340 results on '"Pseudogenes"'
Search Results
2. ORFans in Mitochondrial Genomes of Marine Polychaete Polydora.
- Author
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Selifanova M, Demianchenko O, Noskova E, Pitikov E, Skvortsov D, Drozd J, Vatolkina N, Apel P, Kolodyazhnaya E, Ezhova MA, Tzetlin AB, Neretina TV, and Knorre DA
- Subjects
- Animals, DNA, Mitochondrial genetics, Base Sequence, Proteins genetics, RNA, Transfer genetics, Phylogeny, Genome, Mitochondrial
- Abstract
Most characterized metazoan mitochondrial genomes are compact and encode a small set of proteins that are essential for oxidative phosphorylation, as well as rRNA and tRNA for their expression. However, in rare cases, invertebrate taxa have additional open reading frames (ORFs) in their mtDNA sequences. Here, we sequenced and analyzed the mitochondrial genome of a polychaete worm, Polydora cf. ciliata, part of whose life cycle takes place in low-oxygen conditions. In the mitogenome, we found three "ORFan" regions (544, 1,060, and 427 bp) that have no resemblance to any standard metazoan mtDNA gene but lack stop codons in one of the reading frames. Similar regions are found in the mitochondrial genomes of three other Polydora species and Bocardiella hamata. All five species share the same gene order in their mitogenomes, which differ from that of other known Spionidae mitogenomes. By analyzing the ORFan sequences, we found that they are under purifying selection pressure and contain conservative regions. The codon adaptation indices (CAIs) of the ORFan genes were in the same range of values as the CAI of conventional protein-coding genes in corresponding mitochondrial genomes. The analysis of the P. cf. ciliata mitochondrial transcriptome showed that ORFan-544, ORFan-427, and a portion of the ORFan-1060 are transcribed. Together, this suggests that ORFan-544 and ORFan-427 encode functional proteins. It is likely that the ORFans originated when the Polydora/Bocardiella species complex separated from the rest of the Spionidae, and this event coincided with massive gene rearrangements in their mitochondrial genomes and tRNA-Met duplication., (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
- Published
- 2023
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3. Phylogeny, Ecology, and Gene Families Covariation Shaped the Olfactory Subgenome of Rodents.
- Author
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Courcelle M, Fabre PH, and Douzery EJP
- Subjects
- Female, Pregnancy, Animals, Phylogeny, DNA Copy Number Variations, Placenta metabolism, Mammals genetics, Mammals metabolism, Evolution, Molecular, Rodentia genetics, Receptors, Odorant genetics, Receptors, Odorant metabolism
- Abstract
Olfactory receptor (OR) genes represent the largest multigenic family in mammalian genomes and encode proteins that bind environmental odorant molecules. The OR repertoire is extremely variable among species and is subject to many gene duplications and losses, which have been linked to ecological adaptations in mammals. Although they have been studied on a broad taxonomic scale (i.e., placental), finer sampling has rarely been explored in order to better capture the mechanisms that drove the evolution of the OR repertoire. Among placental mammals, rodents are well-suited for this task, as they exhibit diverse life history traits, and genomic data are available for most major families and a diverse array of lifestyles. In this study, 53 rodent published genomes were mined for their OR subgenomes. We retrieved more than 85,000 functional and pseudogene OR sequences that were subsequently classified into phylogenetic clusters. Copy number variation among rodents is similar to that of other mammals. Using our OR counts along with comparative phylogenetic approaches, we demonstrated that ecological niches such as diet, period of activity, and a fossorial lifestyle strongly impacted the proportion of OR pseudogenes. Within the OR subgenome, phylogenetic inertia was the main factor explaining the relative variations of the 13 OR gene families. However, a striking exception was a convergent 10-fold expansion of the OR family 14 among the phylogenetically divergent subterranean mole-rat lineages belonging to Bathyergidae and Spalacidae families. This study illustrates how the diversity of the OR repertoire has evolved among rodents, both shaped by selective forces stemming from species life history traits and neutral evolution along the rodent phylogeny., (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
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- 2023
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4. The Ga1 locus of the genus Zea is associated with novel genome structures derived from multiple, independent nonhomologous recombination events.
- Author
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Bapat AR, Moran Lauter AN, Hufford MB, Boerman NA, and Scott MP
- Subjects
- Phylogeny, Tandem Repeat Sequences, Recombination, Genetic, Zea mays genetics, Poaceae genetics
- Abstract
The Ga1 locus controls cross-incompatibility between field corn and popcorn. The Ga1-S haplotype contains 2 types of pectin methylesterase (PME) genes, ZmPme3 and several copies of ZmGa1P that are expressed in silk and pollen, respectively. The ga1 haplotype contains nonfunctional tandem repeat sequences related to ZmPme3 and ZmGa1P. This haplotype can cross-pollinate freely and is widely present in field corn. The primary objective of this study is to characterize the repeat sequences from a diverse collection of maize and teosinte lines and use this information to understand the evolution of the Ga1 locus. First, we characterized the complexity of the Ga1 genome region in high-quality maize genome assemblies that led to their categorization into 5 groups based on the number and type of PME-like sequences found at this region. Second, we studied duplication events that led to the ga1 and Ga1-S repeats using maximum likelihood phylogenetic reconstruction. Divergence estimates of the ga1 haplotype suggest that the duplication events occurred more than 600 KYA whereas those in Ga1-S occurred at 3 time points, i.e. >600, ∼260, and ∼100 KYA. These estimates suggest that the ga1 and Ga1-S tandem duplication events occurred independently. Finally, analysis of ZmPme3 and ZmGa1P homologs in Zea and Tripsacum genomes suggests that ga1 and Ga1-S repeats originated from an ancestral pair of PME genes that duplicated and diverged through 2 evolutionary branches prior to the domestication of maize., Competing Interests: Conflicts of interest The authors declare no conflicts of interest., (Published by Oxford University Press on behalf of The Genetics Society of America 2023.)
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- 2023
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5. From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA).
- Author
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Ruiz JL, Reimering S, Escobar-Prieto JD, Brancucci NMB, Echeverry DF, Abdi AI, Marti M, Gómez-Díaz E, and Otto TD
- Subjects
- Humans, Sequence Analysis, DNA, Pseudogenes, Chromosomes, High-Throughput Nucleotide Sequencing, Genome
- Abstract
Recent advances in long read technologies not only enable large consortia to aim to sequence all eukaryotes on Earth, but they also allow individual laboratories to sequence their species of interest with relatively low investment. Long read technologies embody the promise of overcoming scaffolding problems associated with repeats and low complexity sequences, but the number of contigs often far exceeds the number of chromosomes and they may contain many insertion and deletion errors around homopolymer tracts. To overcome these issues, we have implemented the ILRA pipeline to correct long read-based assemblies. Contigs are first reordered, renamed, merged, circularized, or filtered if erroneous or contaminated. Illumina short reads are used subsequently to correct homopolymer errors. We successfully tested our approach by improving the genome sequences of Homo sapiens, Trypanosoma brucei, and Leptosphaeria spp., and by generating four novel Plasmodium falciparum assemblies from field samples. We found that correcting homopolymer tracts reduced the number of genes incorrectly annotated as pseudogenes, but an iterative approach seems to be required to correct more sequencing errors. In summary, we describe and benchmark the performance of our new tool, which improved the quality of novel long read assemblies up to 1 Gbp. The pipeline is available at GitHub: https://github.com/ThomasDOtto/ILRA., (© The Author(s) 2023. Published by Oxford University Press.)
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- 2023
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6. GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery.
- Author
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Marino GB, Ngai M, Clarke DJB, Fleishman RH, Deng EZ, Xie Z, Ahmed N, and Ma'ayan A
- Subjects
- Humans, Cell Line, RNA-Seq, Internet, Proteomics, Pseudogenes, Software
- Abstract
Several atlasing efforts aim to profile human gene and protein expression across tissues, cell types and cell lines in normal physiology, development and disease. One utility of these resources is to examine the expression of a single gene across all cell types, tissues and cell lines in each atlas. However, there is currently no centralized place that integrates data from several atlases to provide this type of data in a uniform format for visualization, analysis and download, and via an application programming interface. To address this need, GeneRanger is a web server that provides access to processed data about gene and protein expression across normal human cell types, tissues and cell lines from several atlases. At the same time, TargetRanger is a related web server that takes as input RNA-seq data from profiled human cells and tissues, and then compares the uploaded input data to expression levels across the atlases to identify genes that are highly expressed in the input and lowly expressed across normal human cell types and tissues. Identified targets can be filtered by transmembrane or secreted proteins. The results from GeneRanger and TargetRanger are visualized as box and scatter plots, and as interactive tables. GeneRanger and TargetRanger are available from https://generanger.maayanlab.cloud and https://targetranger.maayanlab.cloud, respectively., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)
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- 2023
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7. The genome of the oomycete Peronosclerospora sorghi, a cosmopolitan pathogen of maize and sorghum, is inflated with dispersed pseudogenes.
- Author
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Fletcher K, Martin F, Isakeit T, Cavanaugh K, Magill C, and Michelmore R
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- Zea mays genetics, Pseudogenes, Edible Grain genetics, Plant Diseases genetics, Sorghum genetics, Oomycetes genetics, Peronospora genetics
- Abstract
Several species in the oomycete genus Peronosclerospora cause downy mildew on maize and can result in significant yield losses in Asia. Bio-surveillance of these pathogens is a high priority to prevent epidemics on maize in the United States and consequent damage to the US economy. The unresolved taxonomy and dearth of molecular resources for Peronosclerospora spp. hinder these efforts. P. sorghi is a pathogen of sorghum and maize with a global distribution, for which limited diversity has been detected in the southern USA. We characterized the genome, transcriptome, and mitogenome of an isolate, representing the US pathotype 6. The highly homozygous genome was assembled using 10× Genomics linked reads and scaffolded using Hi-C into 13 chromosomes. The total assembled length was 303.2 Mb, larger than any other oomycete previously assembled. The mitogenome was 38 kb, similar in size to other oomycetes, although it had a unique gene order. Nearly 20,000 genes were annotated in the nuclear genome, more than described for other downy mildew causing oomycetes. The 13 chromosomes of P. sorghi were highly syntenic with the 17 chromosomes of Peronospora effusa with conserved centromeric regions and distinct chromosomal fusions. The increased assembly size and gene count of P. sorghi is due to extensive retrotransposition, resulting in putative pseudogenization. Ancestral genes had higher transcript abundance and were enriched for differential expression. This study provides foundational resources for analysis of Peronosclerospora and comparisons to other oomycete genera. Further genomic studies of global Peronosclerospora spp. will determine the suitability of the mitogenome, ancestral genes, and putative pseudogenes for marker development and taxonomic relationships., Competing Interests: Conflicts of interest None declared., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Genetics Society of America.)
- Published
- 2023
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8. FerrDb V2: update of the manually curated database of ferroptosis regulators and ferroptosis-disease associations.
- Author
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Zhou N, Yuan X, Du Q, Zhang Z, Shi X, Bao J, Ning Y, and Peng L
- Subjects
- Data Accuracy, Databases, Factual, Lipid Peroxidation, Pseudogenes, Ferroptosis genetics
- Abstract
Ferroptosis is a mode of regulated cell death characterized by iron-dependent accumulation of lipid peroxidation. It is closely linked to the pathophysiological processes in many diseases. Since our publication of the first ferroptosis database in 2020 (FerrDb V1), many new findings have been published. To keep up with the rapid progress in ferroptosis research and to provide timely and high-quality data, here we present the successor, FerrDb V2. It contains 1001 ferroptosis regulators and 143 ferroptosis-disease associations manually curated from 3288 articles. Specifically, there are 621 gene regulators, of which 264 are drivers, 238 are suppressors, 9 are markers, and 110 are unclassified genes; and there are 380 substance regulators, with 201 inducers and 179 inhibitors. Compared to FerrDb V1, curated articles increase by >300%, ferroptosis regulators increase by 175%, and ferroptosis-disease associations increase by 50.5%. Circular RNA and pseudogene are novel regulators in FerrDb V2, and the percentage of non-coding RNA increases from 7.3% to 13.6%. External gene-related data were integrated, enabling thought-provoking and gene-oriented analysis in FerrDb V2. In conclusion, FerrDb V2 will help to acquire deeper insights into ferroptosis. FerrDb V2 is freely accessible at http://www.zhounan.org/ferrdb/., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2023
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9. Genenames.org: the HGNC resources in 2023.
- Author
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Seal RL, Braschi B, Gray K, Jones TEM, Tweedie S, Haim-Vilmovsky L, and Bruford EA
- Subjects
- Humans, Genome, Genomics, Proteomics, Pseudogenes, Terminology as Topic, Databases, Genetic
- Abstract
The HUGO Gene Nomenclature Committee (HGNC) assigns unique symbols and names to human genes. The HGNC database (www.genenames.org) currently contains over 43 000 approved gene symbols, over 19 200 of which are assigned to protein-coding genes, 14 000 to pseudogenes and nearly 9000 to non-coding RNA genes. The public website, www.genenames.org, displays all approved nomenclature within Symbol Reports that contain data curated by HGNC nomenclature advisors and links to related genomic, clinical, and proteomic information. Here, we describe updates to our resource, including improvements to our search facility and new download features., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2023
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10. Pseudogenes Provide Evolutionary Evidence for the Competitive Endogenous RNA Hypothesis
- Author
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Aoife McLysaght and Cian Glenfield
- Subjects
0301 basic medicine ,Untranslated region ,Proto-Oncogene Proteins B-raf ,evolutionary rates ,Pseudogene ,pseudogenes ,Biology ,BRAF ,Evolution, Molecular ,03 medical and health sciences ,microRNA ,Catarrhini ,Genetics ,Animals ,Humans ,Molecular Biology ,Gene ,3' Untranslated Regions ,Ecology, Evolution, Behavior and Systematics ,Discoveries ,Regulation of gene expression ,Base Sequence ,Competing endogenous RNA ,Three prime untranslated region ,RNA ,ceRNA ,030104 developmental biology ,Gene Expression Regulation - Abstract
The competitive endogenous RNA (ceRNA) hypothesis is an attractively simple model to explain the biological role of many putatively functionless noncoding RNAs. Under this model, there exist transcripts in the cell whose role is to titrate out microRNAs such that the expression level of another target sequence is altered. That it is logistically possible for expression of one microRNA recognition element (MRE)-containing transcript to affect another is seen in the multiple examples of pathogenic effects of inappropriate expression of MRE-containing RNAs. However, the role, if any, of ceRNAs in normal biological processes and at physiological levels is disputed. By comparison of parent genes and pseudogenes we show, both for a specific example and genome-wide, that the pseudo-3′ untranslated regions (3′UTRs) of expressed pseudogenes are frequently retained and are under selective constraint in mammalian genomes. We found that the pseudo-3′UTR of BRAFP1, a previously described oncogenic ceRNA, has reduced substitutions relative to its pseudo-coding sequence, and we show sequence constraint on MREs shared between the parent gene, BRAF, and the pseudogene. Investigation of RNA-seq data reveals expression of BRAFP1 in normal somatic tissues in human and in other primates, consistent with biological ceRNA functionality of this pseudogene in nonpathogenic cellular contexts. Furthermore, we find that on a genome-wide scale pseudo-3′UTRs of mammalian pseudogenes (n = 1,629) are under stronger selective constraint than their pseudo-coding sequence counterparts, and are more often retained and expressed. Our results suggest that many human pseudogenes, often considered nonfunctional, may have an evolutionarily constrained role, consistent with the ceRNA hypothesis.
- Published
- 2018
11. Uncovering Pseudogenes and Intergenic Protein-coding Sequences in TriTryps' Genomes.
- Author
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Abrahim M, Machado E, Alvarez-Valín F, de Miranda AB, and Catanho M
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- Animals, Pseudogenes, Phylogeny, Open Reading Frames, Genome, Trypanosoma brucei brucei genetics, Parasites genetics
- Abstract
Trypanosomatids belong to a remarkable group of unicellular, parasitic organisms of the order Kinetoplastida, an early diverging branch of the phylogenetic tree of eukaryotes, exhibiting intriguing biological characteristics affecting gene expression (intronless polycistronic transcription, trans-splicing, and RNA editing), metabolism, surface molecules, and organelles (compartmentalization of glycolysis, variation of the surface molecules, and unique mitochondrial DNA), cell biology and life cycle (phagocytic vacuoles evasion and intricate patterns of cell morphogenesis). With numerous genomic-scale data of several trypanosomatids becoming available since 2005 (genomes, transcriptomes, and proteomes), the scientific community can further investigate the mechanisms underlying these unusual features and address other unexplored phenomena possibly revealing biological aspects of the early evolution of eukaryotes. One fundamental aspect comprises the processes and mechanisms involved in the acquisition and loss of genes throughout the evolutionary history of these primitive microorganisms. Here, we present a comprehensive in silico analysis of pseudogenes in three major representatives of this group: Leishmania major, Trypanosoma brucei, and Trypanosoma cruzi. Pseudogenes, DNA segments originating from altered genes that lost their original function, are genomic relics that can offer an essential record of the evolutionary history of functional genes, as well as clues about the dynamics and evolution of hosting genomes. Scanning these genomes with functional proteins as proxies to reveal intergenic regions with protein-coding features, relying on a customized threshold to distinguish statistically and biologically significant sequence similarities, and reassembling remnant sequences from their debris, we found thousands of pseudogenes and hundreds of open reading frames, with particular characteristics in each trypanosomatid: mutation profile, number, content, density, codon bias, average size, single- or multi-copy gene origin, number and type of mutations, putative primitive function, and transcriptional activity. These features suggest a common process of pseudogene formation, different patterns of pseudogene evolution and extant biological functions, and/or distinct genome organization undertaken by those parasites during evolution, as well as different evolutionary and/or selective pressures acting on distinct lineages., (© The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
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- 2022
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12. Toll-Like Receptor Evolution in Birds: Gene Duplication, Pseudogenization, and Diversifying Selection
- Author
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Velová, Hana, Gutowska-Ding, Maria W, Burt, David W, and Vinkler, Michal
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adaptive evolution ,convergence ,Toll-Like Receptors ,pattern recognition receptors ,pseudogene ,Birds ,Evolution, Molecular ,positive selection ,Gene Duplication ,Animals ,Amino Acid Sequence ,amino acid physicochemical properties ,Selection, Genetic ,Discoveries ,Pseudogenes - Abstract
Toll-like receptors (TLRs) are key sensor molecules in vertebrates triggering initial phases of immune responses to pathogens. The avian TLR family typically consists of ten receptors, each adapted to distinct ligands. To understand the complex evolutionary history of each avian TLR, we analyzed all members of the TLR family in the whole genome assemblies and target sequence data of 63 bird species covering all major avian clades. Our results indicate that gene duplication events most probably occurred in TLR1 before synapsids diversified from sauropsids. Unlike mammals, ssRNA-recognizing TLR7 has duplicated independently in several avian taxa, while flagellin-sensing TLR5 has pseudogenized multiple times in bird phylogeny. Our analysis revealed stronger positive, diversifying selection acting in TLR5 and the three-domain TLRs (TLR10 [TLR1A], TLR1 [TLR1B], TLR2A, TLR2B, TLR4) that face the extracellular space and bind complex ligands than in single-domain TLR15 and endosomal TLRs (TLR3, TLR7, TLR21). In total, 84 out of 306 positively selected sites were predicted to harbor substitutions dramatically changing the amino acid physicochemical properties. Furthermore, 105 positively selected sites were located in the known functionally relevant TLR regions. We found evidence for convergent evolution acting between birds and mammals at 54 of these sites. Our comparative study provides a comprehensive insight into the evolution of avian TLR genetic variability. Besides describing the history of avian TLR gene gain and gene loss, we also identified candidate positions in the receptors that have been likely shaped by direct molecular host–pathogen coevolutionary interactions and most probably play key functional roles in birds.
- Published
- 2018
13. Are Nonsense Alleles of Drosophila melanogaster Genes under Any Selection?
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Nadezhda A. Potapova, Alexey S. Kondrashov, Georgii A. Bazykin, and Maria A. Andrianova
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0106 biological sciences ,0301 basic medicine ,Pseudogene ,media_common.quotation_subject ,Nonsense mutation ,Population ,Nonsense ,Biology ,01 natural sciences ,loss-of-function ,Evolution, Molecular ,03 medical and health sciences ,Negative selection ,Genetics ,Missense mutation ,Animals ,Amino Acid Sequence ,neutral evolution ,Selection, Genetic ,education ,Gene ,Ecology, Evolution, Behavior and Systematics ,Alleles ,media_common ,education.field_of_study ,Alternative splicing ,negative selection ,Exons ,drosophila ,Alternative Splicing ,030104 developmental biology ,Drosophila melanogaster ,Genetics, Population ,Codon, Nonsense ,Pseudogenes ,010606 plant biology & botany ,Research Article ,nonsense allele - Abstract
A gene which carries a bona fide loss-of-function mutation effectively becomes a functionless pseudogene, free from selective constraint. However, there is a number of molecular mechanisms that may lead to at least a partial preservation of the function of genes carrying even drastic alleles. We performed a direct measurement of the strength of negative selection acting on nonsense alleles of protein-coding genes in the Zambian population of Drosophila melanogaster. Within those exons that carry nonsense mutations, negative selection, assayed by the ratio of missense over synonymous nucleotide diversity levels, appears to be absent, consistent with total loss of function. In other exons of nonsense alleles, negative selection was deeply relaxed but likely not completely absent, and the per site number of missense alleles declined significantly with the distance from the premature stop codon. This pattern may be due to alternative splicing which preserves function of some isoforms of nonsense alleles of genes.
- Published
- 2018
14. dreamBase: DNA modification, RNA regulation and protein binding of expressed pseudogenes in human health and disease
- Author
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Shun Liu, Liang-Hu Qu, Ze-Lin Wang, Jian-Hua Yang, Zhi-Rong Chen, Ding-Yao Zhang, Ling-Ling Zheng, and Ke-Ren Zhou
- Subjects
0301 basic medicine ,Pseudogene ,Gene Expression ,RNA-binding protein ,Biology ,03 medical and health sciences ,Neoplasms ,microRNA ,Databases, Genetic ,Genetics ,Database Issue ,Humans ,RNA Processing, Post-Transcriptional ,Gene ,PKD1 ,Competing endogenous RNA ,Sequence Analysis, RNA ,RNA ,High-Throughput Nucleotide Sequencing ,RNA-Binding Proteins ,DNA ,MicroRNAs ,030104 developmental biology ,Human genome ,Pseudogenes ,Protein Binding - Abstract
Although thousands of pseudogenes have been annotated in the human genome, their transcriptional regulation, expression profiles and functional mechanisms are largely unknown. In this study, we developed dreamBase (http://rna.sysu.edu.cn/dreamBase) to facilitate the investigation of DNA modification, RNA regulation and protein binding of potential expressed pseudogenes from multidimensional high-throughput sequencing data. Based on ∼5500 ChIP-seq and DNase-seq datasets, we identified genome-wide binding profiles of various transcription-associated factors around pseudogene loci. By integrating ∼18 000 RNA-seq data, we analysed the expression profiles of pseudogenes and explored their co-expression patterns with their parent genes in 32 cancers and 31 normal tissues. By combining microRNA binding sites, we demonstrated complex post-transcriptional regulation networks involving 275 microRNAs and 1201 pseudogenes. We generated ceRNA networks to illustrate the crosstalk between pseudogenes and their parent genes through competitive binding of microRNAs. In addition, we studied transcriptome-wide interactions between RNA binding proteins (RBPs) and pseudogenes based on 458 CLIP-seq datasets. In conjunction with epitranscriptome sequencing data, we also mapped 1039 RNA modification sites onto 635 pseudogenes. This database will provide insights into the transcriptional regulation, expression, functions and mechanisms of pseudogenes as well as their roles in biological processes and diseases.
- Published
- 2017
15. The extracellular vesicular pseudogene LGMNP1 induces M2-like macrophage polarization by upregulating LGMN and serves as a novel promising predictive biomarker for ovarian endometriosis recurrence.
- Author
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Sun SG, Guo JJ, Qu XY, Tang XY, Lin YY, Hua KQ, and Qiu JJ
- Subjects
- Adolescent, Animals, Biomarkers metabolism, China, Cysteine Endopeptidases, Endometrium metabolism, Female, Humans, Macrophages metabolism, Mice, Pseudogenes, RNA, Messenger metabolism, Retrospective Studies, Stromal Cells metabolism, Endometriosis pathology, Extracellular Vesicles
- Abstract
Study Question: How does ectopic endometrial stromal cell (Ecto-ESC)-derived extracellular vesicular Legumain pseudogene 1 (EV-LGMNP1), a newly identified pseudogene of Legumain (LGMN), contribute to M2-phenotype macrophage polarization, and does it predict recurrence in patients with ovarian endometriosis (EMs)?, Summary Answer: EV-LGMNP1, which is abundant in Ecto-ESCs and serum from ovarian EMs, can direct macrophages towards an M2 phenotype by upregulating LGMN expression and is a promising biomarker for predicting ovarian EMs recurrence., What Is Known Already: Extracellular vesicles (EVs) can mediate cell-to-cell crosstalk to promote disease progression via cargo molecule transport. Recently, LGMNP1, a newly identified pseudogene of LGMN, has been reported to promote cancer progression by upregulating LGMN. LGMN is a well-studied protein that can induce M2-like polarization., Study Design, Size, Duration: An in vitro study was conducted with Ecto-ESCs isolated from ectopic endometrial samples, collected from two patients with ovarian EMs (diagnosed by laparoscopy and histological analysis). A clinical retrospective cohort study of 52 ovarian EMs patients and 21 controls with available preoperative serum samples was carried out (2013-2017). The follow-up period ended either at the time of recurrence or on 31 December 2018., Participants/materials, Setting, Methods: Ecto-ESC-derived EVs (EV/Ecto-ESCs) were characterized by nanoparticle tracking analysis, transmission electron microscopy and western blotting. EV internalization by THP-1 cells, which are the most widely used primary human macrophages model, was detected by fluorescence labelling. After EV treatment, THP-1 cell polarization was detected by quantitative real-time PCR (qRT-PCR) and western blot analyses of CD86 (M1-related marker) and CD206 (M2-related marker). LGMNP1 mRNA expression level in EVs from both primary ectopic endometrioc stromal cells and serum was examined using qRT-PCR. Additionally, the expression of LGMN, the downstream target gene of LGMNP1, in THP-1 cells was evaluated using qRT-PCR and western blotting. Kaplan-Meier and multivariate Cox regression analyses were applied to evaluate the independent predictive factors of EMs recurrence-free survival. A novel nomogram model based on serum EV-LGMNP1 was then formulated to predict EMs recurrence., Main Results and the Role of Chance: In vitro assays demonstrated that EV/Ecto-ESCs drove macrophages towards an M2-like phenotype. Moreover, LGMNP1 contributed to EV/Ecto-ESC-induced M2 macrophage polarization by upregulating LGMN mRNA expression levels. Clinically, serum EV-LGMNP1 was more highly expressed in recurrent EMs patients than in controls and EMs patients without recurrence. Survival analysis and our novel nomogram reconfirmed that serum EV-LGMNP1 was a novel promising and meaningful non-invasive biomarker for predicting EMs recurrence., Large Scale Data: N/A., Limitations, Reasons for Caution: In vitro experiments were only performed on samples from two patients with ovarian endometriosis, and a larger sample size is needed. ESCs isolated from the eutopic endometrium of EMs and non-EMs patients should be studied in the future. Additionally, in vitro experiments should be performed using endometrial epithelium cells and further in vivo experiments, such as using mice endometriotic models to investigate whether EV/Ecto could induce M2 macrophage polarization, should be conducted. Moreover, multicentre, large-sample data are needed to validate our predictive nomogram model., Wider Implications of the Findings: Our study provides novel insights into the mechanism of M2 polarization involved in ovarian EMs progression mediated by an 'EV-shuttled pseudogene LGMNP1' mode. In addition, serum EV-LGMNP1 may serve as a novel non-invasive biomarker for predicting recurrence, providing a new therapeutic target for ovarian EMs., Study Funding/competing Interest(s): This project was supported by funding from the National Natural Science Foundation of China (81971361), the Natural Science Foundation of Shanghai Science and Technology (19ZR1406900), the Shanghai 'Rising Stars of Medical Talent' Youth Development Program (AB83030002019004), the Clinical Research Plan of SHDC (SHDC2020CR4087), the Shanghai Municipal Health Commission (202040498), the Research and Innovation Project of the Shanghai Municipal Education Commission (2019-01-07-00-07-E00050) and the Clinical Research Plan of SHDC (SHDC2020CR1045B). There are no competing interests to declare., (© The Author(s) 2021. Published by Oxford University Press on behalf of European Society of Human Reproduction and Embryology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)
- Published
- 2022
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16. Remarkable variation of ribosomal DNA organization and copy number in gnetophytes, a distinct lineage of gymnosperms
- Abstract
[ntroduction] Gnetophytes, comprising the genera Ephedra, Gnetum and Welwitschia, are an understudied, enigmatic lineage of gymnosperms with a controversial phylogenetic relationship to other seed plants. Here we examined the organization of ribosomal DNA (rDNA) across representative species. [Methods] We applied high-throughput sequencing approaches to isolate and reconstruct rDNA units and to determine their intragenomic homogeneity. In addition, fluorescent in situ hybridization and Southern blot hybridization techniques were used to reveal the chromosome and genomic organization of rDNA. [Key results] The 5S and 35S rRNA genes were separate (S-type) in Gnetum montanum, Gnetum gnemon and Welwitschia mirabilis and linked (L-type) in Ephedra altissima. There was considerable variability in 5S rDNA abundance, ranging from as few as ~4000 (W. mirabilis) to >100 000 (G. montanum) copies. A similar large variation was also observed in 5S rDNA locus numbers (two to 16 sites per diploid cell). 5S rRNA pseudogenes were interspersed between functional genes forming a single unit in E. altissima and G. montanum. Their copy number was comparable or even higher than that of functional 5S rRNA genes. In E. altissima internal transcribed spacers of 35S rDNA were long and intrinsically repetitive while in G. montanum and W. mirabilis they were short without the subrepeats. [Conclusions] Gnetophytes are distinct from other gymnosperms and angiosperms as they display surprisingly large variability in rDNA organization and rDNA copy and locus numbers between genera, with no relationship between copy numbers and genome sizes apparent. Concerted evolution of 5S rDNA units seems to have led to the amplification of 5S pseudogenes in both G. montanum and E. altissima. Evolutionary patterns of rDNA show both gymnosperm and angiosperm features underlining the diversity of the group.
- Published
- 2019
17. Comparative genomic analysis of SET domain family reveals the origin, expansion, and putative function of the arthropod-specific SmydA genes as histone modifiers in insects
- Author
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Yanli Wang, Qing Liu, Tianqi Song, Le Kang, Xianhui Wang, Feng Jiang, Huimin Wang, Meiling Yang, and Jie Zhang
- Subjects
0106 biological sciences ,0301 basic medicine ,Insecta ,domain ,Health Informatics ,Biology ,010603 evolutionary biology ,01 natural sciences ,Evolution, Molecular ,03 medical and health sciences ,RNA interference ,Gene duplication ,Histone methylation ,Gene family ,Animals ,histone modification ,insects ,Gene ,Arthropods ,Phylogeny ,Genetics ,Regulation of gene expression ,Gene knockdown ,Genome ,Research ,gene duplication ,Histone-Lysine N-Methyltransferase ,Sequence Analysis, DNA ,Computer Science Applications ,PR-SET Domains ,030104 developmental biology ,Histone ,Multigene Family ,biology.protein ,Insect Proteins ,Pseudogenes - Abstract
The SET domain is an evolutionarily conserved motif present in histone lysine methyltransferases, which are important in the regulation of chromatin and gene expression in animals. In this study, we searched for SET domain–containing genes (SET genes) in all of the 147 arthropod genomes sequenced at the time of carrying out this experiment to understand the evolutionary history by which SET domains have evolved in insects. Phylogenetic and ancestral state reconstruction analysis revealed an arthropod-specific SET gene family, named SmydA, that is ancestral to arthropod animals and specifically diversified during insect evolution. Considering that pseudogenization is the most probable fate of the new emerging gene copies, we provided experimental and evolutionary evidence to demonstrate their essential functions. Fluorescence in situ hybridization analysis and in vitro methyltransferase activity assays showed that the SmydA-2 gene was transcriptionally active and retained the original histone methylation activity. Expression knockdown by RNA interference significantly increased mortality, implying that the SmydA genes may be essential for insect survival. We further showed predominantly strong purifying selection on the SmydA gene family and a potential association between the regulation of gene expression and insect phenotypic plasticity by transcriptome analysis. Overall, these data suggest that the SmydA gene family retains essential functions that may possibly define novel regulatory pathways in insects. This work provides insights into the roles of lineage-specific domain duplication in insect evolution.
- Published
- 2017
18. Remarkable variation of ribosomal DNA organization and copy number in gnetophytes, a distinct lineage of gymnosperms
- Author
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Hannes Becher, Wencai Wang, Sònia Garcia, Ilia J. Leitch, Andrew R. Leitch, Tao Wan, Alena Kuderova, Aleš Kovařík, Czech Science Foundation, Ministerio de Economía y Competitividad (España), and China Scholarship Council
- Subjects
0106 biological sciences ,Gnetum ,DNA Copy Number Variations ,Pseudogene ,Locus (genetics) ,Plant Science ,010603 evolutionary biology ,01 natural sciences ,DNA, Ribosomal ,Gnetophytes ,Evolution, Molecular ,Gymnosperm ,Commentaries ,Intragenomic diversity ,Ribosomal DNA ,In Situ Hybridization, Fluorescence ,Phylogeny ,Concerted evolution ,High-throughput sequencing ,biology ,Chromosome evolution ,Welwitschia ,rDNA organization ,Ribosomal RNA ,biology.organism_classification ,Cycadopsida ,Evolutionary biology ,Pseudogenes ,010606 plant biology & botany - Abstract
[ntroduction] Gnetophytes, comprising the genera Ephedra, Gnetum and Welwitschia, are an understudied, enigmatic lineage of gymnosperms with a controversial phylogenetic relationship to other seed plants. Here we examined the organization of ribosomal DNA (rDNA) across representative species. [Methods] We applied high-throughput sequencing approaches to isolate and reconstruct rDNA units and to determine their intragenomic homogeneity. In addition, fluorescent in situ hybridization and Southern blot hybridization techniques were used to reveal the chromosome and genomic organization of rDNA. [Key results] The 5S and 35S rRNA genes were separate (S-type) in Gnetum montanum, Gnetum gnemon and Welwitschia mirabilis and linked (L-type) in Ephedra altissima. There was considerable variability in 5S rDNA abundance, ranging from as few as ~4000 (W. mirabilis) to >100 000 (G. montanum) copies. A similar large variation was also observed in 5S rDNA locus numbers (two to 16 sites per diploid cell). 5S rRNA pseudogenes were interspersed between functional genes forming a single unit in E. altissima and G. montanum. Their copy number was comparable or even higher than that of functional 5S rRNA genes. In E. altissima internal transcribed spacers of 35S rDNA were long and intrinsically repetitive while in G. montanum and W. mirabilis they were short without the subrepeats. [Conclusions] Gnetophytes are distinct from other gymnosperms and angiosperms as they display surprisingly large variability in rDNA organization and rDNA copy and locus numbers between genera, with no relationship between copy numbers and genome sizes apparent. Concerted evolution of 5S rDNA units seems to have led to the amplification of 5S pseudogenes in both G. montanum and E. altissima. Evolutionary patterns of rDNA show both gymnosperm and angiosperm features underlining the diversity of the group., The work was supported by the Czech Science Foundation (P506/16/02149J), NERC and the Dirección General de Investigación Científica y Técnica (CGL2016-75694-P). W.W. is sponsored by the China Scholarship Council
- Published
- 2019
19. Novel Classes and Evolutionary Turnover of Histone H2B Variants in the Mammalian Germline.
- Author
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Raman P, Rominger MC, Young JM, Molaro A, Tsukiyama T, and Malik HS
- Subjects
- Animals, Germ Cells metabolism, Mammals genetics, Mammals metabolism, Phylogeny, Chromatin genetics, Histones genetics, Histones metabolism
- Abstract
Histones and their posttranslational modifications facilitate diverse chromatin functions in eukaryotes. Core histones (H2A, H2B, H3, and H4) package genomes after DNA replication. In contrast, variant histones promote specialized chromatin functions, including DNA repair, genome stability, and epigenetic inheritance. Previous studies have identified only a few H2B variants in animals; their roles and evolutionary origins remain largely unknown. Here, using phylogenomic analyses, we reveal the presence of five H2B variants broadly present in mammalian genomes. Three of these variants have been previously described: H2B.1, H2B.L (also called subH2B), and H2B.W. In addition, we identify and describe two new variants: H2B.K and H2B.N. Four of these variants originated in mammals, whereas H2B.K arose prior to the last common ancestor of bony vertebrates. We find that though H2B variants are subject to high gene turnover, most are broadly retained in mammals, including humans. Despite an overall signature of purifying selection, H2B variants evolve more rapidly than core H2B with considerable divergence in sequence and length. All five H2B variants are expressed in the germline. H2B.K and H2B.N are predominantly expressed in oocytes, an atypical expression site for mammalian histone variants. Our findings suggest that H2B variants likely encode potentially redundant but vital functions via unusual chromatin packaging or nonchromatin functions in mammalian germline cells. Our discovery of novel histone variants highlights the advantages of comprehensive phylogenomic analyses and provides unique opportunities to study how innovations in chromatin function evolve., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
- Published
- 2022
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20. Decreased Transcription Factor Binding Levels Nearby Primate Pseudogenes Suggest Regulatory Degeneration
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Gavin M. Douglas, Alan M. Moses, and Michael D. Wilson
- Subjects
0301 basic medicine ,Nonsynonymous substitution ,Primates ,Lineage (genetic) ,Pseudogene ,0206 medical engineering ,02 engineering and technology ,Degeneration (medical) ,Biology ,Frameshift mutation ,Evolution, Molecular ,03 medical and health sciences ,0302 clinical medicine ,regulatory evolution ,histone modifications ,Genetics ,Transcriptional regulation ,Animals ,Humans ,Regulatory Elements, Transcriptional ,neutral evolution ,Molecular Biology ,Transcription factor ,Gene ,Ecology, Evolution, Behavior and Systematics ,Discoveries ,030304 developmental biology ,Regulation of gene expression ,0303 health sciences ,Models, Genetic ,Sequence Analysis, DNA ,Biological Evolution ,ChIP-seq ,030104 developmental biology ,Gene Expression Regulation ,Macaca ,Sequence Alignment ,020602 bioinformatics ,030217 neurology & neurosurgery ,pseudoenhancer ,Pseudogenes ,Protein Binding ,Transcription Factors - Abstract
Characteristics of pseudogene degeneration at the coding level are well-known, such as a shift towards neutral rates of nonsynonymous substitutions and gain of frameshift mutations. In contrast, degeneration of pseudogene transcriptional regulation is not well understood. Here, we test two predictions of regulatory degeneration along the pseudogenized lineage: (1) decreased transcription factor binding and (2) accelerated evolution in putative cis-regulatory regions. We find evidence for decreased TF binding levels nearby two primate pseudogenes compared to functional liver genes. We also find evidence for pseudogene-lineage-specific relaxation of sequence constraint on a fragment of the promoter of the primate pseudogene urate oxidase (Uox) and a nearby cis-regulatory module (CRM). However, the majority of TF-bound sequences nearby pseudogenes do not show evidence for lineage-specific accelerated rates of evolution. We conclude that decreases in TF binding level could be a marker for regulatory degeneration, while sequence degeneration in most CRMs may be obscured by background rates of TF binding site turnover.
- Published
- 2016
21. Plastid NDH Pseudogenization and Gene Loss in a Recently Derived Lineage from the Largest Hemiparasitic Plant Genus Pedicularis (Orobanchaceae).
- Author
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Li X, Yang JB, Wang H, Song Y, Corlett RT, Yao X, Li DZ, and Yu WB
- Subjects
- Evolution, Molecular, Genes, Plant, NADH Dehydrogenase genetics, Pseudogenes, Genome, Plastid, Pedicularis genetics, Phylogeny, Plastids genetics
- Abstract
The plastid genome (plastome) is highly conserved in both gene order and content and has a lower mutation rate than the nuclear genome. However, the plastome is more variable in heterotrophic plants. To date, most such studies have investigated just a few species or only holoheterotrophic groups, and few have examined plastome evolution in recently derived lineages at an early stage of transition from autotrophy to heterotrophy. In this study, we investigated the evolutionary dynamics of plastomes in the monophyletic and recently derived Pedicularis sect. Cyathophora (Orobanchaceae). We obtained 22 new plastomes, 13 from the six recognized species of section Cyathophora, six from hemiparasitic relatives and three from autotrophic relatives. Comparative analyses of gene content, plastome structure and selection pressure showed dramatic differences among species in section Cyathophora and in Pedicularis as a whole. In comparison with autotrophic relatives and other Pedicularis spp., we found that the inverted repeat (IR) region in section Cyathophora had expansions to the small single-copy region, with a large expansion event and two independent contraction events. Moreover, NA(D)H dehydrogenase, accD and ccsA have lost function multiple times, with the function of accD being replaced by nuclear copies of an accD-like gene in Pedicularis spp. The ccsA and ndhG genes may have evolved under selection in association with IR expansion/contraction events. This study is the first to report high plastome variation in a recently derived lineage of hemiparasitic plants and therefore provides evidence for plastome evolution in the transition from autotrophy to heterotrophy., (© The Author(s) 2021. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.)
- Published
- 2021
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22. The Plastomes of Two Species in the Endoparasite Genus Pilostyles (Apodanthaceae) Each Retain Just Five or Six Possibly Functional Genes
- Author
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Sidonie Bellot and Susanne S. Renner
- Subjects
0301 basic medicine ,Apodanthaceae ,Pseudogene ,Genome, Plastid ,Genes, Plant ,03 medical and health sciences ,Magnoliopsida ,Genus ,Botany ,Genetics ,Animals ,Ecology, Evolution, Behavior and Systematics ,Rafflesiaceae ,photosynthesis ,biology ,Host (biology) ,Fabaceae ,gene loss ,biology.organism_classification ,minimal plastome ,030104 developmental biology ,Chloroplast DNA ,Rafflesia ,endoparasite ,chloroplast genome ,Pseudogenes ,Research Article - Abstract
The 23 species of mycoheterotrophic or exoparasitic land plants (from 15 genera and 6 families) studied so far all retain a minimal set of 17 of the normally 116 plastome genes. Only Rafflesia lagascae, an endoparasite concealed in its host except when flowering, has been reported as perhaps lacking a plastome, although it still possesses plastid-like compartments. We analyzed two other endoparasites, the African Apodanthaceae Pilostyles aethiopica and the Australian Pilostyles hamiltonii, both living inside Fabaceae. Illumina and 454 data and Sanger resequencing yielded circularized plastomes of 11,348 and 15,167 bp length, with both species containing five possibly functional genes (accD, rps3, rps4, rrn16, rrn23) and two/three pseudogenes (rpoC2 in P. aethiopica and rpl2 and rps12 in both species; rps12 may be functional in P. hamiltonii). Previously known smallest land plant plastomes contain 27-29 genes, making these Apodanthaceae plastomes the most reduced in size and gene content. A similar extent of divergence might have caused the plastome of Rafflesia to escape detection. The higher plastome degeneration in both these families of endoparasites, Rafflesiaceae and Apodanthaceae, of similar high age, compared with exoparasites points to a difference of plastome function between those two modes of parasitic life.
- Published
- 2015
23. Ca. Endozoicomonas cretensis: A Novel Fish Pathogen Characterized by Genome Plasticity
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Maria Chiara Cascarano, Weihong Qi, Helena M. B. Seth-Smith, Ralph Schlapbach, Pantelis Katharios, Lloyd Vaughan, University of Zurich, and Seth-Smith, Helena M B
- Subjects
0301 basic medicine ,Aquatic Organisms ,mobile elements ,Sequence analysis ,genome degradation ,Pseudogene ,Cell Plasticity ,Virulence ,610 Medicine & health ,10071 Functional Genomics Center Zurich ,Biology ,Genome ,host–pathogen ,resistance ,virulence ,genome decay ,03 medical and health sciences ,1311 Genetics ,Genetics ,Animals ,14. Life underwater ,Insertion sequence ,Symbiosis ,Pathogen ,Gene ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Bacteria ,Coral Reefs ,Effector ,Fishes ,Sequence Analysis, DNA ,Genome Report ,1105 Ecology, Evolution, Behavior and Systematics ,030104 developmental biology ,Vertebrates ,DNA Transposable Elements ,570 Life sciences ,biology ,Genome, Bacterial ,Pseudogenes - Abstract
Endozoicomonas bacteria are generally beneficial symbionts of diverse marine invertebrates including reef-building corals, sponges, sea squirts, sea slugs, molluscs, and Bryozoans. In contrast, the recently reported Ca. Endozoicomonas cretensis was identified as a vertebrate pathogen, causing epitheliocystis in fish larvae resulting in massive mortality. Here, we described the Ca. E. cretensis draft genome, currently undergoing genome decay as evidenced by massive insertion sequence (IS element) expansion and pseudogene formation. Many of the insertion sequences are also predicted to carry outward-directed promoters, implying that they may be able to modulate the expression of neighbouring coding sequences (CDSs). Comparative genomic analysis has revealed many Ca. E. cretensis-specific CDSs, phage integration and novel gene families. Potential virulence related CDSs and machineries were identified in the genome, including secretion systems and related effector proteins, and systems related to biofilm formation and directed cell movement. Mucin degradation would be of importance to a fish pathogen, and many candidate CDSs associated with this pathway have been identified. The genome may reflect a bacterium in the process of changing niche from symbiont to pathogen, through expansion of virulence genes and some loss of metabolic capacity. ISSN:1759-6653
- Published
- 2018
24. Engineered Functional Redundancy Relaxes Selective Constraints upon Endogenous Genes in Viral RNA Genomes
- Author
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Francisca de la Iglesia, Anamarija Butković, Sttefany M. Rosario, Santiago F. Elena, Silvia Ambrós, Ministerio de Educación Superior, Ciencia y Tecnología (República Dominicana), Ministerio de Economía y Competitividad (España), Consejo Superior de Investigaciones Científicas (España), and European Commission
- Subjects
0301 basic medicine ,Potyvirus ,Endogeny ,Computational biology ,Genome, Viral ,Genome ,Experimental virus evolution ,Viral suppressors of RNA silencing ,Evolution, Molecular ,03 medical and health sciences ,Genetics ,RNA Viruses ,Viral rna ,Gene ,Ecology, Evolution, Behavior and Systematics ,Compensatory evolution ,Plant Diseases ,biology ,Tobacco etch virus ,Functional redundancy ,Multifunctional proteins ,Plants ,biology.organism_classification ,Genetic redundancy ,030104 developmental biology ,Mutation ,RNA, Viral ,RNA Interference ,Pseudogenes ,Research Article - Abstract
Functional redundancy, understood as the functional overlap of different genes, is a double-edge sword. At the one side, it is thought to serve as a robustness mechanism that buffers the deleterious effect of mutations hitting one of the redundant copies, thus resulting in pseudogenization. At the other side, it is considered as a source of genetic and functional innovation. In any case, genetically redundant genes are expected to show an acceleration in the rate of molecular evolution. Here, we tackle the role of functional redundancy in viral RNA genomes. To this end, we have evaluated the rates of compensatory evolution for deleterious mutations affecting an essential function, the suppression of RNA silencing plant defense, of tobacco etch potyvirus (TEV). TEV genotypes containing deleterious mutations in presence/absence of engineered functional redundancy were evolved and the pattern of fitness and pathogenicity recovery evaluated. Genetically redundant genotypes suffered less from the effect of deleterious mutations and showed relatively minor changes in fitness and pathogenicity. By contrast, nongenetically redundant genotypes had very low fitness and pathogenicity at the beginning of the evolution experiment that were fully recovered by the end. At the molecular level, the outcome depended on the combination of the actual mutations being compensated and the presence/absence of functional redundancy. Reversions to wild-type alleles were the norm in the nonredundant genotypes while redundant ones either did not fix any mutation at all or showed a higher nonsynonymous mutational load., This work was supported by Spain’s Agencia Estatal de Investigacion—FEDER grant BFU2015-65037-P to S.F.E. and by a fellowship from the Dominican Republic’s Ministerio de Educacion Superior, Ciencia y Tecnolog ıa to S.M.R.
- Published
- 2018
25. The Evolution of Interdependence in a Four-Way Mealybug Symbiosis.
- Author
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Garber AI, Kupper M, Laetsch DR, Weldon SR, Ladinsky MS, Bjorkman PJ, and McCutcheon JP
- Subjects
- Animals, Genome, Bacterial, Phylogeny, Symbiosis genetics, Betaproteobacteria genetics, Gammaproteobacteria genetics, Hemiptera genetics, Hemiptera microbiology
- Abstract
Mealybugs are insects that maintain intracellular bacterial symbionts to supplement their nutrient-poor plant sap diets. Some mealybugs have a single betaproteobacterial endosymbiont, a Candidatus Tremblaya species (hereafter Tremblaya) that alone provides the insect with its required nutrients. Other mealybugs have two nutritional endosymbionts that together provision these same nutrients, where Tremblaya has gained a gammaproteobacterial partner that resides in its cytoplasm. Previous work had established that Pseudococcus longispinus mealybugs maintain not one but two species of gammaproteobacterial endosymbionts along with Tremblaya. Preliminary genomic analyses suggested that these two gammaproteobacterial endosymbionts have large genomes with features consistent with a relatively recent origin as insect endosymbionts, but the patterns of genomic complementarity between members of the symbiosis and their relative cellular locations were unknown. Here, using long-read sequencing and various types of microscopy, we show that the two gammaproteobacterial symbionts of P. longispinus are mixed together within Tremblaya cells, and that their genomes are somewhat reduced in size compared with their closest nonendosymbiotic relatives. Both gammaproteobacterial genomes contain thousands of pseudogenes, consistent with a relatively recent shift from a free-living to an endosymbiotic lifestyle. Biosynthetic pathways of key metabolites are partitioned in complex interdependent patterns among the two gammaproteobacterial genomes, the Tremblaya genome, and horizontally acquired bacterial genes that are encoded on the mealybug nuclear genome. Although these two gammaproteobacterial endosymbionts have been acquired recently in evolutionary time, they have already evolved codependencies with each other, Tremblaya, and their insect host., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
- Published
- 2021
- Full Text
- View/download PDF
26. Higher Rates of Processed Pseudogene Acquisition in Humans and Three Great Apes Revealed by Long-Read Assemblies.
- Author
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Feng X and Li H
- Subjects
- Alternative Splicing, Animals, Humans, Polymorphism, Genetic, Genetic Techniques, Hominidae genetics, Long Interspersed Nucleotide Elements, Pseudogenes
- Abstract
LINE-1-mediated retrotransposition of protein-coding mRNAs is an active process in modern humans for both germline and somatic genomes. Prior works that surveyed human data mostly relied on detecting discordant mappings of paired-end short reads, or exon junctions contained in short reads. Moreover, there have been few genome-wide comparisons between gene retrocopies in great apes and humans. In this study, we introduced a more sensitive and accurate method to identify processed pseudogenes. Our method utilizes long-read assemblies, and more importantly, is able to provide full-length retrocopy sequences as well as flanking regions which are missed by short-read based methods. From 22 human individuals, we pinpointed 40 processed pseudogenes that are not present in the human reference genome GRCh38 and identified 17 pseudogenes that are in GRCh38 but absent from some input individuals. This represents a significantly higher discovery rate than previous reports (39 pseudogenes not in the reference genome out of 939 individuals). We also provided an overview of lineage-specific retrocopies in chimpanzee, gorilla, and orangutan genomes., (Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 2021. This work is written by US Government employees and is in the public domain in the US.)
- Published
- 2021
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27. Plastome Evolution in Hemiparasitic Mistletoes
- Author
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Gitte Petersen, Argelia Cuenca, and Ole Seberg
- Subjects
Osyris ,Santalales ,DNA, Plant ,Pseudogene ,pseudogenes ,selection ,Genes, Plant ,Evolution, Molecular ,Viscum ,Intergenic region ,Botany ,Genetics ,Plastid ,Selection, Genetic ,Genome, Chloroplast ,Gene ,Ecology, Evolution, Behavior and Systematics ,biology ,gene loss ,Genomics ,biology.organism_classification ,hemiparasite ,Mistletoe ,intergenic regions ,Chloroplast DNA ,structural rearrangements ,Genome, Plant ,Research Article - Abstract
Santalales is an order of plants consisting almost entirely of parasites. Some, such as Osyris, are facultative root parasites whereas others, such as Viscum, are obligate stem parasitic mistletoes. Here, we report the complete plastome sequences of one species of Osyris and three species of Viscum, and we investigate the evolutionary aspects of structural changes and changes in gene content in relation to parasitism. Compared with typical angiosperms plastomes, the four Santalales plastomes are all reduced in size (10-22% compared with Vitis), and they have experienced rearrangements, mostly but not exclusively in the border areas of the inverted repeats. Additionally, a number of protein-coding genes (matK, infA, ccsA, rpl33, and all 11 ndh genes) as well as two transfer RNA genes (trnG-UCC and trnV-UAC) have been pseudogenized or completely lost. Most of the remaining plastid genes have a significantly changed selection pattern compared with other dicots, and the relaxed selection of photosynthesis genes is noteworthy. Although gene loss obviously reduces plastome size, intergenic regions were also shortened. As plastome modifications are generally most prominent in Viscum, they are most likely correlated with the increased nutritional dependence on the host compared with Osyris.
- Published
- 2015
28. Gene Loss Dominates As a Source of Genetic Variation within Clonal Pathogenic Bacterial Species
- Author
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Evgeni Bolotin and Ruth Hershberg
- Subjects
pangenome ,Gene Transfer, Horizontal ,Pseudogene ,bacterial evolution ,Mycobacterium tuberculosis ,Evolution, Molecular ,03 medical and health sciences ,Bacterial Proteins ,sources of variation ,Genetic variation ,Genetics ,Gene ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,0303 health sciences ,biology ,Bacteria ,030306 microbiology ,Genetic Variation ,Molecular Sequence Annotation ,gene loss ,biology.organism_classification ,Phenotype ,Yersinia pestis ,clonal pathogens ,Genes, Bacterial ,Recombination ,Genome, Bacterial ,Pseudogenes ,Research Article - Abstract
Some of the most dangerous pathogens such as Mycobacterium tuberculosis and Yersinia pestis evolve clonally. This means that little or no recombination occurs between strains belonging to these species. Paradoxically, although different members of these species show extreme sequence similarity of orthologous genes, some show considerable intraspecies phenotypic variation, the source of which remains elusive. To examine the possible sources of phenotypic variation within clonal pathogenic bacterial species, we carried out an extensive genomic and pan-genomic analysis of the sources of genetic variation available to a large collection of clonal and nonclonal pathogenic bacterial species. We show that while nonclonal species diversify through a combination of changes to gene sequences, gene loss and gene gain, gene loss completely dominates as a source of genetic variation within clonal species. Indeed, gene loss is so prevalent within clonal species as to lead to levels of gene content variation comparable to those found in some nonclonal species that are much more diverged in their gene sequences and that acquire a substantial number of genes horizontally. Gene loss therefore needs to be taken into account as a potential dominant source of phenotypic variation within clonal bacterial species.
- Published
- 2015
29. Toward a high-quality pan-genome landscape of Bacillus subtilis by removal of confounding strains.
- Author
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Wu H, Wang D, and Gao F
- Subjects
- Bacillus subtilis classification, Chromosomes, Bacterial, Genetic Variation, Phylogeny, Pseudogenes, Bacillus subtilis genetics, Genome, Bacterial
- Abstract
Pan-genome analysis is widely used to study the evolution and genetic diversity of species, particularly in bacteria. However, the impact of strain selection on the outcome of pan-genome analysis is poorly understood. Furthermore, a standard protocol to ensure high-quality pan-genome results is lacking. In this study, we carried out a series of pan-genome analyses of different strain sets of Bacillus subtilis to understand the impact of various strains on the performance and output quality of pan-genome analyses. Consequently, we found that the results obtained by pan-genome analyses of B. subtilis can be influenced by the inclusion of incorrectly classified Bacillus subspecies strains, phylogenetically distinct strains, engineered genome-reduced strains, chimeric strains, strains with a large number of unique genes or a large proportion of pseudogenes, and multiple clonal strains. Since the presence of these confounding strains can seriously affect the quality and true landscape of the pan-genome, we should remove these deviations in the process of pan-genome analyses. Our study provides new insights into the removal of biases from confounding strains in pan-genome analyses at the beginning of data processing, which enables the achievement of a closer representation of a high-quality pan-genome landscape of B. subtilis that better reflects the performance and credibility of the B. subtilis pan-genome. This procedure could be added as an important quality control step in pan-genome analyses for improving the efficiency of analyses, and ultimately contributing to a better understanding of genome function, evolution and genome-reduction strategies for B. subtilis in the future., (© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)
- Published
- 2021
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30. Probing the Evolutionary History of Human Bitter Taste Receptor Pseudogenes by Restoring Their Function
- Author
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Maik Behrens, Dennis Drayna, Eduardo Sainz, Davide Risso, and Wolfgang Meyerhof
- Subjects
0301 basic medicine ,Taste ,Pan troglodytes ,Pseudogene ,Zoology ,Biology ,ENCODE ,Ligands ,Receptors, G-Protein-Coupled ,Evolution, Molecular ,03 medical and health sciences ,Synthetic biology ,Species Specificity ,Genetics ,Animals ,Humans ,Receptor ,Molecular Biology ,Gene ,Ecology, Evolution, Behavior and Systematics ,Discoveries ,Phylogeny ,Taste Buds ,Biological Evolution ,Open reading frame ,030104 developmental biology ,Evolutionary biology ,Synthetic Biology ,Function (biology) ,Pseudogenes - Abstract
Lineage-specific gene losses can be driven by selection or environmental adaptations. However, a lack of studies on the original function of species-specific pseudogenes leaves a gap in our understanding of their role in evolutionary histories. Pseudogenes are of particular relevance for taste perception genes, which encode for receptors that confer the ability to both identify nutritionally valuable substances and avoid potentially harmful substances. To explore the role of bitter taste pseudogenization events in human origins, we restored the open reading frames of the three human-specific pseudogenes and synthesized the reconstructed functional hTAS2R2, hTAS2R62 and hTAS2R64 receptors. We have identified ligands that differentially activate the human and chimpanzee forms of these receptors and several other human functional TAS2Rs. We show that these receptors are narrowly tuned, suggesting that bitter-taste sensitivities evolved independently in different species, and that these pseudogenization events occurred because of functional redundancy. The restoration of function of lineage-specific pseudogenes can aid in the reconstruction of their evolutionary history, and in understanding the forces that led to their pseudogenization.
- Published
- 2017
31. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data
- Author
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Hui Zhou, Jun-Hao Li, Liang-Hu Qu, Shun Liu, and Jian-Hua Yang
- Subjects
I. Nucleic acid sequence, structure and regulation ,RNA, Untranslated ,Pseudogene ,Gene regulatory network ,RNA-binding protein ,Computational biology ,Biology ,Mice ,Genetics ,Animals ,Humans ,Immunoprecipitation ,Gene Regulatory Networks ,RNA, Messenger ,Internet ,MiRTarBase ,Binding Sites ,Genome ,Competing endogenous RNA ,Sequence Analysis, RNA ,High-Throughput Nucleotide Sequencing ,RNA-Binding Proteins ,Molecular Sequence Annotation ,Oncogenes ,RNA, Circular ,Argonaute ,Non-coding RNA ,MicroRNAs ,Argonaute Proteins ,RNA ,RNA, Long Noncoding ,Databases, Nucleic Acid ,ICLIP ,Pseudogenes - Abstract
Although microRNAs (miRNAs), other non-coding RNAs (ncRNAs) (e.g. lncRNAs, pseudogenes and circRNAs) and competing endogenous RNAs (ceRNAs) have been implicated in cell-fate determination and in various human diseases, surprisingly little is known about the regulatory interaction networks among the multiple classes of RNAs. In this study, we developed starBase v2.0 (http://starbase.sysu.edu.cn/) to systematically identify the RNA-RNA and protein-RNA interaction networks from 108 CLIP-Seq (PAR-CLIP, HITS-CLIP, iCLIP, CLASH) data sets generated by 37 independent studies. By analyzing millions of RNA-binding protein binding sites, we identified ∼9000 miRNA-circRNA, 16 000 miRNA-pseudogene and 285,000 protein-RNA regulatory relationships. Moreover, starBase v2.0 has been updated to provide the most comprehensive CLIP-Seq experimentally supported miRNA-mRNA and miRNA-lncRNA interaction networks to date. We identified ∼10,000 ceRNA pairs from CLIP-supported miRNA target sites. By combining 13 functional genomic annotations, we developed miRFunction and ceRNAFunction web servers to predict the function of miRNAs and other ncRNAs from the miRNA-mediated regulatory networks. Finally, we developed interactive web implementations to provide visualization, analysis and downloading of the aforementioned large-scale data sets. This study will greatly expand our understanding of ncRNA functions and their coordinated regulatory networks.
- Published
- 2013
32. Loose ends: almost one in five human genes still have unresolved coding status
- Author
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Laura Martinez, Manolis Kellis, Maria Rigau, Jesús Vázquez, David Juan, Federico Abascal, Jose Manuel Rodriguez, Irwin Jungreis, Michael L. Tress, and National Institutes of Health (Estados Unidos)
- Subjects
0301 basic medicine ,INTEGRATED MAP ,DNA Copy Number Variations ,PREDICTION ,DATABASE ,Pseudogene ,Computational biology ,Data Resources and Analyses ,Biology ,EVOLUTIONARY INFORMATION ,Genome ,Antibodies ,03 medical and health sciences ,NUMBER ,0302 clinical medicine ,Human proteome project ,RefSeq ,Genetics ,Ensembl ,HUMAN GENOME ,TOPOLOGY ,Humans ,GENCODE ,Genome, Human ,Genetic Variation ,Proteins ,Molecular Sequence Annotation ,FUNCTIONALLY IMPORTANT ,PROTEOME ,030104 developmental biology ,Genes ,030211 gastroenterology & hepatology ,Human genome ,UniProt ,Corrigendum ,PROJECT ,Pseudogenes ,Coding (social sciences) - Abstract
Seventeen years after the sequencing of the human genome, the human proteome is still under revision. One in eight of the 22 210 coding genes listed by the Ensembl/GENCODE, RefSeq and UniProtKB reference databases are annotated differently across the three sets. We have carried out an in-depth investigation on the 2764 genes classified as coding by one or more sets of manual curators and not coding by others. Data from large-scale genetic variation analyses suggests that most are not under protein-like purifying selection and so are unlikely to code for functional proteins. A further 1470 genes annotated as coding in all three reference sets have characteristics that are typical of non-coding genes or pseudogenes. These potential non-coding genes also appear to be undergoing neutral evolution and have considerably less supporting transcript and protein evidence than other coding genes. We believe that the three reference databases currently overestimate the number of human coding genes by at least 2000, complicating and adding noise to large-scale biomedical experiments. Determining which potential non-coding genes do not code for proteins is a difficult but vitally important task since the human reference proteome is a fundamental pillar of most basic research and supports almost all large-scale biomedical projects. National Institutes of Health [2 U41 HG007234 to I.J., L.M., J.M.R. and M.L.T., R01 HG004037 to I.J.]. Funding for open access charge: NIH [2 U41 HG007234]. Sí
- Published
- 2018
33. Contrasting Gene Decay in Subterranean Vertebrates: Insights from Cavefishes and Fossorial Mammals.
- Author
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Policarpo M, Fumey J, Lafargeas P, Naquin D, Thermes C, Naville M, Dechaud C, Volff JN, Cabau C, Klopp C, Møller PR, Bernatchez L, García-Machado E, Rétaux S, and Casane D
- Subjects
- Animals, Caves, Pseudogenes, Selection, Genetic, Zebrafish, Circadian Clocks genetics, Fishes genetics, Loss of Function Mutation, Moles genetics, Pigmentation genetics, Vision, Ocular genetics
- Abstract
Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxes functional constraints. Subterranean vertebrates are outstanding models to analyze this process, and gene decay can serve as a readout. We sought to understand some general principles on the extent and tempo of the decay of genes involved in vision, circadian clock, and pigmentation in cavefishes. The analysis of the genomes of two Cuban species belonging to the genus Lucifuga provided evidence for the largest loss of eye-specific genes and nonvisual opsin genes reported so far in cavefishes. Comparisons with a recently evolved cave population of Astyanax mexicanus and three species belonging to the Chinese tetraploid genus Sinocyclocheilus revealed the combined effects of the level of eye regression, time, and genome ploidy on eye-specific gene pseudogenization. The limited extent of gene decay in all these cavefishes and the very small number of loss-of-function mutations per pseudogene suggest that their eye degeneration may not be very ancient, ranging from early to late Pleistocene. This is in sharp contrast with the identification of several vision genes carrying many loss-of-function mutations in ancient fossorial mammals, further suggesting that blind fishes cannot thrive more than a few million years in cave ecosystems., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
- Published
- 2021
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34. Concerted and birth-and-death evolution of 26S ribosomal DNA in Camellia L.
- Author
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Zhang M, Tang YW, Xu Y, Yonezawa T, Shao Y, Wang YG, Song ZP, Yang J, and Zhang WJ
- Subjects
- DNA, Ribosomal, Phylogeny, Pseudogenes, RNA, Ribosomal, Camellia, Evolution, Molecular
- Abstract
Background and Aims: The ribosomal DNA (rDNA) gene family, encoding ribosomal RNA (rRNA), has long been regarded as an archetypal example illustrating the model of concerted evolution. However, controversy is arising, as rDNA in many eukaryotic species has been proved to be polymorphic. Here, a metagenomic strategy was applied to detect the intragenomic polymorphism as well as the evolutionary patterns of 26S rDNA across the genus Camellia., Methods: Degenerate primer pairs were designed to amplify the 26S rDNA fragments from different Camellia species. The amplicons were then paired-end sequenced on the Illumina MiSeq platform., Key Results: An extremely high level of rDNA polymorphism existed universally in Camellia. However, functional rDNA was still the major component of the family, and was relatively conserved among different Camellia species. Sequence variations mainly came from rRNA pseudogenes and favoured regions that are rich in GC. Specifically, some rRNA pseudogenes have existed in the genome for a long time, and have even experienced several expansion events, which has greatly enriched the abundance of rDNA polymorphism., Conclusions: Camellia represents a group in which rDNA is subjected to a mixture of concerted and birth-and-death evolution. Some rRNA pseudogenes may still have potential functions. Conversely, when released from selection constraint, they can evolve in the direction of decreasing GC content and structural stability through a methylation-induced process, and finally be eliminated from the genome., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2021
- Full Text
- View/download PDF
35. Differentiation of developing olfactory neurons analysed in terms of coupled epigenetic landscapes
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Kim Sneppen and Anne K. Alsing
- Subjects
Olfactory system ,Gene Dosage ,Sensory system ,Biology ,Receptors, Odorant ,Olfactory Receptor Neurons ,Epigenesis, Genetic ,Genetics ,medicine ,Epigenetics ,Gene Silencing ,Transcription factor ,Gene ,Feedback, Physiological ,Models, Genetic ,Mechanism (biology) ,Computational Biology ,Cell Differentiation ,Sensory neuron ,medicine.anatomical_structure ,Enhancer Elements, Genetic ,Neuron ,Neuroscience ,Pseudogenes ,Transcription Factors - Abstract
The olfactory system integrates signals from receptors expressed in olfactory sensory neurons. Each sensory neuron expresses only one of many similar olfactory receptors (ORs). The choice of receptor is made stochastically early in the differentiation process and is maintained throughout the life of the neuron. The underlying mechanism of this stochastic commitment to one of multiple similar OR genes remains elusive. We present a theoretical analysis of a mechanism that invokes important epigenetic properties of the system. The proposed model combines nucleosomes and associated read–write enzymes as mediators of a cis-acting positive feedback with a trans-acting negative feedback, thereby coupling the local epigenetic landscape of the individual OR genes in a way that allow one and only one gene to be active at any time. The model pinpoint that singular gene selection does not require transient mechanisms, enhancer elements or transcription factors to separate choice from maintenance. In addition, our hypothesis allow us to combine all reported characteristics of singular OR gene selection, in particular that OR genes are silenced from OR transgenes. Intriguingly, it predicts that OR transgenes placed in close proximity should always be expressed simultaneously, though rarely.
- Published
- 2013
36. An apomixis-linked ORC3-like pseudogene is associated with silencing of its functional homolog in apomictic Paspalum simplex
- Author
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Lorena Adelina Siena, Maria Eugenia Caceres, Simone Grisan, Juan Pablo A. Ortiz, Ornella Calderini, Francesco Paolocci, Pankaj Kaushal, Fulvio Pupilli, and Silvina Claudia Pessino
- Subjects
0106 biological sciences ,0301 basic medicine ,Transcription, Genetic ,Physiology ,Cellular differentiation ,Arabidopsis ,Origin Recognition Complex ,Asexual reproduction ,Plant Science ,Seed Development ,01 natural sciences ,Endosperm ,gene silencing ,Gene Expression Regulation, Plant ,Paspalum ,Cloning, Molecular ,In Situ Hybridization ,Plant Proteins ,Genetics ,Gametophyte ,Reproduction ,Agricultura ,Chromosome Mapping ,food and beverages ,medicine.anatomical_structure ,Apomixis ,Pseudogenes ,Germ cell ,seed development ,Pseudogene ,Biology ,03 medical and health sciences ,Sequence Homology, Nucleic Acid ,medicine ,RNA, Messenger ,Gene Silencing ,Base Sequence ,Gene Expression Profiling ,Oryza ,030104 developmental biology ,CIENCIAS AGRÍCOLAS ,Mutation ,purl.org/becyt/ford/4.1 [https] ,Origin recognition complex ,origin recognition complex ,Agricultura, Silvicultura y Pesca ,Sequence Alignment ,purl.org/becyt/ford/4 [https] ,010606 plant biology & botany - Abstract
Apomixis in plants consists of asexual reproduction by seeds. Here we characterized at structural and functional levels an apomixis-linked sequence of Paspalum simplex homologous to subunit 3 of the ORIGIN RECOGNITION COMPLEX (ORC3). ORC is a multiprotein complex which controls DNA replication and cell differentiation in eukaryotes. Three PsORC3 copies were identified, each one characterized by a specific expression profile. Of these, PsORC3a, specific for apomictic genotypes, is a pseudogene that was poorly and constitutively expressed in all developmental stages of apomictic flowers, whereas PsORC3b, the putative functional gene in sexual flowers, showed a precise time-related regulation. Sense transcripts of PsORC3 were expressed in the female cell lineage of both apomictic and sexual reproductive phenotypes, and in aposporous initials. Although strong expression was detected in sexual early endosperm, no expression was present in the apomictic endosperm. Antisense PsORC3 transcripts were revealed exclusively in apomictic germ cell lineages. Defective orc3 mutants of rice and Arabidopsis showed normal female gametophytes although the embryo and endosperm were arrested at early phases of development. We hypothesize that PsORC3a is associated with the down-regulation of its functional homolog and with the development of apomictic endosperm which deviates from the canonical 2(maternal):1(paternal) genome ratio. Fil: Siena, Lorena Adelina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Investigaciones en Ciencias Agrarias de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Agrarias. Instituto de Investigaciones en Ciencias Agrarias de Rosario; Argentina Fil: Ortiz, Juan Pablo Amelio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Investigaciones en Ciencias Agrarias de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Agrarias. Instituto de Investigaciones en Ciencias Agrarias de Rosario; Argentina Fil: Calderini, Ornella. Istituto di Bioscienze e Biorisorse; Italia Fil: Paolocci, Francesco. Istituto di Bioscienze e Biorisorse; Italia Fil: Cáceres, Maria E.. Istituto di Bioscienze e Biorisorse; Italia Fil: Kaushal, Pankaj. Istituto di Bioscienze e Biorisorse; Italia Fil: Grisan, Simone. Istituto di Bioscienze e Biorisorse; Italia Fil: Pessino, Silvina Claudia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Investigaciones en Ciencias Agrarias de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Agrarias. Instituto de Investigaciones en Ciencias Agrarias de Rosario; Argentina Fil: Pupilli, Fulvio. Istituto di Bioscienze e Biorisorse; Italia
- Published
- 2016
37. Horizontal Transfer and Death of a Fungal Secondary Metabolic Gene Cluster
- Author
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Matthew A. Campbell, Jason C. Slot, and Antonis Rokas
- Subjects
Letter ,Gene Transfer, Horizontal ,Pseudogene ,Xanthones ,pseudogene ,pathway degeneration ,Fungal Proteins ,03 medical and health sciences ,bikaverin ,Fusarium ,Gene cluster ,Genetics ,Gene ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Regulator gene ,Botrytis cinerea ,Synteny ,0303 health sciences ,biology ,030306 microbiology ,secondary metabolites ,Structural gene ,fungi ,food and beverages ,biology.organism_classification ,Multigene Family ,Horizontal gene transfer ,Botrytis ,Pseudogenes - Abstract
A cluster composed of four structural and two regulatory genes found in several species of the fungal genus Fusarium (class Sordariomycetes) is responsible for the production of the red pigment bikaverin. We discovered that the unrelated fungus Botrytis cinerea (class Leotiomycetes) contains a cluster of five genes that is highly similar in sequence and gene order to the Fusarium bikaverin cluster. Synteny conservation, nucleotide composition, and phylogenetic analyses of the cluster genes indicate that the B. cinerea cluster was acquired via horizontal transfer from a Fusarium donor. Upon or subsequent to the transfer, the B. cinerea gene cluster became inactivated; one of the four structural genes is missing, two others are pseudogenes, and the fourth structural gene shows an accelerated rate of nonsynonymous substitutions along the B. cinerea lineage, consistent with relaxation of selective constraints. Interestingly, the bik4 regulatory gene is still intact and presumably functional, whereas bik5, which is a pathway-specific regulator, also shows a mild but significant acceleration of evolutionary rate along the B. cinerea lineage. This selective preservation of the bik4 regulator suggests that its conservation is due to its likely involvement in other non-bikaverin-related biological processes in B. cinerea. Thus, in addition to novel metabolism, horizontal transfer of wholesale metabolic gene clusters might also be contributing novel regulation.
- Published
- 2012
38. Are Human Translated Pseudogenes Functional?
- Author
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Jianzhi Zhang and Jinrui Xu
- Subjects
0301 basic medicine ,Nonsynonymous substitution ,Proteome ,Transcription, Genetic ,Pseudogene ,Molecular Sequence Data ,Macaque ,Evolution, Molecular ,03 medical and health sciences ,Negative selection ,Open Reading Frames ,biology.animal ,Genetics ,Animals ,Humans ,Amino Acid Sequence ,ORFS ,Selection, Genetic ,Molecular Biology ,Gene ,Ecology, Evolution, Behavior and Systematics ,Discoveries ,biology ,Base Sequence ,Computational Biology ,Genomics ,Open reading frame ,030104 developmental biology ,Protein Biosynthesis ,Synonymous substitution ,Transcriptome ,Pseudogenes - Abstract
By definition, pseudogenes are relics of former genes that no longer possess biological functions. Operationally, they are identified based on disruptions of open reading frames (ORFs) or presumed losses of promoter activities. Intriguingly, a recent human proteomic study reported peptides encoded by 107 pseudogenes. These peptides may play currently unrecognized physiological roles. Alternatively, they may have resulted from accidental translations of pseudogene transcripts and possess no function. Comparing between human and macaque orthologs, we show that the nonsynonymous to synonymous substitution rate ratio (ω) is significantly smaller for translated pseudogenes than other pseudogenes. In particular, five of 34 translated pseudogenes amenable to evolutionary analysis have ω values significantly lower than 1, indicative of the action of purifying selection. This and other findings demonstrate that some but not all translated pseudogenes have selected functions at the protein level. Hence, neither ORF disruption nor presence of protein product disproves or proves gene functionality at the protein level.
- Published
- 2015
39. Genomic and Genetic Evidence for the Loss of Umami Taste in Bats
- Author
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Dong Xu, Shuyi Zhang, Huabin Zhao, and Jianzhi Zhang
- Subjects
Taste ,Monosodium glutamate ,Molecular Sequence Data ,bats ,Zoology ,Tas1r1 ,Umami ,Biology ,Receptors, G-Protein-Coupled ,TAS1R1 ,Evolution, Molecular ,chemistry.chemical_compound ,Food Preferences ,TAS1R3 ,Dogs ,TAS1R2 ,Taste receptor ,Chiroptera ,Genetics ,Animals ,Letters ,umami taste ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Genome ,Base Sequence ,Genomics ,Taste Buds ,TAS2R38 ,chemistry ,Biochemistry ,pseudogenization ,diet ,Sequence Alignment ,Pseudogenes - Abstract
Umami taste is responsible for sensing monosodium glutamate, nucleotide enhancers, and other amino acids that are appetitive to vertebrates and is one of the five basic tastes that also include sour, salty, sweet, and bitter. To study how ecological factors, especially diets, impact the evolution of the umami taste, we examined the umami taste receptor gene Tas1r1 in a phylogenetically diverse group of bats including fruit eaters, insect eaters, and blood feeders. We found that Tas1r1 is absent, unamplifiable, or pseudogenized in each of the 31 species examined, including the genome sequences of two species, suggesting the loss of the umami taste in most, if not all, bats regardless of their food preferences. Most strikingly, vampire bats have also lost the sweet taste receptor gene Tas1r2 and the gene required for both umami and sweet tastes (Tas1r3), being the first known mammalian group to lack two of the five tastes. The puzzling absence of the umami taste in bats calls for a better understanding of the roles that this taste plays in the daily life of vertebrates.
- Published
- 2011
40. Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies
- Author
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Joshua M. Stuart, H. James Tripp, Ian Hewson, Jonathan P. Zehr, and Sam Boyarsky
- Subjects
Protein family ,Hydrolases ,Computational biology ,Biology ,03 medical and health sciences ,Annotation ,23S ribosomal RNA ,Operon ,Genetics ,RNA, Antisense ,Internal transcribed spacer ,030304 developmental biology ,Alphaproteobacteria ,0303 health sciences ,Bacteria ,030302 biochemistry & molecular biology ,Genes, rRNA ,Molecular Sequence Annotation ,Genomics ,Sequence Analysis, DNA ,Archaea ,3. Good health ,Metagenomics ,GenBank ,Pyrosequencing ,Databases, Nucleic Acid ,Transcriptome ,Pseudogenes - Abstract
In the course of analyzing 9,522,746 pyrosequencing reads from 23 stations in the Southwestern Pacific and equatorial Atlantic oceans, it came to our attention that misannotations of rRNA as proteins is now so widespread that false positive matching of rRNA pyrosequencing reads to the National Center for Biotechnology Information (NCBI) non-redundant protein database approaches 90%. One conserved portion of 23S rRNA was consistently misannotated often enough to prompt curators at Pfam to create a spurious protein family. Detailed examination of the annotation history of each seed sequence in the spurious Pfam protein family (PF10695, 'Cw-hydrolase') uncovered issues in the standard operating procedures and quality assurance programs of major sequencing centers, and other issues relating to the curation practices of those managing public databases such as GenBank and SwissProt. We offer recommendations for all these issues, and recommend as well that workers in the field of metatranscriptomics take extra care to avoid including false positive matches in their datasets.
- Published
- 2011
41. Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project
- Author
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Mark Gerstein, Yong Kong, Zhi John Lu, Xinmeng Jasmine Mu, and Hugo Y. K. Lam
- Subjects
RNA, Untranslated ,Pseudogene ,Population ,Genomics ,Computational biology ,Biology ,Genome ,Polymorphism, Single Nucleotide ,Negative selection ,Gene Frequency ,INDEL Mutation ,Genetics ,Humans ,1000 Genomes Project ,Indel ,education ,education.field_of_study ,Binding Sites ,Genome, Human ,Genetic Variation ,Proteins ,MicroRNAs ,Human genome ,DNA, Intergenic ,Pseudogenes ,Transcription Factors - Abstract
In the human genome, it has been estimated that considerably more sequence is under natural selection in non-coding regions [such as transcription-factor binding sites (TF-binding sites) and non-coding RNAs (ncRNAs)] compared to protein-coding ones. However, less attention has been paid to them. To study selective pressure on non-coding elements, we use next-generation sequencing data from the recently completed pilot phase of the 1000 Genomes Project, which, compared to traditional methods, allows for the characterization of a full spectrum of genomic variations, including single-nucleotide polymorphisms (SNPs), short insertions and deletions (indels) and structural variations (SVs). We develop a framework for combining these variation data with non-coding elements, calculating various population-based metrics to compare classes and subclasses of elements, and developing element-aware aggregation procedures to probe the internal structure of an element. Overall, we find that TF-binding sites and ncRNAs are less selectively constrained for SNPs than coding sequences (CDSs), but more constrained than a neutral reference. We also determine that the relative amounts of constraint for the three types of variations are, in general, correlated, but there are some differences: counter-intuitively, TF-binding sites and ncRNAs are more selectively constrained for indels than for SNPs, compared to CDSs. After inspecting the overall properties of a class of elements, we analyze selective pressure on subclasses within an element class, and show that the extent of selection is associated with the genomic properties of each subclass. We find, for instance, that ncRNAs with higher expression levels tend to be under stronger purifying selection, and the actual regions of TF-binding motifs are under stronger selective pressure than the corresponding peak regions. Further, we develop element-aware aggregation plots to analyze selective pressure across the linear structure of an element, with the confidence intervals evaluated using both simple bootstrapping and block bootstrapping techniques. We find, for example, that both micro-RNAs (particularly the seed regions) and their binding targets are under stronger selective pressure for SNPs than their immediate genomic surroundings. In addition, we demonstrate that substitutions in TF-binding motifs inversely correlate with site conservation, and SNPs unfavorable for motifs are under more selective constraints than favorable SNPs. Finally, to further investigate intra-element differences, we show that SVs have the tendency to use distinctive modes and mechanisms when they interact with genomic elements, such as enveloping whole gene(s) rather than disrupting them partially, as well as duplicating TF motifs in tandem.
- Published
- 2011
42. RetrogeneDB—A Database of Animal Retrogenes
- Author
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Michal Kabza, Joanna Ciomborowska, and Izabela Makalowska
- Subjects
Retroelements ,Pseudogene ,Fast Tracks ,Context (language use) ,Biology ,computer.software_genre ,Genome ,Evolution, Molecular ,03 medical and health sciences ,Gene duplication ,Databases, Genetic ,Genetics ,Animals ,Humans ,Molecular Biology ,Gene ,Ecology, Evolution, Behavior and Systematics ,database ,030304 developmental biology ,retroposition ,0303 health sciences ,retrogene ,Database ,030302 biochemistry & molecular biology ,gene duplication ,RNA ,computer ,Pseudogenes - Abstract
Retrocopies of protein-coding genes, reverse transcribed and inserted into the genome copies of mature RNA, have commonly been categorized as pseudogenes with no biological importance. However, recent studies showed that they play important role in the genomes evolution and shaping interspecies differences. Here, we present RetrogeneDB, a database of retrocopies in 62 animal genomes. RetrogeneDB contains information about retrocopies, their genomic localization, parental genes, ORF conservation, and expression. To our best knowledge, this is the most complete retrocopies database providing information for dozens of species previously never analyzed in the context of protein-coding genes retroposition. The database is available at http://retrogenedb.amu.edu.pl.
- Published
- 2014
43. Segmental duplications in the human genome reveal details of pseudogene formation
- Author
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Mark Gerstein, Nicholas Carriero, Chao Cheng, Ekta Khurana, Philip Cayting, and Hugo Y. K. Lam
- Subjects
Genetics ,Genome evolution ,Genome, Human ,Pseudogene ,Retrotransposon ,Genomics ,Biology ,Genome ,Evolution, Molecular ,Segmental Duplications, Genomic ,Genetic Loci ,Gene Duplication ,Gene duplication ,Humans ,Human genome ,Gene ,Pseudogenes ,Segmental duplication - Abstract
Duplicated pseudogenes in the human genome are disabled copies of functioning parent genes. They result from block duplication events occurring throughout evolutionary history. Relatively recent duplications (with sequence similarity ≥90% and length ≥1 kb) are termed segmental duplications (SDs); here, we analyze the interrelationship of SDs and pseudogenes. We present a decision-tree approach to classify pseudogenes based on their (and their parents’) characteristics in relation to SDs. The classification identifies 140 novel pseudogenes and makes possible improved annotation for the 3172 pseudogenes located in SDs. In particular, it reveals that many pseudogenes in SDs likely did not arise directly from parent genes, but are the result of a multi-step process. In these cases, the initial duplication or retrotransposition of a parent gene gives rise to a ‘parent pseudogene’, followed by further duplication creating duplicated–duplicated or duplicated–processed pseudogenes, respectively. Moreover, we can precisely identify these parent pseudogenes by overlap with ancestral SD loci. Finally, a comparison of nucleotide substitutions per site in a pseudogene with its surrounding SD region allows us to estimate the time difference between duplication and disablement events, and this suggests that most duplicated pseudogenes in SDs were likely disabled around the time of the original duplication.
- Published
- 2010
44. PseudoChecker: an integrated online platform for gene inactivation inference.
- Author
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Alves LQ, Ruivo R, Fonseca MM, Lopes-Marques M, Ribeiro P, and Castro LFC
- Subjects
- Animals, Codon, Genomics methods, Mutation, Sequence Alignment, Pseudogenes, Software
- Abstract
The rapid expansion of high-quality genome assemblies, exemplified by ongoing initiatives such as the Genome-10K and i5k, demands novel automated methods to approach comparative genomics. Of these, the study of inactivating mutations in the coding region of genes, or pseudogenization, as a source of evolutionary novelty is mostly overlooked. Thus, to address such evolutionary/genomic events, a systematic, accurate and computationally automated approach is required. Here, we present PseudoChecker, the first integrated online platform for gene inactivation inference. Unlike the few existing methods, our comparative genomics-based approach displays full automation, a built-in graphical user interface and a novel index, PseudoIndex, for an empirical evaluation of the gene coding status. As a multi-platform online service, PseudoChecker simplifies access and usability, allowing a fast identification of disruptive mutations. An analysis of 30 genes previously reported to be eroded in mammals, and 30 viable genes from the same lineages, demonstrated that PseudoChecker was able to correctly infer 97% of loss events and 95% of functional genes, confirming its reliability. PseudoChecker is freely available, without login required, at http://pseudochecker.ciimar.up.pt., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2020
- Full Text
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45. Reduced chromatin accessibility underlies gene expression differences in homologous chromosome arms of diploid Aegilops tauschii and hexaploid wheat.
- Author
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Lu FH, McKenzie N, Gardiner LJ, Luo MC, Hall A, and Bevan MW
- Subjects
- Chromatin metabolism, Computational Biology methods, DNA Methylation, Evolution, Molecular, Genome, Plant, Genomics methods, Pseudogenes, Aegilops genetics, Chromatin genetics, Chromatin Assembly and Disassembly, Chromosomes, Plant, Gene Expression Regulation, Plant, Ploidies, Triticum genetics
- Abstract
Background: Polyploidy is centrally important in the evolution and domestication of plants because it leads to major genomic changes, such as altered patterns of gene expression, which are thought to underlie the emergence of new traits. Despite the common occurrence of these globally altered patterns of gene expression in polyploids, the mechanisms involved are not well understood., Results: Using a precisely defined framework of highly conserved syntenic genes on hexaploid wheat chromosome 3DL and its progenitor 3 L chromosome arm of diploid Aegilops tauschii, we show that 70% of these gene pairs exhibited proportionately reduced gene expression, in which expression in the hexaploid context of the 3DL genes was ∼40% of the levels observed in diploid Ae tauschii. Several genes showed elevated expression during the later stages of grain development in wheat compared with Ae tauschii. Gene sequence and methylation differences probably accounted for only a few cases of differences in gene expression. In contrast, chromosome-wide patterns of reduced chromatin accessibility of genes in the hexaploid chromosome arm compared with its diploid progenitor were correlated with both reduced gene expression and the imposition of new patterns of gene expression., Conclusions: Our pilot-scale analyses show that chromatin compaction may orchestrate reduced gene expression levels in the hexaploid chromosome arm of wheat compared to its diploid progenitor chromosome arm., (© The Author(s) 2020. Published by Oxford University Press.)
- Published
- 2020
- Full Text
- View/download PDF
46. Pervasive Suicidal Integrases in Deep-Sea Archaea.
- Author
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Badel C, Da Cunha V, Forterre P, and Oberto J
- Subjects
- Hydrothermal Vents, Integrases genetics, Interspersed Repetitive Sequences, Thermococcus genetics, Thermococcus isolation & purification, Evolution, Molecular, Integrases metabolism, Pseudogenes, Thermococcus enzymology
- Abstract
Mobile genetic elements (MGEs) often encode integrases which catalyze the site-specific insertion of their genetic information into the host genome and the reverse reaction of excision. Hyperthermophilic archaea harbor integrases belonging to the SSV-family which carry the MGE recombination site within their open reading frame. Upon integration into the host genome, SSV integrases disrupt their own gene into two inactive pseudogenes and are termed suicidal for this reason. The evolutionary maintenance of suicidal integrases, concurring with the high prevalence and multiples recruitments of these recombinases by archaeal MGEs, is highly paradoxical. To elucidate this phenomenon, we analyzed the wide phylogenomic distribution of a prominent class of suicidal integrases which revealed a highly variable integration site specificity. Our results highlighted the remarkable hybrid nature of these enzymes encoded from the assembly of inactive pseudogenes of different origins. The characterization of the biological properties of one of these integrases, IntpT26-2 showed that this enzyme was active over a wide range of temperatures up to 99 °C and displayed a less-stringent site specificity requirement than comparable integrases. These observations concurred in explaining the pervasiveness of these suicidal integrases in the most hyperthermophilic organisms. The biochemical and phylogenomic data presented here revealed a target site switching system operating on highly thermostable integrases and suggested a new model for split gene reconstitution. By generating fast-evolving pseudogenes at high frequency, suicidal integrases constitute a powerful model to approach the molecular mechanisms involved in the generation of active genes variants by the recombination of proto-genes., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
- Published
- 2020
- Full Text
- View/download PDF
47. Cortisol and Aldosterone Responses to Hypoglycemia and Na Depletion in Women With Non-Classic 21-Hydroxylase Deficiency.
- Author
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Kamenický P, Blanchard A, Lamaziere A, Piedvache C, Donadille B, Duranteau L, Bry H, Gautier JF, Salenave S, Raffin-Sanson ML, Genc S, Pietri L, Christin-Maitre S, Thomas J, Lorthioir A, Azizi M, Chanson P, Le Bouc Y, Brailly-Tabard S, and Young J
- Subjects
- Adolescent, Adult, Case-Control Studies, Equivalence Trials as Topic, Female, Follow-Up Studies, France epidemiology, Humans, Hypoglycemia blood, Hypoglycemia epidemiology, Incidence, Middle Aged, Prognosis, Prospective Studies, Young Adult, Adrenal Hyperplasia, Congenital physiopathology, Aldosterone blood, Biomarkers blood, Hydrocortisone blood, Hypoglycemia pathology, Pseudogenes, Sodium deficiency
- Abstract
Background: Non-classic 21-hydroxylase deficiency is usually diagnosed in post-pubertal women because of androgen excess. Indication of systematic steroid replacement therapy is controversial because the risk of acute adrenal insufficiency is unknown. In order to specify this risk we evaluated the cortisol and aldosterone secretions in response to appropriate pharmacologic challenges., Methods: In this prospective case-control non-inferiority study we investigated 20 women with non-classic 21-hydroxylase deficiency carrying biallelic CYP21A2 mutations and with serum 17-hydroxyprogesterone (17OHP) >10 ng/mL after stimulation with Synacthen® (tetracosactrin) and 20 age- and body mass index-matched healthy women with 17OHP after Synacthen® <2 ng/mL. Each participant underwent sequentially an insulin tolerance test to evaluate cortisol secretion and a sodium depletion test, obtained by oral administration of 40 mg of furosemide under low sodium diet (<20 mmol during 24 hours), to evaluate renin and aldosterone secretion., Findings: The peak serum cortisol concentration after insulin hypoglycemia was lower in patients than in controls (mean difference -47 ng/mL, 90% CI, -66, P = 0.0026). A peak serum cortisol above a cutoff value of 170 ng/mL was obtained in all controls but only in 55% of patients (P = 0.0039). Twenty-four hours after sodium depletion, blood pressure, plasma sodium, potassium, and serum aldosterone concentrations were comparable between the two groups, but patients had higher stimulated renin concentrations than controls (P = 0.0044)., Interpretation: Patients with non-classic 21-hydroxylase deficiency frequently display partial cortisol insufficiency and compensated defect in aldosterone secretion. Their clinical management should systematically include assessment of adrenal functions., (© Endocrine Society 2019. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2020
- Full Text
- View/download PDF
48. Aquatic Adaptation and Depleted Diversity: A Deep Dive into the Genomes of the Sea Otter and Giant Otter.
- Author
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Beichman AC, Koepfli KP, Li G, Murphy W, Dobrynin P, Kliver S, Tinker MT, Murray MJ, Johnson J, Lindblad-Toh K, Karlsson EK, Lohmueller KE, and Wayne RK
- Subjects
- Animals, Genetic Variation, Whole Genome Sequencing, Adaptation, Biological genetics, Biological Evolution, Otters genetics, Selection, Genetic
- Abstract
Despite its recent invasion into the marine realm, the sea otter (Enhydra lutris) has evolved a suite of adaptations for life in cold coastal waters, including limb modifications and dense insulating fur. This uniquely dense coat led to the near-extinction of sea otters during the 18th-20th century fur trade and an extreme population bottleneck. We used the de novo genome of the southern sea otter (E. l. nereis) to reconstruct its evolutionary history, identify genes influencing aquatic adaptation, and detect signals of population bottlenecks. We compared the genome of the southern sea otter with the tropical freshwater-living giant otter (Pteronura brasiliensis) to assess common and divergent genomic trends between otter species, and with the closely related northern sea otter (E. l. kenyoni) to uncover population-level trends. We found signals of positive selection in genes related to aquatic adaptations, particularly limb development and polygenic selection on genes related to hair follicle development. We found extensive pseudogenization of olfactory receptor genes in both the sea otter and giant otter lineages, consistent with patterns of sensory gene loss in other aquatic mammals. At the population level, the southern sea otter and the northern sea otter showed extremely low genomic diversity, signals of recent inbreeding, and demographic histories marked by population declines. These declines may predate the fur trade and appear to have resulted in an increase in putatively deleterious variants that could impact the future recovery of the sea otter., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2019
- Full Text
- View/download PDF
49. Evolutionary signatures of photoreceptor transmutation in geckos reveal potential adaptation and convergence with snakes.
- Author
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Schott RK, Bhattacharyya N, and Chang BSW
- Subjects
- Animals, Light, Opsins genetics, Phylogeny, Pseudogenes, Selection, Genetic, Species Specificity, Transcriptome, Vision, Ocular, Biological Evolution, Lizards physiology, Retinal Cone Photoreceptor Cells physiology, Retinal Rod Photoreceptor Cells physiology, Snakes physiology
- Abstract
Most vertebrates use a combination of rod and cone photoreceptors to enable vision in conditions ranging from starlight to direct sunlight. Nocturnal geckos, however, have simplex retinas that contain only rods in terms of morphology and physiology, but these rods are thought to be derived from cones through an evolutionary process known as photoreceptor transmutation. To investigate this, we generated eye transcriptomes and analyzed patterns of phototransduction gene evolution in geckos in comparison to other reptiles. We confirm that geckos have lost several major components of the rod phototransduction pathway, including rod opsin (RH1), which we identified as a pseudogene in multiple genomes. We also identified a partial rod transducin transcript, but found no evidence of the protein in retinal sections. However, we find that geckos express several complete rod phototransduction transcripts in the eye, which may contribute to the rod-like physiology of nocturnal gecko photoreceptors. Finally, we found surprising evidence that even though photoreceptor transmutation evolved independently in geckos and snakes, they have experienced parallel shifts in selective constraint on phototransduction genes. These results implicate adaptive change in the underlying molecular machinery of visual transduction, in addition to the convergent changes in cellular morphology, during photoreceptor transmutation., (© 2019 The Author(s). Evolution © 2019 The Society for the Study of Evolution.)
- Published
- 2019
- Full Text
- View/download PDF
50. An enhanced MITOMAP with a global mtDNA mutational phylogeny
- Author
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James Kreuziger, Christina Yi, Vincent Procaccio, Douglas C. Wallace, Marie T. Lott, Jason C. Poole, Pierre Baldi, Eduardo Ruiz-Pesini, Dan Mishmar, and Marty C. Brandon
- Subjects
hereditary optic neuropathy ,Mitochondrial DNA ,Mitochondrial Diseases ,Pseudogene ,adaptive selection ,Biology ,Human mitochondrial genetics ,DNA, Mitochondrial ,Haplogroup ,03 medical and health sciences ,User-Computer Interface ,0302 clinical medicine ,longevity ,alzheimer-disease ,Medicine and Health Sciences ,Genetics ,Humans ,african populations ,genome ,Phylogeny ,030304 developmental biology ,mtDNA control region ,0303 health sciences ,Internet ,Genome ,Phylogenetic tree ,Life Sciences ,ancient ,Articles ,mitochondrial-dna analysis ,haplogroups ,Mutation ,Numt ,human-evolution ,Databases, Nucleic Acid ,030217 neurology & neurosurgery ,Pseudogenes ,Human mitochondrial DNA haplogroup - Abstract
The MITOMAP (http://www.mitomap.org) data system for the human mitochondrial genome has been greatly enhanced by the addition of a navigable mutational mitochondrial DNA (mtDNA) phylogenetic tree of approximately 3000 mtDNA coding region sequences plus expanded pathogenic mutation tables and a nuclear-mtDNA pseudogene (NUMT) data base. The phylogeny reconstructs the entire mutational history of the human mtDNA, thus defining the mtDNA haplogroups and differentiating ancient from recent mtDNA mutations. Pathogenic mutations are classified by both genotype and phenotype, and the NUMT sequences permits detection of spurious inclusion of pseudogene variants during mutation analysis. These additions position MITOMAP for the implementation of our automated mtDNA sequence analysis system, Mitomaster.
- Published
- 2006
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