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The Elsholtzieae, comprising ca. 7 genera and 70 species, is a small tribe of Lamiaceae (mint family). Members of Elsholtzieae are of high medicinal, aromatic, culinary, and ornamentals value. Despite the rich diversity and value of Elsholtzieae, few molecular markers or plastomes are available for phylogenetics. In the present study, we employed high-throughput sequencing to assemble two Mosla plastomes, M. dianthera and M. scabra, for the first time, and compared with other plastomes of Elsholtzieae. The plastomes of Elsholtzieae exhibited a quadripartite structure, ranging in size from 148,288 bp to 152,602 bp. Excepting the absence of the pseudogene rps19 in Elsholtzia densa, the exhaustive tally revealed the presence of 132 genes (113 unique genes). Among these, 85 protein-coding genes (CDS), 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes (rps19 and ycf1) were annotated. Comparative analyses showed that the plastomes of these species have minor variations at the gene level. Notably, the E. eriostchya plastid genome exhibited increased GC content regions in the LSC and SSC, resulting in an increased overall GC content of the entire plastid genome. The E. densa plastid genome displayed modified boundaries due to inverted repeat (IR) contraction. The sequences of CDS and intergenic regions (IGS) with elevated variability were identified as potential molecular markers for taxonomic inquiries within Elsholtzieae. Phylogenetic analysis indicated that four genera formed monophyletic entities, with Mosla and Perilla forming a sister clade. This clade was, in turn, sister to Collinsonia, collectively forming a sister group to Elsholtzia. Both CDS, and CDS + IGS could construct a phylogenetic tree with stronger support. These findings facilitate species identification and DNA barcoding investigations in Elsholtzieae and provide a foundation for further exploration and resource utilization within this tribe. [ABSTRACT FROM AUTHOR]

BACKGROUND: Osteoarthritis is one of the most common joint diseases. With the increasing global incidence and prevalence of osteoarthritis, effective early diagnosis and treatment of osteoarthritis have become an urgent problem. OBJECTIVE: To elucidate the important biological functions of long non-coding RNAs, circular RNAs and pseudogenes and their regulatory roles as competing endogenous RNAs in osteoarthritis pathogenesis to gain a comprehensive, in-depth and new understanding of the involvement of competing endogenous RNAs in osteoarthritis progression and to provide new clues for early diagnosis and treatment of osteoarthritis. METHODS: CNKI, PubMed, VIP and WanFang databases were searched for articles published before 2022. The search terms were “osteoarthritis, competing endogenous RNA, circular RNA, long non-coding RNAs, pseudogenes” in Chinese and English. RESULTS AND CONCLUSION: Non-coding RNAs with the same microRNA response elements, including long non-coding RNAs, cyclic RNAs and pseudogenes, are involved in the construction of a regulatory network of competing endogenous RNAs centered on microRNAs. Non-coding RNAs, cyclic RNAs and pseudogenes can act as competing endogenous RNAs to adsorb microRNAs through “sponge” so as to regulate gene expression. Long non-coding RNAs, cyclic RNAs and pseudogenes can act as competing endogenous RNAs to regulate the proliferation, apoptosis and autophagy of osteoarthritic chondrocytes, the synthesis and degradation of extracellular matrix and the occurrence of inflammatory events. The practical application of the regulatory network of competing endogenous RNA to the clinical setting still faces many challenges and problems. The research on competing endogenous RNA as diagnostic markers or therapeutic targets for osteoarthritis is still at an early stage, and the current research on competing endogenous RNA regulatory network is still focused on the identification and validation of individual competing endogenous RNAs, and this regulatory network needs to be further supplemented and improved. However, with the development of advanced technologies, competing endogenous RNAs are expected to become early diagnostic markers and therapeutic targets for osteoarthritis diseases. [ABSTRACT FROM AUTHOR]

Parasitic red algae are an interesting system for investigating the genetic changes that occur in parasites. These parasites have evolved independently multiple times within the red algae. The functional loss of plastid genomes can be investigated in these multiple independent examples, and fine‐scale patterns may be discerned. The only plastid genomes from red algal parasites known so far are highly reduced and missing almost all photosynthetic genes. Our study assembled and annotated plastid genomes from the parasites Janczewskia tasmanica and its two Laurencia host species (Laurencia elata and one unidentified Laurencia sp. A25) from Australia and Janczewskia verruciformis, its host species (Laurencia catarinensis), and the closest known free‐living relative (Laurencia obtusa) from the Canary Islands (Spain). For the first time we show parasitic red algal plastid genomes that are similar in size and gene content to free‐living host species without any gene loss or genome reduction. The only exception was two pseudogenes (moeB and ycf46) found in the plastid genome of both isolates of J. tasmanica, indicating potential for future loss of these genes. Further comparative analyses with the three highly reduced plastid genomes showed possible gene loss patterns, in which photosynthetic gene categories were lost followed by other gene categories. Phylogenetic analyses did not confirm monophyly of Janczewskia, and the genus was subsumed into Laurencia. Further investigations will determine if any convergent small‐scale patterns of gene loss exist in parasitic red algae and how these are applicable to other parasitic systems. [ABSTRACT FROM AUTHOR]

As an endosymbiont, Wolbachia exerts significant effects on the host, including on reproduction, immunity, and metabolism. However, the study of Wolbachia in Thysanopteran insects, such as flower thrips Frankliniella intonsa, remains limited. Here, we assembled a gap-free looped genome assembly of Wolbachia strain wFI in a length of 1,463,884 bp (GC content 33.80%), using Nanopore long reads and Illumina short reads. The annotation of wFI identified a total of 1838 protein-coding genes (including 85 pseudogenes), 3 ribosomal RNAs (rRNAs), 35 transfer RNAs (tRNAs), and 1 transfer-messenger RNA (tmRNA). Beyond this basic description, we identified mobile genetic elements, such as prophage and insertion sequences (ISs), which make up 17% of the entire wFI genome, as well as genes involved in riboflavin and biotin synthesis and metabolism. This research lays the foundation for understanding the nutritional mutualism between Wolbachia and flower thrips. It also serves as a valuable resource for future studies delving into the intricate interactions between Wolbachia and its host. [ABSTRACT FROM AUTHOR]

Anaplasma capra is an emerging tickborne human pathogen initially recognized in China in 2015; it has been reported in ticks and in a wide range of domestic and wild animals worldwide. We describe whole-genome sequences of 2 A. capra strains from metagenomic sequencing of purified erythrocytes from infected goats in China. The genome of A. capra was the smallest among members of the genus Anaplasma. The genomes of the 2 A. capra strains contained comparable G+C content and numbers of pseudogenes with intraerythrocytic Anaplasma species. The 2 A. capra strains had 54 unique genes. The prevalence of A. capra was high among goats in the 2 endemic areas. Phylogenetic analyses revealed that the A. capra strains detected in this study were basically classified into 2 subclusters with those previously detected in Asia. Our findings clarify details of the genomic characteristics of A. capra and shed light on its genetic diversity. [ABSTRACT FROM AUTHOR]

The complete chloroplast genomes of red currant cultivar 'Belaya Potapenko' and gooseberry cultivar 'Nekrasovskij' were sequenced and assembled for the first time. The plastomes are 157,802 bp and 157,559 bp in length for Ribes rubrum and R. uva-crispa, respectively. The R. rubrum cp genome is 243 b.p. longer. It has one more protein-coding gene ycf1, which is pseudogenized in the R. uva-crispa cp genome. In total, 56 and 54 simple sequence repeats (SSRs) were identified within the assembled plastid genomes. The SSR content of plastid genomes was assessed for the 18 Saxifragales species. Phylogeny inference based on plastome data of 18 Saxifragales revealed that all Ribes species are clustered together on the phylogenetic tree, though R. fasciculatum seems to be the most distant from the other analyzed Ribes species. The position of taxa inside the Ribes genus clade does not support the concept of its division into five subgenera. All Ribes species share approximately the same set of protein-coding genes in their plastome sequences. There was multiple independent pseudogenization of the ycf1 gene within the Ribes genus as well as other Saxifragales taxa. Negative selection was observed for most of the genes in both the Ribes group and Saxifragales. A positive selection ratio was observed only inside the Ribes group for the ycf4 and clpP genes. Together with positive selection signatures, pseudogenization events of ycfs genes perhaps reflect that these genes' evolution was important for Ribes' adaptation. Thus, our study provides genomic resources and valuable reference for marker development, and makes some clarifications of the phylogenomics of the Ribes genus. [ABSTRACT FROM AUTHOR]

The idea that proteins are the main determining factors in the functioning of cells and organisms, and their dysfunctions are the first cause of pathologies, has been predominant in biology and biomedicine until recently. This protein-centered view was too simplistic and failed to explain the physiological and pathological complexity of the cell. About 80% of the human genome is dynamically and pervasively transcribed, mostly as non-protein-coding RNAs (ncRNAs), which competitively interact with each other and with coding RNAs generating a complex RNA network regulating RNA processing, stability, and translation and, accordingly, fine-tuning the gene expression of the cells. Qualitative and quantitative dysregulations of RNA-RNA interaction networks are strongly involved in the onset and progression of many pathologies, including cancers and degenerative diseases. This review will summarize the RNA species involved in the competitive endogenous RNA network, their mechanisms of action, and involvement in pathological phenotypes. Moreover, it will give an overview of the most advanced experimental and computational methods to dissect and rebuild RNA networks.

There are about 14,000 pseudogenes that are mutated or truncated sequences resembling functional parent genes. About two-thirds of pseudogenes are processed, while others are duplicated. Although initially thought dead, emerging studies indicate they have functional and regulatory roles. We study 14-3-3ζ, an adaptor protein that regulates cytokine signaling and inflammatory diseases, including rheumatoid arthritis, cancer, and neurological disorders. To understand how 14-3-3ζ (gene symbol YWHAZ) performs diverse functions, we examined the human genome and identified nine YWHAZ pseudogenes spread across many chromosomes. Unlike the 32 kb exon-to-exon sequence in YWHAZ, all pseudogenes are much shorter and lack introns. Out of six, four YWHAZ exons are highly conserved, but the untranslated region (UTR) shows significant diversity. The putative amino acid sequence of pseudogenes is 78–97% homologous, resulting in striking structural similarities with the parent protein. The OMIM and Decipher database searches revealed chromosomal loci containing pseudogenes are associated with human diseases that overlap with the parent gene. To the best of our knowledge, this is the first report on pseudogenes of the 14-3-3 family protein and their implications for human health. This bioinformatics-based study introduces a new insight into the complexity of 14-3-3ζ’s functions in biology.

ABSTRACT Pseudogenes, once considered "junk DNA" based on the incorrect assumption that the absence of full coding potential means a complete lack of functionality, have recently become a subject of significant interest in the scientific community. Concurrently, it is widely assumed that bacterial genomes are compact and have a high density of coding genes with little room for non-coding genes, including pseudogenes. A key aspect of genome annotation is the correct identification of genes and the distinction between coding genes and pseudogenes, as it directly impacts functional and comparative genomics studies. In this study, we analyzed the genomic data of 4,699 strains of the bacterium Pseudomonas aeruginosa (P. aeruginosa) as they exhibit high variability in the number of annotated pseudogenes. In particular, we looked for correlations between the number of pseudogenes and other genomic and meta-features of the strains. We identified clusters of orthologous genes and pseudogenes and compared cluster size distributions and length homogeneity within clusters. We then mapped and examined orthology relationships between genes and pseudogenes. Additionally, we generated a phylogenetic tree of the strains and found that phylogenetically related strains are more homogeneous in the number of pseudogenes and share a significant amount of pseudogenes. Finally, we delved into clusters of orthologous genes and pseudogenes and quantified their phylogenetic neighborhood, classifying pseudogenes into evolutionary preserved pseudogenes, mis-annotated pseudogenes, or pseudogenes formed by failed horizontal transfer events. This in-depth study provides important insights that can be incorporated into pseudogene annotation pipelines in the future. IMPORTANCE Accurate annotation of genes and pseudogenes is vital for comparative genomics analysis. Recent studies have shown that bacterial pseudogenes have an important role in regulatory processes and can provide insight into the evolutionary history of homologous genes or the genome as a whole. Due to pseudogenes’ nature as non-functional genes, there is no commonly accepted definition of a pseudogene, which poses difficulties in verifying the annotation through experimental methods and resolving discrepancies among different annotation techniques. Our study introduces an in-depth analysis of annotated genes and pseudogenes and insights that can be incorporated into improved pseudogene annotation pipelines in the future.

Gibberellin (GAs) plays an important regulatory role in the development and growth of pineapple (Ananas comosus (L.) Merr.). Bioinformatics was used to confirm the differential expression of GA2 gibberellin oxidase gene AcGA2oxs in the pineapple genome, which laid the foundation for exploring its role in pineapple. In this study, 42 GA2ox genes (AcGA2oxs) were identified in the pineapple genome, named from AcGA2ox1 to AcGA2ox42, and divided into four groups according to phylogenetic analysis. We also analyzed the gene structure, conserved motifs and chromosome localization of AcGA2oxs. AcGA2oxs within the same group had similar gene structure and motifs composition. Collinear analysis and cis-element analysis provided the basis for understanding the evolution and function of GA2ox genes in pineapple. In addition, we selected different tissue parts to analyze the expression profile of AcGA2oxs, and the results show that 41 genes were expressed, except for AcGA2ox18. AcGA2ox18 may not be expressed in these sites or may be pseudogenes. qRT-PCR (real-time fluorescence quantitative PCR) was used to detect the relative expression levels of the GA2ox gene family under different concentrations of GA3 treatment, and it was found that AcGA2ox gene expression was upregulated in different degrees under GA3 treatment. These results provide useful information for further study on the evolution and function of the GA2ox family in pineapple. [ABSTRACT FROM AUTHOR]

Complex regions in the human genome such as repeat motifs, pseudogenes and structural (SVs) and copy number variations (CNVs) present ongoing challenges to accurate genetic analysis, particularly for short-read Next-Generation- Sequencing (NGS) technologies. One such region is the highly polymorphic CYP2D loci, containing CYP2D6, a clinically relevant pharmacogene contributing to the metabolism of >20% of common drugs, and two highly similar pseudogenes, CYP2D7 and CYP2D8. Multiple complex SVs, including CYP2D6/CYP2D7-derived hybrid genes are known to occur in different configurations and frequencies across populations and are difficult to detect and characterize accurately. This can lead to incorrect enzyme activity assignment and impact drug dosing recommendations, often disproportionally affecting underrepresented populations. To improve CYP2D6 genotyping accuracy, we developed a PCR-free CRISPR-Cas9 based enrichment method for targeted long-read sequencing that fully characterizes the entire CYP2D6- CYP2D7-CYP2D8 loci. Clinically relevant sample types, including blood, saliva, and liver tissue were sequenced, generating high coverage sets of continuous single molecule reads spanning the entire targeted region of up to 52 kb, regardless of SV present (n = 9). This allowed for fully phased dissection of the entire loci structure, including breakpoints, to accurately resolve complex CYP2D6 diplotypes with a single assay. Additionally, we identified three novel CYP2D6 suballeles, and fully characterized 17 CYP2D7 and 18 CYP2D8 unique haplotypes. This method for CYP2D6 genotyping has the potential to significantly improve accurate clinical phenotyping to inform drug therapy and can be adapted to overcome testing limitations of other clinically challenging genomic regions. [ABSTRACT FROM AUTHOR]

Objective. Skin cutaneous melanoma (SKCM) is a highly lethal malignancy that poses a significant threat to human health. Recent research has shown that competing endogenous RNA (ceRNA) regulatory networks play a critical role in the development and progression of various types of cancer, including SKCM. The objective of this study is to investigate the ceRNA regulatory network associated with the transmembrane protein semaphorin 6A (SEMA6A) and identify the underlying molecular mechanisms involved in SKCM. Methods. Expression profiles of four RNAs, including pseudogenes, long non-coding RNAs, microRNAs, and mRNAs were obtained from The Cancer Genome Atlas database. The analysis was completed by bioinformatics methods, and the expression levels of the selected genes were verified by cell experiments. Results. Bioinformatics analysis revealed that the LINC00511–hsa-miR-625-5p–SEMA6A ceRNA network was associated with SKCM prognosis. Furthermore, immune infiltration analysis indicated that the LINC00511–hsa-miR-625-5p–SEMA6A axis may have an impact on changes in the tumor immune microenvironment of SKCM. Conclusion. The LINC00511–hsa-miR-625-5p–SEMA6A axis could be a promising therapeutic target and a prognostic biomarker for SKCM. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Background: Voltage-dependent anion selective channels (VDACs) are the most abundant mitochondrial outer membrane proteins, encoded in mammals by three genes, VDAC1, 2 and 3, mostly ubiquitously expressed. As 'mitochondrial gatekeepers', VDACs control organelle and cell metabolism and are involved in many diseases. Despite the presence of numerous VDAC pseudogenes in the human genome, their significance and possible role in VDAC protein expression has not yet been considered. Results: We investigated the relevance of processed pseudogenes of human VDAC genes, both in physiological and in pathological contexts. Using high-throughput tools and querying many genomic and transcriptomic databases, we show that some VDAC pseudogenes are transcribed in specific tissues and pathological contexts. The obtained experimental data confirm an association of the VDAC1P8 pseudogene with acute myeloid leukemia (AML). Conclusions: Our in-silico comparative analysis between the VDAC1 gene and its VDAC1P8 pseudogene, together with experimental data produced in AML cellular models, indicate a specific over-expression of the VDAC1P8 pseudogene in AML, correlated with a downregulation of the parental VDAC1 gene. [ABSTRACT FROM AUTHOR]

The vast majority of the human genome is non-coding. There is a diversity of non-coding features, some of which have functional importance. Although the non-coding regions constitute the majority of the genome, they remain understudied, and for a long time, these regions have been referred to as junk DNA. Pseudogenes are one of these features. A pseudogene is a non-functional copy of a protein-coding gene. Pseudogenes may arise through a variety of genetic mechanisms. Processed pseudogenes are formed through reverse transcription of mRNA by LINE elements, after which the cDNA is integrated into the genome. Processed pseudogenes are known to be variable across populations; however, the variability and distribution remains unknown. Herein, we apply a custom-designed processed pseudogene pipeline on the whole genome sequencing data of 3,500 individuals; 2,500 individuals from the thousand genomes dataset, as well as 1,000 Swedish individuals. Through these analyses, we discover over 3,000 pseudogenes missing from the GRCh38 reference. Utilising our pipeline, we position 74% of the detected processed pseudogenes—allowing for analyses of formation. Notably, we find that common structural variant callers, such as Delly, classify the processed pseudogenes as deletion events, which are later predicted to be truncating variants. By compiling lists of non-reference processed pseudogenes and their frequencies, we find a great variability of pseudogenes; indicating that non-reference processed pseudogenes may be useful for DNA testing and as population-specific markers. In summary, our findings highlight a great diversity of processed pseudogenes, that processed pseudogenes are actively formed in the human genome; and that our pipeline may be used to reduce false positive structural variation caused by the misalignment and subsequent misclassification of non-reference processed pseudogenes. [ABSTRACT FROM AUTHOR]

The plastome (plastid genome) represents an indispensable molecular data source for studying phylogeny and evolution in plants. Although the plastome size is much smaller than that of nuclear genome, and multiple plastome annotation tools have been specifically developed, accurate annotation of plastomes is still a challenging task. Different plastome annotation tools apply different principles and workflows, and annotation errors frequently occur in published plastomes and those issued in GenBank. It is therefore timely to compare available annotation tools and establish standards for plastome annotation. In this review, we review the basic characteristics of plastomes, trends in the publication of new plastomes, the annotation principles and application of major plastome annotation tools, and common errors in plastome annotation. We propose possible methods to judge pseudogenes and RNA-editing genes, jointly consider sequence similarity, customed algorithms, conserved domain or protein structure. We also propose the necessity of establishing a database of reference plastomes with standardized annotations, and put forward a set of quantitative standards for evaluating plastome annotation quality for the scientific community. In addition, we discuss how to generate standardized GenBank annotation flatfiles for submission and downstream analysis. Finally, we prospect future technologies for plastome annotation integrating plastome annotation approaches with diverse evidences and algorithms of nuclear genome annotation tools. This review will help researchers more efficiently use available tools to achieve high-quality plastome annotation, and promote the process of standardized annotation of the plastome. [ABSTRACT FROM AUTHOR]

The complete chloroplast genome sequence of Acer pseudosieboldianum (Sapindaceae) was determined. The chloroplast genome of A. pseudosieboldianum is 157,053 bp in length with two inverted repeats (26,747 bp) between a large single-copy (85,391 bp) and a small single-copy (18,168 bp). The GC content was 37.8% and it was composed of 86 coding genes, eight rRNA genes, 37 tRNA genes, and two pseudogenes, rps2, and ycf1. Molecular phylogenetic analysis based on the plastid genome sequences strongly supported the hypothesis that A. pseudosieboldianum was embedded in the series Palmata of section Palmata. However, the phylogenetic positions of A. ukurunduense and A. buergerianum, which are a members of the series Penninervia of sections Palmata and Pentaphylla, respectively, were incongruent with the recent sectional classification system. [ABSTRACT FROM AUTHOR]

Background: The promoters of mammalian genes contain clusters of CG dinucleotides known as CpG islands. Most mammalian housekeeping genes predominantly contain CpG islands (CGIs), facilitating gene transcription. Numerous studies have explored the physiological implications of the relationship between CGIs and gene expression. However, the evolutionary implications of this relationship remain largely unexplored. Pseudogenes, in contrast, are genomic remnants that have lost their function over evolutionary time. Methods: In our current research, we employed comparative genomic techniques to demonstrate a correlation between the absence of gene expression due to a lack of CGIs in the gene promoters and pseudogenization. Results: We showed that there is a significant enrichment of tissue-specific genes in the functional orthologs of pseudogenes. We also found a significant correlation between the lack of CGIs and enriched tissue specificity in these functional orthologs of pseudogenes. Conclusions: We inferred that perhaps tissue-specific genes are more prone to the process of pseudogenization. In this way, because of their impact on gene expression, CGIs may affect the fate of a gene. To our knowledge, this is the first study to propose a connection between CGIs, gene expression, and the pseudogenization process and discuss the evolutionary implications of this potential trilogy.

Different species of toothed whales (Odontoceti) exhibit a variety of tooth forms and enamel types. Some odontocetes have highly prismatic enamel with Hunter-Schreger bands, whereas enamel is vestigial or entirely lacking in other species. Different tooth forms and enamel types are associated with alternate feeding strategies that range from biting and grasping prey with teeth in most oceanic and river dolphins to the suction feeding of softer prey items without the use of teeth in many beaked whales. At the molecular level, previous studies have documented inactivating mutations in the enamel-specific genes of some odontocete species that lack complex enamel. At a broader scale, however, it is unclear whether enamel complexity across the full diversity of extant Odontoceti correlates with the relative strength of purifying selection on enamel-specific genes. Here, we employ sequence alignments for seven enamel-specific genes (ACP4, AMBN, AMELX, AMTN, ENAM, KLK4, MMP20) in 62 odontocete species that are representative of all extant families. The sequences for 33 odontocete species were obtained from databases, and sequences for the remaining 29 species were newly generated for this study. We screened these alignments for inactivating mutations (e.g., frameshift indels) and provide a comprehensive catalog of these mutations in species with one or more inactivated enamel genes. Inactivating mutations are rare in Delphinidae (oceanic dolphins) and Platanistidae/Inioidea (river dolphins) that have higher enamel complexity scores. By contrast, mutations are much more numerous in clades such as Monodontidae (narwhal, beluga), Ziphiidae (beaked whales), Physeteroidea (sperm whales), and Phocoenidae (porpoises) that are characterized by simpler enamel or even enamelless teeth. Further, several higher-level taxa (e.g., Hyperoodon, Kogiidae, Monodontidae) possess shared inactivating mutations in one or more enamel genes, which suggests loss of function of these genes in the common ancestor of each clade. We also performed selection (dN/dS) analyses on a concatenation of these genes and used linear regression and Spearman’s rank-order correlation to test for correlations between enamel complexity and two different measures of selection intensity (# of inactivating mutations per million years, dN/dS values). Selection analyses revealed that relaxed purifying selection is especially prominent in physeteroids, monodontids, and phocoenids. Linear regressions and correlation analyses revealed a strong negative correlation between selective pressure (dN/dS values) and enamel complexity. Stronger purifying selection (low dN/dS) is found on branches with more complex enamel and weaker purifying selection (higher dN/dS) occurs on branches with less complex enamel or enamelless teeth. As odontocetes diversified into a variety of feeding modes, in particular, the suction capture of prey, a reduced reliance on the dentition for prey capture resulted in the relaxed selection of genes that are critical to enamel development.

Accumulating evidence shows that pseudogenes can function as microRNAs (miRNAs) sponges and regulate gene expression. Mining potential interactions between pseudogenes and miRNAs will facilitate the clinical diagnosis and treatment of complex diseases. However, identifying their interactions through biological experiments is time-consuming and labor intensive. In this study, an ensemble learning framework with similarity kernel fusion is proposed to predict pseudogene–miRNA associations, named ELPMA. First, four pseudogene similarity profiles and five miRNA similarity profiles are measured based on the biological and topology properties. Subsequently, similarity kernel fusion method is used to integrate the similarity profiles. Then, the feature representation for pseudogenes and miRNAs is obtained by combining the pseudogene–pseudogene similarities, miRNA–miRNA similarities. Lastly, individual learners are performed on each training subset, and the soft voting is used to yield final decision based on the prediction results of individual learners. The k-fold cross validation is implemented to evaluate the prediction performance of ELPMA method. Besides, case studies are conducted on three investigated pseudogenes to validate the predict performance of ELPMA method for predicting pseudogene–miRNA interactions. Therefore, all experiment results show that ELPMA model is a feasible and effective tool to predict interactions between pseudogenes and miRNAs. [ABSTRACT FROM AUTHOR]

Background: Since the first report of carbapenem-resistant Klebsiella pneumoniae isolates in China in 2007, the prevalence of CRKP and CRE has increased significantly. However, the molecular characteristics of IMP-producing Klebsiella pneumoniae (IMPKp) are rarely reported. Methods: A total of 29 IMPKp isolates were collected from a Chinese tertiary hospital from 2011 to 2017. Clinical IMPKp were identified by VITEK®MS, and further analyzed by whole-genome DNA sequencing with HiSeq and PacBio RSII sequencer. Sequencing data were analyzed using CSI Phylogeny 1.4, Resfinder, PlasmidFinder and the MLST tool provided by the Centre for Genomic Epidemiology. The analysis results were visualized using iTOL editor v1_1. The open reading frames and pseudogenes were predicted using RAST 2.0 combined with BLASTP/BLASTN searches against the RefSeq database. The databases CARD, ResFinder, ISfinder, and INTEGRALL were performed for annotation of the resistance genes, mobile elements, and other features. The types of blaIMP in clinical isolates were determined by BIGSdb-Pasteur. Integrons were drawn by Snapgene, and the gene organization diagrams were drawn by Inkscape 0.48.1. Results: Four novel ST type, including ST5422, ST5423, ST5426 and ST5427 were identified. The IMP-4 and IMP-1 were the dominant IMP type. The majority of blaIMP-carrying plasmids belonged to IncN and IncHI5. Two novel blaIMP-carrying integrons (In2146 and In2147) were uncovered. A novel variant blaIMP-90 presented in novel integron In2147 has been identified. Conclusions: IMPKp showed low prevalence in China. Novel molecular characteristics of IMPKp have been identified. Continuous monitoring of IMPKp shall also be carried out in the future. [ABSTRACT FROM AUTHOR]

Background: Acute myeloid leukemia (AML) is a hematologic malignancy characterized by the abnormal proliferation of myeloid hematopoietic cells and it is urgently needed to develop new molecular biomarkers to predict clinical outcomes and improve therapeutic effects. Methods: The differentially expressed genes were identified by comparing TCGA with GETx data. Univariate LASSO and multivariate cox regression analysis were performed to identify prognosis-associated pseudogenes. Based on the overall survival of related pseudogenes, we used them to construct a prognostic model for AML patients. Moreover, we built the pseudogenes-miRNA-mRNA ceRNA networks and explored their involved biological functions and pathways via GO and KEGG enrichment analysis. Results: Seven prognosis-associated pseudogenes were identified, including CCDC150P1, DPY19L1P1, FTH1P8, GTF2IP4, HLA-K, NAPSB, and PDCD6IPP2. The risk model based on these 7 pseudogenes could accurately predict the 1-year, 3-year, and 5-year survival rates. The GO and KEGG enrichment analyses demonstrated that these prognosis-associated pseudogenes were significantly enriched in cell cycle, myeloid leukocyte differentiation, regulation of hemopoiesis, and other critical cancer-related biological functions and pathways. We systematically and comprehensively analyzed the prognostic role of pseudogenes in AML. Conclusions: The prognostic model of pseudogenes we identified is an independent predictor of overall survival in AML and could be used as biomarker for AML treatment. [ABSTRACT FROM AUTHOR]

Simple Summary: Silver sillago (Sillago sihama) is highly sensitive to environmental stimuli, which restrict the development of its breeding industry. Olfactory receptor (OR) genes play a critical role in the ecology of stress behavior in fishes. A total of 141 OR genes were identified in S. sihama, including 112 intact genes, 26 truncated genes, and three pseudogenes. The OR genes were classified into six groups, of which β, γ, δ, ε, and ζ groups belonged to type I; and η group belonged to type II. The type I OR genes contained almost all conserved motifs, while type II OR genes mainly retained conserved motifs 7(3), 1, 10, 4, and 2. OR genes were mostly distributed on LG 1, LG9, LG11, and LG12. Of all OR genes, 36.23% (50 genes) showed significant expansion in S. sihama. Ka/Ks analysis demonstrated that 227 sites were under purifying selection, while 12 sites were under positive selection, including eight genes in the OR2A12 gene subfamily. Sixty-one genes (44.20%) displayed differential expression under hypoxic stress. The OR gene expanded mechanisms revealed that positive selection promotes S. sihama efficient adaptation to environmental changes. Olfactory receptor (OR) genes are essential in the specific recognition of diverse stimuli in fish. In this study, a total of 141 OR genes were identified in silver sillago (Sillago sihama), a marine fish sensitive to environmental stimuli, including 112 intact genes, 26 truncated genes, and three pseudogenes. A phylogenetic tree analysis elucidated that the OR genes of S. sihama were classified into six groups, of which β, γ, δ, ε, and ζ groups belonged to type I, and the η group belonged to type II. The type I OR genes contained almost all conserved motifs (n = 62), while type II OR genes mainly retained conserved motifs 7(3), 1, 10, 4, and 2 (n = 39). OR genes were mainly distributed on LG1, LG9, LG11, and LG12. Of all OR genes, 36.23% (50 genes) showed significant expansion in S. sihama. Ka/Ks analysis demonstrated that 227 sites were under purifying selection, while 12 sites were under positive selection, including eight genes in the OR2A12 gene subfamily. Sixty-one genes (44.20%) displayed differential expression under hypoxic stress. The identified OR genes explored the mechanism of environmental stress and ecological adaptation of S. sihama, and provided valuable genomic resources for further research on the olfaction of teleosts. [ABSTRACT FROM AUTHOR]

Background and Objectives: Leprosy remains an important health problem worldwide. It is one of the oldest recorded diseases of humankind. In this study, we expanded the analysis of the geographic distribution of Mycobacterium leprae by investigating SNPs and rpoT genotypes in South Central Coast and Central Highlands clinical isolates, providing insights into the distribution and transmission of leprosy in Vietnam and in this geographic region. Materials and Methods: 27 clinical isolates from the patients, determined the genotypes of M. leprae by SNP and rpoT polymorphism. SNP genotyping was performed by PCR amplification and sequencing, rpoT genotyping by PCR amplification and electrophoresis. Results: All of 27 DNA samples (100%) were positive with RLEP TaqMan PCR (Ct value range is 18-32 on 3 replicates). SNP type 1 was identified in 15 isolates (56%), while SNP type 3 was detected in 12 samples (44%). SNP type 2 and type 4, were not detected. The 6-base repeat region of the rpoT gene was amplified by PCR and analyzed by 4% MetaPhor™ agarose gel electrophoresis. All isolates yielded amplification products of 91-bp, but not 97-bp. Conclusion: This study showed that 56% of isolates belonged to type 1, 44% to type 3. In addition, all samples have the 3-copy hexamer genotype in the rpoT gene. [ABSTRACT FROM AUTHOR]

Mussels (Mytilus spp.) tolerate infections much better than other species living in the same marine coastal environment thanks to a highly efficient innate immune system, which exploits a remarkable diversification of effector molecules involved in mucosal and humoral responses. Among these, antimicrobial peptides (AMPs) are subjected to massive gene presence/absence variation (PAV), endowing each individual with a potentially unique repertoire of defense molecules. The unavailability of a chromosome-scale assembly has so far prevented a comprehensive evaluation of the genomic arrangement of AMP-encoding loci, preventing an accurate ascertainment of the orthology/paralogy relationships among sequence variants. Here, we characterized the CRP-I gene cluster in the blue mussel Mytilus edulis, which includes about 50 paralogous genes and pseudogenes, mostly packed in a small genomic region within chromosome 5. We further reported the occurrence of widespread PAV within this family in the Mytilus species complex and provided evidence that CRP-I peptides likely adopt a knottin fold. We functionally characterized the synthetic peptide sCRP-I H1, assessing the presence of biological activities consistent with other knottins, revealing that mussel CRP-I peptides are unlikely to act as antimicrobial agents or protease inhibitors, even though they may be used as defense molecules against infections from eukaryotic parasites. [ABSTRACT FROM AUTHOR]

Nocardia seriolae is a major causative agent of fish nocardiosis that results in serious economic losses in the aquaculture industry. However, the virulence factors and pathogenic mechanisms of the bacterium are poorly understood. Here, a new N. seriolae strain AHLQ20‐01 was isolated from the diseased Micropterus salmoides and identified by phenotypic examination combined with 16S rRNA sequencing. Subsequently, the potential virulence factors of the strain were analysed at genome level by whole‐genome sequencing. The results showed that the whole‐genome sequence derived from N. seriolae AHLQ20‐01 circular chromosome contains 8,129,380 bp DNA with G + C content of 68.14%, and encompasses 7650 protein‐coding genes, 114 pseudo‐genes, 3 rRNAs, 66 tRNAs and 36 non‐coding RNAs. More importantly, a total of 139 genes, which mainly involved in adhesion, invasion, resistance to oxidative and nitrosative stress, phagosome arresting, iron acquisition system, toxin production and bacterial secretion systems, were identified as core virulence‐associated genes. Furthermore, the pathogenicity of N. seriolae AHLQ20‐01 to M. salmoides was further investigated through experimental infection. It was found that the LD50 value of the strain to M. salmoides was 9.3 × 106 colony forming unit/fish. Histopathological examination demonstrated typical granuloma with varying sizes in the liver, head kidney, spleen and heart of the experimentally infected fish. Terminal deoxynucleotidyl transferase dUTP nick end labelling assay and 4′,6‐diamidino‐2‐phenylindole staining showed that there were distinctly more apoptotic cells in all the tested tissues in the infection group, but not in the control group. Together, these findings provide the foundation to further explore the pathogenic mechanism of N. seriolae, which might contribute to the prevention and treatment of fish nocardiosis. [ABSTRACT FROM AUTHOR]

Introduction: Galeola lindleyana is a mycoheterotrophic orchid belonging to the tribe Vanilleae within the subfamily Vanilloideae. Methods: In this study, the G. lindleyana plastome was assembled and annotated, and compared with other Vanilleae orchids, revealing the evolutionary variations between the photoautotrophic and mycoheterotrophic plastomes. Results: The G. lindleyana plastome was found to include 32 protein-coding genes, 16 tRNA genes and four ribosomal RNA genes, including 11 pseudogenes. Almost all of the genes encoding photosynthesis have been lost physically or functionally, with the exception of six genes encoding ATP synthase and psaJ in photosystem I. The length of the G. lindleyana plastome has decreased to 100,749 bp, while still retaining its typical quadripartite structure. Compared with the photoautotrophic Vanilloideae plastomes, the inverted repeat (IR) regions and the large single copy (LSC) region of the mycoheterotrophic orchid's plastome have contracted, while the small single copy (SSC) region has expanded significantly. Moreover, the difference in length between the two ndhB genes was found to be 682 bp, with one of them spanning the IRb/SSC boundary. The Vanilloideae plastomes were varied in their structural organization, gene arrangement, and gene content. Even the Cyrtosia septentrionalis plastome which was found to be closest in length to the G. lindleyana plastome, differed in terms of its gene arrangement and gene content. In the LSC region, the psbA, psbK, atpA and psaB retained in the G. lindleyana plastome were missing in the C. septentrionalis plastome, while, the matK, rps16, and atpF were incomplete in the C. septentrionalis plastome, yet still complete in that of the G. lindleyana. Lastly, compared with the G. lindleyana plastome, a 15 kb region located in the SSC area between ndhB-rrn16S was found to be inverted in the C. septentrionalis plastome. These changes in gene content, gene arrangment and gene structure shed light on the polyphyletic evolution of photoautotrophic orchid plastomes to mycoheterotrophic orchid plastomes. Discussion: Thus, this study's decoding of the mycoheterotrophic G. lindleyana plastome provides valuable resource data for future research and conservation of endangered orchids. [ABSTRACT FROM AUTHOR]

LTR-retrotransposons (LTR-RTs) are a large group of transposable elements that replicate through an RNA intermediate and alter genome structure. The activities of LTR-RTs in plant genomes provide helpful information about genome evolution and gene function. LTR-RTs near or within genes can directly alter gene function. This work introduces PlantLTRdb, an intact LTR-RT database for 195 plant species. Using homology- and de novo structure-based methods, a total of 150.18 Gbp representing 3,079,469 pseudomolecules/scaffolds were analyzed to identify, characterize, annotate LTR-RTs, estimate insertion ages, detect LTR-RT-gene chimeras, and determine nearby genes. Accordingly, 520,194 intact LTR-RTs were discovered, including 29,462 autonomous and 490,732 nonautonomous LTR-RTs. The autonomous LTR-RTs included 10,286 Gypsy and 19,176 Copia, while the nonautonomous were divided into 224,906 Gypsy, 218,414 Copia, 1,768 BARE-2, 3,147 TR-GAG and 4,2497 unknown. Analysis of the identified LTR-RTs located within genes showed that a total of 36,236 LTR-RTs were LTR-RT-gene chimeras and 11,619 LTR-RTs were within pseudo-genes. In addition, 50,026 genes are within 1 kbp of LTR-RTs, and 250,587 had a distance of 1 to 10 kbp from LTR-RTs. PlantLTRdb allows researchers to search, visualize, BLAST and analyze plant LTR-RTs. PlantLTRdb can contribute to the understanding of structural variations, genome organization, functional genomics, and the development of LTR-RT target markers for molecular plant breeding. [ABSTRACT FROM AUTHOR]

Nuclear mitochondrial pseudogenes (numts) may hinder the reconstruction of mtDNA genomes and affect the reliability of mtDNA datasets for phylogenetic and population genetic comparisons. Here, we present the program Numt Parser , which allows for the identification of DNA sequences that likely originate from numt pseudogene DNA. Sequencing reads are classified as originating from either numt or true cytoplasmic mitochondrial (cymt) DNA by direct comparison against cymt and numt reference sequences. Classified reads can then be parsed into cymt or numt datasets. We tested this program using whole genome shotgun-sequenced data from 2 ancient Cape lions (Panthera leo), because mtDNA is often the marker of choice for ancient DNA studies and the genus Panthera is known to have numt pseudogenes. Numt Parser decreased sequence disagreements that were likely due to numt pseudogene contamination and equalized read coverage across the mitogenome by removing reads that likely originated from numts. We compared the efficacy of Numt Parser to 2 other bioinformatic approaches that can be used to account for numt contamination. We found that Numt Parser outperformed approaches that rely only on read alignment or Basic Local Alignment Search Tool (BLAST) properties, and was effective at identifying sequences that likely originated from numts while having minimal impacts on the recovery of cymt reads. Numt Parser therefore improves the reconstruction of true mitogenomes, allowing for more accurate and robust biological inferences. [ABSTRACT FROM AUTHOR]

Epithelial Ovarian Cancer (EOC) is a heterogeneous disease usually diagnosed at advanced stages. Therefore, early detection is crucial for better survival. Despite the advances in ovarian research, mechanisms underlying EOC carcinogenesis are not elucidated. We performed chromatin immunoprecipitation sequencing to identify genes regulated by E2F5, a transcription factor involved in ovarian carcinogenesis. Results revealed several putative candidate genes (115 protein-coding genes, 20 lncRNAs, 6 pseudogenes, and 4 miRNAs). A literature review and bioinformatics analysis of these genes revealed a novel lncRNA candidate (LINC01465) in EOC. We validated LINC01465 by quantifying its expression in EOC cell lines and selected OVSAHO and SKOV3 as a model with high LINC01465 levels. We silenced LINC01465 and performed proliferation, wound healing, invasion, and drug resistance assays. Knocking-down LINC01465 resulted in reduced migration, suggesting potential involvement in EOC. Furthermore, to identify the significance of LINC01465 in chemoresistance, we assessed the LINC01465 levels in A2780 S cells treated with malformin, which revealed higher LINC01465 expression as compared to untreated A2780S cells implying the involvement of LINC01465 in cell death. Thus, this study unraveled the repertoire of E2F5 regulated candidate genes and suggested a putative role of LINC01465 in malformin-induced cell death in EOC. [ABSTRACT FROM AUTHOR]

Keratins (KRTs) are the intermediate filament-forming proteins of epithelial cells, classified, according to their physicochemical properties, into “soft” and “hard” keratins. They have a key role in several aspects of cancer pathophysiology, including cancer cell invasion and metastasis, and several members of the KRT family serve as diagnostic or prognostic markers. The human genome contains both, functional KRT genes and non-functional KRT pseudogenes, arranged in two uninterrupted clusters on chromosomes 12 and 17. This characteristic renders KRTs ideal for evolutionary studies. Herein, comprehensive phylogenetic analyses of KRT homologous proteins in the genomes of major taxonomic divisions were performed, so as to fill a gap in knowledge regarding the functional implications of keratins in cancer biology among tumor-bearing species. The differential expression profiles of KRTs in diverse types of cancers were investigated by analyzing high-throughput data, as well. Several KRT genes, including the phylogenetically conserved ones, were found to be deregulated across several cancer types and to participate in a common protein-protein interaction network. This indicates that, at least in cancer-bearing species, these genes might have been under similar evolutionary pressure, perhaps to support the same important function(s). In addition, semantic relations between KRTs and cancer were detected through extensive text mining. Therefore, by applying an integrative in silico pipeline, the evolutionary history of KRTs was reconstructed in the context of cancer, and the potential of using non-mammalian species as model organisms in functional studies on human cancer-associated KRT genes was uncovered. [ABSTRACT FROM AUTHOR]

α-Gliadins are a major group of gluten proteins in wheat flour that contribute to the end-use properties for food processing and contain major immunogenic epitopes that can cause serious health-related issues including celiac disease (CD). α-Gliadins are also the youngest group of gluten proteins and are encoded by a large gene family. The majority of the gene family members evolved independently in the A, B, and D genomes of different wheat species after their separation from a common ancestral species. To gain insights into the origin and evolution of these complex genes, the genomic regions of the Gli-2 loci encoding α-gliadins were characterized from the tetraploid wild emmer, a progenitor of hexaploid bread wheat that contributed the AABB genomes. Genomic sequences of Gli-2 locus regions for the wild emmer A and B genomes were first reconstructed using the genome sequence scaffolds along with optical genome maps. A total of 24 and 16 α-gliadin genes were identified for the A and B genome regions, respectively. α-Gliadin pseudogene frequencies of 86% for the A genome and 69% for the B genome were primarily caused by C to T substitutions in the highly abundant glutamine codons, resulting in the generation of premature stop codons. Comparison with the homologous regions from the hexaploid wheat cv. Chinese Spring indicated considerable sequence divergence of the two A genomes at the genomic level. In comparison, conserved regions between the two B genomes were identified that included α-gliadin pseudogenes containing shared nested TE insertions. Analyses of the genomic organization and phylogenetic tree reconstruction indicate that although orthologous gene pairs derived from speciation were present, large portions of α-gliadin genes were likely derived from differential gene duplications or deletions after the separation of the homologous wheat genomes ~ 0.5 MYA. The higher number of full-length intact α-gliadin genes in hexaploid wheat than that in wild emmer suggests that human selection through domestication might have an impact on α-gliadin evolution. Our study provides insights into the rapid and dynamic evolution of genomic regions harboring the α-gliadin genes in wheat.

For example, I HMGA1P6 i , a pseudogene transcriptionally activated by oncogene I MYC i , could contribute to oncogenesis in ovarian cancer.[2] Besides, pseudogenes also have profound impacts on anti-tumour responses via involvement in regulating tumour-immune interactions. To systematically evaluate candidate intrinsic pseudogene modulators of immune cells, we introduced a novel framework to identify immune-related housekeeping pseudogenes (Supplementary Materials). Growing evidence has demonstrated that pseudogenes are intricately associated with tumour progression in hepatocellular carcinoma (HCC).[1] Nonetheless, pseudogenes related to tumour immune infiltration and their value in improving clinical outcomes remain largely unexplored. [Extracted from the article]

Rutaceae is a large family, and the genus‐level classification in the subfamilies or tribes of this family is not unified based on different taxonomic treatments. Until now, phylogenetic relationships of some genera in traditional tribe Ruteae have not been clearly resolved. In this study, seven new complete plastomes of this tribe were sequenced, and a comparative analysis was performed to investigate their plastome characteristics and evolution. In addition, we inferred the phylogenetic relationships of Ruteae based on complete plastome and nuclear ITS data. All plastomes exhibited a typical quadripartite structure and were relatively conserved in their structure and gene arrangement. Their genome sizes ranged from 154,656 bp to 160,677 bp, and the size variation was found to be associated with differences in IR expansion and gene loss. A total of 112 to 114 genes were identified in the genomes, including 78 to 79 protein‐coding genes, 30 tRNA genes, 4 rRNA genes, and 2 pseudogenes. Sequence divergence analysis indicated that non‐coding regions exhibited a higher percentage of variable characters, and nine non‐coding and six coding regions were identified as divergent hotspots. Phylogenetic results based on different datasets showed that this tribe was divided into three reciprocally exclusive groups. The phylogenetic analyses between plastome and nuclear ITS data were partly incongruent with each other. This study provides new insights into plastome evolution of Ruteae as well as Rutaceae. The availability of these plastomes provides useful genomic resources for molecular DNA barcodes and phylogenetically informative markers and deepens our understanding of the phylogeny in Ruteae. [ABSTRACT FROM AUTHOR]

Background: The axolotl, Ambystoma mexicanum is a unique biological model for complete tissue regeneration. Is a neotenic endangered species and is highly susceptible to environmental stress, including infectious disease. In contrast to other amphibians, the axolotl is particularly vulnerable to certain viral infections. Like other salamanders, the axolotl genome is one of the largest (32 Gb) and the impact of genome size on Ig loci architecture is unknown. To better understand the immune response in axolotl, we aimed to characterize the immunoglobulin loci of A. mexicanum and compare it with other model vertebrates. Methods: The most recently published genome sequence of A. mexicanum (V6) was used for alignment-based annotation and manual curation using previously described axolotl Ig sequences or reference sequences from other vertebrates. Gene models were further curated using A. mexicanum spleen RNA-seq data. Human, Xenopus tropicalis, Danio rerio (zebrafish), and eight tetrapod reference genomes were used for comparison. Results: Canonical A. mexicanum heavy chain (IGH), lambda (IGL), sigma (IGS), and the putative surrogate light chain (SLC) loci were identified. No kappa locus was found. More than half of the IGHV genes and the IGHF gene are pseudogenes and there is no clan I IGHV genes. Although the IGH locus size is proportional to genome size, we found local size restriction in the IGHM gene and the V gene intergenic distances. In addition, there were V genes with abnormally large V-intron sizes, which correlated with loss of gene functionality. Conclusion: The A. mexicanum immunoglobulin loci share the same general genome architecture as most studied tetrapods. Consistent with its large genome, Ig loci are larger; however, local size restrictions indicate evolutionary constraints likely to be imposed by high transcriptional demand of certain Ig genes, as well as the V(D)J recombination over very long genomic distance ranges. The A. mexicanum has undergone an extensive process of Ig gene loss which partially explains a reduced potential repertoire diversity that may contribute to its impaired antibody response. [ABSTRACT FROM AUTHOR]

This study aimed to perform genomic, probiotic, and metabolic characterization of a novel Liquorilactobacillus nagelii AGA58 isolated from a lactic acid-fermented shalgam beverage to understand its metabolic potentials and probiotic features. AGA58 is gram-positive, motile, catalase-negative and appears as short rods under the light-microscope. The AGA58 chromosome comprises a single linear chromosome of 2,294,635 bp that is predicted to carry 2135 coding sequences, including 45 tRNA genes, 3 mRNA, and 3 rRNA operons. The genome has a G+C content of 36.9%, including 55 pseudogenes and a single intact prophage. AGA58 is micro-anaerobic due to achieving a shorter doubling time and faster growth rate than micro-aerophilic conditions. It carries flagellar biosynthesis protein-encoding genes predicting motile behavior, which was confirmed with the in vitro motility test. AGA58 is an obligatory homofermentative lactobacillus that can ferment hexose sugars such as galactose, glucose, fructose, sucrose, mannose, N -acetyl glucosamine, maltose, and trehalose to lactate through glycolysis. No acid production from pentoses implies that five-carbon sugars are being utilized for purine and pyrimidine synthesis. Putative pyruvate metabolism revealed formate, malate, oxaloacetate, acetate, acetaldehyde, acetoin, and lactate forms from pyruvate. AGA58 is predicted to encode the LuxS gene and biosynthesis of class IIa and Blp family class-II bacteriocins suggesting this bacterium's antimicrobial potential, linked to antagonism tests that AGA58 can inhibit Escherichia coli ATCC 43895, S almonella enterica serovar Typhimurium ATCC 14028, and K lebsiella pneumonia ATCC 13883. Moreover, AGA58 is tolerant to acid and bile concentrations simulating the human gastrointestinal conditions depicting the probiotic potential of the organism as the first report in literature within the same species. [ABSTRACT FROM AUTHOR]

Most pseudogenes are generated when an RNA transcript is reverse-transcribed and integrated into the genome at a new location. Pseudogenes are often considered as an imperfect and silent copy of a functional gene because of the accumulation of numerous mutations in their sequence. Here we report the presence of Pfh8-ps, a Phf8 retrotransposed pseudogene in the mouse genome, which has no disruptions in its coding sequence. We show that this pseudogene is mainly transcribed in testis and can produce a PHF8-PS protein in vivo. As the PHF8-PS protein has a well-conserved JmjC domain, we characterized its enzymatic activity and show that PHF8-PS does not have the intrinsic capability to demethylate H3K9me2 in vitro compared to the parental PHF8 protein. Surprisingly, PHF8-PS does not localize in the nucleus like PHF8, but rather is mostly located at the cytoplasm. Finally, our proteomic analysis of PHF8-PS-associated proteins revealed that PHF8-PS interacts not only with mitochondrial proteins, but also with prefoldin subunits (PFDN proteins) that deliver unfolded proteins to the cytosolic chaperonin complex implicated in the folding of cytosolic proteins. Together, our findings highlighted PHF8-PS as a new pseudogene-derived protein with distinct molecular functions from PHF8. [ABSTRACT FROM AUTHOR]

Pomegranates (Punica granatum L.) are one of the most fashionable fruits and can be cultivated in both tropical and subtropical regions of the world. It is a shiny and attractive pome due to its cultivation. It belongs to the Lythraceae family. In this study, we analyzed the chloroplast genome of wild pomegranate based on whole genome shotgun sequences. In wild pomegranate, we found 158,645 bp in size, 132 genes containing 84 protein genes, 37 tRNA genes, 8 rRNA genes, and 36.92% of GC content, one infA and two duplicated ycf15 pseudogenes. Moreover, 21 chloroplast genes contained intros that are detected in a large single copy (LSC), small single copy (SSC), and two inverted repeats (IRA and IRB) regions, 17 of which were involved in single introns, while four genes (ycf3, rps12, clpP and rsp12) located in LSC, IRA, and IRB region. In total, 26,272 codons are found in protein-coding genes (PCGs); relative synonymous codon usage (RSCU) analysis revealed that the most abundant amino acid is leucine containing 2773 codons (10.55%), less abundant is methionine amino acid containing 1 codon (0.0032) in the PCGs. Furthermore, a total of 233 cpSSRs were identified in the wild pomegranate cp genome, and their distribution was analyzed in three regions, namely IR, LSC, and SSC. However, 155 cpSSR were found in the LSC (66.5%), followed by 40 cpSSR in the SSC (17.2%) and 38 cpSSR in the IR (16.3%) regions. Phylogenetic validation revealed that wild pomegranate is close to the pemphis acidula species. We believe that the cp genome allocates significant information promising for breeding research of wild pomegranate to Lythraceae. [ABSTRACT FROM AUTHOR]

Background: Heteroplexis Chang is an endangered genus endemic to China with important ecological and medicinal value. However, due to the lack of genetic data, our conservation strategies have repeatedly been delayed by controversial phylogenetic (molecular) relationships within the genera. In this study, we reported three new Heteroplexis chloroplast (cp.) genomes (H. vernonioides, H. impressinervia and H. microcephala) to clarify phylogenetic relationships between species allocated in this genus and other related Compositae. Results: All three new cp. genomes were highly conserved, showing the classic four regions. Size ranged from 152,984 − 153,221 bp and contained 130 genes (85 protein-coding genes, 37 tRNA, eight rRNA) and two pseudogenes. By comparative genomic and phylogenetic analyses, we found a large-scale inversion of the entire large single-copy (LSC) region in H. vernonioides, H. impressinervia and H. microcephala, being experimentally verified by PCR. The inverted repeat (IR) regions showed high similarity within the five Heteroplexis plastomes, showing small-size contractions. Phylogenetic analyses did not support the monophyly of Heteroplexis genus, whereas clustered the five species within two differentiated clades within Aster genus. These phylogenetic analyses suggested that the five Heteroplexis species might be subsumed into the Aster genus. Conclusion: Our results enrich the data on the cp. genomes of the genus Heteroplexis, providing valuable genetic resources for future studies on the taxonomy, phylogeny, and evolution of Aster genus. [ABSTRACT FROM AUTHOR]

Next-generation sequencing (NGS) is a useful molecular diagnostic tool for genetic diseases. However, due to the presence of highly homologous pseudogenes, it is challenging to use short-read NGS for analyzing mutations of the Shwachman-Bodian-Diamond syndrome (SBDS) gene. The SBDS mutation spectrum was analyzed in the Chinese population, which revealed that SBDS variants were primarily from sequence exchange between SBDS and its pseudogene at the base-pair level, predominantly in the coding region and splice junction of exon two. The c.258+2T>C and c.185_184TA>GT variants were the two most common pathogenic SBDS variants in the Chinese population, resulting in a total carrier frequency of 1.19%. When analyzing pathogenic variants in the SBDS gene from the NGS data, the misalignment was identified as a common issue, and there were different probabilities of misalignment for different pathogenic variants. Here, we present a novel mathematical method for identifying pathogenic variants in the SBDS gene from the NGS data, which utilizes read-depth of the paralogous sequence variant (PSV) loci of SBDS and its pseudogene. Combined with PCR and STR orthogonal experiments, SBDS gene mutation analysis results were improved in 40% of clinical samples, and various types of mutations such as homozygous, compound heterozygous, and uniparental diploid were explored. The findings effectively reduce the impact of misalignment in NGS-based SBDS mutation analysis and are helpful for the clinical diagnosis of SBDS-related diseases, the research into population variation, and the carrier screening. [ABSTRACT FROM AUTHOR]

The circadian clock allows the body to coordinate physiology with the light and dark cycles of the day. One of the critical components of the molecular clock machinery is the PER family of circadian clock genes, including PER1, PER2, and PER3. The PER3P1 (or PER4) is the only molecular clock-related pseudogene that has been derived from the PER3 gene. Pseudogenes have an essential role in the regulation of gene expression. In this study, we investigated the PER3P1 fluctuations and their effects on the PER3 expression level. We hypothesized that the PER3P1 pseudogene suppresses clock-related miRNAs and positively affects clock genes levels. The results showed that PER3P1 and its parent gene had a corresponding oscillatory expression pattern. The overexpression of PER3P1 increased the mRNA level of PER3. In contrast, the downregulation of PER3 decreased PER3P1 expression. Furthermore, PER3P1 modulates the expression level of other clock genes, including PER1, PER2, CRY1, and CRY2. Our results suggest that the PER3P1 pseudogene may positively affect the PER3 and other clock-related gene expressions. [ABSTRACT FROM AUTHOR]

Inherited copy number variations (CNVs) can provide valuable information for cancer susceptibility and prognosis. However, their association with oropharynx squamous cell carcinoma (OPSCC) is still poorly studied. Using microarrays analysis, we identified three inherited CNVs associated with OPSCC risk, of which one was validated in 152 OPSCC patients and 155 controls and related to pseudogene-microRNA-mRNA interaction. Individuals with three or more copies of ADAM3A and ADAM5 pseudogenes (8p11.22 chromosome region) were under 6.49-fold increased risk of OPSCC. ADAM5 shared a highly homologous sequence with the ADAM9 3′-UTR, predicted to be a binding site for miR-122b-5p. Individuals carrying more than three copies of ADAM3A and ADAM5 presented higher ADAM9 expression levels. Moreover, patients with total deletion or one copy of pseudogenes and with higher expression of miR-122b-5p presented worse prognoses. Our data suggest, for the first time, that ADAM3A and ADAM5 pseudogene-inherited CNV could modulate OPSCC occurrence and prognosis, possibly through the interaction of ADAM5 pseudogene transcript, miR-122b-5p, and ADAM9. [ABSTRACT FROM AUTHOR]

The cricetine rodents Peromyscus leucopus and P. maniculatus are key reservoirs for several zoonotic diseases in North America. We determined the complete circular mitochondrial genome sequences of representatives of 3 different stock colonies of P. leucopus, one stock colony of P. maniculatus and two wild populations of P. leucopus. The genomes were syntenic with that of the murids Mus musculus and Rattus norvegicus. Phylogenetic analysis confirmed that these two Peromyscus species are sister taxa in a clade with P. polionotus and also uncovered a distinction between P. leucopus populations in the eastern and the central United States. In one P. leucopus lineage four extended regions of mitochondrial pseudogenes were identified in the nuclear genome. RNA-seq analysis revealed transcription of the entire genome and differences from controls in the expression profiles of mitochondrial genes in the blood, but not in liver or brain, of animals infected with the zoonotic pathogen Borrelia hermsii. PCR and sequencing of the D-loop of the mitochondrion identified 32 different haplotypes among 118 wild P. leucopus at a Connecticut field site. These findings help to further establish P. leucopus as a model organism for studies of emerging infectious diseases, ecology, and in other disciplines.

This document is a summary of three articles published in the Plant Cell journal. The first article discusses the evolutionary origins of Delphinieae flowers and the genes that control their symmetry. The study found that certain genes in Delphinieae species have higher expression levels compared to their counterparts in Nigelleae species, and silencing these genes resulted in less symmetrical flowers. The second article focuses on pseudogenes, nonfunctional replicas of protein-coding genes, and their potential role in post-transcriptional regulatory mechanisms. The study found that pseudogenes exhibit sequence alterations and are associated with the expression of long noncoding RNAs. The third article explores the light-responsive localization of the COP1 protein, which plays a role in repressing photomorphogenesis. The study identified specific signals within the COP1 protein that govern its movement between the nucleus and cytoplasm in response to light. [Extracted from the article]

Many animal species employ sperm nuclear basic proteins (SNBPs) or protamines to package sperm genomes tightly. SNBPs vary across animal lineages and evolve rapidly in mammals. We used a phylogenomic approach to investigate SNBP diversification in Drosophila species. We found that most SNBP genes in Drosophila melanogaster evolve under positive selection except for genes essential for male fertility. Unexpectedly, evolutionarily young SNBP genes are more likely to be critical for fertility than ancient, conserved SNBP genes. For example, CG30056 is dispensable for male fertility despite being one of three SNBP genes universally retained in Drosophila species. We found 19 independent SNBP gene amplification events that occurred preferentially on sex chromosomes. Conversely, the montium group of Drosophila species lost otherwise-conserved SNBP genes, coincident with an X-Y chromosomal fusion. Furthermore, SNBP genes that became linked to sex chromosomes via chromosomal fusions were more likely to degenerate or relocate back to autosomes. We hypothesize that autosomal SNBP genes suppress meiotic drive, whereas sex-chromosomal SNBP expansions lead to meiotic drive. X-Y fusions in the montium group render autosomal SNBPs dispensable by making X-versus-Y meiotic drive obsolete or costly. Thus, genetic conflicts between sex chromosomes may drive SNBP rapid evolution during spermatogenesis in Drosophila species.

BackgroundThe axolotl, Ambystoma mexicanum is a unique biological model for complete tissue regeneration. Is a neotenic endangered species and is highly susceptible to environmental stress, including infectious disease. In contrast to other amphibians, the axolotl is particularly vulnerable to certain viral infections. Like other salamanders, the axolotl genome is one of the largest (32 Gb) and the impact of genome size on Ig loci architecture is unknown. To better understand the immune response in axolotl, we aimed to characterize the immunoglobulin loci of A. mexicanum and compare it with other model vertebrates.MethodsThe most recently published genome sequence of A. mexicanum (V6) was used for alignment-based annotation and manual curation using previously described axolotl Ig sequences or reference sequences from other vertebrates. Gene models were further curated using A. mexicanum spleen RNA-seq data. Human, Xenopus tropicalis, Danio rerio (zebrafish), and eight tetrapod reference genomes were used for comparison.ResultsCanonical A. mexicanum heavy chain (IGH), lambda (IGL), sigma (IGS), and the putative surrogate light chain (SLC) loci were identified. No kappa locus was found. More than half of the IGHV genes and the IGHF gene are pseudogenes and there is no clan I IGHV genes. Although the IGH locus size is proportional to genome size, we found local size restriction in the IGHM gene and the V gene intergenic distances. In addition, there were V genes with abnormally large V-intron sizes, which correlated with loss of gene functionality.ConclusionThe A. mexicanum immunoglobulin loci share the same general genome architecture as most studied tetrapods. Consistent with its large genome, Ig loci are larger; however, local size restrictions indicate evolutionary constraints likely to be imposed by high transcriptional demand of certain Ig genes, as well as the V(D)J recombination over very long genomic distance ranges. The A. mexicanum has undergone an extensive process of Ig gene loss which partially explains a reduced potential repertoire diversity that may contribute to its impaired antibody response.

Objective: Gastric cancer is one of the most common and deadly types of cancer. The molecular mechanism of gastric cancer progression remains unclear. Materials and methods: Four hub genes were identified through GEO and TCGA database screening and analysis. Prognostic analysis revealed that COL5A2 was the most likely to affect the prognosis of gastric cancer among the four hub genes. The relationships between COL5A2 and clinical variables and immune cell infiltration were analyzed. Then, COL5A2 was analyzed for single-gene differences and related functional enrichment. Using the starBase database for prediction and analysis, miRNAs and pseudogenes/lncRNAs that might combine with COL5A2 were identified; thus, the ceRNA network was constructed. Finally, the network was verified by Cox analysis and qPCR, and a nomogram was constructed. Results: First, we found that COL5A2, COL12A1, BGN and THBS2 were highly expressed in gastric cancer. COL5A2 had statistical significance in overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI) analysis. Immune infiltration analysis suggested that COL5A2 might influence the changes in the tumor immune microenvironment. The StarBase database was used to predict that 3 pseudogenes and 7 lncRNAs might inhibit the hsa-miR-200b-3p-COL5A2 axis in gastric cancer. The pseudogenes/lncRNA-hsa-miR-200b-3p-COL5A2 ceRNA network was identified and verified using Cox regression analysis and PCR. Finally, we constructed a nomogram. Conclusions: We elucidated the regulatory role of the pseudogenes/lncRNA-hsa-miR-200b-3p-COL5A2 network in gastric cancer progression and constructed a nomogram. These studies may provide effective treatments and potential prognostic biomarkers for gastric cancer. [ABSTRACT FROM AUTHOR]

Dehydration-responsive element-binding (DREB) transcription factors of the A2 subfamily play key roles in plant stress responses. In this study, we identified and characterized a new A2-type DREB gene, ZmDREB2.9, in the Zea mays cv. B73 genome and compared its expression profile with those of the known A2-type maize genes ZmDREB2.1–2.8. ZmDREB2.9 was mapped to chromosome 8, contained 18 predicted hormone- and stress-responsive cis-elements in the promoter, and had two splice isoforms: short ZmDREB2.9-S preferentially expressed in the leaves, embryos, and endosperm and long ZmDREB2.9-L expressed mostly in the male flowers, stamens, and ovaries. Phylogenetically, ZmDREB2.9 was closer to A. thaliana DREB2A than the other ZmDREB2 factors. ZmDREB2.9-S, ZmDREB2.2, and ZmDREB2.1/2A were upregulated in response to cold, drought, and abscisic acid and may play redundant roles in maize stress resistance. ZmDREB2.3, ZmDREB2.4, and ZmDREB2.6 were not expressed in seedlings and could be pseudogenes. ZmDREB2.7 and ZmDREB2.8 showed similar transcript accumulation in response to cold and abscisic acid and could be functionally redundant. Our results provide new data on Z. mays DREB2 factors, which can be used for further functional studies as well as in breeding programs to improve maize stress tolerance. [ABSTRACT FROM AUTHOR]

Because DNA metabarcoding typically employs sequence diversity among mitochondrial amplicons to estimate species composition, nuclear mitochondrial pseudogenes (NUMTs) can inflate diversity. This study quantifies the incidence and attributes of NUMTs derived from the 658‐bp barcode region of cytochrome c oxidase I (COI) in 156 marine animal genomes. NUMTs were examined to ascertain if they could be recognized by their possession of indels or stop codons. In total, 309 NUMTs ≥150 bp were detected, with an average of 1.98 per species (range = 0–33) and a mean length of 391 ± 200 bp. Among this total, 75 (24.3%) lacked indels or stop codons. NUMTs appear to pose the greatest interpretational risk when short (<313 bp) amplicons are used, such as in environmental DNA studies, dietary analyses or processed fish identification. Employing the standard amplicon length (313 bp) for marine metabarcoding, NUMTs could potentially inflate the operational taxonomic unit (OTU) count by 21% above the true species count while also raising intraspecific variation at COI by 15%. However, when both amplicon length and position are considered, inflation in OTU counts and in barcode variation were just 9% and 10%, respectively, suggesting NUMTs will not seriously distort biodiversity assessments. There was a weak positive correlation between genome size and NUMT count but no variation among phyla or trophic groups. Until bioinformatic advances improve NUMT detection, the best defence involves targeting long amplicons and developing reference databases that include both mitochondrial sequences and their NUMT derivatives. [ABSTRACT FROM AUTHOR]