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Analysis of publicly available whole‐genome sequence data from the Human Pangenome Project and the 1000 Genomes Project has identified a DNA segment of approximately 60 kb in the major histocompatibility complex (MHC) between HLA‐W and HLA‐J that is present in some MHC haplotypes but not others. This DNA segment is largely repeat element‐rich but includes the pseudogene HLA‐Y, thus pinpointing the location of this pseudogene, and a new HLA class I sequence we have called HLA‐OLI. HLA‐OLI clusters phylogenetically with the HLA class I pseudogenes, HLA‐P and HLA‐W, and appears to have a similar genetic structure. The availability of whole‐genome sequence data from diverse populations enables a detailed characterization of the MHC at the population level and will have implications for understanding MHC disease associations and the non‐HLA MHC factors that impact unrelated hematopoietic cell transplant outcomes. [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]

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]

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]

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]

Nuclear mitochondrial pseudogenes (numts) are short, nonfunctional DNA sequences resulting from mitochondrial gene transfer to the nuclear genome; these sequences seriously affect the accuracy of mitochondrial gene for population genetic and phylogenetic analyses. The nuclear genome of Dendroctonus valens (Coleoptera: Curculionidae: Scolytidae), a major forest quarantine pest that seriously threatens the ecological security of pine forests, contains a large number of numts, and these interfere with analyses of genetic variation based on the mitochondrial cox1 gene. To eliminate interference by numts, we sequenced, assembled and analysed the complete mitochondrial genome of D. valens. The mitogenome is a circular molecule of 16,547 bp and shows typical gene content and arrangement. We identified its codon preference, tRNA secondary structure and nucleotide evolution rate. Furthermore, we designed primers for long fragment amplification to eliminate numts in the mitochondrial cox1 gene. Finally, amplified products were sequenced with universal primers, and cox1 gene sequences (464 bp) without numts were successfully obtained. The Heilihe Nature Reserve (harbouring Pinus tabulaeformis) in Inner Mongolia, is in the early stage of D. valens northward invasion, with a high population genetic diversity. We hypothesized that the high genetic diversity was related to human activities around the reserve and the reproductive characteristics in the early stage of D. valens invasion. The newly developed method resolves the issue of numt interference and lays a foundation for the analyses of genetic diversity in D. valens populations in the region as well as its invasion routes. [ABSTRACT FROM AUTHOR]

DNA barcoding is based on the premise that the barcode sequences can distinguish individuals (strains) of different species because their sequence variation between species exceeds that within species. The primary barcodes used in fungal and yeast taxonomy are the ITS segments and the LSU (large subunit) D1/D2 domain of the homogenized multicopy rDNA repeats. The secondary barcodes are conserved segments of protein‐encoding genes, which usually have single copies in haploid genomes. This study shows that the analysis of barcode sequences fails to reconstruct accurate species trees and differentiate species when the organisms have chimeric genomes composed of admixed mosaics of different origins. It is shown that the type strains of 10 species of the pulcherrima clade of the ascomycetous yeast genus Metschnikowia cannot be differentiated with standard barcodes because their intragenomic diversity is comparable to or even higher than the interstrain diversity. The analysis of a large group of genes of the sequenced genomes of the clade and the viability and segregation of the hybrids of ex‐type strains indicate that the high intragenomic barcode differences can be attributed to admixed genome structures. Because of the mosaic structures of the genomes, the rDNA repeats do not form continuous arrays and thus cannot be homogenized. Since the highly diverse ITS and D1/D2 sequences of the type strains form a continuous pool including pseudogenes, the evolution of their rDNA appears to involve reticulation. The secondary barcode sequences and the nonbarcode genes included in the analysis show incongruent phylogenetic relationships among the type strains, which can also be attributed to differences in the phylogenetic histories of the genes. [ABSTRACT FROM AUTHOR]

Apart from I GBA i and I PRKRA i , a potential role of pseudogenes has not (yet) caught our attention in the field of movement disorders, although several well-established disease-linked genes also have pseudogenes. The definition of a pseudogene has now broadened to include any DNA sequence that is similar to a known gene and has lost some of its original functionality.25 Therefore, pseudogenes can be translated into proteins, as recently proven for 140 human pseudogenes, and also act at the protein level.26 For instance, pseudogene-derived proteins may have the same activity as the parental proteins, but function in different tissues, cellular compartments, or pathophysiological conditions. Pseudogenes can be divided into two major groups, that is, unprocessed pseudogenes and processed pseudogenes, with the latter representing the majority of pseudogenes in humans (~70%, https://www.gencodegenes.org/human/stats.html). Therefore, the sequence identity for these pseudogenes should be too less to seriously trouble sequence analyses.27 Overall, pseudogenes have emerged as a hot topic because they can challenge genetic testing and trigger mutational events even in biologically functional parental genes. [Extracted from the article]

Processed pseudogenes, also known as retrocopy genes, are copies of messenger RNAs that have been reverse transcribed into DNA and inserted into the genome. In this study, we identified 62 processed pseudogene candidates as intron‐less genes from whole‐genome sequencing (WGS) data of Thoroughbred horses using delly structural variation software. The 62 processed pseudogene candidates were confirmed by PCR amplification of intron‐less products. A total of 11 processed pseudogenes were confirmed in the genome of all 23 analysed horses, whereas three processed pseudogenes with structures of ATP11B, DPH3 and RPL17 were detected in only one of 115 horses by PCR amplification of intron‐less products. Currently, most of the gene doping tests proposed in human and horse sports are adapted PCR‐based methods using hydrolysis probes to detect exon/exon junctions in transgenes because the operation is simple and economical. However, when the pseudogene is present in the host genome, the PCR‐based methods may have a potential risk of detecting false positives. In this study, because processed pseudogenes that exist less frequently in the horse genome may affect PCR‐based transgene detection in gene‐doping tests, we propose and demonstrate that PCR amplification and sequencing using primers designed on transgene and promotors and/or polyadenylation signal for gene expression are useful for gene‐doping detection as an additional confirmatory test to prevent false positives. [ABSTRACT FROM AUTHOR]

Peach trees showing witches'‐broom disease symptoms in the northwest of Iran were sampled for phytoplasma detection. PCR assays and Sanger sequence analyses indicated that ʻCandidatus Phytoplasma phoeniciumʼ was associated with peach witchesʼ‐broom disease. Virtual RFLP analyses of the 16S rRNA gene indicated that ʻCa. Phytoplasma phoeniciumʼ strain, which was prevalent in the northwest of Iran belonged to 16SrIX‐C subgroup. For the genomic characterization of Iranian ʻCa. Phytoplasma phoeniciumʼ strain, total DNA extracted from the infected peach trees was subjected to Illumina next‐generation sequencing. The NGS sequencing resulted in 41157647 read pairs of raw data. The raw reads length was 150 bp and the insert size was 350 bp. Assembly and genes clustering finally resulted in 750 contigs with a total size of 228345 bp. The GC content of sequence was 33.2%, N50 value was 259 and L50 value was 256. According to NCBI‐ PGAP annotation the genome of Prunus persica phytoplasma PP2 contained 410 genes including 377 CDSs with protein, 10 rRNAs, nine tRNAs and 14 pseudogenes. [ABSTRACT FROM AUTHOR]

The major histocompatibility complex (MHC) class I region of cattle is both highly polymorphic and, unlike many species, highly variable in gene content between haplotypes. Cattle MHC class I alleles were historically grouped by sequence similarity in the more conserved 3′ end of the coding sequence to form phylogenetic allele groups. This has formed the basis of current cattle MHC class I nomenclature. We presently describe and compare five fully assembled MHC class I haplotypes using the latest cattle and yak genome assemblies. Of the five previously described "pseudogenes" in the cattle MHC class I region, Pseudogene 3 is putatively functional in all haplotypes and Pseudogene 6 and Pseudogene 7 are putatively functional in some haplotypes. This was reinforced by evidence of transcription. Based on full gene sequences as well as 3′ coding sequence, we identified distinct subgroups of BoLA‐3 and BoLA‐6 that represent distinct genetic loci. We further examined allele‐specific expression using transcriptomic data revealing that certain alleles are consistently weakly expressed compared to others. These observations will help to inform further studies into how MHC class I region variability influences T cell and natural killer cell functions in cattle. [ABSTRACT FROM AUTHOR]

Baculoviruses, like their holometabolous host insects, comprise a monophyletic clade and, since the evolutionary origin of this virus family, have coevolved with their hosts. Despite this intimate coevolutionary relationship, baculoviruses have occasionally diverged independently of the host phylogeny by acquiring new infection mechanisms. Given that current baculovirus genomes contain various anti‐apoptotic genes and pseudogenes, the possibility arises that ancient baculoviruses had the genetic means to counter antiviral host apoptosis mechanisms. In this review, we propose an evolutionary scenario for baculovirus diversification in which the development of novel antiviral apoptosis mechanisms in host insects provided the necessary pressure to produce new baculovirus lineages possessing novel anti‐apoptotic genes. This apoptotic arms race and subsequent viral host adaptation likely play a crucial role in the establishment of baculovirus diversity. [ABSTRACT FROM AUTHOR]

DNA metabarcoding is a rapid, high‐resolution tool used for biomonitoring complex zooplankton communities. However, diversity estimates derived with this approach can be biased by the co‐detection of sequences from environmental DNA (eDNA), nuclear‐encoded mitochondrial (NUMT) pseudogene contamination, and taxon‐specific PCR primer affinity differences. To avoid these methodological uncertainties, we tested the use of metatranscriptomics as an alternative approach for characterizing zooplankton communities. Specifically, we compared metatranscriptomics with PCR‐based methods using genomic (gDNA) and complementary DNA (cDNA) amplicons, and morphology‐based data for estimating species diversity and composition for both mock communities and field‐collected samples. Mock community analyses showed that the use of gDNA mitochondrial cytochrome c oxidase I (mtCO1) amplicons inflates species richness due to the co‐detection of extra‐organismal eDNA. Significantly more amplicon sequence variants, nucleotide diversity, and indels were observed with gDNA amplicons than with cDNA, indicating the presence of putative NUMT pseudogenes. Moreover, PCR‐based methods failed to detect the most abundant species in mock communities due to priming site mismatch. Overall, metatranscriptomics provided estimates of species richness and composition that closely resembled those derived from morphological data. The use of metatranscriptomics was further tested using field‐collected samples, with the results showing consistent species diversity estimates among biological and technical replicates. Additionally, temporal zooplankton species composition changes could be monitored using different mitochondrial markers. These findings demonstrate the advantages of metatranscriptomics as an effective tool for monitoring diversity in zooplankton research. [ABSTRACT FROM AUTHOR]

Processed pseudogenes may serve as a genetic reservoir for evolutionary innovation. Here, we argue that through the activity of long interspersed element‐1 retrotransposons, processed pseudogenes disperse coding and noncoding sequences rich with regulatory potential throughout the human genome. While these sequences may appear to be non‐functional, a lack of contemporary function does not prohibit future development of biological activity. Here, we discuss the dynamic evolution of certain processed pseudogenes into coding and noncoding genes and regulatory elements, and their implication in wide‐ranging biological and pathological processes. Also see the video abstract here: https://youtu.be/iUY_mteVoPI [ABSTRACT FROM AUTHOR]

SUMMARY: Oryza sativa (rice) plays an essential food security role for more than half of the world's population. Obtaining crops with high levels of disease resistance is a major challenge for breeders, especially today, given the urgent need for agriculture to be more sustainable. Plant resistance genes are mainly encoded by three large leucine‐rich repeat (LRR)‐containing receptor (LRR‐CR) families: the LRR‐receptor‐like kinase (LRR‐RLK), LRR‐receptor‐like protein (LRR‐RLP) and nucleotide‐binding LRR receptor (NLR). Using lrrprofiler, a pipeline that we developed to annotate and classify these proteins, we compared three publicly available annotations of the rice Nipponbare reference genome. The extended discrepancies that we observed for LRR‐CR gene models led us to perform an in‐depth manual curation of their annotations while paying special attention to nonsense mutations. We then transferred this manually curated annotation to Kitaake, a cultivar that is closely related to Nipponbare, using an optimized strategy. Here, we discuss the breakthrough achieved by manual curation when comparing genomes and, in addition to 'functional' and 'structural' annotations, we propose that the community adopts this approach, which we call 'comprehensive' annotation. The resulting data are crucial for further studies on the natural variability and evolution of LRR‐CR genes in order to promote their use in breeding future resilient varieties. Significance Statement: The automatic structural annotation of genes evolving through an active birth‐and‐death model, such as LRR‐CRs, is often inconsistent because numerous paralogs accumulate nonsense mutations in their coding sequences. We propose a consensus method of annotating these genes while retaining all sequence fragments that are clearly derived from their ancestral coding sequences. They are then tagged as non‐canonical or canonical, respectively, depending on the presence or absence of nonsense mutations. [ABSTRACT FROM AUTHOR]

Metabarcoding of Metazoa using mitochondrial genes may be confounded by both the accumulation of PCR and sequencing artefacts and the co‐amplification of nuclear mitochondrial pseudogenes (NUMTs). The application of read abundance thresholds and denoising methods is efficient in reducing noise accompanying authentic mitochondrial amplicon sequence variants (ASVs). However, these procedures do not fully account for the complex nature of concomitant sequences and the highly variable DNA contribution of specimens in a metabarcoding sample. We propose, as a complement to denoising, the metabarcoding Multidimensional Abundance Threshold Evaluation (metaMATE) framework, a novel approach that allows comprehensive examination of multiple dimensions of abundance filtering and the evaluation of the prevalence of unwanted concomitant sequences in denoised metabarcoding datasets. metaMATE requires a denoised set of ASVs as input, and designates a subset of ASVs as being either authentic (mitochondrial DNA haplotypes) or nonauthentic ASVs (NUMTs and erroneous sequences) by comparison to external reference data and by analysing nucleotide substitution patterns. metaMATE (i) facilitates the application of read abundance filtering strategies, which are structured with regard to sequence library and phylogeny and applied for a range of increasing abundance threshold values, and (ii) evaluates their performance by quantifying the prevalence of nonauthentic ASVs and the collateral effects on the removal of authentic ASVs. The output from metaMATE facilitates decision‐making about required filtering stringency and can be used to improve the reliability of intraspecific genetic information derived from metabarcode data. The framework is implemented in the metaMATE software (available at https://github.com/tjcreedy/metamate). see also the Perspective by Natalie R. Graham, Rosemary G. Gillespie and Henrik Krehenwinkel [ABSTRACT FROM AUTHOR]

B Cover Legend b Water lily ( I Nymphaea colorata i ), an early diverging angiosperm, whose genome contains pseudogenes as "footprints" of the seed maturation regulators. Image courtesy of Mariko Nonogaki (Nishiyama I et al i ., pp. 889-901). [Extracted from the article]

Pseudogenes exert potential functions in tumorigenicity and tumour process in human beings. In our previous research on oncogene AKR1B10 in hepatocellular carcinoma (HCC), its pseudogene, AKR1B10P1, was preliminarily noticed being anomalistic transcribed, whereas whether AKR1B10P1 plays any specific function in HCC is poorly understood. By using shRNA transfection and lentiviral infection, we regulated the expression of ARK1B10P1 transcript and the relative targets in two ways. As we discovered, pathological transcription of AKR1B10P1 in HCC cells significantly promotes cell growth and motility either in vitro or in vivo. AKR1B10P1 was correlated with relatively dismal features of HCC. The epithelial‐mesenchymal transition (EMT) was enhanced by up‐regulating AKR1B10P1. And, a potential sequence of AKR1B10P1 transcript was discovered directly interacting with miR‐138. SOX4, a pivotal promotor of EMT, was validated as the down‐streaming target of miR‐138. Mechanistically, degradation of SOX4 mRNA induced by miR‐138 was effectively abrogated by AKR1B10P1. In conclusion, pseudogene AKR1B10P1 exerts stabilizing effect on SOX4 in HCC, associated EMT process, by directly sponging miR‐138, which post‐transcriptionally modulates SOX4's regulating gene. [ABSTRACT FROM AUTHOR]

The incidence and mortality rate of hepatocellular carcinoma (HCC) nowadays is still at high levels. The regulatory roles of pseudogene in cancers have been gradually recognized in recent years. However, comprehensive investigation of abnormally expressed pseudogene and related mechanisms in HCC remains lacking. GSE124535 dataset was used to identify differentially expressed pseudogenes in HCC tissues compared with normal tissues. Prognostic value of these differentially expressed pseudogenes was analyzed at GEPIA. StarBase used to analyze microRNAs (miRNAs) can bind with pseudogene, while the targets for these miRNAs were analyzed at miRTarBase. Protein–protein interaction (PPI) network was then established for miRNA targets, after that hub genes were selected. Expression correlation of pseudogene and hub genes was analyzed at StarBase. In total, 16 upregulated and 17 downregulated pseudogenes were identified. Pseudogene HSPB1P1 was identified abnormally expressed in 20 types of human cancers and could be used as an indicator for poorer overall survival of patients with HCC. Functional analyses showed that HSPB1P1 was strongly correlated with signaling pathways related to cancer progression. Further studied revealed that HSPB1P1 could direct regulate the EZH2 expression in HCC. In summary, our study indicated that HSPB1P1 was a predictor for poorer overall survival of patients with HCC and may be potential therapeutic target against HCC. [ABSTRACT FROM AUTHOR]

Summary: Genetic variation in a pathogen, including the causative agent of salmonellosis, Salmonella enterica, can occur as a result of eco‐evolutionary forces triggered by dissimilarities of ecological niches. Here, we applied comparative genomics to study 90 antimicrobial resistant (AMR) S. enterica isolates from bovine and human hosts in New York and Washington states to understand host‐ and geographic‐associated population structure. Results revealed distinct presence/absence profiles of functional genes and pseudogenes (e.g., virulence genes) associated with bovine and human isolates. Notably, bovine isolates contained significantly more transposase genes but fewer transposase pseudogenes than human isolates, suggesting the occurrence of large‐scale transposition in genomes of bovine and human isolates at different times. The high correlation between transposase genes and AMR genes, as well as plasmid replicons, highlights the potential role of horizontally transferred transposons in promoting adaptation to antibiotics. By contrast, a number of potentially geographic‐associated single‐nucleotide polymorphisms (SNPs), rather than geographic‐associated genes, were identified. Interestingly, 38% of these SNPs were in genes annotated as cell surface protein‐encoding genes, including some essential for antibiotic resistance and host colonization. Overall, different evolutionary forces and limited recent inter‐population transmission appear to shape AMR S. enterica population structure in different hosts and geographic origins. [ABSTRACT FROM AUTHOR]

Summary: Vertebrate genomes are mosaics of megabase‐size DNA segments with a fairly homogeneous base composition, called isochores. They are divided into five families characterized by different guanine‐cytosine (GC) levels and linked to several functional and structural properties. The increased availability of fully sequenced genomes allows the investigation of isochores in several species, assessing their level of conservation across vertebrate genomes. In this work, we characterized the isochores in Bos taurus using the ARS‐UCD1.2 genome version. The comparison of our results with the well‐studied human isochores and those of other mammals revealed a large conservation in isochore families, in number, average GC levels and gene density. Exceptions to the established increase in gene density with the increase in isochores (GC%) were observed for the following gene biotypes: tRNA, small nuclear RNA, small nucleolar RNA and pseudogenes that have their maximum number in H2 and H1 isochores. Subsequently, we assessed the ontology of all gene biotypes looking for functional classes that are statistically over‐ or under‐represented in each isochore. Receptor activity and sensory perception pathways were significantly over‐represented in L1 and L2 (GC‐poor) isochores. This was also validated for the horse genome. Our analysis of housekeeping genes confirmed a preferential localization in GC‐rich isochores, as reported in other species. Finally, we assessed the SNP distribution of a bovine high‐density SNP chip across the isochores, finding a higher density in the GC‐rich families, reflecting a potential bias in the chip, widely used for genetic selection and biodiversity studies. [ABSTRACT FROM AUTHOR]

Hepatocellular carcinoma (HCC) is a malignancy with one of the worst prognoses. Long noncoding RNA (lncRNA) are emerging as an important regulator of gene expression and function, leading to the development of cancer. The aim of this study was to determine the relationship between lncRNA and HCC and to further guide clinical therapy. lncRNA in HCC and adjacent tissues were screened, and the correlation between lncRNA‐PDPK2P expression in liver tissues and the pathological characteristics and severity of HCC was assessed. The effects of PDPK2P on HCC proliferation, apoptosis, metastasis, and invasion were also systematically investigated via CCK‐8 assay, flow cytometry, scratch wound healing, and transwell assay, respectively. The relationship between PDPK2P and PDK1 was verified by RNA pull‐down, rescue experiments and western blot. lncRNA‐PDPK2P was highly expressed in HCC tissues with a distinct positive correlation between PDPK2P and PDK1, and the upregulation was clinically associated with a larger tumor embolus, low differentiation, and poor survival. Mechanistically, lncRNA‐PDPK2P interacted with PDK1 and promoted HCC progression through the PDK1/AKT/caspase 3 signaling pathway. lncRNA‐PDPK2P can promote HCC progression, suggesting it may be a clinically valuable biomarker and serve as a molecular target for the diagnosis, prognosis, and therapy of hepatocellular carcinoma. [ABSTRACT FROM AUTHOR]

Recently, pseudogenes have emerged as critical regulators in the onset of human neoplasia. Here, we present a comprehensive analysis of pseudogene alterations at transcriptional levels in lung adenocarcinoma (LUAD) from The Cancer Genome Atlas. By combinations of differential expression analysis, survival analysis, and univariate and multivariable Cox proportional hazards regression models, we identified four dysregulated pseudogenes, whose expression level was closely related to LUAD patients' prognosis and the four pseudogene signature could act as an independent prognostic indicator for LUAD patients. We further characterized CHIAP2, one of those four pseudogenes, whose expression level was the most closely linked to LUAD patients' prognosis. Consistent with our analysis, the expression of CHIAP2 was abnormally downregulated in LUAD tissues compared with that in normal tissues in our 50 pairs of clinical samples. Functional assays demonstrated that upregulation of CHIAP2 significantly impaired cell proliferation and invasion. After performing RNA sequencing (RNA‐seq) and small RNA‐seq between CHIAP2 overexpression and negative control LUAD cell lines, we identified differentially expressed messenger RNAs and microRNAs (miRNAs), among which six miRNAs were downregulated. Target genes of six downregulated miRNAs were predicted with online miRNA target prediction tools and significant pathways including the WNT signal pathway were identified with Gene Set Enrichment Analysis. By combining predictor genes of six downregulated miRNAs and dysregulated genes of the WNT pathway, we inferred that overexpression of CHAP2 may inhibit LUAD cell proliferation and invasion via modulation of NFATC2 or GSK3B (WNT signal pathway) targeted by miR‐3614‐5p or miR‐873‐3p. [ABSTRACT FROM AUTHOR]

LIN28A serves as a crucial marker of dairy goat male germline stem cells (GmGSCs). In our previous study, we demonstrated that LIN28A promotes proliferation, self‐renewal, and maintains the stemness of GmGSCs. Here, we found that LIN28A could activate the transcription of NANOG in a let‐7g independent manner. We cloned the 5′ upstream of two NANOG genes which were located on chromosome 15 (NANOG‐ch15) and chromosome 5 (NANOG‐ch5), respectively, and then examined their promoter activities and promoter methylation levels. Results showed that NANOG‐ch15 is a pseudogene whereas NANOG‐ch5 is active in Capra hircus. Bioinformatics analysis indicated that the 5′ upstream region of NANOG‐ch5 does not have typical CpG islands but contains several CG enrichment regions and several LIN28A binding sites. Deletion analysis suggested that NANOG‐ch5 promoter can be activated by LIN28A directly binding to the site ‐210 but not by the indirect effect from the inhibition of let‐7g, which is known to be downregulated by LIN28A. Mechanistically, LIN28A recruits and interacts with 5‐methylcytosine‐dioxygenase Ten‐Eleven translocation 1 (TET1) to NANOG‐ch5 gene promoter binding sites to orchestrate 5‐methylcytosine and 5‐hydroxymethylcytosine dynamics. These results revealed the role of LIN28A in NANOG transcriptional regulation via epigenetic DNA modifications to maintain the stemness of GmGSC. In this study, we found that LIN28A in a let‐7g independent manner activating the transcription of NANOG that located on chromosome 5 via binding the −573/+210 5′ upstream region. Mechanistically, LIN28A recruits and interacts with 5‐methylcytosine‐dioxygenase Ten‐Eleven translocation 1 (TET1) to NANOG gene promoter binding sites to orchestrate 5‐methylcytosine and 5‐hydroxymethylcytosine dynamics. These results reveal the role of LIN28A in NANOG transcriptional regulation via epigenetic DNA modifications to maintain stemness of goat male germline stem cells (GmGSCs). [ABSTRACT FROM AUTHOR]

Pemphigus foliaceus (PF) is an autoimmune skin disease characterized by autoantibodies directed mainly against desmoglein‐1. The purpose of this study was to determine whether differential susceptibility to endemic PF in Brazil (fogo selvagem) is associated with polymorphisms at the cytogenetic location 1p13.2. Four single nucleotide polymorphisms that together tag 28 SNPs on a segment of approximately 312,000 bp encompassing the protein‐coding genes MAGI3, PHTF1, RSBN1, PTPN22, BCL2L15, AP4B1, DCLRE1B, the pseudogenes MTND5P20, RPS2P14 (AL133517.1) and the long non‐coding RNA genes AL137856.1, and AP4B1‐AS1 were used as markers for association analysis in a case–control study. Allele, genotype and haplotype frequencies of rs33996649, rs2476601, rs3789604 and rs3195954 were compared between patient and control samples. No significant association was found. Lack of association with rs2476601 of the PTPN22 gene agrees with previous results for pemphigus vulgaris and the Tunisian form of endemic pemphigus foliaceus. The other three SNPs had never been analysed before in any form of pemphigus. We conclude that variants in structural and regulatory sites of region 1p13.2 are not susceptibility factors for fogo selvagem. We suggest careful investigation of this genomic region in diseases that had been previously associated with PTPN22, since there are several other genes relevant for immune‐mediated diseases located in 1p13.2. [ABSTRACT FROM AUTHOR]

Ribonuclease 6 (RNase6 or RNase K6) is a protein that belongs to a superfamily thought to be the sole verte‐brate‐specific enzyme known for a wide range of physiological functions, including digestion, cytotoxicity, angiogenesis, male reproduction and host defense. In our study, 51 functional genes and 11 pseudogenes were identified from 27 Rodentia species. Intriguingly, in the 3 main lineages of rodents there were multiple RNase6s identified in all species of Ctenohystrica, whereas only a single RNase6 was observed in other Rodentia species examined except for 2 species in the mouse‐related clade. The evolutionary scenario of "birth (gene duplication) and death (gene deactivation)" and gene sorting have been demonstrated in Ctenohystrica. In addition, bursts of positive selection, diversification of isoelectric point and positive net charge have been identified in Ctenohystrica, especially at two key sites that are involved in antimicrobial function. Site Trp30 has undergone positive selection and Ile45 has changed into other residues in Group B and Group C of the Ctenohystrica. Our results demonstrated a complex and intriguing evolutionary pattern of rodent RNase6, and indicated that functional modification may have occurred, which establishes an important theoretical foundation for future functional assays in rodent RNase6. [ABSTRACT FROM AUTHOR]

Neisseria gonorrhoeae causes the sexually transmitted disease gonorrhea exclusively in humans and uses multiple strategies to infect, including acquisition of host sialic acids that cap and mask lipooligosaccharide termini, while restricting complement activation. We hypothesized that gonococci selectively target human anti‐inflammatory sialic acid‐recognizing Siglec receptors on innate immune cells to blunt host responses and that pro‐inflammatory Siglecs and SIGLEC pseudogene polymorphisms represent host evolutionary adaptations to counteract this interaction. N. gonorrhoeae can indeed engage multiple human but not chimpanzee CD33rSiglecs expressed on innate immune cells and in the genitourinary tract––including Siglec‐11 (inhibitory) and Siglec‐16 (activating), which we detected for the first time on human cervical epithelium. Surprisingly, in addition to LOS sialic acid, we found that gonococcal porin (PorB) mediated binding to multiple Siglecs. PorB also bound preferentially to human Siglecs and not chimpanzee orthologs, modulating host immune reactions in a human‐specific manner. Lastly, we studied the distribution of null SIGLEC polymorphisms in a Namibian cohort with a high prevalence of gonorrhea and found that uninfected women preferentially harbor functional SIGLEC16 alleles encoding an activating immune receptor. These results contribute to the understanding of the human specificity of N. gonorrhoeae and how it evolved to evade the human immune defense. [ABSTRACT FROM AUTHOR]

The major histocompatibility complex (MHC; 6p21.3) contains the most polymorphic genes, the most gene dense parts, and the highest diversity of functional gene clusters of the human genome. The clusters form haplotypes, which differ in linkage disequilibrium and show large variations in strength and extent between populations. Haplotype cis‐ and trans‐expression quantitative trait loci have increased the knowledge of regulatory interactions between multiple MHC genes. The detailed haplotype data offer a reference for future studies in immune‐mediated diseases and may unravel disease associations in conditions traditionally considered not to be immunologic. This article aims to describe the structural and functional variations of the MHC genes and haplotypes and their role on selected immune‐mediated diseases. In immune‐/inflammation‐mediated complex diseases, hundreds of common variants influence the development of the disease trait, but the individual variants have small effects on the disease phenotypes as seen in genome‐wide association studies. The genetic influence may still be significant on the cellular or molecular level. Nonetheless, the HLA alone is not sufficient as a susceptible genetic background to deduce the disease. For a comprehensive insight of the disease mechanisms, both immunological and genome assays methods are required. [ABSTRACT FROM AUTHOR]

Abstract: Bats are a diverse radiation of mammals of enduring interest for understanding the evolution of sensory specialization. Colour vision variation among species has previously been linked to roosting preferences and echolocation form in the suborder Yinpterochiroptera, yet questions remain about the roles of diet and habitat in shaping bat visual ecology. We sequenced OPN1SW and OPN1LW opsin genes for 20 species of leaf‐nosed bats (family Phyllostomidae; suborder Yangochiroptera) with diverse roosting and dietary ecologies, along with one vespertilionid species (Myotis lavali). OPN1LW genes appear intact for all species, and predicted spectral tuning of long‐wavelength opsins varied among lineages. OPN1SW genes appear intact and under purifying selection for Myotis lavali and most phyllostomid bats, with two exceptions: (a) We found evidence of ancient OPN1SW pseudogenization in the vampire bat lineage, and loss‐of‐function mutations in all three species of extant vampire bats; (b) we additionally found a recent, independently derived OPN1SW pseudogene in Lonchophylla mordax, a cave‐roosting species. These mutations in leaf‐nosed bats are independent of the OPN1SW pseudogenization events previously reported in Yinpterochiropterans. Therefore, the evolution of monochromacy (complete colour blindness) has occurred in both suborders of bats and under various evolutionary drivers; we find independent support for the hypothesis that obligate cave roosting drives colour vision loss. We additionally suggest that haematophagous dietary specialization and corresponding selection on nonvisual senses led to loss of colour vision through evolutionary sensory trade‐off. Our results underscore the evolutionary plasticity of opsins among nocturnal mammals. [ABSTRACT FROM AUTHOR]

DNA repair pathways are essential for cellular survival as our DNA is constantly under assault from both exogenous and endogenous DNA damaging agents. Five major mammalian DNA repair pathways exist within a cell to maintain genomic integrity. Of these, the DNA mismatch repair (MMR) pathway is highly conserved among species and is well documented in bacteria. In humans, the importance of MMR is underscored by the discovery that a single mutation in any 1 of 4 genes within the MMR pathway (MLH1, MSH2, MSH6 and PMS2) results in Lynch syndrome (LS). LS is a autosomal dominant condition that predisposes individuals to a higher incidence of many malignancies including colorectal, endometrial, ovarian, and gastric cancers. In this review, we discuss the role of PMS2 in the MMR pathway, the evolving testing criteria used to identify variants in the PMS2 gene, the LS phenotype as well as the autosomal recessive condition called constitutional mismatch repair deficiency syndrome, and current methods used to elucidate the clinical impact of PMS2 mutations. [ABSTRACT FROM AUTHOR]

Summary: Understanding the symbiotic interaction between Coxiella‐like endosymbionts (CLE) and their tick hosts is challenging due to lack of isolates and difficulties in tick functional assays. Here we sequenced the metagenome of a CLE population from wild Rhipicephalus sanguineus ticks (CRs) and compared it to the previously published genome of its close relative, CLE of R. turanicus (CRt). The tick hosts are closely related sympatric species, and their two endosymbiont genomes are highly similar with only minor differences in gene content. Both genomes encode numerous pseudogenes, consistent with an ongoing genome reduction process. In silico flux balance metabolic analysis (FBA) revealed the excess production of L‐proline for both genomes, indicating a possible proline transport from Coxiella to the tick. Additionally, both CR genomes encode multiple copies of the proline/betaine transporter, proP gene. Modelling additional Coxiellaceae members including other tick CLE, did not identify proline as an excreted metabolite. Although both CRs and CRt genomes encode intact B vitamin synthesis pathway genes, which are presumed to underlay the mechanism of CLE‐tick symbiosis, the FBA analysis indicated no changes for their products. Therefore, this study provides new testable hypotheses for the symbiosis mechanism and a better understanding of CLE genome evolution and diversity. [ABSTRACT FROM AUTHOR]

Accumulating evidence indicates that mRNAs and noncoding RNAs act as competitive endogenous RNAs (ceRNAs) and play a key role in tumorigenesis. However, the complex competitive relationship among genes remains unknown. In the present study, the long noncoding RNAs (lncRNAs), pseudogenes and mRNAs that compete with common microRNAs are defined as lncRNA–pseudogene–mRNA competitive triples. We find that some candidate ceRNAs, modules and triples are associated with cancers and can significantly divide patients into high‐risk and low‐risk groups; thus, they may serve as potential cancer biomarkers. In sum, the present study systematically analyzes the association between competitive triples and cancer, which provides a reference for a deeper understanding of cancer progression. [ABSTRACT FROM AUTHOR]

Summary: KIR (Killer Immunoglobulin‐like Receptor) variants influence immune responses and are genetic factors in disease susceptibility. Using sequence‐specific priming PCR, we have previously described the diversity of KIR genes in term of presence/absence in northeastern Thais (NETs). To provide additional resolution beyond conventional methods, quantitative PCR was applied to determine KIR copy number profiles. Novel expanded and contracted KIR copy number profiles were identified at cumulatively high frequencies. These all comprise haplotypes with duplication (6·9%) or deletion (2·7%) of KIR3DL1/S1 along with adjacent genes. Five expanded KIR profiles comprised haplotypes with duplications of KIR2DP1, 2DL1, 3DP1, 2DL4, 3DL1/S1 and 2DS1/4, whereas two contracted profiles contained only a single copy of KIR3DP1, 3DL1/S1 and 2DL4. Using a KIR haplotype prediction program (KIR Haplotype Identifier), 14% of NET haplotypes carried atypical haplotypes based on the gene copy number data. [ABSTRACT FROM AUTHOR]

Summary: Pseudogenes have a reputation of being ‘evolutionary relics’ or ‘junk DNA’. While they are well characterized in mammals, studies in more complex plant genomes have so far been hampered by the absence of reference genome sequences. Barley is one of the economically most important cereals and has a genome size of 5.1 Gb. With the first high‐quality genome reference assembly available for a Triticeae crop, we conducted a whole‐genome assessment of pseudogenes on the barley genome. We identified, characterized and classified 89 440 gene fragments and pseudogenes scattered along the chromosomes, with occasional hotspots and higher densities at the chromosome ends. Full‐length pseudogenes (11 015) have preferentially retained their exon–intron structure. Retrotransposition of processed mRNAs only plays a marginal role in their creation. However, the distribution of retroposed pseudogenes reflects the Rabl configuration of barley chromosomes and thus hints at founding mechanisms. While parent genes related to the defense‐response were found to be under‐represented in cultivated barley, we detected several defense‐related pseudogenes in wild barley accessions. The percentage of transcriptionally active pseudogenes is 7.2%, and these may potentially adopt new regulatory roles.The barley genome is rich in pseudogenes and small gene fragments mainly located towards chromosome tips or as tandemly repeated units. Our results indicate non‐random duplication and pseudogenization preferences and improve our understanding of the dynamics of gene birth and death in large plant genomes and the mechanisms that lead to evolutionary innovations. [ABSTRACT FROM AUTHOR]

Pseudogenes play a crucial role in cancer progression. However, the role of pituitary tumour-transforming 3, pseudogene (PTTG3P) in gastric cancer (GC) remains unknown. Here, we showed that PTTG3P expression was abnormally up-regulated in GC tissues compared with that in normal tissues both in our 198 cases of clinical samples and the cohort from The Cancer Genome Atlas (TCGA) database. High PTTG3P expression was correlated with increased tumour size and enhanced tumour invasiveness and served as an independent negative prognostic predictor. Moreover, up-regulation of PTTG3P in GC cells stimulated cell proliferation, migration and invasion both in vitro in cell experiments and in vivo in nude mouse models, and the pseudogene functioned independently of its parent genes. Overall, these results reveal that PTTG3P is a novel prognostic biomarker with independent oncogenic functions in GC. [ABSTRACT FROM AUTHOR]

The major histocompatibility complex ( MHC) is located in chromosome 6p21 and contains crucial regulators of immune response, including human leucocyte antigen ( HLA) genes, alongside other genes with nonimmunological roles. More recently, a repertoire of noncoding RNA genes, including expressed pseudogenes, has also been identified. The MHC is the most gene dense and most polymorphic part of the human genome. The region exhibits haplotype-specific linkage disequilibrium patterns, contains the strongest cis- and trans- eQTLs/me QTLs in the genome and is known as a hot spot for disease associations. Another layer of complexity is provided to the region by the extreme structural variation and copy number variations. While the HLA-B gene has the highest number of alleles, the HLA- DR/ DQ subregion is structurally most variable and shows the highest number of disease associations. Reliance on a single reference sequence has complicated the design, execution and analysis of GWAS for the MHC region and not infrequently, the MHC region has even been excluded from the analysis of GWAS data. Here, we contrast features of the MHC region with the rest of the genome and highlight its complexities, including its functional polymorphisms beyond those determined by single nucleotide polymorphisms or single amino acid residues. One of the several issues with customary GWAS analysis is that it does not address this additional layer of polymorphisms unique to the MHC region. We highlight alternative approaches that may assist with the analysis of GWAS data from the MHC region and unravel associations with all functional polymorphisms beyond single SNPs. We suggest that despite already showing the highest number of disease associations, the true extent of the involvement of the MHC region in disease genetics may not have been uncovered. [ABSTRACT FROM AUTHOR]

The expression pattern and biological role of long non-coding RNA (lnc RNA) in cancer has been reported to be involved in many cancers. Here, we report the expression and biological role of a newly discovered lnc RNA NmrA-like family domain containing 1 pseudogene (Loc344887) in gallbladder cancer ( GBC). In this study, we found that the expression of Loc344887 was significantly elevated in GBC tissues and cell lines when compared with matched normal tissues and normal epithelial bile duct cell line, respectively. High Loc344887 was associated with larger tumor size. Loc344887 was upregulated significantly after ectopic expression of nuclear factor (erythroid-derived 2)-like 2 (Nrf2) in GBC cells. Downregulation of Loc344887 in GBC cells suppressed cell proliferation, blocked cells in G0/S phase, and decreased the migration and invasion cell numbers. In addition, downregulation of Loc344887 decreased the expression of transcription factor Twist, mesenchymal marker Vimentin, and N-cadherin and increased the expression of epithelial maker E-cadherin, which could prompt a mesenchymal-to-epithelial transition phenotype. These results demonstrated that Loc344887 might contribute to cell proliferation and epithelial-to-mesenchymal transition process in GBC, which might be a potential therapeutic target. [ABSTRACT FROM AUTHOR]

We present a DNA barcoding study on the insect order Orthoptera that was generated in collaboration between four barcoding projects in three countries, viz. Barcoding Fauna Bavarica (Germany), German Barcode of Life, Austrian Barcode of Life and Swiss Barcode of Life. Our data set includes 748 COI sequences from 127 of the 162 taxa (78.4%) recorded in the three countries involved. Ninety-three of these 122 species (76.2%, including all Ensifera) can be reliably identified using DNA barcodes. The remaining 26 caeliferan species (families Acrididae and Tetrigidae) form ten clusters that share barcodes among up to five species, in three cases even across different genera, and in six cases even sharing individual barcodes. We discuss incomplete lineage sorting and hybridization as most likely causes of this phenomenon, as the species concerned are phylogenetically young and hybridization has been previously observed. We also highlight the problem of nuclear mitochondrial pseudogenes (numts), a known problem in the barcoding of orthopteran species, and the possibility of Wolbachia infections. Finally, we discuss the possible taxonomic implications of our barcoding results and point out future research directions. [ABSTRACT FROM AUTHOR]

The competing endogenous RNA network (ce RNET) is involved in tumorigenesis and has become a hot spot of research. The ce RNET between CYP4Z1 and the pseudogene CYP4Z2P promotes angiogenesis and mediates tamoxifen resistance in breast cancer. Nevertheless, the effects of this ce RNET on cell apoptosis and related mechanisms remain unclear. In the present study, we found that downregulation of CYP4Z1 or the CYP4Z2P 3′- UTR promotes cell apoptosis, mirroring the functions of human telomerase reverse transcriptase ( hTERT). Furthermore, the ce RNET between CYP4Z1 and pseudogene CYP4Z2P modulates hTERT expression by operating as a sub-ce RNET for hTERT. Our data demonstrate that the ce RNET between CYP4Z1 and pseudogene CYP4Z2P acts as a sub-ce RNET for hTERT and, thus, inhibits breast cancer apoptosis. [ABSTRACT FROM AUTHOR]

The concept of competitive endogenous RNA (ce RNA) was first proposed by Salmena and colleagues. Evidence suggests that pseudogene RNAs can act as a 'sponge' through competitive binding of common mi RNA, releasing or attenuating repression through sequestering mi RNAs away from parental mRNA. In theory, ce RNAs refer to all transcripts such as mRNA, tRNA, rRNA, long non-coding RNA, pseudogene RNA and circular RNA, because all of them may become the targets of mi RNA depending on spatiotemporal situation. As binding of mi RNA to the target RNA is not 100% complementary, it is possible that one mi RNA can bind to multiple target RNAs and vice versa. All RNAs crosstalk through competitively binding to mi RNA via mi RNA response elements ( MREs) contained within the RNA sequences, thus forming a complex regulatory network. The ratio of a subset of mi RNAs to the corresponding number of MREs determines repression strength on a given mRNA translation or stability. An increase in pseudogene RNA level can sequester mi RNA and release repression on the parental gene, leading to an increase in parental gene expression. A massive number of transcripts constitute a complicated network that regulates each other through this proposed mechanism, though some regulatory significance may be mild or even undetectable. It is possible that the regulation of gene and pseudogene expression occurring in this manor involves all RNAs bearing common MREs. In this review, we will primarily discuss how pseudogene transcripts regulate expression of parental genes via ce RNA network and biological significance of regulation. [ABSTRACT FROM AUTHOR]

The proportions of individual masu salmon Oncorhynchus masou whose genotypic and phenotypic sex differed were compared among juvenile and adult fish in three rivers, and genotypically male but phenotypically female individuals were observed 6-16% more often among adults than among juveniles. This suggests that during the transition from juvenile to adult, survival rates of genotypically male but phenotypically female individuals are higher than those of normal females. In contrast, genotypically female but phenotypically male individuals were only found in the juvenile period, which suggests that they exhibit a decreased survival rate in comparison with normal males. [ABSTRACT FROM AUTHOR]

Pronounced mitochondrial heterogeneity within putative species of Pleuroceridae has prevented meaningful systematic revisions of this critically imperilled freshwater family. Previous studies have demonstrated that this mitochondrial diversity often produces polyphyletic species on mitochondrial gene trees, but its significance is unclear. Hypotheses advanced to explain this pattern have included cryptic species, retained ancestral polymorphisms and introgression; other possible explanations such as doubly uniparental inheritance or the presence of pseudogenes have not been given due consideration. Previous analyses have not included adequate sampling, neither in terms of number of individuals nor in geographic coverage, to adequately test any of these hypotheses. To fully characterize mitochondrial heterogeneity in pleurocerids and robustly assess possible causal explanations, we collected 239 individuals representing four putative species from seven sites and sequenced the COI and 16S rRNA mitochondrial genes and the H3 nuclear gene for all individuals. We also used whole-genome shotgun sequencing to construct and annotate a mitochondrial genome for one individual. Characters with demonstrated utility in morphospecies delineation of gastropods (head-foot coloration, shell and radular morphology, pallial oviduct anatomy) were examined for a subset of individuals to determine whether morphology co-varied by haplotype clade. We found pronounced mitochondrial heterogeneity at both the population level and species level in three of the species examined, but our data reject paralogous nuclear copies of mitochondrial genes (NUMTs) and doubly uniparental inheritance as causal mechanisms, and there was no evidence of cryptic diversity. Mutation rates were found to differ significantly among mitochondrial lineages, and population genetic statistics revealed a signature of balancing selection that could be acting to maintain this diversity. The observed pattern is similar to that seen in lineages with inherited endosymbionts like Wolbachia infections, which merits further investigation. Although questions remain concerning the precise cause(s) of intraspecific mitochondrial diversity in pleurocerids, nuclear and/or genomic data, combined with anatomical and life history investigations in an integrative phylogenetic context, is the most promising avenue for resolving pleurocerid systematics. [ABSTRACT FROM AUTHOR]

Detection of Neisseria gonorrhoeae relies increasingly on nucleic acid amplification tests ( NAATs). The specificity of many gonococcal NAATs has been suboptimal and supplementary testing remains recommended in Europe and several additional countries. The novel dual-target GeneProof Neisseria gonorrhoeae PCR kit, targeting porA pseudogene and 16S rRNA gene, showed a high specificity and sensitivity when isolates of non-gonococcal Neisseria and related species (n = 144), and gonococci (n = 104) were tested. However, rare gonococcal porA mutants were only detected in the 16S rRNA gene target and two non-gonococcal isolates showed a low-level cross-reactivity in the 16S rRNA gene target. The detection limit for both targets was 1.5 copies per reaction. [ABSTRACT FROM AUTHOR]

The PPR-B gene is responsible for male-fertility restoration of the Ogura-type male-sterile radish plants, and it is located in the complex Rfo locus in the vicinity of similar PPR-A gene and PPR-C pseudogene. The aim of this study was to identify PPR-B alleles and understand the structure of the Rfo locus in radish breeding lines. Five lines of radish with normal male-fertile cytoplasm were tested. The entire PPR-B gene was amplified, sequenced and allelic PPR-B sequences were identified. The results indicated that the maintainer lines 7, 15 and 21 contained a non-restoring form of PPR-B protein. A unique PPR-B was found in lines 24/15 and 31 that are restorer and maintainer lines, respectively. The substitutions might be responsible for the loss of a restoring function of the PPR-B-31 allele. Amplification of the PPR-A/ PPR-B and PPR-B/ PPR-C intergenic regions allowed to identify rearrangements within Rfo locus. Obtained results confirm the wide allelic variation within the Rfo locus, as well as high genetic complexity of the fertility restoration mechanism in radish. [ABSTRACT FROM AUTHOR]

Human gallbladder cancer is a rare malignancy disease but having poor prognosis over the world. Previous studies have put forward that PTEN is a tumour suppressor in regulating many cellular processes, similar activities have been observed for its mammal homologue TPTE2. In this study, we attempted to unravel the underlying mechanistic basis of the role of TPTE2 and its pseudogene TPTE2P1 in gallbladder cancer. We employed lentivirus-mediated RNA interference as an efficient tool to silence endogenous TPTE2P1 transcription in the gallbladder cancer cell line GBC- SD/M. The effects of TPTE2P1 on cell migration and invasion were determined by transwell assays. We figured that depletion of TPTE2P1 remarkably inhibited gallbladder cancer cell migration and invasion capacity in vitro and elevated the expression of β-catenin via epithelial-mesenchymal transition signalling. Our findings revealed the functional role of TPTE2P1 in human gallbladder cancer and suggested that TPTE2P1 could serve as a promising therapeutic target and a palliation option in human gallbladder cancer. [ABSTRACT FROM AUTHOR]

Here we used both microsatellites and mtCR (mitochondrial DNA control region) sequences as genetic markers to examine the genetic diversity and population structure of Penaeus monodon shrimp from six Indonesian regions. The microsatellite data showed that shrimp from the Indian and the Pacific Ocean were genetically distinct from each other. It has been reported previously that P. monodon mt CR sequences from the Indo-Pacific group into two major paralogous clades of unclear origin. Here we show that the population structure inferred from mt CR sequences matches the microsatellite-based population structure for one of these clades. This is consistent with the notion that this mt CR clade shares evolutionary history with nuclear DNA and may thus represent nuclear mitochondrial pseudogenes (Numts). [ABSTRACT FROM AUTHOR]

Summary: Rumplessness in Hongshan chickens has been reported as a novel sex‐linked characteristic. Re‐sequencing data suggest that a pseudogene on the Z chromosome, LOC431648, is affiliated with this phenotype. In this study, we chose 23 rumpless and 25 normal Hongshan chickens to localize the potential variation by means of a genome‐wide association study using a high density microarray. A region on the Z chromosome was found to be closely associated with rumplessness in Hongshan chickens. The region, located in gene LINGO2, was approximately 3 Mb away from pseudogene LOC431648. The function of this gene has not yet been studied in birds. Differential expression of the candidate genes in the tail feather follicles was not detected by q‐PCR, which suggests that the rumplessness trait could be attributed to other genetic mechanisms. [ABSTRACT FROM AUTHOR]

Single mutations in the ATP-binding cassette transporter ( ABCC6) gene (OMIM 603234) are known to cause the rare autosomal recessive disease pseudoxanthoma elasticum ( PXE). Recently, we have found that copy number variations ( CNVs) in pseudogenes of the ABCC6 gene are quite common. The aim of this study was to investigate the frequency and possible contribution of CNV in ABCC6 and its pseudogenes in PXE. Genomic DNA from 212 PXE individuals were examined for copy number by pyrosequencing and quantitative polymerase chain reaction ( PCR) and compared with healthy individuals. The frequency of PXE individuals with any CNV was higher than in healthy individuals. The majority of variation comprised known and possibly new deletions in the ABCC6 gene and duplications of the ABCC6P1 and ABCC6P2 genes. ABCC6 deletions and ABCC6P2 duplications were not observed in 142 healthy individuals. In conclusion, by pyrosequencing and quantitative PCR, we were able to detect known and possibly new deletions in the ABCC6 gene that may have caused the PXE phenotype. Pyrosequencing may be used in PXE patients who have obtained incomplete genotype from conventional techniques. The frequency of ABCC6P2 pseudogene duplication was more common in PXE patients than healthy individuals and may affect the PXE phenotype. [ABSTRACT FROM AUTHOR]

Drosophila simulans is a close relative of the genetic model D. melanogaster. Its worldwide distribution in combination with the absence of segregating chromosomal inversions makes this species an increasingly attractive model to study the molecular signatures of adaptation in natural and experimental populations. In an effort to improve the genomic resources for D. simulans, we assembled and annotated the genome of a strain originating from Madagascar (M252), the ancestral range of D. simulans. The comparison of the M252 genome to other available D. simulans assemblies confirmed its high quality, but also highlighted genomic regions that are difficult to assemble with NGS data. The annotation of M252 provides a clear improvement with alternative splicing for 52% of the multiple-exon genes, UTRs for 70% of the genes, 225 novel genes and 781 pseudogenes being reported. We anticipate that the M252 genome will be a valuable resource for many research questions. [ABSTRACT FROM AUTHOR]