Genome Biology and Evolution最新文献_第6页

Genomic Localization Bias of Secondary Metabolite Gene Clusters and Association with Histone Modifications in Aspergillus. 曲霉次生代谢物基因簇的基因组定位偏差及其与组蛋白修饰的关联。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-01 DOI: 10.1093/gbe/evae228

Xin Zhang, Iseult Leahy, Jérȏme Collemare, Michael F Seidl

{"title":"Genomic Localization Bias of Secondary Metabolite Gene Clusters and Association with Histone Modifications in Aspergillus.","authors":"Xin Zhang, Iseult Leahy, Jérȏme Collemare, Michael F Seidl","doi":"10.1093/gbe/evae228","DOIUrl":"10.1093/gbe/evae228","url":null,"abstract":"Fungi are well-known producers of bioactive secondary metabolites (SMs), which have been exploited for decades by humankind for various medical applications like therapeutics and antibiotics. SMs are synthesized by biosynthetic gene clusters (BGCs)-physically co-localized and co-regulated genes. Because BGCs are often regulated by histone post-translational modifications (PTMs), it was suggested that their chromosomal location is important for their expression. Studies in a few fungal species indicated an enrichment of BGCs in sub-telomeric regions; however, there is no evidence that BGCs with distinct genomic localization are regulated by different histone PTMs. Here, we used 174 Aspergillus species covering 22 sections to determine the correlation between BGC genomic localization, gene expression, and histone PTMs. We found a high abundance and diversity of SM backbone genes across the Aspergillus genus, with notable unique genes within sections. Being unique or conserved in many species, BGCs showed a strong bias for being localized in low-synteny regions, regardless of their position in chromosomes. Using chromosome-level assemblies, we also confirmed a significantly biased localization in sub-telomeric regions. Notably, SM backbone genes in sub-telomeric regions and about half of those in low-synteny regions exhibit higher gene expression variability, likely due to the similar higher variability in H3K4me3 and H3K36me3 histone PTMs; while variations in histone H3 acetylation and H3K9me3 are not correlated to genomic localization and expression variation, as analyzed in two Aspergillus species. Expression variability across four Aspergillus species further supports that BGCs tend to be located in low-synteny regions and that regulation of expression in those regions likely involves different histone PTMs than the most commonly studied modifications.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11542625/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142499148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

LukProt: A Database of Eukaryotic Predicted Proteins Designed for Investigations of Animal Origins. LukProt：真核生物预测蛋白质数据库，用于研究动物起源。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-01 DOI: 10.1093/gbe/evae231

Łukasz F Sobala

{"title":"LukProt: A Database of Eukaryotic Predicted Proteins Designed for Investigations of Animal Origins.","authors":"Łukasz F Sobala","doi":"10.1093/gbe/evae231","DOIUrl":"10.1093/gbe/evae231","url":null,"abstract":"The origins and early evolution of animals are subjects with many outstanding questions. One problem faced by researchers trying to answer them is the absence of a comprehensive database with sequences from nonbilaterians. Publicly available data are plentiful but scattered and often not associated with proper metadata. A new database presented in this paper, LukProt, is an attempt at solving this issue. The database contains protein sequences obtained mostly from genomic, transcriptomic, and metagenomic studies and is an extension of EukProt (Richter DJ, Berney C, Strassert JFH, Poh Y-P, Herman EK, Muñoz-Gómez SA, Wideman JG, Burki F, de Vargas C. EukProt: a database of genome-scale predicted proteins across the diversity of eukaryotes. Peer Community J. 2022:2:e56. https://doi.org/10.24072/pcjournal.173). LukProt adopts the EukProt naming conventions and includes data from 216 additional animals. The database is associated with a taxonomic grouping (taxogroup) scheme suitable for studying early animal evolution. Minor updates to the database will contain species additions or metadata corrections, whereas major updates will synchronize LukProt to each new version of EukProt, and releases are permanently stored on Zenodo (https://doi.org/10.5281/zenodo.7089120). A BLAST server to search the database is available at: https://lukprot.hirszfeld.pl/. Users are invited to participate in maintaining and correcting LukProt. As it can be searched without downloading locally, the database aims to be a convenient resource not only for evolutionary biologists, but for the broader scientific community as well.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11534060/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chromosomal-Level Genome Assembly of the Antarctic Sea Urchin Sterechinus neumayeri: A Model for Antarctic Invertebrate Biology. 南极无脊椎动物生物学模型--南极海胆 Sterechinus neumayeri 的染色体级基因组组装。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-01 DOI: 10.1093/gbe/evae237

Jacob F Warner, Ryan C Range, Jennifer Fenner, Cheikouna Ka, Damien S Waits, Kristen Boddy, Kyle T David, Andrew R Mahon, Kenneth M Halanych

引用次数: 0

The Evolution of Gene Expression Plasticity During Adaptation to Salt in Chlamydomonas reinhardtii. 莱茵衣藻在适应盐分过程中基因表达可塑性的演变。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-01 DOI: 10.1093/gbe/evae214

Yeshoda Y Harry-Paul, Josianne Lachapelle, Rob W Ness

{"title":"The Evolution of Gene Expression Plasticity During Adaptation to Salt in Chlamydomonas reinhardtii.","authors":"Yeshoda Y Harry-Paul, Josianne Lachapelle, Rob W Ness","doi":"10.1093/gbe/evae214","DOIUrl":"10.1093/gbe/evae214","url":null,"abstract":"When environmental change is rapid or unpredictable, phenotypic plasticity can facilitate adaptation to new or stressful environments to promote population persistence long enough for adaptive evolution to occur. However, the underlying genetic mechanisms that contribute to plasticity and its role in adaptive evolution are generally unknown. Two main opposing hypotheses dominate-genetic compensation and genetic assimilation. Here, we predominantly find evidence for genetic compensation over assimilation in adapting the freshwater algae Chlamydomonas reinhardtii to 36 g/L salt environments over 500 generations. More canalized genes in the high-salt (HS) lines displayed a pattern of genetic compensation (63%) fixing near or at the ancestral native expression level, rather than genetic assimilation of the salt-induced level, suggesting that compensation was more common during adaptation to salt. Network analysis revealed an enrichment of genes involved in energy production and salt-resistance processes in HS lines, while an increase in DNA repair mechanisms was seen in ancestral strains. In addition, whole-transcriptome similarity among ancestral and HS lines displayed the evolution of a similar plastic response to salt conditions in independently reared HS lines. We also found more cis-acting regions in the HS lines; however, the expression patterns of most genes did not mimic that of their inherited sequence. Thus, the expression changes induced via plasticity offer temporary relief, but downstream changes are required for a sustainable solution during the evolutionary process.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11534027/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Repeat-Rich Regions Cause False-Positive Detection of NUMTs: A Case Study in Amphibians Using an Improved Cane Toad Reference Genome. 富重复区域导致 NUMTs 的假阳性检测：利用改进的蔗蟾蜍参考基因组对两栖动物进行的案例研究。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-01 DOI: 10.1093/gbe/evae246

Kelton Cheung, Lee Ann Rollins, Jillian M Hammond, Kirston Barton, James M Ferguson, Harrison J F Eyck, Richard Shine, Richard J Edwards

{"title":"Repeat-Rich Regions Cause False-Positive Detection of NUMTs: A Case Study in Amphibians Using an Improved Cane Toad Reference Genome.","authors":"Kelton Cheung, Lee Ann Rollins, Jillian M Hammond, Kirston Barton, James M Ferguson, Harrison J F Eyck, Richard Shine, Richard J Edwards","doi":"10.1093/gbe/evae246","DOIUrl":"10.1093/gbe/evae246","url":null,"abstract":"Mitochondrial DNA (mtDNA) has been widely used in genetics research for decades. Contamination from nuclear DNA of mitochondrial origin (NUMTs) can confound studies of phylogenetic relationships and mtDNA heteroplasmy. Homology searches with mtDNA are widely used to detect NUMTs in the nuclear genome. Nevertheless, false-positive detection of NUMTs is common when handling repeat-rich sequences, while fragmented genomes might result in missing true NUMTs. In this study, we investigated different NUMT detection methods and how the quality of the genome assembly affects them. We presented an improved nuclear genome assembly (aRhiMar1.3) of the invasive cane toad (Rhinella marina) with additional long-read Nanopore and 10× linked-read sequencing. The final assembly was 3.47 Gb in length with 91.3% of tetrapod universal single-copy orthologs (n = 5,310), indicating the gene-containing regions were well assembled. We used 3 complementary methods (NUMTFinder, dinumt, and PALMER) to study the NUMT landscape of the cane toad genome. All 3 methods yielded consistent results, showing very few NUMTs in the cane toad genome. Furthermore, we expanded NUMT detection analyses to other amphibians and confirmed a weak relationship between genome size and the number of NUMTs present in the nuclear genome. Amphibians are repeat-rich, and we show that the number of NUMTs found in highly repetitive genomes is prone to inflation when using homology-based detection without filters. Together, this study provides an exemplar of how to robustly identify NUMTs in complex genomes when confounding effects on mtDNA analyses are a concern.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11606642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Chromosome-Scale and Annotated Reference Genome Assembly of Plecia longiforceps Duda, 1934 (Diptera: Bibionidae). Plecia longiforceps Duda, 1934 (Diptera: Bibionidae) 的染色体尺度和注释参考基因组组装。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-10-09 DOI: 10.1093/gbe/evae205

Jonghwan Choi, Taemin Kang, Sun-Jae Park, Seunggwan Shin

{"title":"A Chromosome-Scale and Annotated Reference Genome Assembly of Plecia longiforceps Duda, 1934 (Diptera: Bibionidae).","authors":"Jonghwan Choi, Taemin Kang, Sun-Jae Park, Seunggwan Shin","doi":"10.1093/gbe/evae205","DOIUrl":"10.1093/gbe/evae205","url":null,"abstract":"Urbanization is a leading factor effecting global biodiversity, driving rapid evolutionary processes in the local biota. Species that adapt and proliferate in city environments can become pests, with human activities facilitating their dispersal and excessive outbreaks. Here we present the first genome data of Plecia longiforceps, a lovebug pest in Eastern Asia with intensive aggregations recently occurring in the Seoul Metropolitan Area of Korea. PacBio HiFi and ONT Pore-C sequencing data were used to construct a highly continuous assembly with a total size of 707 Mb and 8 major pseudochromosomes, its integrity supported by the N50 length of 98.1 Mb and 96.8% BUSCO completeness. Structural and functional annotation using transcriptome data and ab initio predictions revealed a high proportion (69.3%) of repeat sequences, and synteny analysis with Bibio marci showed high levels of genomic collinearity. The genome will serve as an essential resource for both population genomics and molecular research on lovebug dispersal and outbreaks, and also implement studies on the eco-evolutionary processes of insects in urbanizing habitats.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11474240/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142345128","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Effect of the Presence and Absence of DNA Repair Genes on the Rate and Pattern of Mutation in Bacteria. DNA 修复基因的存在与否对细菌突变率和突变模式的影响。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-10-09 DOI: 10.1093/gbe/evae216

Georgios Kalogiannis, Adam Eyre-Walker

引用次数: 0

The Evolution of Extreme Genetic Variability in a Parasite-Resistance Complex. 寄生虫抗药性复合体中极端遗传变异的进化。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-10-09 DOI: 10.1093/gbe/evae222

Suha Naser-Khdour, Fabian Scheuber, Peter D Fields, Dieter Ebert

{"title":"The Evolution of Extreme Genetic Variability in a Parasite-Resistance Complex.","authors":"Suha Naser-Khdour, Fabian Scheuber, Peter D Fields, Dieter Ebert","doi":"10.1093/gbe/evae222","DOIUrl":"10.1093/gbe/evae222","url":null,"abstract":"Genomic regions that play a role in parasite defense are often found to be highly variable, with the major histocompatibility complex serving as an iconic example. Single nucleotide polymorphisms may represent only a small portion of this variability, with Indel polymorphisms and copy number variation further contributing. In extreme cases, haplotypes may no longer be recognized as orthologous. Understanding the evolution of such highly divergent regions is challenging because the most extreme variation is not visible using reference-assisted genomic approaches. Here we analyze the case of the Pasteuria Resistance Complex in the crustacean Daphnia magna, a defense complex in the host against the common and virulent bacterium Pasteuria ramosa. Two haplotypes of this region have been previously described, with parts of it being nonhomologous, and the region has been shown to be under balancing selection. Using pan-genome analysis and tree reconciliation methods to explore the evolution of the Pasteuria Resistance Complex and its characteristics within and between species of Daphnia and other Cladoceran species, our analysis revealed a remarkable diversity in this region even among host species, with many nonhomologous hyper-divergent haplotypes. The Pasteuria Resistance Complex is characterized by extensive duplication and losses of Fucosyltransferase (FuT) and Galactosyltransferase (GalT) genes that are believed to play a role in parasite defense. The Pasteuria Resistance Complex region can be traced back to common ancestors over 250 million years. The unique combination of an ancient resistance complex and a dynamic, hyper-divergent genomic environment presents a fascinating opportunity to investigate the role of such regions in the evolution and long-term maintenance of resistance polymorphisms. Our findings offer valuable insights into the evolutionary forces shaping disease resistance and adaptation, not only in the genus Daphnia, but potentially across the entire Cladocera class.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11500718/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142400021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

THI1 Gene Evolutionary Trends: A Comprehensive Plant-Focused Assessment via Data Mining and Large-Scale Analysis. THI1 基因进化趋势：通过数据挖掘和大规模分析进行以植物为重点的全面评估。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-10-09 DOI: 10.1093/gbe/evae212

Henrique Moura Dias, Naiara Almeida de Toledo, Ravi V Mural, James C Schnable, Marie-Anne Van Sluys

{"title":"THI1 Gene Evolutionary Trends: A Comprehensive Plant-Focused Assessment via Data Mining and Large-Scale Analysis.","authors":"Henrique Moura Dias, Naiara Almeida de Toledo, Ravi V Mural, James C Schnable, Marie-Anne Van Sluys","doi":"10.1093/gbe/evae212","DOIUrl":"10.1093/gbe/evae212","url":null,"abstract":"Molecular evolution analysis typically involves identifying selection pressure and reconstructing evolutionary trends. This process usually requires access to specific data related to a target gene or gene family within a particular group of organisms. While recent advancements in high-throughput sequencing techniques have resulted in the rapid accumulation of extensive genomics and transcriptomics data and the creation of new databases in public repositories, extracting valuable insights from such vast data sets remains a significant challenge for researchers. Here, we elucidated the evolutionary history of THI1, a gene responsible for encoding thiamine thiazole synthase. The thiazole ring is a precursor for vitamin B1 and a crucial cofactor in primary metabolic pathways. A thorough search of complete genomes available within public repositories reveals 702 THI1 homologs of Archaea and Eukarya. Throughout its diversification, the plant lineage has preserved the THI1 gene by incorporating the N-terminus and targeting the chloroplasts. Likewise, evolutionary pressures and lifestyle appear to be associated with retention of TPP riboswitch sites and consequent dual posttranscriptional regulation of the de novo biosynthesis pathway in basal groups. Multicopy retention of THI1 is not a typical plant pattern, even after successive genome duplications. Examining cis-regulatory sites in plants uncovers two shared motifs across all plant lineages. A data mining of 484 transcriptome data sets supports the THI1 homolog expression under a light/dark cycle response and a tissue-specific pattern. Finally, the work presented brings a new look at public repositories as an opportunity to explore evolutionary trends to THI1.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11521341/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463301","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Palaeognaths Reveal Evolutionary Ancestry of the Avian Major Histocompatibility Complex Class II. 古猿揭示了鸟类主要组织相容性复合体 II 类的进化祖先。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-10-09 DOI: 10.1093/gbe/evae211

Piotr Minias, Wiesław Babik

{"title":"Palaeognaths Reveal Evolutionary Ancestry of the Avian Major Histocompatibility Complex Class II.","authors":"Piotr Minias, Wiesław Babik","doi":"10.1093/gbe/evae211","DOIUrl":"10.1093/gbe/evae211","url":null,"abstract":"The multigene family of the major histocompatibility complex (MHC) codes for the key antigen-presenting molecules of the vertebrate immune system. In birds, duplicated MHC class II (MHC-II) genes are highly homogenized by concerted evolution, and thus, identification of their orthologous relationships across long evolutionary timescales remains challenging. Relatively low evolutionary rate of avian MHC class IIA genes has been expected to provide a promising avenue to allow such inferences, but availability of MHC-IIA sequences in nonmodel bird species has been limited until recently. Here, taking advantage from accumulating genomic resources, we identified and analyzed MHC-IIA sequences from the most basal lineage of extant birds (Palaeognathae). Conserved region of the MHC-IIA membrane-proximal domain was used to search for orthologous relationships between palaeognath birds and nonavian reptiles. First, analyses of palaeognath sequences revealed the presence of a separate MHC-IIA gene lineage (DAA3) in kiwis, which did not cluster with previously described avian MHC-IIA lineages (DAA1 and DAA2). Next, phylogenetic reconstruction showed that kiwi DAA3 sequences form a single well-supported cluster with turtle MHC-IIA. High similarity of these sequences most likely reflects their remarkable evolutionary conservation and retention of ancient orthologous relationships, which can be traced back to basal archosauromorphs ca. 250 million years ago. Our analyses offer novel insights into macroevolutionary history of the MHC and reinforce the view that rapid accumulation of high-quality genome assemblies across divergent nonmodel species can substantially advance our understanding of gene evolution.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11487930/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142365056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0