Genome Biology and Evolution最新文献_第8页

The Hypolimnas misippus Genome Supports a Common Origin of the W Chromosome in Lepidoptera. Hypolimnas misippus 基因组支持鳞翅目 W 染色体的共同起源。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-10-09 DOI: 10.1093/gbe/evae215

Anna Orteu, Shane A McCarthy, Emily A Hornett, Matthew R Gemmell, Louise A Reynolds, Ian A Warren, Ian J Gordon, Gregory D D Hurst, Richard Durbin, Simon H Martin, Chris D Jiggins

{"title":"The Hypolimnas misippus Genome Supports a Common Origin of the W Chromosome in Lepidoptera.","authors":"Anna Orteu, Shane A McCarthy, Emily A Hornett, Matthew R Gemmell, Louise A Reynolds, Ian A Warren, Ian J Gordon, Gregory D D Hurst, Richard Durbin, Simon H Martin, Chris D Jiggins","doi":"10.1093/gbe/evae215","DOIUrl":"10.1093/gbe/evae215","url":null,"abstract":"Moths and butterflies (Lepidoptera) have a heterogametic sex chromosome system with females carrying ZW chromosomes and males ZZ. The lack of W chromosomes in early-diverging lepidopteran lineages has led to the suggestion of an ancestral Z0 system in this clade and a B chromosome origin of the W. This contrasts with the canonical model of W chromosome evolution in which the W would have originated from the same homologous autosomal pair as the Z chromosome. Despite the distinct models proposed, the rapid evolution of the W chromosome has hindered the elucidation of its origin. Here, we present high-quality, chromosome-level genome assemblies of 2 Hypolimnas species (Hypolimnas misippus and Hypolimnas bolina) and use the H. misippus assembly to explore the evolution of W chromosomes in butterflies and moths. We show that in H. misippus, the W chromosome has higher similarity to the Z chromosome than any other chromosome, which could suggest a possible origin from the same homologous autosome pair as the Z chromosome. However, using genome assemblies of closely related species (ditrysian lineages) containing assembled W chromosomes, we present contrasting evidence suggesting that the W chromosome might have evolved from a B chromosome instead. Crucially, by using a synteny analysis to infer homology, we show that W chromosomes are likely to share a common evolutionary origin in Lepidoptera. This study highlights the difficulty of studying the evolution of W chromosomes and contributes to better understanding its evolutionary origins.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"16 10","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11523094/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142545110","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

Quest for Orthologs in the Era of Biodiversity Genomics. 在生物多样性基因组时代寻找同源物。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-10-09 DOI: 10.1093/gbe/evae224

Felix Langschied, Nicola Bordin, Salvatore Cosentino, Diego Fuentes-Palacios, Natasha Glover, Michael Hiller, Yanhui Hu, Jaime Huerta-Cepas, Luis Pedro Coelho, Wataru Iwasaki, Sina Majidian, Saioa Manzano-Morales, Emma Persson, Thomas A Richards, Toni Gabaldón, Erik Sonnhammer, Paul D Thomas, Christophe Dessimoz, Ingo Ebersberger

{"title":"Quest for Orthologs in the Era of Biodiversity Genomics.","authors":"Felix Langschied, Nicola Bordin, Salvatore Cosentino, Diego Fuentes-Palacios, Natasha Glover, Michael Hiller, Yanhui Hu, Jaime Huerta-Cepas, Luis Pedro Coelho, Wataru Iwasaki, Sina Majidian, Saioa Manzano-Morales, Emma Persson, Thomas A Richards, Toni Gabaldón, Erik Sonnhammer, Paul D Thomas, Christophe Dessimoz, Ingo Ebersberger","doi":"10.1093/gbe/evae224","DOIUrl":"10.1093/gbe/evae224","url":null,"abstract":"The era of biodiversity genomics is characterized by large-scale genome sequencing efforts that aim to represent each living taxon with an assembled genome. Generating knowledge from this wealth of data has not kept up with this pace. We here discuss major challenges to integrating these novel genomes into a comprehensive functional and evolutionary network spanning the tree of life. In summary, the expanding datasets create a need for scalable gene annotation methods. To trace gene function across species, new methods must seek to increase the resolution of ortholog analyses, e.g. by extending analyses to the protein domain level and by accounting for alternative splicing. Additionally, the scope of orthology prediction should be pushed beyond well-investigated proteomes. This demands the development of specialized methods for the identification of orthologs to short proteins and noncoding RNAs and for the functional characterization of novel gene families. Furthermore, protein structures predicted by machine learning are now readily available, but this new information is yet to be integrated with orthology-based analyses. Finally, an increasing focus should be placed on making orthology assignments adhere to the findable, accessible, interoperable, and reusable (FAIR) principles. This fosters green bioinformatics by avoiding redundant computations and helps integrating diverse scientific communities sharing the need for comparative genetics and genomics information. It should also help with communicating orthology-related concepts in a format that is accessible to the public, to counteract existing misinformation about 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/PMC11523110/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463299","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

Evolution of Apoptotic Signaling Pathways Within Lophotrochozoans. 藻类凋亡信号途径的进化

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-10-09 DOI: 10.1093/gbe/evae204

Helen R Horkan, Nikolay Popgeorgiev, Michel Vervoort, Eve Gazave, Gabriel Krasovec

{"title":"Evolution of Apoptotic Signaling Pathways Within Lophotrochozoans.","authors":"Helen R Horkan, Nikolay Popgeorgiev, Michel Vervoort, Eve Gazave, Gabriel Krasovec","doi":"10.1093/gbe/evae204","DOIUrl":"10.1093/gbe/evae204","url":null,"abstract":"Apoptosis is the main form of regulated cell death in metazoans. Apoptotic pathways are well characterized in nematodes, flies, and mammals, leading to a vision of the conservation of apoptotic pathways in metazoans. However, we recently showed that intrinsic apoptosis is in fact divergent among metazoans. In addition, extrinsic apoptosis is poorly studied in non-mammalian animals, making its evolution unclear. Consequently, our understanding of apoptotic signaling pathways evolution is a black box which must be illuminated by extending research to new biological systems. Lophotrochozoans are a major clade of metazoans which, despite their considerable biological diversity and key phylogenetic position as sister group of ecdysozoans (i.e. flies and nematodes), are poorly explored, especially regarding apoptosis mechanisms. Traditionally, each apoptotic signaling pathway was considered to rely on a specific initiator caspase, associated with an activator. To shed light on apoptosis evolution in animals, we explored the evolutionary history of initiator caspases, caspase activators, and the BCL-2 family (which control mitochondrial apoptotic pathway) in lophotrochozoans using phylogenetic analysis and protein interaction predictions. We discovered a diversification of initiator caspases in molluscs, annelids, and brachiopods, and the loss of key extrinsic apoptosis components in platyhelminths, along with the emergence of a clade-specific caspase with an ankyrin pro-domain. Taken together, our data show a specific history of apoptotic actors' evolution in lophotrochozoans, further demonstrating the appearance of distinct apoptotic signaling pathways during metazoan 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/PMC11463336/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142345129","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

Exploring the Relationship Between Gene Expression and Low-Frequency Somatic Mutations in Arabidopsis with Duplex Sequencing. 利用双工测序技术探索拟南芥基因表达与低频体细胞突变之间的关系。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-10-09 DOI: 10.1093/gbe/evae213

Gus Waneka, Braden Pate, J Grey Monroe, Daniel B Sloan

{"title":"Exploring the Relationship Between Gene Expression and Low-Frequency Somatic Mutations in Arabidopsis with Duplex Sequencing.","authors":"Gus Waneka, Braden Pate, J Grey Monroe, Daniel B Sloan","doi":"10.1093/gbe/evae213","DOIUrl":"10.1093/gbe/evae213","url":null,"abstract":"Intragenomic mutation rates can vary dramatically due to transcription-associated mutagenesis or transcription-coupled repair, which vary based on local epigenomic modifications that are nonuniformly distributed across genomes. One feature associated with decreased mutation is higher expression level, which depends on environmental cues. To understand the magnitude of expression-dependent mutation rate variation, we perturbed expression through a heat treatment in Arabidopsis thaliana. We quantified gene expression to identify differentially expressed genes, which we then targeted for mutation detection using duplex sequencing. This approach provided a highly accurate measurement of the frequency of rare somatic mutations in vegetative plant tissues, which has been a recent source of uncertainty. Somatic mutations in plants may be useful for understanding drivers of DNA damage and repair in the germline since plants experience late germline segregation and both somatic and germline cells share common repair machinery. We included mutant lines lacking mismatch repair (MMR) and base excision repair (BER) capabilities to understand how repair mechanisms may drive biased mutation accumulation. We found wild-type (WT) and BER mutant mutation frequencies to be very low (mean variant frequency 1.8 × 10-8 and 2.6 × 10-8, respectively), while MMR mutant frequencies were significantly elevated (1.13 × 10-6). Interestingly, in the MMR mutant lines, there was no difference in the somatic mutation frequencies between temperature treatments or between highly versus lowly expressed genes. The extremely low somatic variant frequencies in WT plants indicate that larger datasets will be needed to address fundamental evolutionary questions about whether environmental change leads to gene-specific changes in mutation rate.","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/PMC11489876/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371626","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

Bursts of rapid diversification, dispersals out of southern Africa, and two origins of dioecy punctuate the evolution of Asparagus 快速多样化的爆发、从南部非洲的扩散以及雌雄异体的两次起源，都是芦笋进化的标志性事件

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2024-09-18 DOI: 10.1093/gbe/evae200

Philip C Bentz, John E Burrows, Sandra M Burrows, Eshchar Mizrachi, Zhengjie Liu, Jun-Bo Yang, Zichao Mao, Margot Popecki, Ole Seberg, Gitte Petersen, Jim Leebens-Mack

{"title":"Bursts of rapid diversification, dispersals out of southern Africa, and two origins of dioecy punctuate the evolution of Asparagus","authors":"Philip C Bentz, John E Burrows, Sandra M Burrows, Eshchar Mizrachi, Zhengjie Liu, Jun-Bo Yang, Zichao Mao, Margot Popecki, Ole Seberg, Gitte Petersen, Jim Leebens-Mack","doi":"10.1093/gbe/evae200","DOIUrl":"https://doi.org/10.1093/gbe/evae200","url":null,"abstract":"The genus Asparagus arose approximately 9–15 million years ago (Ma) and transitions from hermaphroditism to dioecy (separate sexes) occurred ∼3–4 Ma. Roughly 27% of extant Asparagus species are dioecious, while the remaining are bisexual with monoclinous flowers. As such, Asparagus is an ideal model taxon for studying early stages of dioecy and sex chromosome evolution in plants. Until now, however, understanding of diversification and shifts from hermaphroditism to dioecy in Asparagus has been hampered by the lack of robust species tree estimates for the genus. In this study, a genus-wide phylogenomic analysis including 1726 nuclear loci and comprehensive species sampling supports two independent origins of dioecy in Asparagus—first in a widely distributed Eurasian clade, then again in a clade restricted to the Mediterranean Basin. Modeling of ancestral biogeography indicates that both dioecy origins were associated with range expansion out of southern Africa. Our findings also revealed several bursts of diversification across the phylogeny, including an initial radiation in southern Africa that gave rise to 12 major clades in the genus, and more recent radiations that have resulted in paraphyly and polyphyly among closely related species, as expected given active speciation processes. Lastly, we report that the geographic origin of domesticated garden asparagus (Asparagus officinalis L.) was likely in western Asia near the Mediterranean Sea. The presented phylogenomic framework for Asparagus is foundational for ongoing genomic investigations of diversification and functional trait evolution in the genus and contributes to its utility for understanding the origin and early evolution of dioecy and sex chromosomes.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"45 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142263373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Where the ‘ruber’ meets the road: Using the genome of the Red Diamond Rattlesnake to unravel the evolutionary processes driving venom evolution 在 "Ruber "与道路的交汇处：利用红钻响尾蛇的基因组揭示驱动毒液进化的演化过程

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2024-09-10 DOI: 10.1093/gbe/evae198

Samuel R Hirst, Rhett M Rautsaw, Cameron M VanHorn, Marc A Beer, Preston J McDonald, Ramsés Alejandro Rosales-García, Bruno Rodriguez Lopez, Alexandra Rubio Rincón, Hector Franz-Chávez, Víctor Vásquez-Cruz, Alfonso Kelly-Hernández, Andrew Storfer, Miguel Borja, Gamaliel Castañeda-Gaytán, Paul B Frandsen, Christopher L Parkinson, Jason L Strickland, Mark J Margres

{"title":"Where the ‘ruber’ meets the road: Using the genome of the Red Diamond Rattlesnake to unravel the evolutionary processes driving venom evolution","authors":"Samuel R Hirst, Rhett M Rautsaw, Cameron M VanHorn, Marc A Beer, Preston J McDonald, Ramsés Alejandro Rosales-García, Bruno Rodriguez Lopez, Alexandra Rubio Rincón, Hector Franz-Chávez, Víctor Vásquez-Cruz, Alfonso Kelly-Hernández, Andrew Storfer, Miguel Borja, Gamaliel Castañeda-Gaytán, Paul B Frandsen, Christopher L Parkinson, Jason L Strickland, Mark J Margres","doi":"10.1093/gbe/evae198","DOIUrl":"https://doi.org/10.1093/gbe/evae198","url":null,"abstract":"Understanding the proximate and ultimate causes of phenotypic variation is fundamental in evolutionary research, as such variation provides the substrate for selection to act upon. Although trait variation can arise due to selection, the importance of neutral processes is sometimes understudied. We presented the first reference-quality genome of the Red Diamond Rattlesnake (Crotalus ruber) and used range-wide ‘omic data to estimate the degree to which neutral and adaptive evolutionary processes shaped venom evolution. We characterized population structure and found substantial genetic differentiation across two populations, each with distinct demographic histories. We identified significant differentiation in venom expression across age classes with substantially reduced but discernible differentiation across populations. We then used conditional redundancy analysis to test whether venom expression variation was best predicted by neutral divergence patterns or geographically-variable (a)biotic factors. Snake size was the most significant predictor of venom variation, with environment, prey availability, and neutral sequence variation also identified as significant factors, though to a lesser degree. By directly including neutrality in the model, our results confidently highlight the predominant, yet not singular, role of life history in shaping venom evolution.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"115 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142227541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Azooxanthellate Palythoa (Cnidaria: Anthozoa) Genomes Reveal Toxin-related Gene Clusters and Loss of Neuronal Genes in Hexacorals. 偶氮藻类石莲花虫（Cnidaria: Anthozoa）基因组揭示了毒素相关基因簇和六孔动物神经元基因的缺失。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-09-03 DOI: 10.1093/gbe/evae197

Yuki Yoshioka, Hiroshi Yamashita, Taiga Uchida, Chuya Shinzato, Mayumi Kawamitsu, Chloé Julie Loïs Fourreau, Guillermo Mironenko Castelló, Britta Katharina Fiedler, Timotheus Maximilian van den Eeckhout, Stefano Borghi, James Davis Reimer, Eiichi Shoguchi

{"title":"Azooxanthellate Palythoa (Cnidaria: Anthozoa) Genomes Reveal Toxin-related Gene Clusters and Loss of Neuronal Genes in Hexacorals.","authors":"Yuki Yoshioka, Hiroshi Yamashita, Taiga Uchida, Chuya Shinzato, Mayumi Kawamitsu, Chloé Julie Loïs Fourreau, Guillermo Mironenko Castelló, Britta Katharina Fiedler, Timotheus Maximilian van den Eeckhout, Stefano Borghi, James Davis Reimer, Eiichi Shoguchi","doi":"10.1093/gbe/evae197","DOIUrl":"10.1093/gbe/evae197","url":null,"abstract":"Zoantharia is an order among the Hexacorallia (Anthozoa: Cnidaria), and includes at least 300 species. Previously reported genomes from scleractinian corals and actiniarian sea anemones have illuminated part of the hexacorallian diversification. However, little is known about zoantharian genomes and the early evolution of hexacorals. To explore genome evolution in this group of hexacorals, here, we report de novo genome assemblies of the zoantharians Palythoa mizigama (Pmiz) and Palythoa umbrosa (Pumb), both of which are members of the family Sphenopidae, and uniquely live in comparatively dark coral reef caves without symbiotic Symbiodiniaceae dinoflagellates. Draft genomes generated from ultra-low input PacBio sequencing totaled 373 and 319 Mbp for Pmiz and Pumb, respectively. Protein-coding genes were predicted in each genome, totaling 30,394 in Pmiz and 24,800 in Pumb, with each set having ∼93% BUSCO completeness. Comparative genomic analyses identified 3,036 conserved gene families, which were found in all analyzed hexacoral genomes. Some of the genes related to toxins, chitin degradation, and prostaglandin biosynthesis were expanded in these two Palythoa genomes and many of which aligned tandemly. Extensive gene family loss was not detected in the Palythoa lineage and five of ten putatively lost gene families likely had neuronal function, suggesting biased gene loss in Palythoa. In conclusion, our comparative analyses demonstrate evolutionary conservation of gene families in the Palythoa lineage from the common ancestor of hexacorals. Restricted loss of gene families may imply that lost neuronal functions were effective for environmental adaptation in these two Palythoa species.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11413580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142143051","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 Genomic and Cultural Diversity of the Inka Qhapaq Hucha Ceremony in Chile and Argentina. 智利和阿根廷因卡人 Qhapaq hucha 仪式的基因组和文化多样性。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-09-03 DOI: 10.1093/gbe/evae196

Constanza de la Fuente Castro, Constanza Cortés, Maanasa Raghavan, Daniela Castillo, Mario Castro, Ricardo A Verdugo, Mauricio Moraga

{"title":"The Genomic and Cultural Diversity of the Inka Qhapaq Hucha Ceremony in Chile and Argentina.","authors":"Constanza de la Fuente Castro, Constanza Cortés, Maanasa Raghavan, Daniela Castillo, Mario Castro, Ricardo A Verdugo, Mauricio Moraga","doi":"10.1093/gbe/evae196","DOIUrl":"10.1093/gbe/evae196","url":null,"abstract":"The South American archaeological record has ample evidence of the socio-cultural dynamism of human populations in the past. This has also been supported through the analysis of ancient genomes, by showing evidence of gene flow across the region. While the extent of these signals is yet to be tested, the growing number of ancient genomes allows for more fine-scaled hypotheses to be evaluated. In this study, we assessed the genetic diversity of individuals associated with the Inka ritual, Qhapaq hucha. As part of this ceremony, one or more individuals were buried with Inka and local-style offerings on mountain summits along the Andes, leaving a very distinctive record. Using paleogenomic tools, we analyzed three individuals: two newly generated genomes from El Plomo Mountain (Chile) and El Toro Mountain (Argentina), and a previously published genome from Argentina (Aconcagua Mountain). Our results reveal a complex demographic scenario with each of the individuals showing different genetic affinities. Furthermore, while two individuals showed genetic similarities with present-day and ancient populations from the southern region of the Inka empire, the third individual may have undertaken long-distance movement. The genetic diversity we observed between individuals from similar cultural contexts supports the highly diverse strategies Inka implemented while incorporating new territories. More broadly, this research contributes to our growing understanding of the population dynamics in the Andes by discussing the implications and temporality of population movements in the region.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11411372/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132541","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

Correlation Between Subgenome-biased DNA Loss and DNA Transposon Activation Following Hybridization in the Allotetraploid Xenopus Frogs. 异源四倍体异蛙杂交后DNA亚基因组偏向丢失与DNA转座子激活之间的相关性

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-09-03 DOI: 10.1093/gbe/evae179

Kosuke Suda, Takahiro Suzuki, Shun Hayashi, Honoka Okuyama, Daisuke Tsukamoto, Takuya Matsuo, Kei Tamura, Michihiko Ito

{"title":"Correlation Between Subgenome-biased DNA Loss and DNA Transposon Activation Following Hybridization in the Allotetraploid Xenopus Frogs.","authors":"Kosuke Suda, Takahiro Suzuki, Shun Hayashi, Honoka Okuyama, Daisuke Tsukamoto, Takuya Matsuo, Kei Tamura, Michihiko Ito","doi":"10.1093/gbe/evae179","DOIUrl":"https://doi.org/10.1093/gbe/evae179","url":null,"abstract":"In certain tetraploid species resulting from interspecific hybridization, one parent's subgenome is known to selectively undergo DNA loss. The molecular mechanisms behind this remain unclear. In our study, we compared the genomes of a standard diploid species with two allotetraploid species from the Xenopus genus, both possessing L (longer) and S (shorter) homoeologous subgenomes. We observed substantial gene losses and intergenic DNA deletions in both the S and L subgenomes of the tetraploid species. Gene losses were around 1,000 to 3,000 for L and 4,000 to 6,000 for S, with especially prominent losses in the S subgenome. Many of these losses likely occurred shortly after interspecific hybridization in both L/S subgenomes. We also deduced frequent large inversions in the S subgenome. Upon reassessing transposon dynamics using updated genome databases, we reaffirmed heightened DNA transposon activity during the hybridization, as previously reported. We next investigated whether S subgenome-biased DNA loss could be correlated with the activation of DNA transposons following hybridization. Notably, distinct patterns were observed in the dynamics of DNA transposons between the L and S subgenomes. Several DNA transposon subfamilies correlated positively with DNA deletions in the S subgenome and negatively in the L subgenome. Based on these results, we propose a model that, upon and after hybridization between two related diploid Xenopus species, the mixture of their genomes resulted in the derepression of DNA transposons, especially in the S subgenome, leading to selective DNA loss in the S subgenome.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"16 9","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11415220/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142284406","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

Correction to: Chromosome-Level Reference Genome of the Ponza Grayling (Hipparchia sbordonii), an Italian Endemic and Endangered Butterfly. Correction to：意大利特有的濒危蝴蝶 Ponza Grayling（Hipparchia sbordonii）的染色体水平参考基因组。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-09-03 DOI: 10.1093/gbe/evae201

引用次数: 0