{"title":"Chromosome-Level Genome Assembly of Five Emberiza Species Reveals the Genomic Characteristics and Intrinsic Drivers of Adaptive Radiation.","authors":"Tingli Hu, Haohao Ma, Yongxuan Xiao, Ruolei Sun, Chunlin Li, Lei Shan, Baowei Zhang","doi":"10.1111/1755-0998.14063","DOIUrl":null,"url":null,"abstract":"<p><p>Emberiza buntings (Aves: Emberizidae) exhibit extensive diversity and rapid diversification within the Old World, particularly in the eastern Palearctic, making them valuable models for studying rapid radiation among sympatric species. Despite their ecological and morphological diversity, there remains a significant gap in understanding the genomic underpinnings driving their rapid speciation. To fill this gap, we assembled high-quality chromosome-level genomes of five representative Emberiza species (E. aureola, E. pusilla, E. rustica, E. rutila and E. spodocephala). Comparative genomic analysis revealed distinct migration-related evolutionary adaptations in their genomes, including variations in lipid metabolism, oxidative stress response, locomotor ability and circadian regulation. These changes may facilitate the rapid occupation of emerging ecological niches and provide opportunities for species diversification. Additionally, these five species exhibited abnormal abundances of long terminal repeat retrotransposons (LTRs), comprising over 20% of their genomes, with insertion times corresponding to their divergence (~2.5 million years ago). The presence of LTRs influenced genome size, chromosomal structure and single-gene expression, suggesting their role in promoting the rapid diversification of Emberiza species. These findings offer valuable insights into the adaptive radiation of Emberiza and establish a robust theoretical foundation for further exploration of the patterns and mechanisms underlying their diversification.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14063"},"PeriodicalIF":5.5000,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular Ecology Resources","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1111/1755-0998.14063","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Emberiza buntings (Aves: Emberizidae) exhibit extensive diversity and rapid diversification within the Old World, particularly in the eastern Palearctic, making them valuable models for studying rapid radiation among sympatric species. Despite their ecological and morphological diversity, there remains a significant gap in understanding the genomic underpinnings driving their rapid speciation. To fill this gap, we assembled high-quality chromosome-level genomes of five representative Emberiza species (E. aureola, E. pusilla, E. rustica, E. rutila and E. spodocephala). Comparative genomic analysis revealed distinct migration-related evolutionary adaptations in their genomes, including variations in lipid metabolism, oxidative stress response, locomotor ability and circadian regulation. These changes may facilitate the rapid occupation of emerging ecological niches and provide opportunities for species diversification. Additionally, these five species exhibited abnormal abundances of long terminal repeat retrotransposons (LTRs), comprising over 20% of their genomes, with insertion times corresponding to their divergence (~2.5 million years ago). The presence of LTRs influenced genome size, chromosomal structure and single-gene expression, suggesting their role in promoting the rapid diversification of Emberiza species. These findings offer valuable insights into the adaptive radiation of Emberiza and establish a robust theoretical foundation for further exploration of the patterns and mechanisms underlying their diversification.
在旧大陆,特别是在古北大陆东部,Emberiza狩猎(鸟类:Emberizidae)表现出广泛的多样性和快速的多样化,使它们成为研究同域物种快速辐射的有价值的模型。尽管它们的生态和形态多样性,但在理解其快速物种形成的基因组基础方面仍然存在重大差距。为了填补这一空白,我们组装了五个代表性的Emberiza物种(E. aureola, E. pusilla, E. rustica, E. rutila和E. spodocephala)的高质量染色体水平基因组。比较基因组分析揭示了它们基因组中不同的迁移相关进化适应,包括脂质代谢、氧化应激反应、运动能力和昼夜节律调节的变化。这些变化可能会促进新兴生态位的快速占领,并为物种多样化提供机会。此外,这5个物种表现出异常丰度的长末端重复反转录转座子(LTRs),占其基因组的20%以上,其插入时间与它们的分化(~ 250万年前)相对应。LTRs的存在影响了Emberiza物种的基因组大小、染色体结构和单基因表达,表明它们在促进Emberiza物种快速多样化中发挥了作用。这些发现为了解Emberiza的适应性辐射提供了有价值的见解,并为进一步探索其多样化的模式和机制奠定了坚实的理论基础。
期刊介绍:
Molecular Ecology Resources promotes the creation of comprehensive resources for the scientific community, encompassing computer programs, statistical and molecular advancements, and a diverse array of molecular tools. Serving as a conduit for disseminating these resources, the journal targets a broad audience of researchers in the fields of evolution, ecology, and conservation. Articles in Molecular Ecology Resources are crafted to support investigations tackling significant questions within these disciplines.
In addition to original resource articles, Molecular Ecology Resources features Reviews, Opinions, and Comments relevant to the field. The journal also periodically releases Special Issues focusing on resource development within specific areas.