Reference Genome of an Irruptive Migrant, the Pine Siskin (Spinus pinus).

IF 2.5 2区 生物学 Q2 EVOLUTIONARY BIOLOGY
Jair Cortez, Joel W G Slade, Tricia A Van Laar
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引用次数: 0

Abstract

Pine siskins (Spinus pinus) are irruptive migratory songbirds of biological interest in studies of endocrine regulation, immune function, and behavioral flexibility. Here, we present a chromosome-level reference genome from a female pine siskin, assembled de novo using long-read sequencing and scaffolded with a reference-guided approach. Synteny analyses also showed that our assembly can reliably reveal genomic rearrangements relative to other finches. Using reference-based annotation, we identified thousands of protein-coding genes, including loci relevant to metabolism and immune function that demonstrate the utility of this assembly for downstream studies. We also found evidence of gene duplications and pseudogenization in immune loci, showing the utility of our assembly for immunogenetic studies. Our analysis provides the first genome-wide view of transposable element (TE) activity in Spinus, revealing multiple bursts of long terminal repeat (LTR) retrotransposon expansion, including a recent one that coincides with the estimated diversification of North and South American siskins approximately 2.7 million years ago. We also detected putative lineage-specific LTR sequences, suggesting recent or ongoing TE diversification. This assembly fills a critical gap in passerine genomic resources and provides a resource for comparative, transcriptomic, and population-level studies across species with diverse migratory strategies.

入侵候鸟松雀(Spinus pinus)的参考基因组。
松雀(Spinus pinus)是一种入侵性迁徙鸣禽,在内分泌调节、免疫功能和行为灵活性的研究中具有生物学意义。在这里,我们提出了一个染色体水平的参考基因组从一个雌性松siskin,组装从头使用长读测序和支架与参考指导的方法。Synteny分析还表明,我们的组装可以可靠地揭示相对于其他雀类的基因组重排。使用基于参考的注释,我们鉴定了数千个蛋白质编码基因,包括与代谢和免疫功能相关的位点,证明了该组装在下游研究中的实用性。我们还在免疫位点发现了基因复制和假原化的证据,显示了我们的组装在免疫遗传学研究中的实用性。我们的分析提供了Spinus转座因子(TE)活性的第一个全基因组视图,揭示了长末端重复(LTR)逆转录转座子扩展的多次爆发,包括最近的一次与大约270万年前北美和南美siskin的多样化相吻合。我们还检测到假定的谱系特异性LTR序列,表明最近或正在进行的TE多样化。该组合填补了雀形目动物基因组资源的关键空白,并为具有不同迁徙策略的物种的比较,转录组学和种群水平研究提供了资源。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Journal of Heredity
Journal of Heredity 生物-遗传学
CiteScore
5.20
自引率
6.50%
发文量
63
审稿时长
6-12 weeks
期刊介绍: Over the last 100 years, the Journal of Heredity has established and maintained a tradition of scholarly excellence in the publication of genetics research. Virtually every major figure in the field has contributed to the journal. Established in 1903, Journal of Heredity covers organismal genetics across a wide range of disciplines and taxa. Articles include such rapidly advancing fields as conservation genetics of endangered species, population structure and phylogeography, molecular evolution and speciation, molecular genetics of disease resistance in plants and animals, genetic biodiversity and relevant computer programs.
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