染色体尺度的基因组显示了熊类物种之间的快速多样化和古老的基因流动。

IF 2.8 2区 生物学 Q2 EVOLUTIONARY BIOLOGY
T Brock Wooldridge, Merly Escalona, Blair W Perry, Alexis N Enstrom, Dalya Salih, William E Seligmann, Samuel Sacco, Katherine L Moon, Ruta Sahasrabudhe, Noravit Chumchim, Oanh Nguyen, Joanna L Kelley, Ross D E MacPhee, Beth Shapiro
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引用次数: 0

摘要

由于缺乏高质量的参考基因组,进化历史的重建可能受到限制。迄今为止,熊(熊科)的八种中只有四种具有染色体水平的基因组组装。在这里,我们展示了另外三个物种——太阳熊、树懒和眼镜熊的集合,并使用所有熊类和其他食肉动物的全基因组比对来重建熊科的进化。基于融合模式的分化年代测定表明,熊类的分化速度比之前报道的要快,所有熊类的起源时间为~ 19 Ma,而熊科的6个物种的起源时间为~ 3.3 Ma。令人惊讶的是,我们观察到近50%的基因树拓扑结构与我们高度支持的物种树相冲突,这一模式是由熊科中一个重要的早期杂交事件驱动的。我们还发现熊科的祖先核型在大约1500万年的时间里与所有熊类的祖先核型在很大程度上保持保守。与这种稳定性相反,与LINE/L1反转录转座子相关的数十个染色体分裂和融合戏剧性地重组了大熊猫和眼镜熊的基因组。最后,我们利用这些基因组来确定与颜色、饮食和新陈代谢相关的基因正选择的物种特异性证据。其中一个基因TCPN2在色素沉着中起作用,在过去的0.5 Ma中,北极熊出现了一系列氨基酸突变。总的来说,这些新的基因组资源能够更好地重建熊的复杂进化历史,并阐明这个神秘的群体是如何多样化的。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Chromosome-scale genomes show rapid diversification and ancient gene flow among bear species.

Reconstructions of evolutionary history can be restricted by a lack of high quality reference genomes. To-date, only four of the eight species of bears (family Ursidae) have chromosome-level genome assemblies. Here, we present assemblies for three additional species - the sun, sloth, and spectacled bears - and use a whole-genome alignment of all bear species and other carnivores to reconstruct the evolution of Ursidae. Divergence dating based on patterns of coalescence indicates a more rapid diversification than previously reported, with a ∼19 Ma origin for all bears but a ∼3.3 Ma origin for the six species of the subfamily Ursinae. Surprisingly, we observe that nearly 50% of gene tree topologies conflict with our highly supported species tree, a pattern driven by a significant early hybridization event within Ursinae. We also find that the ancestral karyotype of Ursinae has remained largely conserved with the ancestral karyotype of all bears over roughly fifteen million years. In contrast to this stability, dozens of chromosomal fissions and fusions associated with LINE/L1 retrotransposons dramatically restructured the genomes of the giant panda and spectacled bear. Finally, we leverage these genomes to identify species-specific evidence for positive selection on genes associated with color, diet, and metabolism. One of these genes, TCPN2, has a role in pigmentation and shows a series of amino acid mutations in the polar bear over the last 0.5 Ma. Collectively, these new genomic resources enable improved reconstruction of the complex evolutionary history of bears and clarify how this enigmatic group diversified.

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来源期刊
Genome Biology and Evolution
Genome Biology and Evolution EVOLUTIONARY BIOLOGY-GENETICS & HEREDITY
CiteScore
5.80
自引率
6.10%
发文量
169
审稿时长
1 months
期刊介绍: About the journal Genome Biology and Evolution (GBE) publishes leading original research at the interface between evolutionary biology and genomics. Papers considered for publication report novel evolutionary findings that concern natural genome diversity, population genomics, the structure, function, organisation and expression of genomes, comparative genomics, proteomics, and environmental genomic interactions. Major evolutionary insights from the fields of computational biology, structural biology, developmental biology, and cell biology are also considered, as are theoretical advances in the field of genome evolution. GBE’s scope embraces genome-wide evolutionary investigations at all taxonomic levels and for all forms of life — within populations or across domains. Its aims are to further the understanding of genomes in their evolutionary context and further the understanding of evolution from a genome-wide perspective.
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