A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals.
A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals.
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DOI：
10.1093/gigascience/giaa142
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发表时间：
2021-01-06
期刊：
影响因子：
9.2
通讯作者：
Zhou Q
中科院分区：
文献类型：
--
作者：
Li J;Zhang J;Liu J;Zhou Y;Cai C;Xu L;Dai X;Feng S;Guo C;Rao J;Wei K;Jarvis ED;Jiang Y;Zhou Z;Zhang G;Zhou Q
鸭子具有典型的鸟类核型，由大染色体和小染色体组成，但与鸡相比，它们有一对分化程度较低的 ZW 性染色体。为了阐明鸭和鸡之间、鸟类和哺乳动物之间染色体结构的进化，我们通过结合长读长测序和多平台支架技术，产生了雌性北京鸭几乎完整的染色体组装。基因组组装和注释质量的重大改进得益于谱系特异性繁殖重复的成功解析，该重复使之前基于 Illumina 的组装变得支离破碎。我们发现鸭拓扑相关结构域（TAD）由绝缘体蛋白 CTCF、持家基因或活性/非活性染色质区室的转换的推定结合位点划分，表明哺乳动物空间染色体折叠的保守机制。鸭和鸡之间以及 TAD 边界和染色体倒位断点之间存在广泛的重叠。这表明维持调控域完整性的强大自然选择压力，或者 TAD 边界对 DNA 双链断裂的脆弱性。鸭W染色体保留的基因是鸡的2.5倍。与独立进化的人类 Y 染色体类似，鸭 W 进化出了大量分散的回文结构，以及与 Z 染色体的序列分歧模式，反映了同源重组的逐步抑制。我们的结果为鸟类和哺乳动物的保守和趋同进化的染色体特征提供了新的见解，并且还重要地增加了家禽研究的基因组资源。
Ducks have a typical avian karyotype that consists of macro- and microchromosomes, but a pair of much less differentiated ZW sex chromosomes compared to chickens. To elucidate the evolution of chromosome architectures between ducks and chickens, and between birds and mammals, we produced a nearly complete chromosomal assembly of a female Pekin duck by combining long-read sequencing and multiplatform scaffolding techniques. A major improvement of genome assembly and annotation quality resulted from the successful resolution of lineage-specific propagated repeats that fragmented the previous Illumina-based assembly. We found that the duck topologically associated domains (TAD) are demarcated by putative binding sites of the insulator protein CTCF, housekeeping genes, or transitions of active/inactive chromatin compartments, indicating conserved mechanisms of spatial chromosome folding with mammals. There are extensive overlaps of TAD boundaries between duck and chicken, and also between the TAD boundaries and chromosome inversion breakpoints. This suggests strong natural selection pressure on maintaining regulatory domain integrity, or vulnerability of TAD boundaries to DNA double-strand breaks. The duck W chromosome retains 2.5-fold more genes relative to chicken. Similar to the independently evolved human Y chromosome, the duck W evolved massive dispersed palindromic structures, and a pattern of sequence divergence with the Z chromosome that reflects stepwise suppression of homologous recombination. Our results provide novel insights into the conserved and convergently evolved chromosome features of birds and mammals, and also importantly add to the genomic resources for poultry studies.
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