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
	Li, J; Zhang, JL; Liu, J; Zhou, Y; Cai, C; Xu, LH; Dai, XL; Feng, SH; Guo, CX; Rao, JP; Wei, K; Jarvis, ED; Jiang, Y; Zhou, ZK; Zhang, GJ; Zhou, Q
	2021
发表期刊	GIGASCIENCE
ISSN	2047-217X
卷号	10 期号:1
摘要	Background: 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. Results: 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. Conclusions: 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.
收录类别	sci
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/13448
专题	科研部门_遗传多样性基因组学研究组（张国捷）
推荐引用方式 GB/T 7714	Li, J,Zhang, JL,Liu, J,et al. A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals[J]. GIGASCIENCE,2021,10(1).
APA	Li, J.,Zhang, JL.,Liu, J.,Zhou, Y.,Cai, C.,...&Zhou, Q.(2021).A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals.GIGASCIENCE,10(1).
MLA	Li, J,et al."A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals".GIGASCIENCE 10.1(2021).

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