MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China.
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 5 Nobels väg, Stockholm 17177, Sweden.
Gigascience. 2021 Jan 6;10(1). doi: 10.1093/gigascience/giaa142.
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.
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，其 ZW 性染色体的分化程度要低得多。为了阐明鸭子和鸡之间以及鸟类和哺乳动物之间染色体结构的进化，我们通过结合长读测序和多平台支架技术，构建了一只雌性北京鸭的近乎完整的染色体组。
通过成功解析以前基于 Illumina 的组装所产生的谱系特异性传播重复序列，大大提高了基因组组装和注释质量。我们发现，鸭拓扑关联域（TAD）由绝缘子蛋白 CTCF、管家基因或活性/非活性染色质区室的转换的假定结合位点来划定，这表明与哺乳动物一样，存在着空间染色体折叠的保守机制。鸭和鸡之间、TAD 边界和染色体倒位断点之间存在广泛的重叠。这表明对维持调控域完整性存在强大的自然选择压力，或者 TAD 边界易受 DNA 双链断裂的影响。鸭的 W 染色体相对于鸡保留了 2.5 倍的基因。与独立进化的人类 Y 染色体相似，鸭的 W 染色体进化出大量分散的回文结构，以及与 Z 染色体的序列分化模式，反映了同源重组的逐步抑制。
我们的研究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，同时也为家禽研究增加了重要的基因组资源。
