【作者】 李静；

【导师】 周琦；

【作者基本信息】 浙江大学 ， 细胞生物学， 2020， 博士

【摘要】 北京鸭(Anas platyrhynchos)具有典型的鸟类核型,包括大染色体和小染色体。和鸡相比,北京鸭的性染色体具有较低的分化程度。为了阐明北京鸭和鸡之间、以及鸟类和哺乳动物之间染色体结构的演化,本研究利用三代测序和多种基因组数据,完成了一只雌性北京鸭的几乎完整的染色体组装。和之前利用二代Illumina测序技术组装的北京鸭基因组相比,新版本的基因组和注释质量均得到了大幅提升,并鉴定出两类在北京鸭中发生特异性扩张的重复元件。本研究发现北京鸭的拓扑相关结构域(topologically associated domain,TAD)主要有三种形成机制,分别是通过富集绝缘体蛋白CTCF的结合位点、管家基因和转录活跃(A)型和转录不活跃(B)型染色质区块(active/inactive,A/B Chromatin compartment),这表明了北京鸭和哺乳动物在染色质的空间折叠机制方面是保守的。进一步研究发现,北京鸭和鸡的TAD边界存在大量重叠,北京鸭的TAD边界与染色体倒位断点之间也存在大量重叠,这表明TAD作为一个完整的调控基因组单元,受到强烈的自然选择,或者这也可能是由于DNA双链脆弱位点与TAD边界高度重合所引起。北京鸭雌性特异的W染色体上的基因数大约是鸡的4.5倍。与独立演化的人类Y染色体一样,北京鸭的W染色体上也发现了大量分散的回文结构和同源重组抑制产生的演化断层现象。本研究的研究结果为鸟类之间,以及鸟类和哺乳动物之间的染色体演化提供了新的见解,也为禽类研究增加了重要的基因组资源。卵生单孔目哺乳动物是现存哺乳动物中最早分歧出来的一支,主要包括鸭嘴兽科和针鼹科。其中,针鼹科包含短吻针鼹科和长吻针鼹科,它们是为数不多的既产蛋又哺乳的哺乳动物。单孔目动物,是原兽亚纲中仅存的尚未灭绝的哺乳动物,利用单孔目动物进行哺乳动物演化生物学的研究是不可或缺的重要一环,也为哺乳动物的演化生物学研究提供了关键的线索。本研究组装出了两个单孔目物种的高质量参考基因组序列,即鸭嘴兽(Ornithorhynchus anatinus)和短吻针鼹(Tachyglossus aculeatts,本文简称为针鼹)。新版本的鸭嘴兽基因组几乎把整个基因组挂载到了染色体上,和之前发表的基于Sanger测序的鸭嘴兽基因组相比,新版本基因组的组装水平和基因注释质量均得到了显著提升。此外,本研究首次组装并鉴定出几乎完整的五对鸭嘴兽性染色体序列。本研究发现单孔目动物的复杂性染色体复合物很可能起源于一个环状构象,鸭嘴兽复杂性染色体复合物的形成很可能和其广泛的性染色体之间的相互作用有关,并且这些互作在人的同源序列中也广泛存在。单孔目动物作为哺乳动物中重要的一支,其性染色体并不与真兽类哺乳动物的X染色体同源,而是与鸟类的Z染色体同源。同时,SRY作为真兽类哺乳动物中重要的性别决定基因,也并不存在于单孔目哺乳动物中。此外,与鸟类相似,单孔目哺乳动物的性染色体同样不存在剂量补偿效应。总的来说,本研究为单孔目动物和鸟类之间的性染色体演化提供了新的线索。更多还原

【Abstract】 Pekin duck(Anas platyrhyachos)has a typical avian karyotype that consists of macro-and micro-chromosomes,but a pair of much less differentiated ZW sex chromosomes compared to chicken.To elucidate the evolution of chromosome architectures between Pekin duck and chicken,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.The major improvement of genome assembly and annotation quality resulted in successful resolution of lineage-specific propagated repeats that fragmented the previous Illumina-based assembly.We found that the Pekin 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 the conserved mechanisms of spatial chromosome folding with mammals.There are extensive overlaps of TAD boundaries between Pekin duck and chicken,and also between the TAD boundaries and chromosome inversion breakpoints.This suggests strong natural selection on maintaining regulatory domain integrity,or vulnerability of TAD boundaries to DNA double-strand breaks.The Pekin duck W chromosome contains 2.5-fold more genes relative to chicken.Parallel to the independently evolved human Y chromosome,the Pekin duck W evolved massive dispersed palindromic structures,and a sequence divergence pattern 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.Egg-laying mammals were the first to diverge from the common ancestor of modern mammals and provide key insights into mammalian evolution and the innovations that have occurred in the three mammalian lineages present on earth today.Here we report the generation and analyses of high-quality reference genomes for two monotreme species,platypus(Ornithorhynchus anatinus)and echidna(Tachyglossus aculeatus).The new platypus genome assembly anchors almost the entire genome onto chromosomes,dramatically improving the previous draft genome and gene annotation.The two monotreme genomes allowed us to reconstruct genomic innovations at the time of mammalian diversification.We provide evidence that the extraordinary monotreme sex chromosome complex originated from an ancestral chromosome ring configuration.The formation of such a unique chromosome complex may have been facilitated by the unusual extensive interactions between the multi-X and-Y chromosomes that are shared by their human autosomal homologues.The monotremes are belonging to one important clade of mammals.However,their sex chromosomes are not homologous to human chrX,but homologous to chicken chrZ.The eutherian sex determining gene SRY is also missing in monotremes.In addition,like birds,the monotremes lack dosage compensation as well.Overall,my analyses of the Pekin duck and monotremes provide new insights into the transition of sex chromosome evolution between mammals and birds.更多还原