A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes

作者：Jing Liu, Zongji Wang, Jing Li, Luohao Xu, Jiaqi Liu, Shaohong Feng, Chunxue Guo, Shengchan Chen, Zhanjun Ren, Jinpeng Rao, Kai Wei, Yuezhou Chen, Erich D. Jarvis, Guojie Zhang, Qi Zhou · 发表于：Genome Research · 年份：2021 · DOI：10.1101/gr.271569.120 · 被引用次数：63 · 研究领域：Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities、Chromosomal and Genetic Variations、Genetic diversity and population structure

Emu and other ratites are more informative than any other birds in reconstructing the evolution of the ancestral avian or vertebrate karyotype because of their much slower rate of genome evolution. Here, we generated a new chromosome-level genome assembly of a female emu, and estimated the tempo of chromosome evolution across major avian phylogenetic branches, by comparing it to chromosome-level genome assemblies of 11 other bird and one turtle species. We found ratites exhibited the lowest numbers of intra- and inter-chromosomal changes among birds since their divergence with turtles. The small-sized and gene-rich emu microchromosomes have frequent inter-chromosomal contacts that are associated with housekeeping genes, which appears to be driven by clustering their centromeres in the nuclear interior, away from the macrochromosomes in the nuclear periphery. Unlike nonratite birds, only less than one-third of the emu W Chromosome regions have lost homologous recombination and diverged between the sexes. The emu W is demarcated into a highly heterochromatic region (WS0) and another recently evolved region (WS1) with only moderate sequence divergence with the Z Chromosome. WS1 has expanded its inactive chromatin compartment, increased chromatin contacts within the region, and decreased contacts with the nearby regions, possibly influenced by the spreading of heterochromatin from WS0. These patterns suggest that alteration of chromatin conformation comprises an important early s...