A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes
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A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes. / Liu, Jing; Wang, Zongji; Li, Jing; Xu, Luohao; Liu, Jiaqi; Feng, Shaohong; Guo, Chunxue; Chen, Shengchan; Ren, Zhanjun; Rao, Jinpeng; Wei, Kai; Chen, Yuezhou; Jarvis, Erich D.; Zhang, Guojie; Zhou, Qi.
In: Genome Research, Vol. 31, No. 3, 2021, p. 497-511.Research output: Contribution to journal › Journal article › Research › peer-review
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T1 - A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes
AU - Liu, Jing
AU - Wang, Zongji
AU - Li, Jing
AU - Xu, Luohao
AU - Liu, Jiaqi
AU - Feng, Shaohong
AU - Guo, Chunxue
AU - Chen, Shengchan
AU - Ren, Zhanjun
AU - Rao, Jinpeng
AU - Wei, Kai
AU - Chen, Yuezhou
AU - Jarvis, Erich D.
AU - Zhang, Guojie
AU - Zhou, Qi
PY - 2021
Y1 - 2021
N2 - 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 step of sex chromosome evolution. Overall, our results provide novel insights into the evolution of avian genome structure and sex chromosomes in three-dimensional space.
AB - 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 step of sex chromosome evolution. Overall, our results provide novel insights into the evolution of avian genome structure and sex chromosomes in three-dimensional space.
U2 - 10.1101/GR.271569.120
DO - 10.1101/GR.271569.120
M3 - Journal article
C2 - 33408157
AN - SCOPUS:85102538622
VL - 31
SP - 497
EP - 511
JO - Genome Research
JF - Genome Research
SN - 1088-9051
IS - 3
ER -
ID: 260187585