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

Publication ,  Journal Article
Liu, J; Wang, Z; Li, J; Xu, L; Liu, J; Feng, S; Guo, C; Chen, S; Ren, Z; Rao, J; Wei, K; Chen, Y; Jarvis, ED; Zhang, G; Zhou, Q
Published in: Genome Res
March 2021

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.

Duke Scholars

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Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

March 2021

Volume

31

Issue

3

Start / End Page

497 / 511

Location

United States

Related Subject Headings

  • Sex Chromosomes
  • Phylogeny
  • Heterochromatin
  • Genome
  • Female
  • Evolution, Molecular
  • Dromaiidae
  • Chromosomes
  • Bioinformatics
  • Animals
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Liu, J., Wang, Z., Li, J., Xu, L., Feng, S., Guo, C., … Zhou, Q. (2021). A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes. Genome Res, 31(3), 497–511. https://doi.org/10.1101/gr.271569.120
Liu, Jing, Zongji Wang, Jing Li, Luohao Xu, Jiaqi Liu, Shaohong Feng, Chunxue Guo, et al. “A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes.Genome Res 31, no. 3 (March 2021): 497–511. https://doi.org/10.1101/gr.271569.120.
Liu J, Wang Z, Li J, Xu L, Feng S, Guo C, et al. A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes. Genome Res. 2021 Mar;31(3):497–511.
Liu, Jing, et al. “A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes.Genome Res, vol. 31, no. 3, Mar. 2021, pp. 497–511. Pubmed, doi:10.1101/gr.271569.120.
Liu J, Wang Z, Li J, Xu L, Feng S, Guo C, Chen S, Ren Z, Rao J, Wei K, Chen Y, Jarvis ED, Zhang G, Zhou Q. A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes. Genome Res. 2021 Mar;31(3):497–511.

Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

March 2021

Volume

31

Issue

3

Start / End Page

497 / 511

Location

United States

Related Subject Headings

  • Sex Chromosomes
  • Phylogeny
  • Heterochromatin
  • Genome
  • Female
  • Evolution, Molecular
  • Dromaiidae
  • Chromosomes
  • Bioinformatics
  • Animals