De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions

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  • Ming Li
  • Congjiao Sun
  • Naiyi Xu
  • Peipei Bian
  • Xiaomeng Tian
  • Xihong Wang
  • Yuzhe Wang
  • Xinzheng Jia
  • Mingshan Wang
  • Fei Wang
  • Xuelei Dai
  • Rongsong Luo
  • Yingwei Guo
  • Xiangnan Wang
  • Peng Yang
  • Dexiang Hu
  • Zhenyu Liu
  • Weiwei Fu
  • Shunjin Zhang
  • Xiaochang Li
  • Chaoliang Wen
  • Fangren Lan
  • Amam Zonaed Siddiki
  • Chatmongkon Suwannapoom
  • Xin Zhao
  • Qinghua Nie
  • Xiaoxiang Hu
  • Yu Jiang
  • Ning Yang

The gene numbers and evolutionary rates of birds were assumed to be much lower than those of mammals, which is in sharp contrast to the huge species number and morphological diversity of birds. It is, therefore, necessary to construct a complete avian genome and analyze its evolution. We constructed a chicken pan-genome from 20 de novo assembled genomes with high sequencing depth, and identified 1,335 protein-coding genes and 3,011 long noncoding RNAs not found in GRCg6a. The majority of these novel genes were detected across most individuals of the examined transcriptomes but were seldomly measured in each of the DNA sequencing data regardless of Illumina or PacBio technology. Furthermore, different from previous pan-genome models, most of these novel genes were overrepresented on chromosomal subtelomeric regions and microchromosomes, surrounded by extremely high proportions of tandem repeats, which strongly blocks DNA sequencing. These hidden genes were proved to be shared by all chicken genomes, included many housekeeping genes, and enriched in immune pathways. Comparative genomics revealed the novel genes had 3-fold elevated substitution rates than known ones, updating the knowledge about evolutionary rates in birds. Our study provides a framework for constructing a better chicken genome, which will contribute toward the understanding of avian evolution and the improvement of poultry breeding.

Original languageEnglish
Article numbermsac066
JournalMolecular Biology and Evolution
Issue number4
Number of pages16
Publication statusPublished - 2022

Bibliographical note

Publisher Copyright:
© 2022 The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.

    Research areas

  • avian evolution, chicken, missing genes, noncanonical DNA secondary structure, pan-genome

ID: 308898002