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

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...

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Autores principales: Li, Ming, Sun, Congjiao, Xu, Naiyi, Bian, Peipei, Tian, Xiaomeng, Wang, Xihong, Wang, Yuzhe, Jia, Xinzheng, Heller, Rasmus, Wang, Mingshan, Wang, Fei, Dai, Xuelei, Luo, Rongsong, Guo, Yingwei, Wang, Xiangnan, Yang, Peng, Hu, Dexiang, Liu, Zhenyu, Fu, Weiwei, Zhang, Shunjin, Li, Xiaochang, Wen, Chaoliang, Lan, Fangren, Siddiki, Amam Zonaed, Suwannapoom, Chatmongkon, Zhao, Xin, Nie, Qinghua, Hu, Xiaoxiang, Jiang, Yu, Yang, Ning
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9021737/
https://www.ncbi.nlm.nih.gov/pubmed/35325213
http://dx.doi.org/10.1093/molbev/msac066
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author Li, Ming
Sun, Congjiao
Xu, Naiyi
Bian, Peipei
Tian, Xiaomeng
Wang, Xihong
Wang, Yuzhe
Jia, Xinzheng
Heller, Rasmus
Wang, Mingshan
Wang, Fei
Dai, Xuelei
Luo, Rongsong
Guo, Yingwei
Wang, Xiangnan
Yang, Peng
Hu, Dexiang
Liu, Zhenyu
Fu, Weiwei
Zhang, Shunjin
Li, Xiaochang
Wen, Chaoliang
Lan, Fangren
Siddiki, Amam Zonaed
Suwannapoom, Chatmongkon
Zhao, Xin
Nie, Qinghua
Hu, Xiaoxiang
Jiang, Yu
Yang, Ning
author_facet Li, Ming
Sun, Congjiao
Xu, Naiyi
Bian, Peipei
Tian, Xiaomeng
Wang, Xihong
Wang, Yuzhe
Jia, Xinzheng
Heller, Rasmus
Wang, Mingshan
Wang, Fei
Dai, Xuelei
Luo, Rongsong
Guo, Yingwei
Wang, Xiangnan
Yang, Peng
Hu, Dexiang
Liu, Zhenyu
Fu, Weiwei
Zhang, Shunjin
Li, Xiaochang
Wen, Chaoliang
Lan, Fangren
Siddiki, Amam Zonaed
Suwannapoom, Chatmongkon
Zhao, Xin
Nie, Qinghua
Hu, Xiaoxiang
Jiang, Yu
Yang, Ning
author_sort Li, Ming
collection PubMed
description 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.
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spelling pubmed-90217372022-04-21 De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions Li, Ming Sun, Congjiao Xu, Naiyi Bian, Peipei Tian, Xiaomeng Wang, Xihong Wang, Yuzhe Jia, Xinzheng Heller, Rasmus Wang, Mingshan Wang, Fei Dai, Xuelei Luo, Rongsong Guo, Yingwei Wang, Xiangnan Yang, Peng Hu, Dexiang Liu, Zhenyu Fu, Weiwei Zhang, Shunjin Li, Xiaochang Wen, Chaoliang Lan, Fangren Siddiki, Amam Zonaed Suwannapoom, Chatmongkon Zhao, Xin Nie, Qinghua Hu, Xiaoxiang Jiang, Yu Yang, Ning Mol Biol Evol Discoveries 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. Oxford University Press 2022-03-24 /pmc/articles/PMC9021737/ /pubmed/35325213 http://dx.doi.org/10.1093/molbev/msac066 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Discoveries
Li, Ming
Sun, Congjiao
Xu, Naiyi
Bian, Peipei
Tian, Xiaomeng
Wang, Xihong
Wang, Yuzhe
Jia, Xinzheng
Heller, Rasmus
Wang, Mingshan
Wang, Fei
Dai, Xuelei
Luo, Rongsong
Guo, Yingwei
Wang, Xiangnan
Yang, Peng
Hu, Dexiang
Liu, Zhenyu
Fu, Weiwei
Zhang, Shunjin
Li, Xiaochang
Wen, Chaoliang
Lan, Fangren
Siddiki, Amam Zonaed
Suwannapoom, Chatmongkon
Zhao, Xin
Nie, Qinghua
Hu, Xiaoxiang
Jiang, Yu
Yang, Ning
De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions
title De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions
title_full De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions
title_fullStr De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions
title_full_unstemmed De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions
title_short De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions
title_sort de novo assembly of 20 chicken genomes reveals the undetectable phenomenon for thousands of core genes on microchromosomes and subtelomeric regions
topic Discoveries
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9021737/
https://www.ncbi.nlm.nih.gov/pubmed/35325213
http://dx.doi.org/10.1093/molbev/msac066
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