基于PacBio三代测序的高质量汶上芦花鸡基因组的组装

doi:10.16431/j.cnki.1671-7236.2023.10.001

Abstract

Abstract: 【Objective】 Wenshang Barred chickens is the only barred chicken breed in the abundant Chinese native chicken resources.The barred-related gene is sex-linked,so the trait could be used for automatical sexing of chicks.This study was aimed to enrich the genome information of domestic chickens,and obtain the whole genome sequence information in Wenshang Barred chickens,so as to provide materials for studying the molecular mechanism of sex-linked barred feather in chickens.【Method】 Wenshang Barred chicken was used as material to construct a small fragment library based on BGI MGISEQ for genomic characterization assessment.The whole genome information database of Wenshang Barred chickens was assembled and constructed by PacBio and Hi-C sequencing technology.The obtained genome sequences were assembled and annotated based on bioinformatics methods.【Result】 A total of 59.70 Gb BGI second-generation sequencing data were obtained.31.13 Gb of PacBio data were obtained with an average reads length of 15 362 bp.The obtained Hi-C data was 95.37 Gb.Splicing and initial assembly resulted in a genome size of 1.12 Gb.After Hi-C auxiliary assembly,a total of 1.07 Gb sequence could be attached to 41 chromosomes,with a mount rate of 95.62%.The contigs N50 and scaffold N50 of the genome were 9.61 and 91.29 Mb,respectively.BUSCO was assessed at 98.50%.So the continuity and integrity of the genome were good.The assembled genome was predicted to have 22.57% repeats,with 426 tRNAs,56 rRNAs,260 miRNAs and 308 snRNAs.A total of 17 338 protein-coding genes were predicted,and 96.00% of them were annotated in the gene function databases.The length of chromosome Z in Wenhang Barred chickens was 88.23 Mb,and 742 protein-coding genes were predicted and annotated,which were significantly enriched in as amino acid and fat related metabolism pathways.The positions of feather color related genes such as TYRP1,CDKN2A and SLC45A2 were accurately located on chromosome Z in Wenhang Barred chickens.【Conclusion】 In this study,high quality chromosome level genome of Wenshang Barred chickens was obtained,which enriched the genetic information of the domestic chicken genome.Some feather color related genes on chromosome Z were accurately located.The results would provide a basis for exploring the regulation mechanism of superior traits in Wenshang Barred chickens at the genome-wide level.

Key words: Wenshang Barred chickens; genome assembly; PacBio third generation sequencing technology; genome annotation; chromosome Z; sex-linked barred feather

CLC Number:

S831.2

XUE Qian, XING Weijie, LI Guohui, ZHOU Chenghao, ZHANG Huiyong, YIN Jianmei, JIANG Yixiu, ZHU Yunfen, HAN Wei. Assembly of High-quality Wenshang Barred Chickens Genome Based on PacBio Third-Generation Sequencing[J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(10): 3869-3881.

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Assembly of High-quality Wenshang Barred Chickens Genome Based on PacBio Third-Generation Sequencing

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