Near telomere-to-telomere genome assemblies of Silkie Gallus gallus and Mallard Anas platyrhynchos restored the structure of chromosomes and “missing” genes in birds  

作　　者：Qiangsen Zhao Zhongtao Yin Zhuocheng Hou 

机构地区：[1]Frontiers Science Center for Molecular Design Breeding(MOE),State Key Laboratory of Animal Biotech Breeding,and National Engineering Laboratory for Animal Breeding,College of Animal Science and Technology,China Agricultural University,Beijing 100193,China

出　　处：《Journal of Animal Science and Biotechnology》2025年第2期517-530,共14页畜牧与生物技术杂志(英文版)

基　　金：supported by the National Key R&D Program of China(2022YFF1000100,2023YFD1300300);the National Natural Science Foundation of China(31572388,31972525);the China Agriculture Research System of MOF and MARA(CARS-41)。

摘　　要：Background Chickens and ducks are vital sources of animal protein for humans.Recent pangenome studies suggest that a single genome is insufficient to represent the genetic information of a species,highlighting the need for more comprehensive genomes.The bird genome has more than tens of microchromosomes,but comparative genomics,annotations,and the discovery of variations are hindered by inadequate telomere-to-telomere level assemblies.We aim to complete the chicken and duck genomes,recover missing genes,and reveal common and unique chromosomal features between birds.Results The near telomere-to-telomere genomes of Silkie Gallus gallus and Mallard Anas platyrhynchos were successfully assembled via multiple high-coverage complementary technologies,with quality values of 36.65 and 44.17 for Silkie and Mallard,respectively;and BUSCO scores of 96.55%and 96.97%for Silkie and Mallard,respectively;the mapping rates reached over 99.52%for both assembled genomes,these evaluation results ensured high completeness and accuracy.We successfully annotated 20,253 and 19,621 protein-coding genes for Silkie and Mallard,respectively,and assembled gap-free sex chromosomes in Mallard for the first time.Comparative analysis revealed that microchromosomes differ from macrochromosomes in terms of GC content,repetitive sequence abundance,gene density,and levels of 5mC methylation.Different types of arrangements of centromeric repeat sequence centromeres exist in both Silkie and the Mallard genomes,with Mallard centromeres being invaded by CR1.The highly heterochromatic W chromosome,which serves as a refuge for ERVs,contains disproportionately long ERVs.Both Silkie and the Mallard genomes presented relatively high 5mC methylation levels on sex chromosomes and microchromosomes,and the telomeres and centromeres presented significantly higher 5mC methylation levels than the whole genome.Finally,we recovered 325 missing genes via our new genomes and annotated TNFA in Mallard for the first time,revealing conserved protein structures and tissue

关 键 词：AVIAN CENTROMERE Missing gene Telomere-to-telomere genome 5mC methylation level 

分 类 号：S831[农业科学—畜牧学]