Annotations of four high-quality indigenous chicken genomes identify more than one thousand missing genes in subtelomeric regions and micro-chromosomes with high G/C contents

	Annotations of four high-quality indigenous chicken genomes identify more than one thousand missing genes in subtelomeric regions and micro-chromosomes with high G/C contents
	Wu, SW; Dou, TF; Yuan, SS; Yan, SX; Xu, ZQ; Liu, Y; Jian, ZH; Zhao, JY; Zhao, RH; Zi, XN; Gu, DH; Liu, LX; Li, QH; Wu, DD; Jia, JJ; Ge, CR; Su, ZC; Wang, K
	2024
发表期刊	BMC GENOMICS
ISSN	1471-2164
卷号	25 期号:1
摘要	Background Although multiple chicken genomes have been assembled and annotated, the numbers of protein-coding genes in chicken genomes and their variation among breeds are still uncertain due to the low quality of these genome assemblies and limited resources used in their gene annotations. To fill these gaps, we recently assembled genomes of four indigenous chicken breeds with distinct traits at chromosome-level. In this study, we annotated genes in each of these assembled genomes using a combination of RNA-seq- and homology-based approaches. Results We identified varying numbers (17,497-17,718) of protein-coding genes in the four indigenous chicken genomes, while recovering 51 of the 274 "missing" genes in birds in general, and 36 of the 174 "missing" genes in chickens in particular. Intriguingly, based on deeply sequenced RNA-seq data collected in multiple tissues in the four breeds, we found 571 similar to 627 protein-coding genes in each genome, which were missing in the annotations of the reference chicken genomes (GRCg6a and GRCg7b/w). After removing redundancy, we ended up with a total of 1,420 newly annotated genes (NAGs). The NAGs tend to be found in subtelomeric regions of macro-chromosomes (chr1 to chr5, plus chrZ) and middle chromosomes (chr6 to chr13, plus chrW), as well as in micro-chromosomes (chr14 to chr39) and unplaced contigs, where G/C contents are high. Moreover, the NAGs have elevated quadruplexes G frequencies, while both G/C contents and quadruplexes G frequencies in their surrounding regions are also high. The NAGs showed tissue-specific expression, and we were able to verify 39 (92.9%) of 42 randomly selected ones in various tissues of the four chicken breeds using RT-qPCR experiments. Most of the NAGs were also encoded in the reference chicken genomes, thus, these genomes might harbor more genes than previously thought. Conclusion The NAGs are widely distributed in wild, indigenous and commercial chickens, and they might play critical roles in chicken physiology. Counting these new genes, chicken genomes harbor more genes than originally thought.
收录类别	sci
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/14237
专题	科研部门_进化与发育转录组学（吴东东）
推荐引用方式 GB/T 7714	Wu, SW,Dou, TF,Yuan, SS,et al. Annotations of four high-quality indigenous chicken genomes identify more than one thousand missing genes in subtelomeric regions and micro-chromosomes with high G/C contents[J]. BMC GENOMICS,2024,25(1).
APA	Wu, SW.,Dou, TF.,Yuan, SS.,Yan, SX.,Xu, ZQ.,...&Wang, K.(2024).Annotations of four high-quality indigenous chicken genomes identify more than one thousand missing genes in subtelomeric regions and micro-chromosomes with high G/C contents.BMC GENOMICS,25(1).
MLA	Wu, SW,et al."Annotations of four high-quality indigenous chicken genomes identify more than one thousand missing genes in subtelomeric regions and micro-chromosomes with high G/C contents".BMC GENOMICS 25.1(2024).

条目包含的文件
文件名称/大小	文献类型	版本类型	开放类型	使用许可
2024073103.pdf（4077KB）	期刊论文	出版稿	开放获取	CC BY-NC-SA	请求全文