False gene and chromosome losses in genome assemblies caused by GC content variation and repeats

	False gene and chromosome losses in genome assemblies caused by GC content variation and repeats
	Kim, J; Lee, C; Ko, BJ; Yoo, DA; Won, S; Phillippy, AM; Fedrigo, O; Zhang, GJ; Howe, K; Wood, J; Durbin, R; Formenti, G; Brown, S; Cantin, L; Mello, CV; Cho, S; Rhie, A; Kim, H; Jarvis, ED
	2022
发表期刊	GENOME BIOLOGY
ISSN	1474-760X
卷号	23 期号:1
摘要	Background Many short-read genome assemblies have been found to be incomplete and contain mis-assemblies. The Vertebrate Genomes Project has been producing new reference genome assemblies with an emphasis on being as complete and error-free as possible, which requires utilizing long reads, long-range scaffolding data, new assembly algorithms, and manual curation. A more thorough evaluation of the recent references relative to prior assemblies can provide a detailed overview of the types and magnitude of improvements. Results Here we evaluate new vertebrate genome references relative to the previous assemblies for the same species and, in two cases, the same individuals, including a mammal (platypus), two birds (zebra finch, Anna's hummingbird), and a fish (climbing perch). We find that up to 11% of genomic sequence is entirely missing in the previous assemblies. In the Vertebrate Genomes Project zebra finch assembly, we identify eight new GC- and repeat-rich micro-chromosomes with high gene density. The impact of missing sequences is biased towards GC-rich 5 '-proximal promoters and 5 ' exon regions of protein-coding genes and long non-coding RNAs. Between 26 and 60% of genes include structural or sequence errors that could lead to misunderstanding of their function when using the previous genome assemblies. Conclusions Our findings reveal novel regulatory landscapes and protein coding sequences that have been greatly underestimated in previous assemblies and are now present in the Vertebrate Genomes Project reference genomes.
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/152453/13437
专题	科研部门_遗传多样性基因组学研究组（张国捷）
推荐引用方式 GB/T 7714	Kim, J,Lee, C,Ko, BJ,et al. False gene and chromosome losses in genome assemblies caused by GC content variation and repeats[J]. GENOME BIOLOGY,2022,23(1).
APA	Kim, J.,Lee, C.,Ko, BJ.,Yoo, DA.,Won, S.,...&Jarvis, ED.(2022).False gene and chromosome losses in genome assemblies caused by GC content variation and repeats.GENOME BIOLOGY,23(1).
MLA	Kim, J,et al."False gene and chromosome losses in genome assemblies caused by GC content variation and repeats".GENOME BIOLOGY 23.1(2022).

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