A genomic resource derived from the integration of genome sequences, expressed transcripts and genetic markers in ramie

文献类型： 外文期刊

第一作者： Wang, Yanzhou

作者： Wang, Yanzhou;Zeng, Zheng;Li, Fu;Gao, Xinyue;Ma, Yonghong;Rao, Jing;Liu, Touming;Wang, Yanzhou;Zeng, Zheng;Li, Fu;Gao, Xinyue;Ma, Yonghong;Rao, Jing;Liu, Touming;Yang, Xiufeng;Wang, Hengyun

作者机构：

关键词： Ramie; Genome sequence; Transcriptome; Genetic map; Molecular marker

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2019 年 20 卷

页码：

收录情况： SCI

摘要： BackgroundThe redundancy of genomic resources, including transcript and molecular markers, and their uncertain position in the genome have dramatically hindered the study of traits in ramie, an important natural fiber crop.ResultsWe obtained a high-quality transcriptome consisting of 30,591 non-redundant transcripts using single-molecule long-read sequencing and proposed it as a universal ramie transcriptome. Additionally, 55,882 single nucleotide polymorphisms (SNPs) were identified and a high-density genetic map was developed. Based on this genetic map, 181.7Mb ramie genome sequences were assembled into 14 chromosomes. For the convenient use of these resources, 29,286 (similar to 95.7%) of the transcripts and all 55,882 SNPs, along with 1827 previously reported sequence repeat markers (SSRs), were mapped into the ramie genome, and 22,343 (similar to 73.0%) transcripts, 50,154 (similar to 89.7%) SNPs, and 1466 (similar to 80.3%) SSRs were assigned to a specific location in the corresponding chromosome.ConclusionThis is the first study to characterize the ramie transcriptome by long-read sequencing, and the substantial number of transcripts of significant length obtained will accelerate our understanding of ramie growth and development. This integration of genome sequences, expressed transcripts, and genetic markers will provide an extremely useful resource for genetic, molecular, and breeding studies of ramie.

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