Chromosomal-level genome assembly of the high-quality Xian/Indica rice (Oryza sativa L.) Xiangyaxiangzhan
文献类型： 外文期刊
作者： Liang, Jiayan 1 ; Kong, Leilei 1 ; Hu, Xiaodan 1 ; Fu, Chongyun 1 ; Bai, Song 1 ;
作者机构： 1.Guangdong Acad Agr Sci, Guangdong Key Lab New Technol Rice Breeding, Guangdong Rice Engn Lab, Rice Res Inst, Guangzhou 510640, Peoples R China
关键词： High-quality rice; de novo assembly; Comparative genomics analysis; Long terminal repeat retrotransposons
期刊名称：BMC PLANT BIOLOGY （ 影响因子：5.3； 五年影响因子：5.9 ）
ISSN： 1471-2229
年卷期： 2023 年 23 卷 1 期
页码：
收录情况： SCI
摘要： The indica rice variety XYXZ carries elite traits including appearance and eating quality. Here, we report the de novo assembly of XYXZ using Illumine paired-end whole-genome shotgun sequencing and Nanopore sequencing. We annotated 39,722 protein-coding genes in the 395.04 Mb assembly. In comparison to other cultivars, XYXZ showed a larger gene size including the transcripts and introns, and more exons per gene. And hundreds of ultra-long genes were also detected. A total of 4362 complete LTRs were annotated, and among them, many were located next to or in protein-coding genes including several genes related to rice quality. We observed the different distributions of LTRs in these genes among XYXZ, Nipponbare, and R498, implying these LTRs might potentially affect expressions of the proximal genes and rice quality. Overall, This chromosome-length genome assembly of XYXZ provides a valuable resource for gene discovery, genetic variation and evolution, and the breeding of high-quality rice.
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