Genome survey sequencing and identification of genomic SSR markers for Rhododendron micranthum
Genome survey sequencing and identification of genomic SSR markers for Rhododendron micranthum
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微花杜鹃基因组普查测序及基因组SSR标记鉴定
DOI：
10.1042/bsr20200988
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发表时间：
2020-06
影响因子：
4
通讯作者：
Hui-yuan Ya
中科院分区：
文献类型：
--
作者：
Xiao-jun Zhou;Meng-xue Liu;Xiao-yu Lu;Shan-shan Sun;Yan-wei Cheng;Hui-yuan Ya
摘要微花杜鹃是我国广泛分布的万年青灌木树种，具有较高的观赏和药用价值。然而，目前该植物的分子生物学和基因组学数据的缺乏，严重制约了其相关研究的发展。本研究的目的是进行第一次基因组调查的R。并确定其全基因组测序方案。使用下一代测序（Illumina Hi-Seq Xten）来测量R.利用K-mer分析技术对该菌的基因组进行了分析。最后，我们利用生物信息学方法对基因组数据进行了SSR（简单重复序列）预测。R.结果表明，该物种的总生物量为554.22Mb。杂合率为0.93%，重复率为49.17%。R.结果表明，在2281551个支架中，组装的N50值为916 bp。共鉴定出479724个SSR标记。微草基因组，设计了871656对引物用于应用。其中100对引物经过验证，71对引物成功扩增。综上所述，R.结果表明，该属植物基因组复杂，杂合性高，重复序列少。在今后的R.对于micranthum，更高深度的“2+3”（Illumina+PacBio）测序可能会产生更好的组装结果。
Abstract Rhododendron micranthum is an evergreen shrub species widely distributed in China that has high ornamental and medicinal value. However, there is a lack of molecular and genomic data for this plant, which severely restricts the development of its relevant research. The objective of the present study was to conduct a first genomic survey of R. micranthum and determine its whole-genome sequencing scheme. Next-generation sequencing (Illumina Hi-Seq Xten) was used to measure the genome size of R. micranthum, K-mer analysis were employed to investigate its genomic profile. Finally, we conducted bioinformatics methods to performed SSR (simple sequence repeat) prediction based on the genomic data. The genome size of R. micranthum was estimated to be 554.22 Mb. The heterozygosity ratio was 0.93%, and the sequence repeat ratio was calculated to be 49.17%. The clean reads of R. micranthum were assembled into 2281551 scaffolds with a N50 value of 916 bp. A total of 479724 SSR molecular markers were identified in the R. micranthum genome, and 871656 pairs of primers designed for application. Among of them, 100 primer pairs were validated, and 71 primer pairs were successfully amplified. In summary, the R. micranthum genome is complex with high heterozygosity and low repeated sequences. In future whole-genome research in R. micranthum, higher-depth ‘2+3’ (Illumina+PacBio) sequencing may yield better assembly results.
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影响因子：
--
作者：
Mijuan Shi;Yingyin Cheng;Wanting Zhang;Xiaoqin Xia
通讯作者：
Mijuan Shi;Yingyin Cheng;Wanting Zhang;Xiaoqin Xia
影响因子：
4
作者：
Li, Guo-qi;Song, Li-xiao;Wang, Ya-fang
通讯作者：
Wang, Ya-fang
使用表达序列标签评估选定植物物种的基因组测序质量
影响因子：
3.7
作者：
Shangguan L;Han J;Kayesh E;Sun X;Zhang C;Pervaiz T;Wen X;Fang J
通讯作者：
Fang J
DOI：
--
发表时间：
2011
期刊：
Journal of Plant Genetic Resources
影响因子：
--
作者：
G. Yangdong
通讯作者：
G. Yangdong
影响因子：
7
作者：
Li, Ruiqiang;Zhu, Hongmei;Wang, Jun
通讯作者：
Wang, Jun