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从头转录组组装和 EST-SSR 标记的开发及在. 中的应用

De Novo Transcriptome Assembly and EST-SSR Marker Development and Application in .

机构信息

Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China.

Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China.

出版信息

Genes (Basel). 2023 Jan 21;14(2):279. doi: 10.3390/genes14020279.

DOI:10.3390/genes14020279
PMID:36833206
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9956384/
Abstract

Oliv., belonging to the family Saxifragaceae, is a traditional and unique Chinese herbal medicine. However, the lack of adequate molecular markers has hampered the progress regarding population genetics and evolution within this species. In this research, we used the DNBSEQ-T7 Sequencer (MGI) sequencing assay to analyze the transcriptome profiles of . SSR markers were developed on the basis of transcriptomic sequences and further validated on and other species. The genetic diversity and structure of the 12 populations were analyzed by using polymorphic expressed sequence tag simple sequence repeat (EST-SSR) markers. A potential pool of 3127 non-redundant EST-SSR markers were identified for in this study. The developed EST-SSR markers had high amplification rates and cross-species transferability in . Our results also showed that the natural populations of had a high level of genetic diversity. Genetic distance, principal component analysis, and popular structure analysis revealed that all 60 samples clustered into two major groups that were consistent with their geographical origins. This study provided a batch of highly polymorphic EST-SSR molecular markers that were developed via transcriptome sequencing. These markers will be of great significance for the study of the genetic diversity and evolutionary history of and other species.

摘要

珙桐，隶属于忍冬科，是一种传统的、独特的中草药。然而，缺乏充分的分子标记阻碍了该物种在种群遗传学和进化方面的研究进展。在本研究中，我们使用 DNBSEQ-T7 测序仪（MGI）测序分析了珙桐的转录组谱。基于转录组序列开发了 SSR 标记，并在珙桐和其他物种上进行了验证。通过使用多态性表达序列标签简单重复序列（EST-SSR）标记分析了 12 个种群的遗传多样性和结构。本研究为珙桐鉴定了 3127 个非冗余的 EST-SSR 标记。开发的 EST-SSR 标记在珙桐中具有较高的扩增率和跨物种转移能力。我们的结果还表明，珙桐的自然种群具有较高的遗传多样性。遗传距离、主成分分析和流行结构分析表明，所有 60 个样本聚类为两个主要群体，与它们的地理起源一致。本研究通过转录组测序提供了一批高度多态性的 EST-SSR 分子标记，这些标记将对研究珙桐和其他物种的遗传多样性和进化历史具有重要意义。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5155/9956384/28716add7c9c/genes-14-00279-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5155/9956384/2c656fb87bab/genes-14-00279-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5155/9956384/b58c9b0c91e4/genes-14-00279-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5155/9956384/b56db8ea3e4a/genes-14-00279-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5155/9956384/17428ab08089/genes-14-00279-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5155/9956384/72692845396a/genes-14-00279-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5155/9956384/ea03dfe995ce/genes-14-00279-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5155/9956384/28716add7c9c/genes-14-00279-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5155/9956384/2c656fb87bab/genes-14-00279-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5155/9956384/b58c9b0c91e4/genes-14-00279-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5155/9956384/b56db8ea3e4a/genes-14-00279-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5155/9956384/17428ab08089/genes-14-00279-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5155/9956384/72692845396a/genes-14-00279-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5155/9956384/ea03dfe995ce/genes-14-00279-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5155/9956384/28716add7c9c/genes-14-00279-g007.jpg

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