Development of EST-SSR markers in Bergenia ciliata using de novo transcriptome sequencing.

IF 4.6 Q2 MATERIALS SCIENCE, BIOMATERIALS

ACS Applied Bio Materials Pub Date : 2024-04-01 Epub Date: 2023-12-13 DOI:10.1139/gen-2023-0059

Harish Chandra Singh, Vandana Tiwari, Avinash Tiwari, Tikam S Rana

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引用次数: 0

Abstract

Bergenia ciliata (Haw.) Sternb. is an important herb predominantly found in the Indian Himalayan Region. It is widely used in medicines, healthcare systems, cosmetics, fodder, and ornamental purposes. The Illumina sequencing and de novo transcriptome assembly were carried out in B. ciliata to develop and identify simple sequence repeat markers. A total of 18 226 simple sequence repeats (SSRs) were identified wherein di-nucleotides were found to be abundant (47.88%), followed by mono-nucleotide (35.03%) and tri-nucleotide (15.88%) repeats. A total of 11 839 EST-SSR primers were designed, of which 96 primer pairs were commercially synthesized. Finally, 17 primer pairs revealed clear, distinct polymorphic bands, and these primers were validated with 40 diverse B. ciliata accessions. The present study revealed moderate level of genetic diversity (H_o = 0.389, H_e = 0.542, and PIC = 0.513). Furthermore, the transcriptome data and EST-SSR markers generated during the present investigation could be an important genetic resource for functional genomics, population studies, and conservation genetics of the genus Bergenia.

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利用全新转录组测序技术开发纤毛虫 EST-SSR 标记。

Bergenia ciliata 是一种重要的草本植物，主要分布在印度喜马拉雅地区（IHR）。它被广泛用于医药、保健系统、化妆品、食品、饲料和观赏用途。对纤毛虫进行了 Illumina 测序和从头开始的转录组组装，以开发和鉴定简单序列重复标记。共鉴定出 18,226 个 SSR，其中二核苷酸占多数（47.88%），其次是单核苷酸（35.03%）和三核苷酸重复（15.88%）。共设计了 11 839 个 EST-SSR 引物，其中 96 对引物是通过商业途径合成的。最后，17 对引物显示出清晰、明显的多态性条带，这些引物已在 40 个不同的纤毛虫品种中得到验证。本研究揭示了中等水平的遗传多样性（Ho =0.389，He =0.542，PIC=0.513）。此外，本研究中产生的转录组数据和 EST-SSR 标记可作为 Bergenia 属功能基因组学、种群研究和保护遗传学的重要遗传资源。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

ACS Applied Bio Materials Chemistry-Chemistry (all)

CiteScore

9.40

自引率

2.10%

发文量

464