Molecular Genetics Laboratory, Department of Botany, Central University of Punjab, VPO Ghudda, Distt, Bathinda, 151401, India.
Mol Biol Rep. 2021 Jan;48(1):721-729. doi: 10.1007/s11033-021-06138-x. Epub 2021 Jan 13.
Ulmus wallichiana is a traditional medicinal plant listed as a vulnerable in the IUCN red list data. Genomic and transcriptomic resources for this species are lacking, hindering its genetic exploration. Further, no polymorphic marker resource is available for this species, thus limiting the elucidation of its underlying genetic diversity, which is a pre-requisite for its conservation. This study was therefore aimed to generate a functionally annotated transcriptomic resource and screen it for SSR regions. We used paired-end Illumina based RNAseq technology and trinity based de novo assembly approach to generate full length transcripts, which were screened for SSR regions and functionally annotated. Around 6.6 million raw reads were de novo assembled transcripts, which were clustered into 146,083 unigenes. 19,909 transcripts were provided with 3986 unique KEGG ids, 70,519 transcripts with 6621 unique Pfam domains, and 45,125 transcripts with 7302 unique INTERPRO domains. 1456 transcripts were identified as transcriptions factors (TFs). Further, 8868 unique GO terms were obtained for the unigenes. The transcripts mapped to 23,056 known pre-determined orthology clusters in the eggNOG database. A total of 16,570 SSRs were identified from the unigenes. Out of the 90 SSRs selected for characterization on 20 genotypes, 28 were polymorphic. Mean effective alleles (Ne) of 2.53, mean observed heterozygosity (Ho) of 0.77, and average polymorphic information content (PIC) of 0.57 were found. This study may facilitate the genetic exploration of this species. The polymorphic SSRs would prove useful to explore its genetic diversity patterns, required for its conservation.
青檀是一种传统的药用植物，被列入 IUCN 红色名录数据中的脆弱物种。该物种缺乏基因组和转录组资源，这阻碍了对其遗传的探索。此外，该物种没有多态性标记资源，因此限制了其潜在遗传多样性的阐明，而这是其保护的前提。因此，本研究旨在生成一个功能注释的转录组资源，并对其 SSR 区域进行筛选。我们使用基于配对末端 Illumina 的 RNAseq 技术和基于 trinity 的从头组装方法生成全长转录本，然后筛选 SSR 区域并进行功能注释。大约 660 万条原始reads 通过从头组装转录本，这些转录本被聚类为 146083 个 unigenes。19909 个转录本提供了 3986 个独特的 KEGG id，70519 个转录本提供了 6621 个独特的 Pfam 结构域，45125 个转录本提供了 7302 个独特的 INTERPRO 结构域。1456 个转录本被鉴定为转录因子（TFs）。此外，为 unigenes 获得了 8868 个独特的 GO 术语。这些转录本映射到 eggNOG 数据库中 23056 个已知预定的同源聚类。从 unigenes 中总共鉴定出 16570 个 SSR。在对 20 个基因型进行的 90 个 SSR 特征选择中，有 28 个是多态性的。发现 2.53 的平均有效等位基因（Ne），0.77 的平均观察杂合度（Ho）和 0.57 的平均多态信息含量（PIC）。本研究可能有助于该物种的遗传探索。多态性 SSR 将有助于探索其遗传多样性模式，这是其保护所必需的。
