PJB-2021-318
Analysis of SSR loci information in transcriptome of Sinopodophyllum hexandrum (Royle) Ying by RNA-Seq
Zheng Zhang, Zhenzhen Sui, Mingge Chen, Huanxing Chang, Luyao Yu, Tong Zhang, Dongxue Yin and Wei Liu
Abstract
Sinopodophyllum hexandrum (Royle) Ying is a rare and endangered medicinal plant in China, and the podophyllotoxin contained in its rhizome is a precursor substance of synthetic anti-cancer drugs, which has special effects on antineoplastic activities. In this study, 75245 Unigenes were assembled by splicing clean reads with Trinity software based on the transcriptome sequencing data of S. hexandrum. A total of 19934 SSR loci were identified in the total Unigenes by using MISA software, and the number of SSR containing sequences was 14809, accounting for 19.68% of the total Unigenes. The dominant repeat motif was mononucleotide, accounting for 55.51% of the total SSR loci, followed by dinucleotide and trinucleotide, accounting for 22.87% and 19.02%, respectively. A/T, AG/CT and AAG/CTT were repeat units with high frequency in mononucleotide, dinucleotide and trinucleotide, respectively. Furthermore, ten was the most frequent number of repeats, up to 5063 SSR loci, accounting for 25.40% of the total SSR loci, followed by 5 repetitions, the number of loci was 2584, accounting for 12.96% of the total. This study utilized transcriptome high-throughput sequencing technique to analyze SSR loci information, which can provide a new basis for genetic diversity research, systematic differentiation analysis, effective molecular marker development and molecular directional breeding of S. hexandrum
To Cite this article:
Zhang, Z., Z. Sui, M. Chen, H. Chang, L. Yu, T. Zhang, D. Yin and W. Liu. 2022. Analysis of SSR loci information in transcriptome of Sinopodophyllum hexandrum (Royle) Ying by RNA-Seq. Pak. J. Bot., 54(4): DOI: http://dx.doi.org/10.30848/PJB2022-4(23)
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