Open Access

ARTICLE

Transcriptome based high-throughput SSRs and SNPs discovery in the medicinal plant Lagenaria siceraria

HONGYUAN ZHANG, MIN ZHANG, JIE TAN, SHUPING HUANG, GUOLIN ZHOU^*, XIA CHEN^*

Wuhan Academy of Agricultural Sciences, Wuhan, 430065, China

* Address correspondence to: Xia Chen, ; Guolin Zhou,

BIOCELL 2021, 45(2), 371-386. https://doi.org/10.32604/biocell.2021.013869

Received 25 August 2020; Accepted 19 October 2020; Issue published 19 February 2021

Abstract

Lagenaria siceraria (Molina) Standley has unique biological characteristics with high nutritional and medicinal values. It is an important pharmaceutical plant with various biologically active ingredients. Genetic improvement and deeper genomic studies require a rich resource of molecular markers. The application of next-generation sequencing technology, especially for transcriptome profiling, has greatly facilitated high throughput single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) discovery. In this study, we sequenced the transcriptome of three major cultivars of L. siceraria and obtained 64.88 GB of clean data. The assembled high-quality reads were clustered into 89,347 unigenes, which were annotated by non-redundant protein database, Swiss-Port, Eukaryotic Ortholog Groups, Kyoto Encyclopedia of Genes and Genomes, and gene ontology databases. A total of 8,891 SSR and 35,873 SNP markers were predicted from unigenes by MISA and SAM tools, respectively. Characterization of the predicted markers in L. siceraria showed that the SSR and SNP densities were 60 and 243 markers per Mb of genome, respectively, and the estimated ratio of transition to transversion of SNP was 2.016. These markers will be very useful for genetic studies in L. siceraria, especially for the high-density linkage map construction and genome-wide association studies. Further genomic studies based on these results will facilitate the identification of novel genes or alleles of pharmaceutical importance.

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Keywords

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