@Article{biocell.2021.013869,
AUTHOR = {HONGYUAN ZHANG, MIN ZHANG, JIE TAN, SHUPING HUANG, GUOLIN ZHOU, XIA CHEN},
TITLE = {Transcriptome based high-throughput SSRs and SNPs discovery in the medicinal plant <i>Lagenaria siceraria</i>},
JOURNAL = {BIOCELL},
VOLUME = {45},
YEAR = {2021},
NUMBER = {2},
PAGES = {371--386},
URL = {http://www.techscience.com/biocell/v45n2/41550},
ISSN = {1667-5746},
ABSTRACT = {<i>Lagenaria siceraria</i> (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 <i>L. siceraria</i> 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 <i>L. siceraria</i> 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 <i>L. siceraria</i>, 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.},
DOI = {10.32604/biocell.2021.013869}
}