De Novo Assembly and Characterization of the Transcriptome, and Development of SSR Markers in Wax Gourd (Benicasa hispida)

Biao Jiang,Xiaoming He,Dasen Xie,Qingwu Peng,Wenrui Liu,Christian Schönbach

doi:10.1371/journal.pone.0071054

Abstract

BackgroundWax gourd is a widely used vegetable of Cucuribtaceae, and also has important medicinal and health values. However, the genomic resources of wax gourd were scarcity, and only a few nucleotide sequences could be obtained in public databases.Methodology/Principal FindingsIn this study, we examined transcriptome in wax gourd. More than 44 million of high quality reads were generated from five different tissues of wax gourd using Illumina paired-end sequencing technology. Approximately 4 Gbp data were generated, and de novo assembled into 65,059 unigenes, with an N50 of 1,132 bp. Based on sequence similarity search with known protein database, 36,070 (55.4%) showed significant similarity to known proteins in Nr database, and 24,969 (38.4%) had BLAST hits in Swiss-Prot database. Among the annotated unigenes, 14,994 of wax gourd unigenes were assigned to GO term annotation, and 23,977 were found to have COG classifications. In addition, a total of 18,713 unigenes were assigned to 281 KEGG pathways. Furthermore, 6,242 microsatellites (simple sequence repeats) were detected as potential molecular markers in wax gourd. Two hundred primer pairs for SSRs were designed for validation of the amplification and polymorphism. The result showed that 170 of the 200 primer pairs were successfully amplified and 49 (28.8%) of them exhibited polymorphisms.Conclusion/SignificanceOur study enriches the genomic resources of wax gourd and provides powerful information for future studies. The availability of this ample amount of information about the transcriptome and SSRs in wax gourd could serve as valuable basis for studies on the physiology, biochemistry, molecular genetics and molecular breeding of this important vegetable crop.

Highlights

The Cucurbitaceae is an important family in the plant kingdom, whose importance is just after Gramineae, Leguminosae and Solanaceae
In order to obtain a broad survey of genes associated with the growth and development of wax gourd, total RNA samples were extracted from shoot tips, leaves, flowers, fruits and stems in the flowering stage
The lack of genomic information in wax gourd has hindered the research on this important vegetable crop at molecular biology and genetic level

Summary

Introduction

The Cucurbitaceae is an important family in the plant kingdom, whose importance is just after Gramineae, Leguminosae and Solanaceae. The wax gourd, called white gourd, white pumpkin, tallow gourd, ash gourd, and so on, is named after the Italian count, Giuseppe Benincasa [4] It is a monotypic genus which belongs to the family Cucurbitaceae, and is a widely used vegetable in India, China and other tropical countries [5]. There is no simple sequence repeat (SSR) marker developed in wax gourd. Conclusion/Significance: Our study enriches the genomic resources of wax gourd and provides powerful information for future studies. The availability of this ample amount of information about the transcriptome and SSRs in wax gourd could serve as valuable basis for studies on the physiology, biochemistry, molecular genetics and molecular breeding of this important vegetable crop

Methods

Results

Conclusion