De Novo Assembly of Bitter Gourd Transcriptomes: Gene Expression and Sequence Variations in Gynoecious and Monoecious Lines

Anjali Shukla; V K Singh; D R Bharadwaj; Rajesh Kumar; Ashutosh Rai; A K Rai; Raja Mugasimangalam; Sriram Parameswaran; Major Singh; P S Naik

doi:10.1371/journal.pone.0128331

De Novo Assembly of Bitter Gourd Transcriptomes: Gene Expression and Sequence Variations in Gynoecious and Monoecious Lines

PLoS One. 2015 Jun 5;10(6):e0128331. doi: 10.1371/journal.pone.0128331. eCollection 2015.

Authors

Affiliations

¹ Division of Crop Improvement, Indian Institute of Vegetable Research, Post Bag No- 01, Jakhini (Shahanshahpur), Varanasi, Uttar Pradesh-221 305, India.
² Centre for Bioinformatics, School of Biotechnology, Banaras Hindu University, Varanasi, Uttar Pradesh 221 005, India.
³ Centre of Advanced Studies, Department of Botany, Banaras Hindu University, Varanasi, Uttar Pradesh 221 005, India.
⁴ Genotypic Technology (P) Ltd., Bangalore 560094, Karnataka, India.

Abstract

Bitter gourd (Momordica charantia L.) is a nutritious vegetable crop of Asian origin, used as a medicinal herb in Indian and Chinese traditional medicine. Molecular breeding in bitter gourd is in its infancy, due to limited molecular resources, particularly on functional markers for traits such as gynoecy. We performed de novo transcriptome sequencing of bitter gourd using Illumina next-generation sequencer, from root, flower buds, stem and leaf samples of gynoecious line (Gy323) and a monoecious line (DRAR1). A total of 65,540 transcripts for Gy323 and 61,490 for DRAR1 were obtained. Comparisons revealed SNP and SSR variations between these lines and, identification of gene classes. Based on available transcripts we identified 80 WRKY transcription factors, several reported in responses to biotic and abiotic stresses; 56 ARF genes which play a pivotal role in auxin-regulated gene expression and development. The data presented will be useful in both functions studies and breeding programs in bitter gourd.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Gene Expression Regulation, Plant
Genes, Plant
Genetic Variation*
High-Throughput Nucleotide Sequencing
Medicine, Traditional
Microsatellite Repeats / genetics
Momordica charantia / genetics*
Plant Proteins / genetics
Plant Proteins / metabolism
Polymorphism, Single Nucleotide
Real-Time Polymerase Chain Reaction
Sequence Analysis, RNA
Transcription Factors / genetics
Transcription Factors / metabolism
Transcriptome*

Substances

Plant Proteins
Transcription Factors

Grants and funding

Genotypic Technology (P) Ltd., provided indirect support in the form letting the authors from Genotypic RM & SP to work on this project, but did not provide any financial support or have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section. The Indian Council of Agricultural Research, New Delhi provided financial support for basic research facilities, infrastructure etc for Indian Institute of Vegetable Research, Varanasi. The funding agency had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.