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

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.苦瓜（Momordica charantia L.）是起源于亚洲的营养型蔬菜作物，在印度与中国传统医学中常作为药用草本应用。由于分子资源有限，尤其是针对雌性系性状的功能标记匮乏，苦瓜的分子育种仍处于起步阶段。本研究采用Illumina第二代测序平台，对雌性系（Gy323）与雌雄同株系（DRAR1）的根、花蕾、茎及叶组织开展了从头转录组测序。最终分别获得雌性系Gy323的65540条转录本、雌雄同株系DRAR1的61490条转录本。序列比对分析揭示了两个品系间的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）与简单序列重复（Simple Sequence Repeat, SSR）变异，并完成了基因类群的鉴定与分类。基于获取的转录本数据，本研究共鉴定出80个WRKY转录因子家族成员，此类基因多参与生物与非生物胁迫响应；同时鉴定得到56个生长素响应因子（Auxin Response Factor, ARF）基因，该类基因在生长素调控的基因表达与生长发育过程中发挥关键作用。本研究生成的转录组数据将为苦瓜的功能基因研究与分子育种工作提供有力支撑。