Using Next Generation Sequencing to Identify Peanut (Arachis hypogaea L.) Transcripts That Are Enhanced Under Water Stress.

Over the past decade, the emergence of next generation sequencing (NGS) technologies revolutionized genomics research. RNA sequencing (RNA-seq) using NGS allows RNA analysis of whole transcripts of previously known or unknown, rare or abundant RNA molecules at large scales with an unprecedented level of sensitivity and accuracy. Peanut, as the world’s fifth most important oilseed crop and second most important legume crop, serves as an essential oil and food source for millions of people. However, peanut’s genomic resources are very limited to advance breeding and biological studies. At present only 178,490 expression sequence tag (EST) entries from cultivated peanut have been deposited in GenBank representing about 40% of peanut genes. The objectives of this study were: 1) to study the peanut transcriptome while enriching the peanut EST database by utilizing the RNA-seq of two peanut cultivars, 2) to identify the abundant transcripts of the two peanut cultivars under water stress, and 3) to discover the transcript sequence polymorphism between the two cultivars. A total of 288,701 reads with an average length of 215bp were generated using the 454 genome sequencer. Assembly of the two cultivars’ reads yielded a unique set of 37,653 transcript sequences. About half of the sequences in this unique set were annotated and their functions covered 29 biological processes. This unique transcript sequence set significantly enriched the current peanut EST database by adding over 10 thousand new ESTs to Genbank. The most abundant transcripts during water stress and several genes with alternative splicing sites were also discovered. Sequence polymorphisms existed between the two cultivars and could be utilized for peanut molecular marker development in the future.