The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies

作者：Jamie A. O’Rourke, Fengli Fu, Bruna Bucciarelli, Sean Yang, Deborah A. Samac, JoAnn FS Lamb, María J. Monteros, Michelle A. Graham, John W Gronwald, Nick Krom, Jun Li, Xinbin Dai, Patrick X. Zhao, Carroll P. Vance · 发表于：BMC Genomics · 年份：2015 · DOI：10.1186/s12864-015-1718-7 · 被引用次数：103 · 研究领域：Legume Nitrogen Fixing Symbiosis、Plant and fungal interactions、Plant Molecular Biology Research

BACKGROUND: Alfalfa (Medicago sativa L.) is the primary forage legume crop species in the United States and plays essential economic and ecological roles in agricultural systems across the country. Modern alfalfa is the result of hybridization between tetraploid M. sativa ssp. sativa and M. sativa ssp. falcata. Due to its large and complex genome, there are few genomic resources available for alfalfa improvement. RESULTS: A de novo transcriptome assembly from two alfalfa subspecies, M. sativa ssp. sativa (B47) and M. sativa ssp. falcata (F56) was developed using Illumina RNA-seq technology. Transcripts from roots, nitrogen-fixing root nodules, leaves, flowers, elongating stem internodes, and post-elongation stem internodes were assembled into the Medicago sativa Gene Index 1.2 (MSGI 1.2) representing 112,626 unique transcript sequences. Nodule-specific and transcripts involved in cell wall biosynthesis were identified. Statistical analyses identified 20,447 transcripts differentially expressed between the two subspecies. Pair-wise comparisons of each tissue combination identified 58,932 sequences differentially expressed in B47 and 69,143 sequences differentially expressed in F56. Comparing transcript abundance in floral tissues of B47 and F56 identified expression differences in sequences involved in anthocyanin and carotenoid synthesis, which determine flower pigmentation. Single nucleotide polymorphisms (SNPs) unique to each M. sativa subspecies (110,241) were identified. ...