De Novo Transcriptome Sequencing And Comparison Of Gene Expression Between Fall Dormant And Non- Fall Dormant Medicago Sativa L.

Alfalfa (Medicago sativa L.) is one of the most widely cultivated perennial forage legume in the world. In this study, we generated about 160 million high quality paired-end (2x100) sequence reads using sequencing by synthesis technology. The de novo transcriptome assembly generated a set of 192,875 transcripts with an average length of 856 bp representing about 165.1 Mb of the alfalfa transcriptome. We identified 41,973 simple sequence repeats, which can be used to generate markers for alfalfa. We also analyzed the sequence conservation with other plant proteomes and 1,350 transcripts encoded for transcription factors were identified using hmmer combined with PlnTFDB. Finally, gene expression between dormant and non-dormant alfalfa were analyzed to find differentially expressed genes related to fall dormancy, fold change more than or equal to 2 and adjusted P value less than 0.05 were filtered as true differential genes. In all four selected sets,176 to 521 differential expressed genes were identified, including annotated and non annotated genes. These findings provide new insights to explore the mechanisms in fall dormancy in alfalfa.