Coding and Noncoding RNA Sequences of Glycine latifolia, a Wild Perennial Relative of Soybean

Glycine latifolia, a wild perennial relative of soybean (Glycine max), is recognized for its resistance to multiple phytopathogenic diseases and tolerance to abiotic stresses. Better understanding of the G. latifolia genome and its characteristics may assist in the identification of genes underlying favorable traits in wild perennial soybean relatives. For that purpose, RNASeq and small RNA libraries were prepared using RNAs purified from various G. latifolia tissue types and analyzed by Illumina high-throughput sequencing, yielding over 400 million and 200 million reads, respectively. Trinity transcriptome de novo assembly generated more than 300,000 contigs with an N50 of 1,394 nt. Among the 158,427 protein sequences predicted by TransDecoder, 70% aligned to predicted products of G. max nuclear, mitochondrial or chloroplast coding sequences. The transcriptome assembly also facilitated annotation by MAKER of a draft G. latifolia genome sequence that predicted 59,400 protein-coding loci - similar to the number (56,044) for G. max. The products of predicted genes included 66 pathogenesis-related proteins and 311 putative disease resistance proteins. Small RNA data were analyzed using miRPlant for expression levels, secondary structure of the primary transcripts and genome locations utilizing the draft G. latifolia genome sequence as reference. Subsequent manual selection based on miRPlant results yielded 231 microRNAs (miRNAs), including 45 novel miRNAs and 186 conserved miRNAs from 41 families. The most abundantly expressed miRNAs were miR166, miR396, miR482, and miR1507, which display similar expression patterns in G. max. Degradome sequence analysis will be required to confirm the activity of the novel miRNAs.