The wall-associated kinases (WAKs) can perceive and transmit extracellular signals as one kind of unique receptor-like kinases (RLKs) involved in the regulation of cell expansion, pathogen resistance and abiotic stress tolerance. To understand their potential roles and screen some key candidates in Medicago truncatula (M. truncatula), genome-wide identification and characterization of MtWAKs were conducted in this study. A total of 54 MtWAK genes were identified and classified into four groups based on their protein domains. They were distributed on all chromosomes, while most of them were clustered on chromosome 1 and 3. The synteny analysis showed that 11 orthologous pairs were identified between M. truncatula and Arabidopsis thaliana (A. thaliana) and 31 pairs between M. truncatula and Glycine max (G. max). The phylogenetic analysis showed that WAK-RLKs were classified into five clades, and they exhibited a species-specific expansion. Most MtWAK-RLKs had similar exon–intron organization and motif distribution. Multiple cis-acting elements responsive to phytohormones, stresses, growth and development were observed in the promoter regions of MtWAK-RLKs. In addition, the expression patterns of MtWAK-RLKs varied with different plant tissues, developmental stages and biotic and abiotic stresses. Interestingly, plasm membrane localized MtWAK24 significantly inhibited Phytophthora infection in tobacco. The study provides valuable information for characterizing the molecular functions of MtWAKs in regulation of plant growth, development and stress tolerance in legume plants.

Hairy vetch (Vicia villosa Roth) and smooth vetch (V. villosa Roth var. glabrescens) are important cover crops and legume forage with great economic and ecological values. Due to the large and highly heterozygous genome, full-length transcriptome reconstruction is a cost-effective route to mining their genetic resources. In this study, a hybrid sequencing approach combining SMRT and NGS technologies was applied. The results showed that 28,747 and 40,600 high-quality non-redundant transcripts with an average length of 1808 bp and 1768 bp were generated from hairy vetch and smooth vetch, including 24,864 and 35,035 open reading frames (ORFs), respectively. More than 96% of transcripts were annotated to the public databases, and around 25% of isoforms underwent alternative splicing (AS) events. In addition, 987 and 1587 high-confidence lncRNAs were identified in two vetches. Interestingly, smooth vetch contains more specific transcripts and orthologous clusters than hairy vetch, revealing intraspecific transcript diversity. The phylogeny revealed that they were clustered together and closely related to the genus Pisum. Furthermore, the estimation of Ka/Ks ratios showed that purifying selection was the predominant force. A putative 3-dehydroquinate dehydratase/shikimate dehydrogenase (DHD/SDH) gene underwent strong positive selection and might regulate phenotypic differences between hairy vetch and smooth vetch. Overall, our study provides a vital characterization of two full-length transcriptomes in Vicia villosa, which will be valuable for their molecular research and breeding.