ThzLecRLK.xlsx

The CDS sequences of the 297 ThzLecRLK genes identified by bioinformatics methods. The unigene sequences of T. hybrid 'Zhongshanshan' were derived from the previously determined salinity stress transcriptome,short-term waterlogging transcriptome and adventitious roots transcriptome. Hidden Markov Model (HMM) profiles (PF00069, PF01453, PF00139, PF00059), which correspond to kinase, G-type lectin, L-type lectin and C-type lectin domains, respectively, were downloaded from Pfam (pfam.xfam.org/).

We retrieved genes containing a kinase domain by running the hmmsearch program (HMMER 2.3.2) to search the kinase profile (PF00069) against the proteomic sequences. Within this set of hypothetical kinase proteins, we searched for G-type lectin, L-type lectin and C-type lectin HMM profiles (PF01453, PF00139, PF00059) (E value cut-off < 1). Sequences in which we identified a protein kinase domain (PF00069), along with either a G-type lectin (PF01453), an L-type lectin (PF00139), or a C-type lectin domain (PF00059) were considered putative LecRLKs (GmLecRLKs) and finally confirmed as ThzLecRLK genes after removing redundant sequences with 97% similarity between different database.