Abstract
BackgroundCotton is an important commodity in the world economy. In this study we have carried out genome-wide identification and bioinformatics characterization of basic leucine zipper domain proteins (bZIPs) from cultivated cotton species G. hirsutum along with two subgenome species of allotetraploid cotton, G. arboreum and G. raimondii. Transcription factors (TFs) are the key regulators in plant development and stress adaptation. Understanding interactions of TFs in cotton crop is important for enhancing stress tolerance and yield enhancement. Among plant TFs, bZIPs plays a major role in seed germination, flower development, biotic and abiotic stress response. Most of the bZIP proteins from cotton remains uncharacterized and can be utilised for crop improvement. In this paper we performed genome-wide identification, phylogenetic analysis, structural characterization and functional role prediction of bZIPs from all three genome species of cotton.ResultsIn the present study genome-wide identification, phylogenetic analysis, structural characterization and functional role prediction of bZIP TFs from G. hirsutum (AADD) along with two subgenome species G. arboreum (A2) and G. raimondii (D5) were performed. A total of 228 bZIP genes of G. hirsutum, 91 bZIP genes of G. arboreum and 86 bZIP genes of G. raimondii were identified from CottonGen database. Cotton bZIP genes were annotated in standard pattern according to their match with Arabidopsis bZIPs. Multiple genes with similar bZIP designations were observed in cotton. Cotton bZIPs are distributed across all 13 chromosomes with varied density. Phylogenetic characterization of all three cotton species bZIPs with Arabidopsis bZIPs classified them into 12 subfamilies, namely A B, C, D, E, F, G, H, I, J, K and S and further into eight subgroups according to functional similarities, viz., A1, A2, A3, C1, C2, S1, S2 and S3.The classification was exclusively based on alignment with Arabidopsis bZIPs further supported by structural characteristics like exon number, amino acid length, common functional motifs shared among subfamilies and basic leucine zipper domain (BRLZ) alignment. Subfamily A and S are having maximum number of bZIP genes, subfamily B, H, J and K are single member families. Cotton is carrying only bZIP17 among the group of bZIP17, 28 and 49 which are known to be crucially worked under endoplasmic reticulum (ER) stress. Cotton bZIP protein functions were predicted from identified motifs and orthologs from varied species.MEME motif analysis identified MYND-Zinc binding domain, tetratricopeptide repeats motif, GluR7, DOG1, (DELAY OF GERMINATION 1) seed dormancy control motif, TGACG sequence specific motif, etc. specifically in some of the subfamily members and presence of bZIP signature domain in all identified bZIPs. Further we explored the BRLZ domain of G. raimondii bZIPs, conserved basic region motif N-X7-R/K is present in almost all subfamily members, variants are GrbZIP62 which is carrying N-X7-I motif and GrbZIP76 with K-X7-R motif. Leucine heptad repeats motif, L-X6-L-X6-L are also present in variant numbers from two to nine with leucine or other hydrophobic amino acid at designated position among 12 subfamily members.STRING protein interaction network analysis of G.raimondii bZIPs observed strong interaction between A-D subfamily members, C-S subfamily members and between GrbZIP17- GrbZIP60. NLS analysis of G. raimondii bZIPs observed conserved NLS sequences among subfamilies.ConclusionThis study analyzed, annotated and phylogenetically classified bZIP proteins from cultivated cotton species G. hirsutum along with two subgenome species G. arboreum and G. raimondii. Cotton bZIPs are classified into twelve subfamilies and eight subgroups. bZIP gene duplications are observed in all three cotton species. We have identified conserved functional motifs among different subfamilies of cotton bZIP proteins and correlated for the prediction of function along with reported function. Explored BRLZ domain structural analysis of G. raimondii bZIPs will be useful in further basic characterization of bZIP proteins of cultivated cotton species G. hirsutum. STRING protein interaction analysis of G. raimondii bZIPs resulted in prediction of interactions among A- D, B-K and C-S subfamily members. Phylogenetic analysis of this study will certainly help in the selection of specific cotton bZIP genes according to the close alignment with Arabidopsis orthologs or subgenome homolog.
Genome-wide regulation of light-controlled seedling morphogenesis by three families of transcription factors
