Molecular Characterization and Global Expression Analysis of Lectin Receptor Kinases in Bread Wheat (Triticum aestivum)

Abstract

Lectin receptor kinases (LRKs) play a critical role in plants during development and stress conditions, but a comprehensive analysis at genome level is still not carried out in Triticum aestivum. Herein, we performed the genome wide identification, characterization and expression analysis of these genes in T. aestivum (TaLRK). In-total 263 TaLRK genes were identified, which were further classified into three groups based on the nature of lectin domain. We identified, two TaLRKs consisted of calcium-dependent lectin (C-LRK), while 84 legume-lectin (L-LRK) and 177 bulb-lectin (B-LRK) domains. The L-LRK and B-LRK genes were distributed throughout the genome of T. aestivum. Most of the TaLRKs were clustered as homologs, which were distributed either in proximity on same chromosome or on homoeologous chromosomes of A, B and D sub-genomes. A total of 9 and 58 duplication events were also predicted in L-LRK and B-LRK, respectively. Phylogenetic analysis indicated conserved evolutionary relationship of homologous and orthologous genes from multiple plant species. Gene ontology analysis indicated TaLRKs role in binding, signaling and receptor activities. Most of the TaLRKs consisted of a trans-membrane domain and predicted to be localized in the plasma-membrane. A diverse expression pattern of TaLRK genes was found in various developmental stages and stress conditions. Some TaLRKs were found to be highly affected during a particular stress, which indicated a specialized role of each LRK gene in a specific stress condition. These results described various characteristic feature and expression pattern of TaLRK genes, which will pave the way for functional characterization in wheat.

Ca2+/Cation Antiporters (CaCA): Identification, Characterization and Expression Profiling in Bread Wheat (Triticum aestivum L.)

“…Genome-wide analysis established that the TaCaCA genes were derived from each subgenomes of T. aestivum as reported in case of other gene families (Shumayla et al, 2016a,b; Zeng et al, 2016). A total of 10 (5 TaCAX, 2 TaCCX, 2 TaNCL, and 1 TaMHX), 10 (4 TaCAX, 3 TaCCX, 2 TaNCL, and 1 TaMHX) and 14 (5 TaCAX, 5 TaCCX, 3 TaNCL, and 1 TaMHX) genes were located on A, B, and D subgenomes, respectively (Figure 1A).…”

“…In other higher plants, a total of 14 (6 AtCAX, 5 AtCCX, 2 AtNCL, and 1 AtMHX), 15 (6 OsCAX, 5 OsCCX, 2 OsNCL, and 2 OsMHX), and 14 (6 ZmCAX, 6 ZmCCX, 1 ZmNCL, and 1 ZmMHX) CaCA protein are reported in Arabidopsis, rice, and maize, respectively (Emery et al, 2012; Singh et al, 2015; Pittman and Hirschi, 2016a). It was earlier established that T. aestivum consisted of higher number of genes in each gene family (Shumayla et al, 2016a,b) due to their large allohexaploid (2n = 6x = 42; AABBDD) nature of genome (Marcussen et al, 2014). Therefore, it was also expected in TaCaCA superfamily.…”

“…The hydropathy analysis of putatively identified sequences was performed using TMHMMv2.01 (Krogh et al, 2001; Petersen et al, 2011) to further confirm their identity as CaCA proteins. The presence of EF-hand (PfamID: PF00036) and Na_Ca_ex (PfamID: PF01699) domains were confirmed by BLAST search against local pfam database (ftp://ftp.sanger.ac.uk/pub/databases/Pfam) following the method established in our laboratory (Finn et al, 2014; Shumayla et al, 2016a,b). CaCA superfamily proteins were also identified in T. urartu (TuCaCA) and Aegilops tauschii (AeCaCA) genomes, which are reported as progenitors of A and D subgenome of T. aestivum , respectively (Marcussen et al, 2014).…”

“…Bi-directional best hit approach at e -value 10 −10 was used for the prediction of homeologous and orthologous genes as reported in earlier studies (Shumayla et al, 2016a,b). The identification of homeologous TaCaCA genes was based on their chromosome group, chromosome arm location and high percent (≥90%) identity.…”

“…The unavailability of genomic information, composite nature of genome and complexity in application of modern functional genomics tools could be the probable reason for the same. In recent years, the genome sequence and numerous development and stress related high throughput RNA sequence data have been available from T. aestivum (IWGSC, 2014; Zhang et al, 2014b, 2016; Liu Z. et al, 2015; Pingault et al, 2015), which enabled the genome wide characterization of various gene families (Shumayla et al, 2016a,b; Zeng et al, 2016). Since the CaCA proteins are involved in several vital functions from development to stress response, there characterization becomes essential in an important food crop like T. aestivum .…”