Genome-wide identification, classification, evolutionary analysis and gene expression patterns of the protein kinase gene family in wheat and Aegilops tauschii

Abstract

In this study we systematically identified and classified PKs in Triticum aestivum, Triticum urartu and Aegilops tauschii. Domain distribution and exon-intron structure analyses of PKs were performed, and we found conserved exon-intron structures within the exon phases in the kinase domain. Collinearity events were determined, and we identified various T. aestivum PKs from polyploidizations and tandem duplication events. Global expression pattern analysis of T. aestivum PKs revealed that some PKs might participate in the signaling pathways of stress response and developmental processes. QRT-PCR of 15 selected PKs were performed under drought treatment and with infection of Fusarium graminearum to validate the prediction of microarray. The protein kinase (PK) gene superfamily is one of the largest families in plants and participates in various plant processes, including growth, development, and stress response. To better understand wheat PKs, we conducted genome-wide identification, classification, evolutionary analysis and expression profiles of wheat and Ae. tauschii PKs. We identified 3269, 1213 and 1448 typical PK genes in T. aestivum, T. urartu and Ae. tauschii, respectively, and classified them into major groups and subfamilies. Domain distributions and gene structures were analyzed and visualized. Some conserved intron-exon structures within the conserved kinase domain were found in T. aestivum, T. urartu and Ae. tauschii, as well as the primitive land plants Selaginella moellendorffii and Physcomitrella patens, revealing the important roles and conserved evolutionary history of these PKs. We analyzed the collinearity events of T. aestivum PKs and identified PKs from polyploidizations and tandem duplication events. Global expression pattern analysis of T. aestivum PKs revealed tissue-specific and stress-specific expression profiles, hinting that some wheat PKs may regulate abiotic and biotic stress response signaling pathways. QRT-PCR of 15 selected PKs were performed under drought treatment and with infection of F. graminearum to validate the prediction of microarray. Our results will provide the foundational information for further studies on the molecular functions of wheat PKs.

The sugarcane and sorghum kinomes: insights into evolutionary expansion and diversification

“…The group containing the most kinases is the RLK-Pelle group (Gish and Clark, 2011) and, similar to findings in other kinomes (Singh et al, 2014;Wei et al, 2014;Zulawski et al, 2014;Liu et al, 2015;Yan et al, 2017Yan et al, , 2018Zhu et al, 2018a, b), we found that the RLK-Pelle group had the most members in our study. This expansion in the Sbi and Ssp kinomes is apparently related to a few specific families within this group, most notably the LRR, RLCK, DLSV, L-LEC and SD-2b families.…”

“…In Sbi, PK genes were more commonly located in subtelomeric regions. This pattern was even more evident when only tandemly duplicated PKs were considered; similar (though less pronounced) patterns were observed in the kinomes of soybean (Liu et al, 2015), T. aestivum (Yan et al, 2017), Gossypium raimondii and Gossypium barbadense (Yan et al, 2018). Yan et al (2017) noted that this pattern is consistent with T. aestivum's higher gene and expressed sequence tag (EST) densities in distal regions of chromosomes and inferred that this location pattern of PKs could indicate chromosomal rearrangements.…”

“…This pattern was even more evident when only tandemly duplicated PKs were considered; similar (though less pronounced) patterns were observed in the kinomes of soybean (Liu et al, 2015), T. aestivum (Yan et al, 2017), Gossypium raimondii and Gossypium barbadense (Yan et al, 2018). Yan et al (2017) noted that this pattern is consistent with T. aestivum's higher gene and expressed sequence tag (EST) densities in distal regions of chromosomes and inferred that this location pattern of PKs could indicate chromosomal rearrangements. Our findings are equally compatible with the general genomic landscape of sorghum: in this species, the density of genes-especially paralogs-is much higher in chromosome extremities, while pericentromeric regions are very rich in long terminal repeat retrotransposons (Paterson et al, 2009;Mace and Jordan, 2011).…”

“…This figure is also comparable to the 1,093 PK genes previously estimated for this species using an earlier genomic reference (Lehti-Shiu and Shiu, 2012). The Ssp genome, on the other hand, contains one of the largest numbers of PK genes reported for any plant species (2,919), ranking below only the allohexaploid genome of Triticum aestivum (3,269 PKs) (Yan et al, 2017). However, we must consider that this identification was performed using a genome that provides information at the allele level; when only Ssp GMs (i.e., single representatives of all copies of a gene) were analyzed, we found a much lower number of PK genes (1,345), which is also within the range of PKs in other Poaceae species.…”

“…The DLSV family includes Domain of Unknown Function 26 (DUF26), SD-1, LRR-VIII, and VMA (a RLK subfamily specific in moss)-like proteins (Lehti-Shiu and Shiu, 2012), which mediate the control of stress responses and development (Vinagre et al, 2006;Vaattovaara et al, 2019), with some members being associated with signaling pathways regulating the responses to cold (Yan et al, 2017) and infection (Yan et al, 2017). L-LEC and SD-2b have established associations with the defense response (Chen et al, 2006;Wei et al, 2014) but also with stomatal immunity regulation via an L-LEC member (Desclos-Theveniau et al, 2012) and with self-incompatibility via SD-2b (Stein et al, 1991).…”