Genome-wide investigation of calcium-dependent protein kinase gene family in pineapple: evolution and expression profiles during development and stress

Abstract

Background: Calcium-dependent protein kinase (CPK) is one of the main Ca 2+ combined protein kinase that play significant roles in plant growth, development and response to multiple stresses. Despite an important member of the stress responsive gene family, little is known about the evolutionary history and expression patterns of CPK genes in pineapple. Results: Herein, we identified and characterized 17 AcoCPK genes from pineapple genome, which were unevenly distributed across eight chromosomes. Based on the gene structure and phylogenetic tree analyses, AcoCPKs were divided into four groups with conserved domain. Synteny analysis identified 7 segmental duplication events of AcoCPKs and 5 syntenic blocks of CPK genes between pineapple and Arabidopsis, and 8 between pineapple and rice. Expression pattern of different tissues and development stages suggested that several genes are involved in the functional development of plants. Different expression levels under various abiotic stresses also indicated that the CPK family underwent functional divergence during long-term evolution. AcoCPK1, AcoCPK3 and AcoCPK6, which were repressed by the abiotic stresses, were shown to be function in regulating pathogen resistance. Conclusions: 17 AcoCPK genes from pineapple genome were identified. Our analyses provide an important foundation for understanding the potential roles of AcoCPKs in regulating pineapple response to biotic and abiotic stresses

Genome-wide identification and expression analysis of the citrus calcium-dependent protein kinase (CDPK) genes in response to arbuscular mycorrhizal fungi colonization and drought

“…All of the CsCDPKs were predicted to contain at least one EF-hand, 17 CsCDPKs were predicted to contain myristoylation sites, and 24 CsCDPKs were predicted to contain palmitoylation sites. CsCDPK1 did not have myristoylation and palmitoylation sites ( [27]. Although the size of citrus genome (380 Mb) (https://www.citrusgenomedb.org/ organism/Citrus/sinensis) was larger than the genome of Arabidopsis (125 Mb) (https://www.arabidopsis.org), the total number of citrus CDPK genes was similar to the number of these genes in Arabidopsis.…”

“…Gene expression analysis revealed that 29 CsCDPKs were variably expressed in the roots. CsCDPK1, 2,5,6,7,8,9,13,17,18,19,21,24,25,26,27 and 29 were upregulated by AMF colonization, and CsCDPK3, 7 and 28 were downregulated. Drought-repressed expression of CsCDPK10, 11, 12, 15 and 16 induced CsCDPK20 and 22.…”

“…Twenty-nine CsCDPKs were expressed in the roots, implying a role in root development and other associated biological processes. 'Defence and stress responsive' cis-elements were identified in the promoters of CsCDPK10, 11,19,20,23,24,26 and 29,but CsCDPK1,2,5,6,7,8,9,13,17,18,19,21,24,25,26,27 and 29 were upregulated by AMF colonization (Figure 4). The patterns of CsCDPK expression were not consistent with the ciselements in their promoters for 'defence and stress responsive', which may be due to the integration of other gene regulatory elements, such as trans-acting factors [50].…”

“…The CDPK family has been characterized in several plants, including Arabidopsis [4], rice [21], wheat [22], Populus [23], cotton [24], Capsicum annuum [25], grape [26], pineapple [27] and banana [28]. CDPKs play important roles in drought stress and microbe interactions and may function in the citrus drought stress response.…”

Peer Review #1 of "Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.) (v0.2)"

“…4, Table S3). The diversity of gene combinations may be one of the factors that make the regulatory relationship complicated (Zhang et al, 2018;Zhang et al, 2020). Polyploidization, a widespread phenomenon among plant, is considered an important process of plant speciation and evolution, and the formation of polyploid includes hybridization and genomic doubling process before or after hybridization (Kohler et al, 2010;Zeng et al, 2020).…”