Genome-Wide Analysis of the <i>CDPK</i> Gene Family in <i>Populus tomentosa</i> and Their Expressions in Response to Arsenic Stress and Arbuscular Mycorrhizal Fungi Colonization

Calcium-dependent protein kinases (CDPKs) are crucial regulators in calcium-mediated signal transduction pathways, playing a pivotal role in plant response to abiotic stresses. However, there is still limited knowledge regarding the genes of the <i>Populus tomentosa CDPK</i> family and their underlying functions in response to arsenic (As) stress and arbuscular mycorrhizal fungi (AMF) colonization. In our study, 20 <i>PtCDPKs</i> were identified in the <i>P. tomentosa</i> genome. Phylogenetic analysis categorized these <i>PtCDPK</i> genes into four subgroups based on sequence homology. Motif analysis revealed that <i>PtCDPK</i> genes within the same group share a similar exon–intron structure, conserved domains, and composition. The promoters of <i>PtCDPK</i> genes were found to contain a multitude of cis-acting elements, including light-response elements, phytohormone-response elements, and stress-response elements. The analysis of genes provided insights into the evolutionary dynamics and expansion of the <i>PtCDPK</i> gene family within <i>P. tomentosa</i>. The <i>PtCDPK</i> genes exhibited a strong collinear relationship with the <i>CDPK</i> genes of two model plants, namely, <i>Arabidopsis thaliana</i> and <i>Oryza sativa</i> L. Specifically, 10 gene pairs showed collinearity with <i>Arabidopsis</i>; in contrast, 14 gene pairs were collinear with rice. Transcriptome analysis of gene expression levels in <i>P. tomentosa</i> roots under both As stress and arbuscular mycorrhizal fungi (AMF) colonization conditions revealed that 20 <i>PtCDPK</i> genes had differential expression patterns. Under As stress, AMF inoculation led to the upregulation of 11 P<i>tCDPK</i> genes (<i>PtCDPKSK5</i>, <i>X2</i>, <i>1</i>-<i>3</i>, <i>20</i>-<i>1</i>, <i>24</i>, <i>26</i>-<i>X1</i>-<i>1</i>, <i>26</i>-<i>X1</i>-<i>2</i>, <i>29</i>-<i>1</i>, <i>29</i>-<i>2</i>, <i>32</i>, and <i>32</i>-<i>X1</i>) and the downregulation of 8 <i>PtCDPK</i> genes, including <i>PtCDPK1</i>-<i>1</i>, <i>1</i>-<i>2</i>, <i>8</i>-<i>X1</i>, <i>10</i>-<i>X4</i>, <i>13</i>, <i>20</i>-<i>2</i>, <i>26</i>-<i>X2</i>, and <i>26</i>-<i>X3</i>. The RT-qPCR results for 10 <i>PtCDPK</i> genes were consistent with the transcriptome data, indicating that AMF symbiosis plays a regulatory role in modulating the expression of <i>PtCDPK</i> genes in response to As stress. The principal findings of this study were that <i>PtCDPK</i> genes showed differential expression patterns under As stress and AMF colonization, with AMF regulating <i>PtCDPK</i> gene expression in response to As stress. Our study contributes to developing a deeper understanding of the function of <i>PtCDPKs</i> in the Ca²⁺ signaling pathway of <i>P. tomentosa</i> under As stress and AMF inoculation, which is pivotal for elucidating the molecular mechanisms underlying As tolerance in AMF-inoculated <i>P. tomentosa</i>.