Phylogenetic tree of the <i>CPK</i> gene family in apple, peach and strawberry annotated with collinear and tandem relationships.

<p>Curves connecting pairs of genes suggest either the collinear relationship (red) or tandem relationship (blue).</p

Duplication genes in apple, peach and plum.

<p>Duplication genes in apple, peach and plum.</p

Characterization and Comparison of the <i>CPK</i> Gene Family in the Apple (<i>Malus × domestica</i>) and Other Rosaceae Species and Its Response to <i>Alternaria alternata</i> Infection

<div><p>As one of the Ca²⁺ sensors, calcium-dependent protein kinase (CPK) plays vital roles in immune and stress signaling, growth and development, and hormone responses, etc. Recently, the whole genome of apple (<i>Malus × domestica)</i>, pear (<i>Pyrus communis</i>), peach (<i>Prunus persica</i>), plum (<i>Prunus mume</i>) and strawberry (<i>Fragaria vesca</i>) in Rosaceae family has been fully sequenced. However, little is known about the <i>CPK</i> gene family in these Rosaceae species. In this study, 123 <i>CPK</i> genes were identified from five Rosaceae species, including 37 apple <i>CPKs</i>, 37 pear <i>CPKs</i>, 17 peach <i>CPKs</i>, 16 strawberry <i>CPKs</i>, and 16 plum <i>CPKs</i>. Based on the phylogenetic tree topology and structural characteristics, we divided the <i>CPK</i> gene family into 4 distinct subfamilies: Group I, II, III, and IV. Whole-genome duplication (WGD) or segmental duplication played vital roles in the expansion of the <i>CPK</i> in these Rosaceae species. Most of segmental duplication pairs in peach and plum may have arisen from the γ triplication (~140 million years ago [MYA]), while in apple genome, many duplicated genes may have been derived from a recent WGD (30~45 MYA). Purifying selection also played a critical role in the function evolution of <i>CPK</i> family genes. Expression of apple <i>CPK</i> genes in response to apple pathotype of <i>Alternaria alternata</i> was verified by analysis of quantitative real-time RT-PCR (qPCR). Expression data demonstrated that <i>CPK</i> genes in apple might have evolved independently in different biological contexts. The analysis of evolution history and expression profile laid a foundation for further examining the function and complexity of the <i>CPK</i> gene family in Rosaceae.</p></div

Localization and duplication of the <i>CPK</i> genes in the apple, peach, plum and strawberry genome.

<p>Circular visualization of the <i>CPK</i> genes mapped on the different chromosomes in the genome using the Circos software. Chromosome number is indicated on the chromosome. The synteny relationship between each pair of <i>CPK</i> genes were detected by using the MicroSyn software. The genes have synteny relationship are linked by lines. Red link: >30 anchors in a synteny block, blue link: 20–30anchors, green link: 10–20 anchors, gray link: 5–10 anchors.</p

Phylogenetic trees of <i>CPK</i> genes in apple, pear, peach, plum, strawberry and Arabidopsis.

<p>The phylogenetic tree of <i>CPK</i> full length protein sequences was constructed with MEGA6 program with the neighbor-joining method. A <i>CPK</i> gene from <i>Ostreococcus lucimarinus</i> was used as the outgroup. The numbers beside the branches represent bootstrap values based on 1000 replications.</p

Relative changes in expression of <i>MdCPK</i> genes in response to <i>A</i>. <i>alternata</i> infection using quantitative real-time RT-PCR.

<p>The expression of <i>MdCPK</i> genes were normalized to tubulin expression. The fold changes of <i>MdCPK</i> genes were obtained by calculating the log2 ratio between treated (18, 36 and 72 hours after inoculation (hai) of <i>A</i>. <i>alternata</i>) and untreated samples. <b>(A)</b> The colour scheme in the heat map is blue/red: white indicate a low variation in expression, blue indicate a decrease and red indicate an increase. <i>MdCPK</i> gene names are displayed to the right of each row and are clustered in different clusters A, B, C and D using Hierarchical Clustering method. <b>(B)</b> Y axis represents the log2 value of fold change of <i>MdCPK</i> genes. For example, > 0 means up-regulation and < 0 indicates down-regulation of expression, and “1” represents genes up-regulated with 2 fold change in treated sample relative to control. Bars indicate standard error (SE) in three biological replicates.</p

<i>CPK</i> genes and related information in apple.

<p><i>CPK</i> genes and related information in apple.</p

Distribution of SV and the type of variants per chromosome in the two grape lines.

<p>Distribution of SV and the type of variants per chromosome in the two grape lines.</p

Diferent InDel sizes distribution and frameshift mutation between the whole genome and CDS region.

<p>Diferent InDel sizes distribution and frameshift mutation between the whole genome and CDS region.</p

The grapes materials used in this study.

<p>The grapes materials used in this study.</p