Genome-Wide Identification of YABBY Gene Family in Cucurbitaceae and Expression Analysis in Cucumber ( Cucumis sativus L.)

Abstract

YABBY transcription factors play important roles in plant growth and development. However, little is known about YABBY genes in Cucurbitaceae. Here, we identified 59 YABBY genes from eight cucurbit species, including cucumber (C. sativus L.), melon (C. melon L.), watermelon (C. lanatus), wax gourd (B. hispida), pumpkin (C. maxima), zucchini (C. pepo L.), silver-seed gourd (C. argyrosperma), and bottle gourd (L. siceraria). The 59 YABBY genes were clustered into five subfamilies wherein the gene structures and motifs are conserved, suggesting similar functions within each subfamily. Different YABBY gene numbers in eight cucurbit species indicated that gene loss or duplication events exist in an evolutionary process across Cucurbitaceae. The cis-acting elements analysis implied that the YABBYs may be involved in plant development, and phytohormone, stress, and light responses. Importantly, YABBY genes exhibited organ-specific patterns in expression in cucumber. Furthermore, a gene CsaV3_6G038650 was constitutively expressed at higher levels at different fruit development stages and might play a crucial role in cucumber fruit development. Collectively, our work will provide a better understanding for further function identifications of YABBY genes in Cucurbitaceae.

Keywords: Cucurbitaceae; YABBY genes; cucumber; evolution; expression pattern.

Figure 1

Phylogenetic tree of the YABBY proteins from Arabidopsis, rice, and eight cucurbit species. Red star, red star filled with pink color, yellow star, green star filled with light purple color, black star filled with dark purple color, bluish grey star, red star filled with blue color, black star, black triangle filled with red color and black circle filled with green color represent the YABBYs from cucumber, melon, watermelon, wax gourd, pumpkin, zucchini, silver-seed gourd, bottle gourd, Arabidopsis, and rice, respectively. Cs, cucumber (C. sativus L.); MELO, melon (C. melo L.); Cla, watermelon (C. lanatus); Bhi, wax gourd (B. hispida); Cma, pumpkin (C. maxima); Cp, zucchini (C. pepo L.); Carg, silver-seed gourd (C. argyrosperma); Lsi, bottle gourd (L. siceraria); AT, Arabidopsis (Arabidopsis thaliana); Os, rice (Oryza sativa L.).

Figure 2

Synteny analysis of YABBY genes between cucumber and melon, watermelon, wax gourd, pumpkin, zucchini, and bottle gourd. The synteny gene pairs are highlighted in the red lines.

Figure 3

Phylogenetic clustering, conserved motifs, and gene structure of YABBY genes from eight cucurbit species. Left panel: unrooted phylogenetic tree of YABBY proteins. Light green, gray, light red, blue and purple part represent YAB5, YAB2, CRC, YAB1, and INO subfamilies, respectively. Middle panel: gene structure of YABBY genes. Untranslated regions and exons are indicated by green boxes and yellow boxes, respectively. Right panel: the conserved motifs of YABBYs are represented by different colored boxes.

Figure 4

The conserved C2C2 domain and YABBY domain of 59 YABBY proteins from eight cucurbit species. The typical amino acid residues within C2C2 domain are indicated with red asterisks.

Figure 5

The cis-acting elements analysis of 59 YABBY genes promoters across Cucurbitaceae. The numbers of cis-acting elements are shown in a heatmap.

Figure 6

The expression patterns of CsYABBY genes in different tissues of cucumber. (A–H) Tissues-specific of CsYABBY expression was examined in cucumber by qRT-PCR. Values are means ± SD of three biological replicates.

Figure 7

The expression patterns of CsYABBY genes in different development stages of ovary/fruit of cucumber. (A) The relative expression levels of CsYABBYs at different development stages of ovary/fruit. (B) The TPM values of CsYABBYs at 4 DBF ovary in near-isogenic lines 408 and 409. DBF: days before flowering. DAF: days after flowering. Values are means ± SD of three biological replicates.