Identification, Characterization and Function of Orphan Genes Among the Current Cucurbitaceae Genomes

Abstract

Orphan genes (OGs) that are missing identifiable homologs in other lineages may potentially make contributions to a variety of biological functions. The Cucurbitaceae family consists of a wide range of fruit crops of worldwide or local economic significance. To date, very few functional mechanisms of OGs in Cucurbitaceae are known. In this study, we systematically identified the OGs of eight Cucurbitaceae species using a comparative genomics approach. The content of OGs varied widely among the eight Cucurbitaceae species, ranging from 1.63% in chayote to 16.55% in wax gourd. Genetic structure analysis showed that OGs have significantly shorter protein lengths and fewer exons in Cucurbitaceae. The subcellular localizations of OGs were basically the same, with only subtle differences. Except for aggregation in some chromosomal regions, the distribution density of OGs was higher near the telomeres and relatively evenly distributed on the chromosomes. Gene expression analysis revealed that OGs had less abundantly and highly tissue-specific expression. Interestingly, the largest proportion of these OGs was significantly more tissue-specific expressed in the flower than in other tissues, and more detectable expression was found in the male flower. Functional prediction of OGs showed that (1) 18 OGs associated with male sterility in watermelon; (2) 182 OGs associated with flower development in cucumber; (3) 51 OGs associated with environmental adaptation in watermelon; (4) 520 OGs may help with the large fruit size in wax gourd. Our results provide the molecular basis and research direction for some important mechanisms in Cucurbitaceae species and domesticated crops.

Keywords: Cucurbitaceae; environmental adaptation; male sterility; orphan genes; transcriptome.

FIGURE 1

Procedures for identifying orphan genes in eight Cucurbitaceae species.

FIGURE 2

Box plot comparison of protein length (A), exon number (B), exon length (C), GC content (D), and isoelectric point (E) of orphan genes (OGs) and non-orphan genes (NOGs) for eight Cucurbitaceae species. Statistical analysis was performed using the Wilcox rank sum test. Statistical significance: ** P-value < 0.001.

FIGURE 3

Subcellular localization (A) and chromosome distribution (B) of eight Cucurbitaceae species.

FIGURE 4

Orphan genes originating from gene duplication. (A) Statistics on the types of OGs originating from gene duplication in eight Cucurbitaceae species. (B) Density distribution of synonymous substitution rate (Ks) values between OGs and paralogous genes in melon. (C) Density distribution of Ks values between OGs and paralogous genes in wax gourd.

FIGURE 5

Expression patterns and functional prediction of OGs in different tissues of melon, includes root, leaf, male flower, female flower and fruit. (A) Gene significance map. (B) Heat map of OGs expression in different tissues inside the MEgreen module. (C) Functional annotation of KEGG for co-expressed genes of OGs. (D) KEGG enrichment analysis of co-expressed genes of OGs.

FIGURE 6

Functional prediction of OGs in the development of cucumber flowers. (A) Trends in the expression of differentially expressed genes at the stage of flower development. (B) Heat map of the expression of OGs under the trend of pattern Cluster 1 and Cluster 5. (C) KEGG enrichment analysis of co-expressed genes of OGs in Cluster 1 and Cluster 5.

FIGURE 7

Functional prediction of OGs under osmotic stress. (A) Trends in the expression of differentially expressed genes at different time points under osmotic stress. (B) Heat map of the expression of OGs under the trend of pattern Cluster 1 and Cluster 3. (C) KEGG enrichment analysis of co-expressed genes of OGs in Cluster 1 and Cluster 3.