Taxonomically Restricted Genes Are Associated With Responses to Biotic and Abiotic Stresses in Sugarcane (Saccharum spp.)

Abstract

Orphan genes (OGs) are protein-coding genes that are restricted to particular clades or species and lack homology with genes from other organisms, making their biological functions difficult to predict. OGs can rapidly originate and become functional; consequently, they may support rapid adaptation to environmental changes. Extensive spread of mobile elements and whole-genome duplication occurred in the Saccharum group, which may have contributed to the origin and diversification of OGs in the sugarcane genome. Here, we identified and characterized OGs in sugarcane, examined their expression profiles across tissues and genotypes, and investigated their regulation under varying conditions. We identified 319 OGs in the Saccharum spontaneum genome without detected homology to protein-coding genes in green plants, except those belonging to Saccharinae. Transcriptomic analysis revealed 288 sugarcane OGs with detectable expression levels in at least one tissue or genotype. We observed similar expression patterns of OGs in sugarcane genotypes originating from the closest geographical locations. We also observed tissue-specific expression of some OGs, possibly indicating a complex regulatory process for maintaining diverse functional activity of these genes across sugarcane tissues and genotypes. Sixty-six OGs were differentially expressed under stress conditions, especially cold and osmotic stresses. Gene co-expression network and functional enrichment analyses suggested that sugarcane OGs are involved in several biological mechanisms, including stimulus response and defence mechanisms. These findings provide a valuable genomic resource for sugarcane researchers, especially those interested in selecting stress-responsive genes.

Keywords: RNA-Seq; gene expression; orphan genes; stress condition; sugarcane hybrid.

Figure 1

Evidence of orphan gene (OG) vestiges within grass genomes. (A) Scatterplot showing the average percentage identity and coverage of each OG in six grass species. Each dot represents an individual OG. The dot sizes represent the number of fragments of each sugarcane OG in other grass species. The number of fragments of each OG in the focal species is also shown in the bar plot (B).

Figure 2

Expression profiles of orphan genes (OGs) in several sugarcane tissues and genotypes. The expression of each gene (TPM) was estimated using a pseudoalignment method implemented in Salmon software.

Figure 3

Orphan genes (OGs) differentially expressed (DE) under cold stress. Hierarchical clustering of the genes expressed at normal and cold temperatures with four replicates for each treatment (row). DE analysis was carried out in leaf tissues at an ambient temperature (ranging from 23°C to 35°C) and a cold temperature (4°C in a well-controlled climate chamber) in two sugarcane genotypes: ROC22 (A) and Guitang08-1180 (B).

Figure 4

Heatmap of orphan genes (OGs) differentially expressed (DE) under osmotic stress. Plants were subjected to osmotic stress for 24, 48, and 72 h, and other plants were maintained without osmotic stress (0 h). RNA samples were extracted from the leaves (A) and roots (B) of S. officinarum.

Figure 5

Genes differentially expressed (DE) under low-nitrogen conditions. RNA samples were extracted from leaves of the ROC22 (A) and Badila (B) genotypes.