Data_Sheet_1_Taxonomically Restricted Genes Are Associated With Responses to Biotic and Abiotic Stresses in Sugarcane (Saccharum spp.).pdf

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.

孤儿基因（Orphan genes, OGs）是一类局限于特定演化支或物种、与其他生物基因无同源性的蛋白编码基因（protein-coding genes），这使得其生物学功能难以预测。孤儿基因能够快速起源并获得功能，因此可能助力生物快速适应环境变化。甘蔗属类群（Saccharum group）中广泛发生了移动元件（mobile elements）的大规模扩散与全基因组复制（whole-genome duplication）事件，这或许推动了甘蔗基因组中孤儿基因的起源与多样化。本研究对甘蔗中的孤儿基因进行了鉴定与特征分析，检测了其在不同组织与基因型中的表达谱，并探究了它们在不同条件下的调控机制。我们在野生甘蔗（Saccharum spontaneum）基因组中鉴定出319个孤儿基因，这些基因与除甘蔗亚族（Saccharinae）外的所有绿色植物蛋白编码基因均无同源性。转录组分析显示，其中288个甘蔗孤儿基因在至少一种组织或基因型中可检测到表达水平。研究发现，地理起源相近的甘蔗基因型中，孤儿基因的表达模式较为相似。同时还观察到部分孤儿基因具有组织特异性表达特征，这或许表明存在复杂的调控过程，以维持这些基因在甘蔗不同组织与基因型中的多样功能活性。有66个孤儿基因在胁迫条件下（尤其是低温胁迫与渗透胁迫）呈现差异表达。基因共表达网络与功能富集分析结果表明，甘蔗孤儿基因参与了多种生物学过程，包括刺激响应与防御机制。本研究结果为甘蔗研究人员，尤其是关注抗逆响应基因筛选的研究者，提供了极具价值的基因组学资源。