Table_6_Genome-wide analysis of tandem duplicated genes and their expression under salt stress in seashore paspalum.XLSX

Seashore paspalum (Paspalum vaginatum) is a halophytic, warm-season grass which is closely related to various grain crops. Gene duplication plays an important role in plant evolution, conferring significant plant adaptation at the genomic level. Here, we identified 2,542 tandem duplicated genes (TDGs) in the P. vaginatum genome and estimated the divergence time of pairs of TDGs based on synonymous substitution rates (Ks). Expression of P. vaginatum TDGs resulted in enrichment in many GO terms and KEGG pathways when compared to four other closely-related species. The GO terms included: “ion transmembrane transporter activity,” “anion transmembrane transporter activity” and “cation transmembrane transport,” and KEGG pathways included “ABC transport.” RNA-seq analysis of TDGs showed tissue-specific expression under salt stress, and we speculated that P. vaginatum leaves became adapted to salt stress in the earlier whole-genome duplication (WGD; ~83.3 million years ago; Ma), whereas the entire P. vaginatum plant acquired a large number of TDGs related to salt stress in the second WGD (~23.3 Ma). These results can be used as a reference resource to accelerate salt-resistance research in other grasses and crops.

海雀稗（Paspalum vaginatum）是一类盐生（halophytic）暖季型草本植物，与多种谷类作物亲缘关系紧密。基因重复在植物演化过程中发挥关键作用，可在基因组层面赋予植物显著的环境适应性。本研究在P. vaginatum基因组中鉴定出2542个串联重复基因（tandem duplicated genes, TDGs），并基于同义替换速率（synonymous substitution rates, Ks）估算了各TDG对的分化时间。相较于其他4个近缘物种，P. vaginatum的TDGs表达显著富集于诸多基因本体（Gene Ontology, GO）条目与京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）通路。其中GO条目涵盖“离子跨膜转运蛋白活性”“阴离子跨膜转运蛋白活性”与“阳离子跨膜转运”，KEGG通路则包含“ABC转运”。对TDGs的RNA-seq（RNA测序）分析显示，其在盐胁迫条件下呈现组织特异性表达模式。研究团队推测，P. vaginatum的叶片在较早的全基因组重复（whole-genome duplication, WGD；约8330万年前，Ma）事件中便已适应盐胁迫环境，而该物种整体则在第二次全基因组重复事件（约2330万年前）中获得了大量与盐胁迫相关的TDGs。本研究结果可作为参考资源，助力其他草本植物与作物的抗盐性研究推进。