Genome-wide and molecular evolution analyses of the KT/HAK/KUP family in tomato (Solanum lycopersicum L.)
Genome-wide and molecular evolution analyses of the KT/HAK/KUP family in tomato (Solanum lycopersicum L.)
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DOI：
10.1007/s13258-014-0174-0
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发表时间：
2014-06-01
期刊：
影响因子：
2.1
通讯作者：
Kim, Ju-Sung
中科院分区：
文献类型：
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作者：
Hyun, Tae Kyung;Rim, Yeonggil;Kim, Ju-Sung
属于KT/HAK/KUP家族的钾转运蛋白在植物生长发育、矿质营养和逆境适应中起着重要作用。本研究利用生物信息学的方法，在番茄中鉴定了分布在10条染色体上的19个KT/HAK/KUP家族基因。对番茄KT/HAK/KUP（SlHAK）基因的染色体定位、遗传、基因结构和进化模式进行了综述。19 SlHAK蛋白的系统发育分析表明，组IV的KT/HAK/KUP家庭是在番茄基因组中的缺失。此外，在番茄KT/HAK/KUP家族中还发现了5对片段重复旁系同源物和2对串联重复旁系同源物。这表明片段性重复是SlHAK基因扩增的主要原因。利用同义替换率计算重复事件的大致发生日期表明，番茄KT/HAK/KUP基因片段重复起源于3589 - 6277万年前。适应性进化分析表明，纯化选择有助于节段重复对的进化。此外，田岛的相对速率测试表明，所有的节段重复对以相似的速率进化。作为番茄KT/HAK/KUP基因家族全基因组分析的第一步，我们的研究结果为理解番茄和其他物种中KT/HAK/KUP基因家族的功能和进化提供了有价值的信息。
Potassium transporters belonging to the KT/HAK/KUP family play an important role in plant growth, development, mineral nutrition, and stress adaptation. In this study, we identified 19 KT/HAK/KUP family genes in tomato, distributed on 10 chromosomes, by using bioinformatics methods. A complete overview of the KT/HAK/KUP (SlHAK) genes in tomato is presented, including chromosome location, phylogeny, gene structure, and evolution pattern. Phylogenetic analysis of 19 SlHAK proteins suggested that group IV of the KT/HAK/KUP family is absent in the tomato genome. In addition, five pairs of segmental duplicated paralogs and two pairs of tandem duplicated paralogs were identified in the tomato KT/HAK/KUP family. This suggests that segmental duplication is predominant for the expansion of the SlHAK genes. Calculation of the approximate dates of duplication events using the synonymous substitution rate indicated that the segmental duplication of the KT/HAK/KUP genes in tomato originated 35.89-62.77 million years ago. Adaptive evolution analysis showed that purifying selection contributed to the evolution of segmental duplicated pairs. Furthermore, Tajima's relative rate test indicated that all segmental duplicated pairs evolved at similar rates. As a first step toward a genome-wide analysis of the KT/HAK/KUP gene family in tomato, our results provide valuable information for understanding the function and evolution of the KT/HAK/KUP gene family in tomato and other species.