番茄KNOX基因家族鉴定及茄科作物KNOX基因进化关系分析

Genome-wide Identification of KNOX Gene Family in Tomatoand Their Evolutionary Relationship in Solanaceae

为了探明番茄KNOX基因家族特征及茄科作物中KNOX的进化关系,利用生物信息学方法,在全基因组水平上对番茄及其它茄科作物KNOX基因家族成员进行鉴定和分析。结果表明,番茄基因组中共含有8个KNOX基因(Sl KNOX1~Sl KNOX8),分别分布在番茄8条染色体上;多序列比对发现,除Sl KNOX5外,所有基因均含有同源异型盒蛋白特有的4种结构域,即KNOX1、KNOX2、ELK和Homeobox KN。利用系统发育树将茄科作物KNOX基因分为2类:ClassⅠ和ClassⅡ。茄科作物KNOX基因与拟南芥同源基因可能经历了不同的进化历程,在茄科作物中,特有的进化分支(Class I C)已经出现。qRTPCR分析发现,番茄Sl KNOX1在花蕾和花中具有较高表达,在果实生长发育过程中表达量逐渐降低,Sl KNOX2~Sl KNOX4在果实生长发育过程中几乎不表达,Sl KNOX6和Sl KNOX7在所测组织中均有表达,Sl KNOX8在果实成熟过程中表达量逐渐增加,且在根中表达量最大。本研究在全基因组水平上揭示了番茄中KNOX基因家族特征以及茄科作物中KNOX基因的系统发育关系,为进一步揭示KNOX基因家族在番茄组织器官中的功能及进化模式奠定了基础。

To investigate the characteristics of KNOX gene family in tomato and their evolutionary relationships in Solanaeae,KNOX gene family in tomato and other Solanaceae（ potato and pepper） were identified using bioinformatics method. The results showed that the tomato genome contained 8 Sl KNOX genes（ Sl KNOX1-Sl KNOX8）,distributed across 8 chromosomes of tomato. Multiple sequence alignment showed,except for Sl KNOX5,all other proteins included4 conservative domains（ KNOX1,KNOX2,ELK and Homeobox KN）,which were specific for plant KNOX proteins.Phylogenetic analysis characterized 2 classes of KNOX genes： Class I with 3 sub-classes（ A,B and C） and Class II with2 sub-classes（ A and B）. Compared with KNOX genes in Arabidopsis,KNOX genes in Solanaceae have a different evolutionary process. Furthermore,a novel branch（ Class IC） has occurred in Solanaceae. qRT-PCR analysis revealed Sl KNOX1 was high expression in bud and flower,gradually reduced in the process of fruit mature. Expression of Sl KNOX2,Sl KNOX3 and Sl KNOX4 was not deleted in the process of fruit mature. Sl KNOX6 and Sl KNOX7 were expressed in all tested tissues. Expression level of Sl KNOX8 was gradually enhanced in the process of fruit mature,and the expression in root was the highest. In this study,the characteristics of KNOX gene family in tomato were revealed on the genome level and their phylogenetic relationships in Solanaceae were clarified,which will contribute to further elaborate their functions in different tissues and their evolutionary relationships in Solanaceae.