毛竹KNOX基因家族全基因组鉴定和组织表达特异性分析

Genome-wide Identification and Tissue Specific Expression Analysis of KNOX Gene Family in Phyllostachys edulis

为了探究KNOX基因在竹子快速生长中的作用,本研究以毛竹(Phyllostachys edulis)为对象,通过同源比对从毛竹基因组中获得12条KNOX同源基因序列。序列分析表明,PeKNOXs的基因结构差异较大,内含子数目1～6个不等,且长度差异较大(30～3 801 bp),但都符合GT-AG剪切原则。PeKNOXs编码蛋白的长度为145～355 aa,分子量为92～130 k D。系统进化分析表明,毛竹PeKNOXs被聚类到2个较大的分支,分别属于Ⅰ、Ⅱ类KNOX亚家族,Ⅰ类中包含PeKNOX1-1～PeKNOX1-5,其中PeKNOX1-1与OSH71、PeKNOX1-2与OSH10、PeKNOX1-3与OSH15均聚类到一起,而PeKNOX1-4和PeKNOX1-5与OSH43聚类到较近的分支;Ⅱ类中包含PeKNOX2-1～PeKNOX2-7,其中PeKNOX2-1和PeKNOX2-2聚类到一个分支,与其它PeKNOXs距离较远,而且PeKNOXs与已知拟南芥的KNATs距离均较远。利用毛竹转录组数据构建热图进行分析,表明除了PeKNOX2-1外,其余PeKNOXs均检测到表达,但2个亚家族不同成员的表达均存在着一定的差异,如PeKNOX1-3的相对表达量最高,PeKNOX1-5的最低。实时定量PCR验证表明,PeKNOX1-3和PeKNOX1-5在不同组织中均有表达,其中在节中表达量最高,其次是茎,而在叶片和叶鞘中的表达量均较低,这与转录组数据相类似。由此表明,PeKNOXs可能在竹子生长发育中起重要调控作用,为进一步利用PeKNOXs开展竹子基因工程研究提供了参考。

In order to explore the role of KNOX gene in the rapid growth of bamboo, moso bamboo （Phyllostachys edtdis） was selected as the object in this study. Twelve homologous gene sequences of KNOX were obtained from the genome of moso bamboo by homologous alignment method. Sequences analysis showed that there were large differences in gene structure of PeKNOXs, the number of introns ranged from 1 to 6, and the length of the introns was different （30-3 801 bp）. However, the splice ofintron was consistent with the GT-AG principle. The length of protein encoded by PeKNOXs ranged from 145 to 354 aa, with the predicted molecular weight of 15.66-39.62 kD. Phylogenetic analysis indicated that PeKNOXs belonged to two subfamilies, which were subfamily I and subfamily Ⅱ of KNOX. Subfamily I included PeKNOXI-I-PeKNOX1-5, in which PeKNOXI-1 and 0SH71, PeKNOX1-2 and OSHIO, PeKNOX1-3 and OSH15 were clustered together, while PeKNOX1-4 and PeKNOX1-5 were closed to OSH43. Subfamily Ⅱ was composed of PeKNOX2-1-PeKNOX2-7, in which PeKNOX2-1 and PeKNOX2-2 were clustered together and they were far from other PeKNOXs. All PeKNOXs were far from the KNA Ts of A rabidopsis thaliana. Heatmap analysis was conducted using the transcriptome data of moso bamboo, and it suggested that all the expression of PeKNOXs were detected except PeKNOX2-1. However, there were some differences in the expression of members in each subfamily, such as PeKNOX1-3 had the relatively highest expression level and PeKNOX1-5 was the lowest. The result of real time PCR further confirmed that PeKNOX1-3 and PeKNOX1-5 had expression in all tissues, with the highest expression level in nodes, followed by that in stems, and lower in leaves and leaf sheaths, which was similar to those of transcriptome data. These result demonstrated that PeKNOXs might play a regulatory role in the growth and development of bamboo, which could provide a reference for further research on the genetic engineering of bamboo with PeKNOXs.