Waqas Muhammad, Azhar Muhammad Tehseen, Rana Iqrar Ahmad, Azeem Farrukh, Ali Muhammad Amjad, Nawaz Muhammad Amjad, Chung Gyuhwa, Atif Rana Muhammad
Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
Centre for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan.
Genes Genomics. 2019 Apr;41(4):467-481. doi: 10.1007/s13258-018-00780-9. Epub 2019 Jan 12.
WRKY proteins play a vital role in the regulation of several imperative plant metabolic processes and pathways, especially under biotic and abiotic stresses. Although WRKY genes have been characterized in various major crop plants, their identification and characterization in pulse legumes is still in its infancy. Chickpea (Cicer arietinum L.) is the most important pulse legume grown in arid and semi-arid tropics.
In silico identification and characterization of WRKY transcription factor-encoding genes in chickpea genome.
For this purpose, a systematic genome-wide analysis was carried out to identify the non-redundant WRKY transcription factors in the chickpea genome.
We have computationally identified 70 WRKY-encoding non-redundant genes which were randomly distributed on all the chickpea chromosomes except chromosome 8. The evolutionary phylogenetic analysis classified the WRKY proteins into three major groups (I, II and III) and seven sub-groups (IN, IC, IIa, IIb, IIc, IId and IIe). The gene structure analysis revealed the presence of 2-7 introns among the family members. Along with the presence of absolutely conserved signatory WRKY domain, 19 different domains were also found to be conserved in a group-specific manner. Insights of gene duplication analysis revealed the predominant role of segmental duplications for the expansion of WRKY genes in chickpea. Purifying selection seems to be operated during the evolution and expansion of paralogous WRKY genes. The transcriptome data-based in silico expression analysis revealed the differential expression of CarWRKY genes in root and shoot tissues under salt, drought, and cold stress conditions. Moreover, some of these genes showed identical expression pattern under these stresses, revealing the possibility of involvement of these genes in conserved abiotic stress-response pathways.
This genome-wide computational analysis will serve as a base to accelerate the functional characterization of WRKY TFs especially under biotic and abiotic stresses.
WRKY蛋白在调控多种重要的植物代谢过程和途径中发挥着至关重要的作用，尤其是在生物和非生物胁迫条件下。尽管WRKY基因已在各种主要农作物中得到鉴定，但在豆类作物中的鉴定和表征仍处于起步阶段。鹰嘴豆（Cicer arietinum L.）是干旱和半干旱热带地区种植的最重要的豆类作物。
对鹰嘴豆基因组中WRKY转录因子编码基因进行电子鉴定和表征。
为此，开展了系统的全基因组分析，以鉴定鹰嘴豆基因组中无冗余的WRKY转录因子。
我们通过计算鉴定出70个编码WRKY的无冗余基因，这些基因随机分布在除8号染色体外的所有鹰嘴豆染色体上。进化系统发育分析将WRKY蛋白分为三大类（I、II和III）和七个亚类（IN、IC、IIa、IIb、IIc、IId和IIe）。基因结构分析显示家族成员中存在2至7个内含子。除了存在绝对保守的标志性WRKY结构域外，还发现19个不同的结构域以组特异性方式保守存在。基因复制分析的结果表明，片段复制在鹰嘴豆WRKY基因的扩增中起主要作用。在同源WRKY基因的进化和扩增过程中似乎存在纯化选择。基于转录组数据的电子表达分析显示，CarWRKY基因在盐、干旱和冷胁迫条件下的根和茎组织中差异表达。此外，其中一些基因在这些胁迫下表现出相同的表达模式，表明这些基因可能参与保守的非生物胁迫响应途径。
这种全基因组计算分析将为加速WRKY转录因子的功能表征提供基础，尤其是在生物和非生物胁迫条件下。
