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Genome-wide analysis of the CCCH zinc finger family identifies tissue specific and stress responsive candidates in chickpea (Cicer arietinum L.)

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Title Genome-wide analysis of the CCCH zinc finger family identifies tissue specific and stress responsive candidates in chickpea (Cicer arietinum L.)
 
Creator Pradhan, Seema
Kant, Chandra
Verma, Subodh
Bhatia, Sabhyata
 
Description Accepted date: June 15, 2017
The CCCH zinc finger is a group of proteins characterised by a typical motif consisting of three cysteine residues and one histidine residue. These proteins have been reported to play important roles in regulation of plant growth, developmental processes and environmental responses. In the present study, genome wide analysis of the CCCH zinc finger gene family was carried out in the available chickpea genome. Various bioinformatics tools were employed to predict 58 CCCH zinc finger genes in chickpea (designated CarC3H1-58), which were analysed for their physio-chemical properties. Phylogenetic analysis classified the proteins into 12 groups in which members of a particular group had similar structural organization. Further, the numbers as well as the types of CCCH motifs present in the CarC3H proteins were compared with those from Arabidopsis and Medicago truncatula. Synteny analysis revealed valuable information regarding the evolution of this gene family. Tandem and segmental duplication events were identified and their Ka/Ks values revealed that the CarC3H gene family in chickpea had undergone purifying selection. Digital, as well as real time qRT-PCR expression analysis was performed which helped in identification of several CarC3H members that expressed preferentially in specific chickpea tissues as well as during abiotic stresses (desiccation, cold, salinity). Moreover, molecular characterization of an important member CarC3H45 was carried out. This study provides comprehensive genomic information about the important CCCH zinc finger gene family in chickpea. The identified tissue specific and abiotic stress specific CCCH genes could be potential candidates for further characterization to delineate their functional roles in development and stress.
The study was funded by grant (BT/AGR/CG-Phase II/01/2014) from the Department of Biotechnology (DBT), Ministry of Science and Technology, India (http://www.dbtindia.nic.in). SP and SV acknowledge the award of research fellowship from the Department of Biotechnology (DBT) and CK acknowledges the award of research fellowship from Council for Scientific and Industrial Research (CSIR). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
 
Date 2017-07-17T05:40:29Z
2017-07-17T05:40:29Z
2017
 
Type Article
 
Identifier PLoS One, 12(7): e0180469
1932-6203
http://59.163.192.83:8080/jspui/handle/123456789/769
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0180469
https://doi.org/10.1371/journal.pone.0180469
 
Language en_US
 
Publisher PLOS