Studies on Genome wide analysis of AP2 gene family sequences of Vigna radiata and its comparative Phylogenetic relationship with other crop plants
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Date
2017-09
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Abstract
The genus Vigna is a potentially valuable new model system for studying plant adaptation to
stressful environments. Recently, wild relatives of crop species have received a great deal of
attention in research communities as potential genetic resources for crop improvement through
harnessing the desirable traits of wild species and by adopting new breeding concepts such as
‘neo-domestication’ and ‘reverse breeding’, Transcription factors belonging to the
APETALA2/Ethylene Responsive Factor (AP2/ERF) family are conservatively widespread in
the plant kingdom. These regulatory proteins are involved in the control of primary and
secondary metabolism, growth and developmental programs, as well as responses to
environmental stimuli. Due to their plasticity and to the specificity of individual members of this
family, AP2/ERF transcription factors represent valuable targets for genetic engineering and
breeding of crops. The AP2/ERF super family is defined by the AP2/ERF domain, which
consists of about 60 to 70 amino acids and is involved in DNA binding. The AP2 family proteins
contain two repeated AP2/ERF domains, the ERF family proteins contain a single AP2/ERF
domain, and the RAV family proteins contain a B3 domain, which is a DNA-binding domain
conserved in other plant-specific transcription factors, in addition to the single AP2/ERF domain.
Genes in the AP2 family have been shown to participate in the regulation of developmental
processes, e.g. flower development, spikelet meristem determinacy, leaf epidermal cell identity,
and embryo development. Considering their significance in plant growth and development,
whole genome search was carried out in the present study to identify AP2 genes in many plants
like Arabidopsis thaliana (30), Soyabean (99), Common bean (31), Chickpea (35), Red gram
(25). There are 21 AP2 family members of genes and proteins belonging to Vigna radiata were
retrieved from plant TFDB database. It was observed that protein length varied from 191 to 664
amino acids where as gene length varied from 573 to 1992 base pairs. Three domain viz.
smart00380, cd00018, pfam00847 were identified in AP2 protein of Vigna radiata. These
domains are DNA-binding domain and act as transcription regulators in plants. Three motifs viz.
‘GNKYLYLGTYATQEEAAAAYDMAAIEYRGANAVTNFDVSRY’ (Red Color),
‘KEEYIGSLRRKSSGFSRGVSKYRGVAR’ (Blue Color) and
‘QSKKGRQGAYDDEEAAARAYDLAALKYWGQDTILNFPLTNY’ (Green Color) were
identified in all AP2 proteins of Vigna radiata.. The phylogenetic analysis of 21 AP2 genes of
Vigna radiata were clustered into two subgroups and vradi04g02560.1 was found to be distantly
related to vradi05g12030.1 Maximum likelihood phylogenetic analysis had been carried out to
understand AP2 proteins divergence pattern and here 21 AP2 proteins were clustered into two
different groups. The AP2 proteins viz. vardi03g01560.1 and vradi08g06840.1 were diverged
from the rest of 19 proteins.
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