APETALA2/Ethylene Response Factor (AP2/ERF) and Heat Shock Protein 90 (HSP90) are important classes of transcription factor and chaperone proteins known to play a significant role under stress. Productivity and yield of legume crops are severely affected by environmental and pathogen stresses. 24 June 2015

1. Financial support
from CGIAR Generation Challenge Programme
(GCP) is gratefully acknowledged. This work was
undertaken as part of the CGIAR Research
Program on Grain Legumes
Acknowledgements• This study has resulted in identification and detailed characterization of two important classes of transcription factor
(AP2/ERF) and molecular chaperone (HSP 90) proteins in the five select legumes
•Segmental duplications outnumbered tandem duplication events with ERFs in most of the duplication events compared to DREBs
•HSP 90 proteins were clustered in two major groups based on their localization in the cell
•A total of 100, 80, 103 and 84 orthologs of chickpea AP2/ERF were identified in pigeonpea, medicago, common bean and lotus
• A total of 6 orthologs of chickpea HSP 90 were found in medicago, pigeonpea and common bean and 3 in lotus
APETALA2/Ethylene Response Factor (AP2/ERF) and Heat Shock Protein 90 (HSP90) are important classes of transcription factor and
chaperone proteins known to play a significant role under stress. Productivity and yield of legume crops are severely affected by environmental and
pathogen stresses. Genome sequences of chickpea, pigeonpea, common bean along with model legumes like medicago and lotus has aided in genome-
wide identification of stress responsive AP2/ERF and HSP90 genes. HMM (Hidden Markov Model), blastp searches followed by domain scanning
identified a total of 147 AP2/ERF genes in chickpea, 176 in pigeonpea, 179 in common bean, 131 in medicago and 140 in lotus. Sequences with one and
two AP2 domains were classified as ERFs and AP2s respectively while sequences with AP2 and B3 domain were identified as RAVs. ERFs were further
sub-classified into DREBs. Number of ERFs and DREBs ranged from 67 to 98 and 41 to 55 respectively in these crops. Two soloists were identified each
in chickpea, pigeonpea and lotus; common bean with one and none in medicago. However, a very less number of HSP90 genes were identified in
chickpea (5), pigeonpea (7), common bean (6), medicago (5) and lotus (5). Gene, protein structures, phylogenetic analyses, functional annotation and
interaction networks provided basic insights in understanding the function of AP2/ERF and HSP90 genes. Expression studies using RNA-seq and qRT-
PCR in response to heat and pathogen stress were also conducted in chickpea and pigeonpea respectively in search of probable candidate genes.
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Abstract
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
*Address for correspondence: r.k.varshney@cgiar.org
Chromosomal distribution and ortholog identification
Summary
A1 to E1: Phylogenetic relationships of AP2/ERF genes in the five legumes
(chickpea, pigeonpea, common bean, medicago and lotus). In the unrooted trees,
the ERFs are represented in green, DREBs in red, AP2s in blue; RAVs in pink and
soloist in teak color. A2: Phylogenetic relationship of HSP 90 genes. A3:
Expression profile of 22 AP2/ERF genes in vegetative tissues, root, leaf and
flower (before flowering) is compared with reproductive flower tissue and root,
leaf (after flowering) tissue of chickpea.
A3
Gaurav Agarwal, Vanika Garg, Himabindu Kudapa, Pazhamala Lekha, Dadakhalandar Doddamani,
Aamir W Khan, Rajeev K Varshney *
Phylogenetic classification and expression analysis of AP2/ERF and HSP 90 genes
A2
Genome-wide survey and characterization of AP2/ERF and
HSP 90 gene family in five legume species
A4: Comparative analysis of orthologus relationship of
AP2/ERF and HSP 90 genes among the five legumes.
Chickpea orthologs in four legumes, pigeonpea, lotus (top
left and right), medicago and common bean (bottom left
and right). HSP 90 orthologs among the five legumes are
represented in the center.
A4: Expression profiles of 81 AP2/ERF genes based on log (base 2) of FPKM values.
Heat map (right) showing hierarchical clustering of AP2/ERF genes in pigeonpea
genotypes resistant and susceptible to Fusarium wilt (FW) and sterility mosaic disease
(SMD).
A3
A1: Representation of number of AP2, ERF, DREB, RAV,
soloist and HSP 90 genes in chickpea, pigeonpea,
medicago, common bean and lotus.
A2
A3
A4
A1
A2
A4
A1-A3: Distribution of 179, 140, 140 AP2/ERF and 6, 5, 5 HSP 90 genes in phaseolus,
lotus and pigeonpea across chromosomes. Tandemly duplicated genes are highlighted
in color. Lines linking the genes represent segmentally duplicated genes.
Chromosomal distribution and expression analysis
A1 B1 C1
D1
E1
A1
A3
A2-A3: Distribution of AP2/ERF and HSP 90 genes in
chickpea and medicago. 19/147, 9/131 AP2/ERF and
2/5, 1/5 HSP 90 on the scaffold could not be anchored
onto any specific chromosome. Tandemly duplicated
genes are highlighted in color. Lines linking the
genes represent segmentally duplicated genes.
A3