Advertisement
Genome-wide survey and characterization of AP2/ERF and HSP 90 gene family in five legume species
Upcoming SlideShare
Genome-wide survey and characterization of AP2/ERF and HSP 90 gene family in ...Genome-wide survey and characterization of AP2/ERF and HSP 90 gene family in ...
Loading in ... 3
1 of 1
Advertisement

More Related Content

Similar to Genome-wide survey and characterization of AP2/ERF and HSP 90 gene family in five legume species(20)

Advertisement

More from ICRISAT(20)

Advertisement

Genome-wide survey and characterization of AP2/ERF and HSP 90 gene family in five legume species

  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. Inclusive Market-Oriented Development (IMOD) – our approach to bringing prosperity in the drylands. ICRISAT is a member of the CGIAR Consortium. 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
Advertisement