Small RNAs have emerged as one of the most important regulators of gene expression in both plants and animals. 24 June 2015

1. Small RNAs have emerged as one of the most important regulators of gene expression in both plants and animals. DCL
(Dicer-like), RDR (RNA-dependent RNA polymerase) and AGO (Argonaute) gene families are known to be essential for the biogenesis and
function of small RNAs. It is therefore imperative to investigate the role of protein/gene families involved in regulation of expression of small
RNAs in important legume crops like chickpea and pigeonpea. HMM (Hidden Markov Model), blastp searches followed by domain scanning
identified a total of 4 DCL, 5 RDR, 13 AGO proteins in chickpea and 5 DCL, 5 RDR, 13 AGO proteins in pigeonpea. Phylogenetic analysis
provided insights into the evolutionary aspects and resulted in clustering of these members into different groups based on their orthologs
from other species. Motif analysis, promoter prediction, functional annotation and gene structure analysis of these families in both chickpea
and pigeonpea were carried out. These results were in concurrence with the previous reports in arabidopsis, rice, maize and soybean
indicating the conservation of small RNA function and structure in plants. Our study unraveled 17 out of 22 and 20 out of 23 identified
proteins as potential targets for the microRNAs (miRNAs) in chickpea and pigeonpea, respectively. This study has not only identified the
genes involved in regulation of gene expression in these two crops, but also would result in identification of probable candidate genes
imparting resistance against different stresses.
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ICRISAT is a member of the CGIAR Consortium.
Genome wide identification of gene families involved in the
regulation of small RNA expression in chickpea and pigeonpea
Summary
Vanika Garg1,2, Gaurav Agarwal1, Aamir W Khan1, Dadakhalandar Doddamani1, Himabindu Kudapa1, Lekha Pazhamala1,
PB Kavi Kishor 2, Rajeev K Varshney1,3*
Department of Science and Technology
Government of India
Comparative analysis of orthologus
relationship of DCL, RDR and AGO genes
among chickpea, pigeonpea and soybean.
The syntenic chromosomes are
represented by similar colors. Red, blue
and green colored links correspond to
DCL, RDR and AGO proteins respectively.
Phylogenetic analysis of DCL, AGO and RDR genes
Identified and characterized three classes of proteins (DCL, RDR and AGO) involved
in biogenesis of small RNAs in chickpea and pigeonpea
A total of 20 orthologs of chickpea DCL, RDR and AGO were found in pigeonpea
Duplication studies identified 3, 6 paralogs in chickpea and pigeonpea respectively
DCLs were localized in nucleus and AGOs were found both in nucleus and cytoplasm
Interaction studies revealed a strong association between DCL, RDR and AGO
proteins
Identification and orthologous relationship
Chromosomal localization and duplication
Chickpea Pigeonpea Arabidopsis Rice
Gene Motif Gene Motif Gene Motif Gene Motif
CaAGO3b DDD/F CcAGO4a DDH/P AGO2 DDD/H OsAGO1 DDH/P
CaAGO4a DDH/A CcAGO4c DDH/A AGO3 DDD/H OsAGO2 DDD/H
CaAGO10c DDH/Q CcAGO9 DDH/S AGO4 DDH/S OsAGO3 DDD/H
CaAGO4c DDH/A CcAGO6 DDH/S AGO6 DDH/P OsAGO4a DDH/P
CaAGO6b DDH/P CcAGO3b DDD/N AGO9 DDH/R OsAGO4b DDH/P
CaAGO6a DDH/P CcAGO3a DDD/H OsAGO11 GDH/H
CaAGO3a DDD/H OsAGO13 -DH/H
OsAGO15 DDH/P
OsAGO16 DDH/P
OsAGO17 HDR/C
OsAGO18 DDH/S
Abundance of genes
Comparison of conserved motifs
Comparison among AGO proteins with missing catalytic
residue(s) in Piwi domains of chickpea, pigeonpea, arabidopsis
and rice
Distribution of DCL, RDR and AGO genes across chickpea
(C1) and pigeonpea (C2) chromosomes. Lines linking the
genes represent the duplicated genes. Tandem blocks are
highlighted in colored background.
A1 A2 A3
C1
C2
B
Unrooted phylogenetic tree of proteins involved in biogenesis of sRNA in chickpea, pigeonpea,
soybean and arabidopsis. MEGA 6.0 was used to construct the tree with NJ method and 5000 bootstrap
replicates. Phylogenetic relationship of dicer like proteins (A1), RNA dependent RNA polymerases (A2),
Argonautes (A3). B represents phylogenetic relationship, domain composition and intron–exon
structure of Argonautes. Green boxes represent exons and black lines represent introns.
1 International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
2 Department of Genetics, Osmania University, Hyderabad, India
3 School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley, Australia
* Address for correspondence: r.k.varshney@cgiar.org
Abstract