Genome-Wide Identification and Expression Analysis of the Mitogen-Activated Protein Kinase Gene Family in Cassava.

Yan Yan,Weiwei Tie,Ming Peng,Zehong Ding,Yunxie Wei,Wei Hu,Hongliang Zhao,Lianzhe Wang,Changying Zeng,Xupo Ding

doi:10.3389/fpls.2016.01294

Abstract

Mitogen-activated protein kinases (MAPKs) play central roles in plant developmental processes, hormone signaling transduction, and responses to abiotic stress. However, no data are currently available about the MAPK family in cassava, an important tropical crop. Herein, 21 MeMAPK genes were identified from cassava. Phylogenetic analysis indicated that MeMAPKs could be classified into four subfamilies. Gene structure analysis demonstrated that the number of introns in MeMAPK genes ranged from 1 to 10, suggesting large variation among cassava MAPK genes. Conserved motif analysis indicated that all MeMAPKs had typical protein kinase domains. Transcriptomic analysis suggested that MeMAPK genes showed differential expression patterns in distinct tissues and in response to drought stress between wild subspecies and cultivated varieties. Interaction networks and co-expression analyses revealed that crucial pathways controlled by MeMAPK networks may be involved in the differential response to drought stress in different accessions of cassava. Expression of nine selected MAPK genes showed that these genes could comprehensively respond to osmotic, salt, cold, oxidative stressors, and abscisic acid (ABA) signaling. These findings yield new insights into the transcriptional control of MAPK gene expression, provide an improved understanding of abiotic stress responses and signaling transduction in cassava, and lead to potential applications in the genetic improvement of cassava cultivars.

Highlights

Mitogen-activated protein kinases (MAPKs), a specific class of serine/threonine protein kinases, are conserved throughout eukaryotes, including animals, yeasts, and plants (Hamel et al, 2006)
In order to evaluate the evolutionary relationships among the MeMAPK proteins, an unrooted Neighbor-Joining phylogenetic tree was created with amino acid sequences of 21 MeMAPKs from cassava, 20 AtMPKs from Arabidopsis, OsMPKs from rice, SlMAPKs from tomato, 26 MdMPKs from apple, and 14 CsMPKs from cucumber (Table S3)
We identified 21 MAPK genes from the cassava genome and established their classification and phylogeny using phylogenetic, gene structure, and conserved protein motif analyses

Summary

Introduction

Mitogen-activated protein kinases (MAPKs), a specific class of serine/threonine protein kinases, are conserved throughout eukaryotes, including animals, yeasts, and plants (Hamel et al, 2006). There are multiple MAPK cascades existing in eukaryotic cells, which play a vital role in regulating gene expression, mitosis, metabolism, motility, survival, apoptosis, and differentiation (Marie and Roux, 2011). MAPK cascades are evolutionarily conserved signaling modules and are composed of at least three protein kinases: MAPKK kinases (MAPKKKs), MAPK kinases (MAPKKs) and MAPK Gene Family in Cassava. Activated MAPK cascade (MAPKKK → MAPKK → MAPK) kinases can regulate transcription factors and other components related to the MAPK pathway by phosphorylation. Based on the phylogenetic analysis of amino acid sequences and phosphorylation motifs, MAPKs in plants can be divided into four subfamilies (A, B, C, and D). Members of the A, B, and C subfamily have a Thr-Glu-Tyr (TEY) phosphorylation motif in their active sites, while members in the D subfamily have a Thr-Asp-Tyr (TDY) motif in their active sites and a long C terminal sequence (Ichimura et al, 2002)

Methods

Results

Conclusion