Genome-wide analysis of the mitogen-activated protein kinase gene family in Solanum lycopersicum

Kong, Fuling; Wang, Jie; Cheng, Lin; Liu, Songyu; Wu, Jian; Peng, Zhen; Lü, Gang

doi:10.1016/j.gene.2012.01.048

Cited by 119 publications

(130 citation statements)

References 49 publications

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“…The phylogenetic relationships of MAPK genes have been systematically investigated in Arabidopsis [12], tomato [15], tobacco [16], wheat [17], rice [18] and soybean [19]. Here, to examine the evolutionary relationships of MAPK members in G. raimondii and other species, 20 MAPK genes in Arabidopsis, 38 in G. max, 17 in O. sative and 28 in G. raimondii were individually selected to construct an unrooted tree based on the alignment of the full MAPK amino acid sequences using the Maximum likelihood method via MEGA5.1 [33].…”

Section: Classification Structure and Variation Of Mapk Genes In Gosmentioning

confidence: 99%

“…Based on the genome scans of several plant genomes, MAPK family genes have been systematically investigated in Arabidopsis [12], tomato [15], tobacco [16], wheat [17], rice [18] and soybean [19]. In the current study, a total of 28 MAPKs from G. raimondii were identified.…”

Section: Characterization Of Mapks In G Raimondii and Evolution Of Mmentioning

confidence: 99%

“…Utilizing genome-wide scans, the MAPK gene family has been systematically investigated in Arabidopsis [12], tomato [15], tobacco [16], wheat [17], rice [18] and soybean [19]. In Arabidopsis, MPK3, MPK4 and MPK6 are involved in stress responses, and both MPK3 and MPK6 are dependent on salicylic acid signaling [7].…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification of mitogen-activated protein kinase gene family in Gossypium raimondii and the function of their corresponding orthologs in tetraploid cultivated cotton

Zhang

Wang

et al. 2014

BMC Plant Biol

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Section: Classification Structure and Variation Of Mapk Genes In Gosmentioning

confidence: 99%

Section: Characterization Of Mapks In G Raimondii and Evolution Of Mmentioning

confidence: 99%

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Genome-wide identification of mitogen-activated protein kinase gene family in Gossypium raimondii and the function of their corresponding orthologs in tetraploid cultivated cotton

Zhang

Wang

et al. 2014

BMC Plant Biol

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“…Nearly all of the MAPKs identified in Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), poplar (Populus trichocarpa), tomato (Solanum lycopersicum), and Brachypodium (Brachypodium distachyon) share a triplet T-x-Y domain that is crucial for phosphorylation between subdomains VII and VIII (MAPK Group 2002;Rohila and Yang 2007;Nicole et al 2006;Kong et al 2012;Chen et al 2012). The exceptions OsMPK2, BdMPK11, and SlMPK6 contain a Met-x-Tyr (M-x-Y) domain instead (Rohila and Yang 2007;Kong et al 2012;Chen et al 2012). Sequence comparison of the T-x-Y domains of MAPKs revealed two subtypes, TEY and TDY.…”

Section: Introductionmentioning

confidence: 99%

“…For example, a MAPK cascade that is composed of CTR1, MKK9, and MPK3/6 is involved in ethylene response and biosynthesis (Alonso et al 1999;Yoo et al 2008). In total,20,17,21,16,16,38,26, and 25 MAPK genes have been identified from the genomes of Arabidopsis, rice, poplar, tomato, Brachypodium, soybean, apple, and banana (MAPK Group 2002;Rohila and Yang 2007;Nicole et al 2006;Kong et al 2012;Chen et al 2012;Neupane et al 2013;Zhang et al 2013;Asif et al 2013), respectively. With the fully sequenced genome (Schnable et al 2009), a number of genes encoding MAPKs were identified in maize (Berberich et al 1999;Lalle et al 2005;Wang et al 2010;Wu et al 2011;Pan et al 2012;Zhang et al 2010).…”

Section: Introductionmentioning

confidence: 99%

Expression analysis of genes encoding mitogen-activated protein kinases in maize provides a key link between abiotic stress signaling and plant reproduction

Sun

Chen

Juan

et al. 2014

Funct Integr Genomics

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Mitogen-activated protein kinases (MAPKs) play important roles in stress responses and development in plants. Maize (Zea mays), an important cereal crop, is a model plant species for molecular studies. In the last decade, several MAPKs have been identified in maize; however, their functions have not been studied extensively. Genome-wide identification and expression analysis of maize MAPK genes could provide valuable information for understanding their functions. In this study, 20 non-redundant maize MAPK genes (ZmMPKs) were identified via a genome-wide survey. Phylogenetic analysis of MAPKs from maize, rice (Oryza sativa), Arabidopsis (Arabidopsis thaliana), poplar (Populus trichocarpa), and tomato (Solanum lycopersicum) classified them into four major classes. ZmMPKs in the same class had similar domains, motifs, and genomic structures. Gene duplication investigations suggested that segmental duplications made a large contribution to the expansion of ZmMPKs. A number of cis-acting elements related to plant development and response to stress and hormones were identified in the promoter regions of ZmMPKs. Furthermore, transcript profile analysis in eight tissues and organs at various developmental stages demonstrated that most ZmMPKs were preferentially expressed in reproductive tissues and organs. The transcript abundance of most ZmMPKs changed significantly under salt, drought, cold, or abscisic acid (ABA) treatments, implying that they might participate in abiotic stress and ABA signaling. These expression analyses indicated that ZmMPKs might serve as linkers between abiotic stress signaling and plant reproduction. Our data will deepen our understanding of the complexity of the maize MAPK gene family and provide new clues to investigate their functions.

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A genome‐wide analysis of the GRAS gene family in upland cotton and a functional study of the role of the GhGRAS55 gene in regulating early maturity in cotton

Xie

Yang

Zhou

et al. 2023

Biotechnology Journal

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The members of the GRAS gene family play important roles in regulating plant growth and development, but their functions in regulating early plant maturity traits are still unknown. In this study, we used a series of bioinformatics tools to identify GRAS gene family members and investigate the function of the gene family (GhGRAS55) using a genome‐wide database of upland cotton samples. A total of 58 members of the GRAS gene family were identified and screened, which were distributed on 21 chromosomes within the whole cotton genome. The results of the phylogenetic analysis showed that the genes of upland cotton, island cotton, African cotton, Raymond cotton and Arabidopsis were distributed in subfamilies I–VIII, although subfamily II did not contain any upland cotton or Arabidopsis GRAS family members. The structures and other characteristics of the genes in this family were clarified using bioinformatics technology. The transcriptomic sequencing results for early and late maturing cotton species showed that the expression of most GRAS family genes, such as GhGRAS10, GhGRAS5511 and GhGRAS55, was lower in early maturing species than late maturing species. We also found that cotton plants with GhGRAS55 genes that were silenced by virus‐induced gene silencing technology showed early bud emergence phenotypes, so it could be speculated that the GhGRAS55 gene has the function of regulating early maturity in cotton.This article is protected by copyright. All rights reserved

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Genome-wide analysis of the mitogen-activated protein kinase gene family in Solanum lycopersicum

Cited by 119 publications

References 49 publications

Genome-wide identification of mitogen-activated protein kinase gene family in Gossypium raimondii and the function of their corresponding orthologs in tetraploid cultivated cotton

Genome-wide identification of mitogen-activated protein kinase gene family in Gossypium raimondii and the function of their corresponding orthologs in tetraploid cultivated cotton

Expression analysis of genes encoding mitogen-activated protein kinases in maize provides a key link between abiotic stress signaling and plant reproduction

A genome‐wide analysis of the GRAS gene family in upland cotton and a functional study of the role of the GhGRAS55 gene in regulating early maturity in cotton

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