Computational identification and systematic analysis of the ACR gene family in Oryza sativa

AbstractMultidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice. In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. The rice MATE family was divided into four subfamilies based on the phylogenetic tree. Tandem repeats and fragment replication contribute to the expansion of the rice MATE gene family. Gene structure and cis-regulatory elements reveal the potential functions of MATE genes. Analysis of gene expression showed that most of MATE genes were constitutively expressed and the expression patterns of genes in different tissues were analyzed using RNA-seq. Furthermore, qRT-PCR-based analysis showed differential expression patterns in response to salt and drought stress. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

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A comprehensive analysis of NAC gene family in Oryza sativa japonica: a structural and functional genomics approach

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2021.2014968 ◽

2021 ◽

pp. 1-15

Author(s):

Sujay Ray ◽

Abishek Basnet ◽

Shreya Bhattacharya ◽

Arundhati Banerjee ◽

Koustav Biswas

Keyword(s):

Oryza Sativa ◽

Functional Genomics ◽

Gene Family ◽

Comprehensive Analysis ◽

Nac Gene Family

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Molecular Analyses of the Metallothionein Gene Family in Rice (Oryza sativa L.)

BMB Reports ◽

10.5483/bmbrep.2006.39.5.595 ◽

2006 ◽

Vol 39 (5) ◽

pp. 595-606 ◽

Cited By ~ 39

Author(s):

Gongke Zhou ◽

Yufeng Xu ◽

Ji Li ◽

Lingyan Yang ◽

Jin-Yuan Liu

Keyword(s):

Oryza Sativa ◽

Gene Family ◽

Oryza Sativa L ◽

Molecular Analyses ◽

Metallothionein Gene

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Characterization of the rice (Oryza sativa) actin gene family

Plant Molecular Biology ◽

10.1007/bf00036912 ◽

1990 ◽

Vol 15 (2) ◽

pp. 257-268 ◽

Cited By ~ 62

Author(s):

David McElroy ◽

Madge Rothenberg ◽

Kimberly S. Reece ◽

Ray Wu

Keyword(s):

Oryza Sativa ◽

Gene Family ◽

Actin Gene

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Genome-wide identification, evolution, and expression analysis of the NPR1-like gene family in pears

PeerJ ◽

10.7717/peerj.12617 ◽

2021 ◽

Vol 9 ◽

pp. e12617

Author(s):

Yarui Wei ◽

Shuliang Zhao ◽

Na Liu ◽

Yuxing Zhang

Keyword(s):

Gene Family ◽

Stress Responses ◽

Systemic Acquired Resistance ◽

Acquired Resistance ◽

Signal Transduction Pathway ◽

Promoter Regions ◽

Systematic Analysis ◽

Genome Wide ◽

Pathogenesis Related ◽

Genome Level

The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) plays a master regulatory role in the salicylic acid (SA) signal transduction pathway and plant systemic acquired resistance (SAR). Members of the NPR1-like gene family have been reported to the associated with biotic/abiotic stress in many plants, however the genome-wide characterization of NPR1-like genes has not been carried out in Chinese pear (Pyrus bretschneideri Reld). In this study, a systematic analysis was conducted on the characteristics of the NPR1-like genes in P. bretschneideri Reld at the whole-genome level. A total nine NPR1-like genes were detected which eight genes were located on six chromosomes and one gene was mapped to scaffold. Based on the phylogenetic analysis, the nine PbrNPR1-like proteins were divided into three clades (Clades I–III) had similar gene structure, domain and conserved motifs. We sorted the cis-acting elements into three clades, including plant growth and development, stress responses, and hormone responses in the promoter regions of PbrNPR1-like genes. The result of qPCR analysis showed that expression diversity of PbrNPR1-like genes in various tissues. All the genes were up-regulated after SA treatment in leaves except for Pbrgene8896. PbrNPR1-like genes showed circadian rhythm and significantly different expression levels after inoculation with Alternaria alternata. These findings provide a solid insight for understanding the functions and evolution of PbrNPR1-like genes in Chinese pear.

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Systematic Analysis and Biochemical Characterization of the Caffeoyl Shikimate Esterase Gene Family in Poplar

International Journal of Molecular Sciences ◽

10.3390/ijms222413366 ◽

2021 ◽

Vol 22 (24) ◽

pp. 13366

Author(s):

Xuechun Wang ◽

Nan Chao ◽

Aijing Zhang ◽

Jiaqi Kang ◽

Xiangning Jiang ◽

...

Keyword(s):

Gene Family ◽

Biochemical Characterization ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Lignin Biosynthesis ◽

Phenylpropanoid Pathway ◽

Biochemical Properties ◽

Phylogenetic Groups ◽

Systematic Analysis ◽

A Genome

Caffeoyl shikimate esterase (CSE) hydrolyzes caffeoyl shikimate into caffeate and shikimate in the phenylpropanoid pathway. In this study, we performed a systematic analysis of the CSE gene family and investigated the possible roles of CSE and CSE-like genes in Populus. We conducted a genome-wide analysis of the CSE gene family, including functional and phylogenetic analyses of CSE and CSE-like genes, using the poplar (Populus trichocarpa) genome. Eighteen CSE and CSE-like genes were identified in the Populus genome, and five phylogenetic groups were identified from phylogenetic analysis. CSEs in Group Ia, which were proposed as bona fide CSEs, have probably been lost in most monocots except Oryza sativa. Primary functional classification showed that PoptrCSE1 and PoptrCSE2 had putative function in lignin biosynthesis. In addition, PoptrCSE2, along with PoptrCSE12, might also respond to stress with a function in cell wall biosynthesis. Enzymatic assay of PoptoCSE1 (Populus tomentosa), -2 and -12 showed that PoptoCSE1 and -2 maintained CSE activity. PoptoCSE1 and 2 had similar biochemical properties, tissue expression patterns and subcellular localization. Most of the PoptrCSE-like genes are homologs of AtMAGL (monoacylglycerol lipase) genes in Arabidopsis and may function as MAG lipase in poplar. Our study provides a systematic understanding of this novel gene family and suggests the function of CSE in monolignol biosynthesis in Populus.

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