Comparative Genomics of The Shikimate Pathway in Arabidopsis, Populus Trichocarpa and Oryza Sativa: Shikimate Pathway Gene Family Structure and Identification of Candidates for Missing Links in Phenylalanine Biosynthesis

2006 ◽  
pp. 85-113 ◽  
Author(s):  
Björn Hamberger ◽  
Jürgen Ehlting ◽  
Brad Barbazuk ◽  
Carl J. Douglas
Keyword(s):  
Oryza Sativa ◽  
Comparative Genomics ◽  
Family Structure ◽  
Gene Family ◽  
Populus Trichocarpa ◽  
Shikimate Pathway ◽  
Pathway Gene

scholarly journals Genome-Wide Analysis of LIM Gene Family in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa

DNA Research ◽  
2007 ◽  
Vol 14 (3) ◽  
pp. 103-116 ◽  
Author(s):  
Dominique Arnaud ◽  
Annabelle Déjardin ◽  
Jean-Charles Leplé ◽  
Marie-Claude Lesage-Descauses ◽  
Gilles Pilate
Keyword(s):  
Arabidopsis Thaliana ◽  
Oryza Sativa ◽  
Gene Family ◽  
Populus Trichocarpa ◽  
Genome Wide Analysis ◽  
Genome Wide

Molecular Evolution of the CPP-like Gene Family in Plants: Insights from Comparative Genomics of Arabidopsis and Rice

2008 ◽  
Vol 67 (3) ◽  
pp. 266-277 ◽  
Author(s):  
Zefeng Yang ◽  
Shiliang Gu ◽  
Xuefeng Wang ◽  
Wenjuan Li ◽  
Zaixiang Tang ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Comparative Genomics ◽  
Gene Family

scholarly journals Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhixuan Du ◽  
Qitao Su ◽  
Zheng Wu ◽  
Zhou Huang ◽  
Jianzhong Bao ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Tandem Repeats ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Genome Wide ◽  
Comprehensive Information ◽  
Family Gene

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.

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

BMB Reports ◽  
2006 ◽  
Vol 39 (5) ◽  
pp. 595-606 ◽  
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

Characterization of the rice (Oryza sativa) actin gene family

1990 ◽  
Vol 15 (2) ◽  
pp. 257-268 ◽  
Author(s):  
David McElroy ◽  
Madge Rothenberg ◽  
Kimberly S. Reece ◽  
Ray Wu
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Actin Gene

In silico study of the CESA and CSL gene family in Arabidopsis thaliana and Oryza sativa: Focus on post-translation modifications

Plant Gene ◽  
2019 ◽  
Vol 19 ◽  
pp. 100189 ◽  
Author(s):  
Parviz Heidari ◽  
Mostafa Ahmadizadeh ◽  
Fatemeh Izanlo ◽  
Thomas Nussbaumer
Keyword(s):  
Arabidopsis Thaliana ◽  
Oryza Sativa ◽  
Gene Family ◽  
In Silico ◽  
In Silico Study

scholarly journals Comprehensive Analysis of the TIFY Gene Family and Its Expression Profiles under Phytohormone Treatment and Abiotic Stresses in Roots of Populus trichocarpa

Forests ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 315
Author(s):  
Hanzeng Wang ◽  
Xue Leng ◽  
Xuemei Xu ◽  
Chenghao Li
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Interaction Network ◽  
Pcr Analysis ◽  
Phylogenetic Tree Analysis ◽  
Element Analysis ◽  
Cis Element

The TIFY gene family is specific to land plants, exerting immense influence on plant growth and development as well as responses to biotic and abiotic stresses. Here, we identify 25 TIFY genes in the poplar (Populus trichocarpa) genome. Phylogenetic tree analysis revealed these PtrTIFY genes were divided into four subfamilies within two groups. Promoter cis-element analysis indicated most PtrTIFY genes possess stress- and phytohormone-related cis-elements. Quantitative real-time reverse transcription polymerase chain reaction (qRT–PCR) analysis showed that PtrTIFY genes displayed different expression patterns in roots under abscisic acid, methyl jasmonate, and salicylic acid treatments, and drought, heat, and cold stresses. The protein interaction network indicated that members of the PtrTIFY family may interact with COI1, MYC2/3, and NINJA. Our results provide important information and new insights into the evolution and functions of TIFY genes in P. trichocarpa.

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