Systematic analysis of O -methyltransferase gene family and identification of potential members involved in the formation of O -methylated flavonoids in Citrus

Gene ◽  
2016 ◽  
Vol 575 (2) ◽  
pp. 458-472 ◽  
Author(s):  
Xiaogang Liu ◽  
Yan Luo ◽  
Hongkun Wu ◽  
Wanpeng Xi ◽  
Jie Yu ◽  
...  
Keyword(s):  
Gene Family ◽  
Systematic Analysis ◽  
Methyltransferase Gene

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

PeerJ ◽  
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.

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

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.

scholarly journals Identification and Expression Analysis of the NAC Gene Family in Coffea canephora

Agronomy ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 670 ◽  
Author(s):  
Dong ◽  
Jiang ◽  
Yang ◽  
Xiao ◽  
Bai ◽  
...  
Keyword(s):  
Cold Stress ◽  
Gene Family ◽  
Stress Responses ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Coffea Canephora ◽  
Coffee Bean ◽  
Systematic Analysis ◽  
Nac Gene Family ◽  
Basic Features

The NAC gene family is one of the largest families of transcriptional regulators in plants, and it plays important roles in the regulation of growth and development as well as in stress responses. Genome-wide analyses have been performed in diverse plant species, but there is still no systematic analysis of the NAC genes of Coffea canephora Pierre ex A. Froehner. In this study, we identified 63 NAC genes from the genome of C. canephora. The basic features and comparison analysis indicated that the NAC gene members increased via duplication events during the evolution of the plant. Phylogenetic analysis divided the NAC proteins from C. canephora, Arabidopsis and rice into 16 subgroups. Analysis of the expression patterns of CocNACs under cold stress and coffee bean development indicated that 38 CocNACs were differentially expressed under cold stress; six genes may play important roles in the process of cold acclimation, and four genes among 54 CocNACs showing a variety of expression patterns during different developmental stages of coffee beans may be positively related to the bean development. This study can expand our understanding of the functions of the CocNAC gene family in cold responses and bean development, thereby potentially intensifying the molecular breeding programs of Coffea spp. plants.

scholarly journals Identification and Expression Analysis of Sugar Transporter Gene Family in Aspergillus oryzae

2020 ◽  
Vol 2020 ◽  
pp. 1-15
Author(s):  
Gongbo Lv ◽  
Chunmiao Jiang ◽  
Tiantian Liang ◽  
Yayi Tu ◽  
Xiaojie Cheng ◽  
...  
Keyword(s):  
Gene Family ◽  
Aspergillus Oryzae ◽  
Expression Profiles ◽  
Protein Domain ◽  
Growth Stages ◽  
Sugar Transporter ◽  
Motif Analysis ◽  
Comprehensive Overview ◽  
Systematic Analysis ◽  
Functional Features

Sugar transporter (SUT) genes are associated with multiple physiological and biochemical processes in filamentous fungi, such as the response to various stresses. However, limited systematic analysis and functional information of SUT gene family have been available on Aspergillus oryzae (A. oryzae). To investigate the potential roles of SUTs in A. oryzae, we performed an integrative analysis of the SUT gene family in this study. Based on the conserved protein domain search, 127 putative SUT genes were identified in A. oryzae and further categorized into eight distinct subfamilies. The result of gene structure and conserved motif analysis illustrated functional similarities among the AoSUT proteins within the same subfamily. Additionally, expression profiles of the AoSUT genes at different growth stages elucidated that most of AoSUT genes have high expression levels at the stationary phase while low in the adaptive phase. Furthermore, expression profiles of AoSUT genes under salt stress showed that AoSUT genes may be closely linked to salt tolerance and involved in sophisticated transcriptional process. The protein-protein interaction network of AoSUT propounded some potentially interacting proteins. A comprehensive overview of the AoSUT gene family will offer new insights into the structural and functional features as well as facilitate further research on the roles of AoSUT genes in response to abiotic stresses.

Comparative genomics and evolutionary analyses of the O-methyltransferase gene family in Populus

Gene ◽  
2011 ◽  
Vol 479 (1-2) ◽  
pp. 37-46 ◽  
Author(s):  
Abdelali Barakat ◽  
Alex Choi ◽  
Norzawani Buang M. Yassin ◽  
Joseph S. Park ◽  
Zichao Sun ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Gene Family ◽  
Methyltransferase Gene

Identification of 11 pseudogenes in the DNA methyltransferase gene family in rodents and humans and implications for the functional loci

Genomics ◽  
2004 ◽  
Vol 84 (1) ◽  
pp. 193-204 ◽  
Author(s):  
Diane J Lees-Murdock ◽  
Gerard A McLoughlin ◽  
Jennifer R McDaid ◽  
Lisa M Quinn ◽  
Alan O'Doherty ◽  
...  
Keyword(s):  
Gene Family ◽  
Dna Methyltransferase ◽  
Methyltransferase Gene

scholarly journals Grape Small Auxin Upregulated RNA (SAUR) 041 Is a Candidate Regulator of Berry Size in Grape

2021 ◽  
Vol 22 (21) ◽  
pp. 11818
Author(s):  
Ming Li ◽  
Rui Chen ◽  
Hong Gu ◽  
Dawei Cheng ◽  
Xizhi Guo ◽  
...  
Keyword(s):  
Gene Family ◽  
Interaction Network ◽  
Early Response ◽  
Structural Features ◽  
Grape Berry ◽  
Amino Acid Residues ◽  
Systematic Analysis ◽  
Berry Size ◽  
Grape Quality ◽  
Genome Wide

Grape (Vitis vinifera) is an important horticultural crop that can be used to make juice and wine. However, the small size of the berry limits its yield. Cultivating larger berry varieties can be an effective way to solve this problem. As the largest family of auxin early response genes, SAUR (small auxin upregulated RNA) plays an important role in the growth and development of plants. Berry size is one of the important factors that determine grape quality. However, the SAUR gene family’s function in berry size of grape has not been studied systematically. We identified 60 SAUR members in the grape genome and divided them into 12 subfamilies based on phylogenetic analysis. Subsequently, we conducted a comprehensive and systematic analysis on the SAUR gene family by analyzing distribution of key amino acid residues in the domain, structural features, conserved motifs, and protein interaction network, and combined with the heterologous expression in Arabidopsis and tomato. Finally, the member related to grape berry size in SAUR gene family were screened. This genome-wide study provides a systematic analysis of grape SAUR gene family, further understanding the potential functions of candidate genes, and provides a new idea for grape breeding.

scholarly journals Genome-Wide Identification and Functional Analysis of the Basic Helix-Loop-Helix (bHLH) Transcription Family Reveals Candidate PtFBH Genes Involved in the Flowering Process of Populus trichocarpa

Forests ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1439
Author(s):  
Yang Ye ◽  
Haodong Xin ◽  
Xiting Gu ◽  
Jianwen Ma ◽  
Lingli Li
Keyword(s):  
Gene Family ◽  
Growth And Development ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Interaction Network ◽  
Systematic Analysis ◽  
Protein Motifs ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Flowering Process

As one of the largest TF families+ in plants, the basic helix-loop-helix (bHLH) family plays an important part in the growth and development of many plants. FLOWERING BHLH (FBH) encodes a bHLH-type transcriptional factor related to the flowering process. Poplar is a model woody plant as well as an important economic tree species with a small genome. However, the characteristics of the bHLHs and FBHs gene family in the newest version of Populustrichocarpa genome have not been analyzed yet. We identified 233 PtbHLHs and 10 PtFBHs in the newest version genome, and PtbHLHs were classified into 21 groups with FBH subfamily occupying one, supported by phylogenetic analysis, exon–intron patterns, and conserved protein motifs. These PtHLHs were distributed on 19 chromosomes unevenly and expressed in nucleus mainly. Gene duplication and synteny analysis have indicated that the PtbHLHs gene family has undergone strong purification selection during the evolution process. The cis-elements analysis has suggested that PtbHLHs may be related to the growth and development. Conserved residues of FBHs among Arabidopsis and poplar were also identified. Expression of 227 PtHLH genes (6 unmatched, 13 no expressed) showed diverse patterns in different tissues, implying their multiple functions. Protein–protein interaction network prediction and expression patterns in three states of the flowering process (Flowers-Dormant, Flowers-Expanding and Flowers-Expanded) suggested that some members of PtbHLH and PtFBH family may be involved in the flowering process. Our comprehensive and systematic analysis can provide some valuable clues and basic reference toward further investigations on physiological and molecular functions of PtbHLHs.

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