Evolutionary Analysis of Cellulose Gene Family in Grasses

Carotenoid cleavage dioxygenases (CCDs) selectively catalyze carotenoids, forming smaller apocarotenoids that are essential for the synthesis of apocarotenoid flavor, aroma volatiles, and phytohormone ABA/SLs, as well as responses to abiotic stresses. Here, 19, 11, and 10 CCD genes were identified in Nicotiana tabacum, Nicotiana tomentosiformis, and Nicotiana sylvestris, respectively. For this family, we systematically analyzed phylogeny, gene structure, conserved motifs, gene duplications, cis-elements, subcellular and chromosomal localization, miRNA-target sites, expression patterns with different treatments, and molecular evolution. CCD genes were classified into two subfamilies and nine groups. Gene structures, motifs, and tertiary structures showed similarities within the same groups. Subcellular localization analysis predicted that CCD family genes are cytoplasmic and plastid-localized, which was confirmed experimentally. Evolutionary analysis showed that purifying selection dominated the evolution of these genes. Meanwhile, seven positive sites were identified on the ancestor branch of the tobacco CCD subfamily. Cis-regulatory elements of the CCD promoters were mainly involved in light-responsiveness, hormone treatment, and physiological stress. Different CCD family genes were predominantly expressed separately in roots, flowers, seeds, and leaves and exhibited divergent expression patterns with different hormones (ABA, MeJA, IAA, SA) and abiotic (drought, cold, heat) stresses. This study provides a comprehensive overview of the NtCCD gene family and a foundation for future functional characterization of individual genes.

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SQUAMOSA Promoter Binding Protein-Like (SPL) Gene Family: TRANSCRIPTOME-Wide Identification, Phylogenetic Relationship, Expression Patterns and Network Interaction Analysis in Panax ginseng C. A. Meyer

Plants ◽

10.3390/plants9030354 ◽

2020 ◽

Vol 9 (3) ◽

pp. 354

Author(s):

Shaokun Li ◽

Li Li ◽

Yang Jiang ◽

Jun Wu ◽

Honghua Sun ◽

...

Keyword(s):

Gene Family ◽

Panax Ginseng ◽

Interaction Analysis ◽

Binding Protein ◽

Expression Patterns ◽

Evolutionary Analysis ◽

Main Function ◽

Squamosa Promoter Binding Protein ◽

Expression Characteristics ◽

Spl Gene

SPL (SQUAMOSA promoter binding protein-like) gene family is specific transcription factor in the plant that have an important function for plant growth and development. Although the SPL gene family has been widely studied and reported in many various plant species from gymnosperm to angiosperm, there are no systematic studies and reports about the SPL gene family in Panax ginseng C. A. Meyer. In this study, we conducted transcriptome-wide identification, evolutionary analysis, structure analysis, and expression characteristics analysis of SPL gene family in Panax ginseng by bioinformatics. We annotated the PgSPL gene family and found that they might involve in multiple functions including encoding structural proteins, but the main function were still focused on the binding function. The result showed that 106 PgSPL transcripts were classified into two clades - A and B, both of which respectively consisted of three groups. Besides, we profiled PgSPL transcripts’ genotypic, temporal, and spatial expression characteristics. Furthermore, we calculated the correlation of PgSPL transcripts in the 14 tissues of a 4 years old ginseng and 42 farmers’ cultivars farmers’ cultivars of 4 years old ginsengs’ roots with both results showing that SPL transcripts formed a single network, which indicated that PgSPLs inter-coordinated when performing their functions. What’s more, we found that most PgSPL transcripts tended to express in older ginseng instead of younger ginseng, which was not only reflected in the expression of more types of SPL transcripts in older ginseng, but also in the higher expression of SPL transcripts in older ginseng. Additionally, we found that four PgSPL transcripts were only massively expressed in roots. According to PgSPL transcripts’ expression characteristics, we found that PgSPL23-35 and PgSPL24-09 were most proper two transcripts to further study as ginseng age’s molecular marker. These results provide the basis for further elucidation of the PgSPL transcripts’ biological function in ginseng and ginseng genetics improvement and gene breeding in the future.

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Combining Expression and Comparative Evolutionary Analysis. The COBRA Gene Family

PLANT PHYSIOLOGY ◽

10.1104/pp.106.087262 ◽

2006 ◽

Vol 143 (1) ◽

pp. 172-187 ◽

Cited By ~ 74

Author(s):

Siobhan M. Brady ◽

Shuang Song ◽

Kanwarpal S. Dhugga ◽

J. Antoni Rafalski ◽

Philip N. Benfey

Keyword(s):

Gene Family ◽

Evolutionary Analysis

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Genome-Wide Identification, Evolutionary Analysis, and Stress Responses of the GRAS Gene Family in Castor Beans

International Journal of Molecular Sciences ◽

10.3390/ijms17071004 ◽

2016 ◽

Vol 17 (7) ◽

pp. 1004 ◽

Cited By ~ 24

Author(s):

Wei Xu ◽

Zexi Chen ◽

Naeem Ahmed ◽

Bing Han ◽

Qinghua Cui ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Evolutionary Analysis ◽

Genome Wide ◽

Gras Gene

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Genome-wide survey and expression analysis of the SLAC/SLAH gene family in pear (Pyrus bretschneideri) and other members of the Rosaceae

10.1101/288308 ◽

2018 ◽

Author(s):

Guodong Chen ◽

Xiaolong Li ◽

Xin qiao ◽

Jiaming Li ◽

Li Wang ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Prunus Persica ◽

Higher Plants ◽

Chloride Transport ◽

Structural Characteristics ◽

Evolutionary Analysis ◽

Anion Channels ◽

Genome Wide ◽

A Genome

AbstractS-type anion channels (SLAC/SLAHs), which play important roles in plant anion (such as nitrate and chloride) transport, growth and development, abiotic stress responses and hormone signaling. However, there is far less information about this family in Rosaceae species. We performed a genome-wide analysis and identified SLAC/SLAH gene family members in pear (Pyrus bretschneideri) and four other species of Rosaceae (Malus domestica, Prunus persica, Fragaria vesca and Prunus mume). A total of 21 SLAC/SLAH genes were identified from the five Rosaceae species. Based on the structural characteristics and a phylogenetic analysis of these genes, the SLAC/SLAH gene family could be classified into three main groups (I, II and III). The evolutionary analysis showed that the SLAC/SLAH gene family was comparatively conserved during the evolution of Rosaceae species. Transcriptome data demonstrated that PbrSLAC/SLAH genes were detected in all parts of the pear. However, PbrSLAC1 showed a higher expression level in leaf, while PbrSLAH2/3 was mainly expressed in roots. In addition, PbrSLAC/SLAH genes were only located on the plasma membrane in transient expression experiments in Arabidopsis protoplasts cells. These results provide valuable information that increases our understanding of the evolution, expression and functions of the SLAC/SLAH gene family in higher plants.

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Systematic Identification and Analysis of NAC Gene Family in Moso Bamboo (Phyllostachys edulis)

10.21203/rs.3.rs-18155/v1 ◽

2020 ◽

Author(s):

Yameng Gao ◽

Huanlong Liu ◽

Lin Wu ◽

Rui Xiong ◽

Yanan Shi ◽

...

Keyword(s):

Gene Family ◽

Brachypodium Distachyon ◽

Moso Bamboo ◽

Evolutionary Analysis ◽

Biotic And Abiotic Stress ◽

Phyllostachys Edulis ◽

Genome Data ◽

Resistant Varieties ◽

Nac Gene Family ◽

Systematic Identification

Abstract Background: NAC (NAM/ATAF1/2/CUC2) gene family is a large plant-specific transcription factor family, which is implicated in many functions, such as morphogenesis, the thickness formation of secondary cell walls as well as biotic and abiotic stress and more. In moso bamboo ( Phyllostachys edulis ), 94 PeNACs have been identified and three members are predicted to relate to the secondary cell wall. However, there were few studies on moso bamboo NAC genes under stress.Results: In this study, we re-identified 165 PheNACs with the latest moso bamboo genome data and divided them into 12 subfamilies using NAM domains. Gene structure and motif distribution manifested the NAC gene family was fairly conserved. Evolutionary analysis showed that the segmental duplication played a significant role in the expansion of NAC genes and the relationship between moso bamboo and Brachypodium distachyon was closest than beween moso bamboo and other four species ( Arabidopsis thaliana, Oryza sativa , Sorghum bicolor and Zea mays ). Based on the promoter analysis of the 27 NAC members in A subfamily, quantitative real-time PCR exhibited these genes reacted differently under drought, high salt, abscisic acid and methyl jasmonate treatments. Finally, we selected out four potential stress-associated genes (PheNAC001, -056, -080 and -100) and found they all localized in the tobacco nucleus and had transcriptional activity in yeast.Conclusions: These preliminary results provide valuable information for mining potential resistance NAC genes and lay theoretical basis for breeding new stress-resistant varieties in moso bamboo.

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Peer Review #2 of "Comparative and evolutionary analysis of the reptilian hedgehog gene family (Shh, Dhh, and Ihh) (v0.1)"

10.7287/peerj.7613v0.1/reviews/2 ◽

2019 ◽

Keyword(s):

Gene Family ◽

Peer Review ◽

Evolutionary Analysis

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Genome-wide identification and expression analysis of the 14-3-3 gene family in soybean (Glycine max)

PeerJ ◽

10.7717/peerj.7950 ◽

2019 ◽

Vol 7 ◽

pp. e7950 ◽

Cited By ~ 2

Author(s):

Yongbin Wang ◽

Lei Ling ◽

Zhenfeng Jiang ◽

Weiwei Tan ◽

Zhaojun Liu ◽

...

Keyword(s):

Plant Growth ◽

Gene Family ◽

Stress Responses ◽

Growth And Development ◽

Genomic Data ◽

Evolutionary Analysis ◽

Rna Seq ◽

Plant Growth And Development ◽

Genome Wide ◽

Gene Structures

In eukaryotes, proteins encoded by the 14-3-3 genes are ubiquitously involved in the plant growth and development. The 14-3-3 gene family has been identified in several plants. In the present study, we identified 22 GmGF14 genes in the soybean genomic data. On the basis of the evolutionary analysis, they were clustered into ε and non-ε groups. The GmGF14s of two groups were highly conserved in motifs and gene structures. RNA-seq analysis suggested that GmGF14 genes were the major regulator of soybean morphogenesis. Moreover, the expression level of most GmGF14s changed obviously in multiple stress responses (drought, salt and cold), suggesting that they have the abilities of responding to multiple stresses. Taken together, this study shows that soybean 14-3-3s participate in plant growth and can response to various environmental stresses. These results provide important information for further understanding of the functions of 14-3-3 genes in soybean.

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Genome-wide identification, phylogeny and expression analysis of G6PC gene family in common carp, Cyprinus carpio

Turkish Journal of Biochemistry ◽

10.1515/tjb-2018-0102 ◽

2020 ◽

Vol 45 (2) ◽

Author(s):

Sijia Liu ◽

Fei Tian ◽

Cunfang Zhang ◽

Zhigang Qiao ◽

Kai Zhao

Keyword(s):

Gene Family ◽

Common Carp ◽

Cyprinus Carpio ◽

Expression Profiles ◽

Expression Patterns ◽

Critical Role ◽

Cold Treatment ◽

Evolutionary Relationship ◽

Whole Genome Sequence ◽

Evolutionary Analysis

AbstractObjectiveThe Glucose 6-phosphatase (G6Pase) catalytic subunit (G6PC) catalyzes glucose 6-phosphate (G6P) to inorganic phosphate and glucose, playing a critical role in endogenous energy supply. Here, the G6PC gene family was investigated and characterized in common carp (Cyprinus carpio).MethodsSequence alignment and phylogenetic analysis were performed using MEGA5. The HMM profiles, motif structure were analyzed using Pfam and MEME, respectively. Quantitative real-time PCR was used to test the expression profiles.ResultsFour assumptive members of G6PC family in common carp whole-genome sequence were identified as cg6pca.1, cg6pca.2a, cg6pca.2b and cg6pcb which were classified into g6pca and g6pcb subtypes, respectively. Evolutionary analysis revealed that cg6pca.2a and cg6pca.2b have a closer evolutionary relationship, and the same subtype members have higher homology among different species. A classical PAP2-glucose phosphates domain is found in four genes and were highly conserved. The expression patterns revealed that only cg6pca.2a elevated significantly after 12 and 24 h of both starvation and cold treatment (p < 0.05).ConclusionsThis study performed a comprehensive analysis of G6PC gene family in common carp. Moreover, cg6pca.2 may be the major functional gene in cold and fasting stress. And the transfactors, PLAG1 and Sox8, may be concerned with expression regulation of cg6pca.2.

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