Phylogenetics and evolution of Trx SET genes in fully sequenced land plants

Genome ◽  
2012 ◽  
Vol 55 (4) ◽  
pp. 269-280 ◽  
Author(s):  
Xinyu Zhu ◽  
Caoyi Chen ◽  
Baohua Wang
Keyword(s):  
Gene Family ◽  
Physcomitrella Patens ◽  
Functional Divergence ◽  
Experimental Studies ◽  
Land Plants ◽  
Orthologous Group ◽  
Evolutionary Stage ◽  
Evolutionary Analysis ◽  
Genes Encoding ◽  
Gene Structures

Plant Trx SET proteins are involved in H3K4 methylation and play a key role in plant floral development. Genes encoding Trx SET proteins constitute a multigene family in which the copy number varies among plant species and functional divergence appears to have occurred repeatedly. To investigate the evolutionary history of the Trx SET gene family, we made a comprehensive evolutionary analysis on this gene family from 13 major representatives of green plants. A novel clustering (here named as cpTrx clade), which included the III-1, III-2, and III-4 orthologous groups, previously resolved was identified. Our analysis showed that plant Trx proteins possessed a variety of domain organizations and gene structures among paralogs. Additional domains such as PHD, PWWP, and FYR were early integrated into primordial SET–PostSET domain organization of cpTrx clade. We suggested that the PostSET domain was lost in some members of III-4 orthologous group during the evolution of land plants. At least four classes of gene structures had been formed at the early evolutionary stage of land plants. Three intronless orphan Trx SET genes from the Physcomitrella patens (moss) were identified, and supposedly, their parental genes have been eliminated from the genome. The structural differences among evolutionary groups of plant Trx SET genes with different functions were described, contributing to the design of further experimental studies.

scholarly journals Functional Specialization within the EXO70 Gene Family in Arabidopsis

2021 ◽  
Vol 22 (14) ◽  
pp. 7595
Author(s):  
Vedrana Marković ◽  
Ivan Kulich ◽  
Viktor Žárský
Keyword(s):  
Gene Family ◽  
Functional Divergence ◽  
Secretory Vesicle ◽  
Land Plants ◽  
Functional Specialization ◽  
Transport Vesicles ◽  
Genes Encoding ◽  
Target Membrane ◽  
Localized Delivery ◽  
High Degree

Localized delivery of plasma-membrane and cell-wall components is a crucial process for plant cell growth. One of the regulators of secretory-vesicle targeting is the exocyst tethering complex. The exocyst mediates first interaction between transport vesicles and the target membrane before their fusion is performed by SNARE proteins. In land plants, genes encoding the EXO70 exocyst subunit underwent an extreme proliferation with 23 paralogs present in the Arabidopsis (Arabidopsis thaliana) genome. These paralogs often acquired specialized functions during evolution. Here, we analyzed functional divergence of selected EXO70 paralogs in Arabidopsis. Performing a systematic cross-complementation analysis of exo70a1 and exo70b1 mutants, we found that EXO70A1 was functionally substituted only by its closest paralog, EXO70A2. In contrast, none of the EXO70 isoforms tested were able to substitute EXO70B1, including its closest relative, EXO70B2, pointing to a unique function of this isoform. The presented results document a high degree of functional specialization within the EXO70 gene family in land plants.

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

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7950 ◽  
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.

scholarly journals Gene Expression Divergence and Evolutionary Analysis of the Drosomycin Gene Family inDrosophila melanogaster

2009 ◽  
Vol 2009 ◽  
pp. 1-9 ◽  
Author(s):  
Xiao-Juan Deng ◽  
Wan-Ying Yang ◽  
Ya-Dong Huang ◽  
Yang Cao ◽  
Shuo-Yang Wen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Binding Sites ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Species Group ◽  
Evolutionary Analysis ◽  
Promoter Regions ◽  
Transcription Start Sites

Drosomycin(Drs) encoding an inducible 44-residue antifungal peptide is clustered with six additional genes,Dro1, Dro2, Dro3, Dro4, Dro5,andDro6, forming a multigene family on the 3L chromosome arm inDrosophila melanogaster. To get further insight into the regulation of each member of the drosomycin gene family, here we investigated gene expression patterns of this family by either microbe-free injury or microbial challenges using real time RT-PCR. The results indicated that among the sevendrosomycingenes,Drs, Dro2, Dro3, Dro4,andDro5showed constitutive expressions. Three out of five,Dro2, Dro3,andDro5, were able to be upregulated by simple injury. Interestingly,Drsis an only gene strongly upregulated whenDrosophilawas infected with microbes. In contrast to these five genes,Dro1andDro6were not transcribed at all in either noninfected or infected flies. Furthermore, by5′rapid amplification of cDNA ends, two transcription start sites were identified inDrsandDro2, and one inDro3, Dro4,andDro5. In addition, NF-κB binding sites were found in promoter regions ofDrs, Dro2, Dro3,andDro5, indicating the importance of NF-κB binding sites for the inducibility ofdrosomycingenes. Based on the analyses of flanking sequences of each gene inD. melanogasterand phylogenetic relationship ofdrosomycinsinD. melanogasterspecies-group, we concluded that gene duplications were involved in the formation of the drosomycin gene family. The possible evolutionary fates ofdrosomycingenes were discussed according to the combining analysis of gene expression pattern, gene structure, and functional divergence of these genes.

scholarly journals Unravelling Cotton Nonexpressor of Pathogenesis-Related 1(NPR1)-Like Genes Family: Evolutionary Analysis and Putative Role in Fiber Development and Defense Pathway

Plants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 999 ◽  
Author(s):  
Neha Agarwal ◽  
Rakesh Srivastava ◽  
Akash Verma ◽  
Krishan Mohan Rai ◽  
Babita Singh ◽  
...  
Keyword(s):  
Gene Family ◽  
Functional Divergence ◽  
Regulatory Elements ◽  
Structural Features ◽  
Fiber Development ◽  
Upstream Region ◽  
Evolutionary Analysis ◽  
Gossypium Species ◽  
Pathogenesis Related ◽  
Six Genes

The nonexpressor of pathogenesis-related 1 (NPR1) family plays diverse roles in gene regulation in the defense and development signaling pathways in plants. Less evidence is available regarding the significance of the NPR1-like gene family in cotton (Gossypium species). Therefore, to address the importance of the cotton NPR1-like gene family in the defense pathway, four Gossypium species were studied: two tetraploid species, G.hirsutum and G. barbadense, and their two potential ancestral diploids, G. raimondii and G. arboreum. In this study, 12 NPR1-like family genes in G. hirsutum were recognized, including six genes in the A-subgenome and six genes in the D-subgenome. Based on the phylogenetic analysis, gene and protein structural features, cotton NPR-like proteins were grouped into three different clades. Our analysis suggests the significance of cis-regulatory elements in the upstream region of cotton NPR1-like genes in hormonal signaling, biotic stress conditions, and developmental processes. The quantitative expression analysis for different developmental tissues and fiber stages (0 to 25 days post-anthesis), as well as salicylic acid induction, confirmed the distinct function of different cotton NPR genes in defense and fiber development. Altogether, this study presents specifications of conservation in the cotton NPR1-like gene family and their functional divergence for development of fiber and defense properties.

Comparative and evolutionary analysis of genes encoding small GTPases and their activating proteins in eukaryotic genomes

2006 ◽  
Vol 24 (3) ◽  
pp. 235-251 ◽  
Author(s):  
Shu-Ye Jiang ◽  
Srinivasan Ramachandran
Keyword(s):  
Large Scale ◽  
Functional Divergence ◽  
Small Gtpases ◽  
Small Gtpase ◽  
Evolutionary Analysis ◽  
Major Mechanism ◽  
Genome Duplications ◽  
Genes Encoding ◽  
Rapid Divergence ◽  
Eukaryotic Organisms

Both small GTPase and its activating protein (GAP) superfamilies exist in various eukaryotes. The small GTPases regulate a wide variety of cellular processes by cycling between active GTP- and inactive GAP-bound conformations. The GAPs promote GTPase inactivation by stimulating the GTP hydrolysis. In this study, we identified 111 small GTPases and 85 GAPs in rice, 65 GAPs in Arabidopsis, 90 small GTPases in Drosophila melanogaster, and 35 GAPs in Saccharomyces cerevisiaeby genome-wide analysis. We then analyzed and compared a total of 498 small GTPases and 422 GAPs from these four eukaryotic and human genomes. Both animals and yeast genomes contained five families of small GTPases and their GAPs. However, plants had only four of these five families because of a lack of the Ras and RasGAP genes. Small GTPases were conserved with common motifs, but GAPs exhibited higher and much more rapid divergence. On the basis of phylogenetic analysis of all small GTPases and GAPs in five eukaryotic organisms, we estimated that their ancestors had small sizes of small GTPases and GAPs and their large-scale expansions occurred after the divergence from their ancestors. Further investigation showed that genome duplications represented the major mechanism for such expansions. Nonsynonymous substitutions per site ( Ka) and synonymous substitutions per site ( Ks) analyses showed that most of the divergence due to a positive selection occurred in common ancestors, suggesting a major functional divergence in an ancient era.

scholarly journals The evolutionary analysis of PEBP Gene Family among Rosaceae tree species

2019 ◽  
Author(s):  
Man Zhang ◽  
Ping Li ◽  
Xiaolan Yan ◽  
Jia Wang ◽  
Tangren Cheng ◽  
...  
Keyword(s):  
Gene Family ◽  
Flowering Time ◽  
Tree Species ◽  
Floral Induction ◽  
Functional Divergence ◽  
Purifying Selection ◽  
Gene Family Evolution ◽  
Evolutionary Analysis ◽  
Functional Roles ◽  
Rosaceae Species

Abstract Phosphatidylethanolamine-binding proteins (PEBPs) are a common gene family found among animals, plants and microbes. Plant PEBP proteins play an important role in regulating flowering time, as well as seed and bud dormancy. PEBP proteins can be divided into three major clades: FLOWERING LOCUS T-like (FT-like), TERMINAL FLOWER1-like (TFL1-like), and MOTHER OF FT AND TFL1-like (MFT-like). Though PEBP family genes have been well studied in Arabidopsis and other model species, their functional role in perennial trees is not fully understood. To characterize the evolution of PEBP genes and their role in flowering control among Rosaceae species, we identified a total of 46 PEBP members in seven Rosaceae species. Sequence and gene structure analysis revealed highly conserved intron/exon distributions and featured motifs among Rosaceae PEBP proteins. Analysis of synonymous/nonsysnonymous substitution rates showed purifying selection constraining divergence within most lineages, while positive selection appears to have driven divergence of FT-like and TFL-like genes from the MFT clade. The expression of PEBP genes varied among different tissues indicating their functional divergence during gene family evolution. Furthermore, by employing a weighted gene co-expression network approach, we inferred a putative FT regulatory module essential for dormancy release and floral induction in P. mume. Our study sheds new light on the evolution of PEBP genes and their functional roles in controlling flowering time among Rosaceae tree species.

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