Characterisation of the whole-genome wide hexokinase gene family unravels the functional divergence in pear (Pyrus bretschneideri Rehd.)

2017 ◽  
Vol 93 (3) ◽  
pp. 244-254 ◽  
Author(s):  
Li’ang Yu ◽  
Jiaming Li ◽  
Leiting Li ◽  
Yuhua Huang ◽  
Xiaolong Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Functional Divergence ◽  
Whole Genome ◽  
Genome Wide

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 Genome-wide analysis of wheat DNA-binding with one finger (Dof) transcription factor genes: evolutionary characteristics and diverse abiotic stress responses

2020 ◽  
Author(s):  
Yue Liu ◽  
Nannan Liu ◽  
Xiong Deng ◽  
Dongmiao Liu ◽  
Mengfei Li ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Abiotic Stress ◽  
Positive Selection ◽  
Gene Family ◽  
Stress Responses ◽  
Functional Divergence ◽  
Acid Sites ◽  
Genome Wide Analysis ◽  
Dof Transcription Factor ◽  
Genome Wide

Abstract Background: DNA binding with one finger (Dof) transcription factors play important roles in plant growth and abiotic stress responses. Although genome-wide identification and analysis of the DOF transcription factor family has been reported in other species, no relevant studies have emerged in wheat. The aim of this study was to investigate the evolutionary and functional characteristics associated with plant growth and abiotic stress responses by genome-wide analysis of the wheat Dof transcription factor gene family. Results: Using the recently released wheat genome database (IWGSC RefSeq v1.1), we identified 96 wheat Dof gene family members, which were phylogenetically clustered into five distinct subfamilies. Gene duplication analysis revealed a broad and heterogeneous distribution of TaDofs on the chromosome groups 1 to 7, and obvious tandem duplication genes were present on chromosomes 2 and 3.Members of the same gene subfamily had similar exon-intron structures, while members of different subfamilies had obvious differences. Functional divergence analysis indicated that type-II functional divergence played a major role in the differentiation of the TaDof gene family. Positive selection analysis revealed that the Dof gene family experienced different degrees of positive selection pressure during the process of evolution, and five significant positive selection sites (30A, 31T, 33A, 102G and 104S) were identified. Additionally, nine groups of coevolving amino acid sites, which may play a key role in maintaining the structural and functional stability of Dof proteins, were identified. The results from the RNA-seq data and qRT-PCR analysis revealed that TaDof genes exhibited obvious expression preference or specificity in different organs and developmental stages, as well as in diverse abiotic stress responses. Most TaDof genes were significantly upregulated by heat, PEG and heavy metal stresses. Conclusions: The genome-wide analysis and identification of wheat DOF transcription factor family and the discovery of important amino acid sites are expected to provide new insights into the structure, evolution and function of the plant Dof gene family.

scholarly journals Genome-Wide Analysis of LRR-RLK Gene Family in Four Gossypium Species and Expression Analysis during Cotton Development and Stress Responses

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 592
Author(s):  
Ruibin Sun ◽  
Shaohui Wang ◽  
Dan Ma ◽  
Chuanliang Liu
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Functional Divergence ◽  
Comprehensive Analysis ◽  
Functional Study ◽  
Gossypium Species ◽  
Genome Wide ◽  
Plant Pathogen Interaction ◽  
Gossypium Raimondii ◽  
Plant Hormone Signaling

Leucine-rich repeat receptor-like kinases (LRR-RLKs) have been reported to play important roles in plant growth, development, and stress responses. However, no comprehensive analysis of this family has been performed in cotton (Gossypium spp.), which is an important economic crop that suffers various stresses in growth and development. Here we conducted a comprehensive analysis of LRR-RLK family in four Gossypium species (Gossypium arboreum, Gossypium barbadense, Gossypium hirsutum, and Gossypium raimondii). A total of 1641 LRR-RLK genes were identified in the four Gossypium species involved in our study. The maximum-likelihood phylogenetic tree revealed that all the LRR-RLK genes were divided into 21 subgroups. Exon-intron organization structure of LRR-RLK genes kept relatively conserved within subfamilies and between Arabidopsis and Gossypium genomes. Notably, subfamilies XI and XII were found dramatically expanded in Gossypium species. Tandem duplication acted as an important mechanism in expansion of the Gossypium LRR-RLK gene family. Functional analysis suggested that Gossypium LRR-RLK genes were enriched for plant hormone signaling and plant-pathogen interaction pathways. Promoter analysis revealed that Gossypium LRR-RLK genes were extensively regulated by transcription factors (TFs), phytohormonal, and various environmental stimuli. Expression profiling showed that Gossypium LRR-RLK genes were widely involved in stress defense and diverse developmental processes including cotton fiber development and provides insight into potential functional divergence within and among subfamilies. Our study provided valuable information for further functional study of Gossypium LRR-RLK genes.

scholarly journals Genome-Wide Identification and Characterization of the SHI-Related Sequence Gene Family in Rice

2020 ◽  
Vol 16 ◽  
pp. 117693432094149
Author(s):  
Jun Yang ◽  
Peng Xu ◽  
Diqiu Yu
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Brachypodium Distachyon ◽  
Functional Divergence ◽  
Japonica Rice ◽  
Segmental Duplications ◽  
Related Sequence ◽  
Genome Wide ◽  
A Genome

Rice ( Oryza sativa) yield is correlated to various factors. Transcription regulators are important factors, such as the typical SHORT INTERNODES-related sequences (SRSs), which encode proteins with single zinc finger motifs. Nevertheless, knowledge regarding the evolutionary and functional characteristics of the SRS gene family members in rice is insufficient. Therefore, we performed a genome-wide screening and characterization of the OsSRS gene family in Oryza sativa japonica rice. We also examined the SRS proteins from 11 rice sub-species, consisting of 3 cultivars, 6 wild varieties, and 2 other genome types. SRS members from maize, sorghum, Brachypodium distachyon, and Arabidopsis were also investigated. All these SRS proteins exhibited species-specific characteristics, as well as monocot- and dicot-specific characteristics, as assessed by phylogenetic analysis, which was further validated by gene structure and motif analyses. Genome comparisons revealed that segmental duplications may have played significant roles in the recombination of the OsSRS gene family and their expression levels. The family was mainly subjected to purifying selective pressure. In addition, the expression data demonstrated the distinct responses of OsSRS genes to various abiotic stresses and hormonal treatments, indicating their functional divergence. Our study provides a good reference for elucidating the functions of SRS genes in rice.

scholarly journals Genetic drift dominates genome-wide regulatory evolution following an ancient whole genome duplication in Atlantic salmon

2021 ◽  
Author(s):  
Jukka-Pekka Verta ◽  
Henry J Barton ◽  
Victoria Pritchard ◽  
Craig R Primmer
Keyword(s):  
Atlantic Salmon ◽  
Genetic Drift ◽  
Functional Divergence ◽  
Regulatory Elements ◽  
Functional Redundancy ◽  
Neutral Evolution ◽  
Whole Genome ◽  
Regulatory Evolution ◽  
Evolutionary Diversification ◽  
Genome Wide

Abstract Whole genome duplications (WGD) have been considered as springboards that potentiate lineage diversification through increasing functional redundancy. Divergence in gene regulatory elements is a central mechanism for evolutionary diversification, yet the patterns and processes governing regulatory divergence following events that lead to massive functional redundancy, such as WGD, remain largely unknown. We studied the patterns of divergence and strength of natural selection on regulatory elements in the Atlantic salmon (Salmo salar) genome, which has undergone WGD 100-80 Mya. Using ChIPmentation, we first show that H3K27ac, a histone modification typical to enhancers and promoters, is associated with genic regions, tissue specific transcription factor binding motifs, and with gene transcription levels in immature testes. Divergence in transcription between duplicated genes from WGD (ohnologs) correlated with difference in the number of proximal regulatory elements, but not with promoter elements, suggesting that functional divergence between ohnologs after WGD is mainly driven by enhancers. By comparing H3K27ac regions between duplicated genome blocks, we further show that a longer polyploid state post-WGD has constrained regulatory divergence. Patterns of genetic diversity across natural populations inferred from re-sequencing indicate that recent evolutionary pressures on H3K27ac regions are dominated by largely neutral evolution. In sum, our results suggest that post-WGD functional redundancy in regulatory elements continues to have an impact on the evolution of the salmon genome, promoting largely neutral evolution of regulatory elements despite their association with transcription levels. These results highlight a case where genome-wide regulatory evolution following an ancient WGD is dominated by genetic drift.

scholarly journals Genome-Wide Analysis of the COBRA-Like Gene Family Supports Gene Expansion through Whole-Genome Duplication in Soybean (Glycine max)

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 167
Author(s):  
Sara Sangi ◽  
Paula M. Araújo ◽  
Fernanda S. Coelho ◽  
Rajesh K. Gazara ◽  
Fabrício Almeida-Silva ◽  
...  
Keyword(s):  
Cell Wall ◽  
Gene Family ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Expression Patterns ◽  
Whole Genome ◽  
Comprehensive Overview ◽  
Genome Wide ◽  
Duplication Events ◽  
Cell Wall Expansion

The COBRA-like (COBL) gene family has been associated with the regulation of cell wall expansion and cellulose deposition. COBL mutants result in reduced levels and disorganized deposition of cellulose causing defects in the cell wall and inhibiting plant development. In this study, we report the identification of 24 COBL genes (GmCOBL) in the soybean genome. Phylogenetic analysis revealed that the COBL proteins are divided into two groups, which differ by about 170 amino acids in the N-terminal region. The GmCOBL genes were heterogeneously distributed in 14 of the 20 soybean chromosomes. This study showed that segmental duplication has contributed significantly to the expansion of the COBL family in soybean during all Glycine-specific whole-genome duplication events. The expression profile revealed that the expression of the paralogous genes is highly variable between organs and tissues of the plant. Only 20% of the paralogous gene pairs showed similar expression patterns. The high expression levels of some GmCOBLs suggest they are likely essential for regulating cell expansion during the whole soybean life cycle. Our comprehensive overview of the COBL gene family in soybean provides useful information for further understanding the evolution and diversification of COBL genes in soybean.

scholarly journals Genome-Wide Identification and Evolutionary Analysis of AOMT Gene Family in Pomegranate (Punica granatum)

Agronomy ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 318
Author(s):  
Xinhui Zhang ◽  
Weicheng Yuan ◽  
Yujie Zhao ◽  
Yuan Ren ◽  
Xueqing Zhao ◽  
...  
Keyword(s):  
Gene Family ◽  
Gene Evolution ◽  
Punica Granatum ◽  
Gene Family Evolution ◽  
Raw Material ◽  
Whole Genome ◽  
Evolutionary Analysis ◽  
New Genes ◽  
Genome Wide ◽  
Duplication Events

Gene duplication is the major resource with which to generate new genes, which provide raw material for novel functions evolution. Thus, to elucidate the gene family evolution after duplication events is of vital importance. Anthocyanin O-methyltransferases (AOMTs) have been recognized as being capable of anthocyanin methylation, which increases anthocyanin diversity and stability and improves the protection of plants from environmental stress. Meanwhile, no detailed identification or genome-wide analysis of the AOMT gene family members in pomegranate (Punicagranatum) have been reported. Three published pomegranate genome sequences offer substantial resources with which to explore gene evolution based on the whole genome. Altogether, 58 identified OMTs from pomegranate and five other species were divided into the AOMT group and the OMT group, according to their phylogenetic tree and AOMTs derived from OMTs. AOMTs in the same subclade have a similar gene structure and protein conserved motifs. The PgAOMT family evolved and expanded primarily via whole-genome duplication (WGD) and tandem duplication. PgAOMTs expression pattern in peel and aril development by qRT-PCR verification indicated that PgAOMTs had tissue-specific patterns. The main fates of AOMTs were neo- or non-functionalization after duplication events. High expression genes of PgOMT04 and PgOMT09 were speculated to contribute to “Taishanhong” pomegranate’s bright red peel color. Finally, we integrated the above analysis in order to infer the evolutionary scenario of AOMT family.

scholarly journals Conservation, Divergence, and Genome-Wide Distribution ofPALandPOX AGene Families in Plants

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
H. C. Rawal ◽  
N. K. Singh ◽  
T. R. Sharma
Keyword(s):  
Gene Family ◽  
Populus Trichocarpa ◽  
Brachypodium Distachyon ◽  
Functional Divergence ◽  
Functional Characterization ◽  
Gene Families ◽  
Wide Distribution ◽  
Genome Wide ◽  
High Level ◽  
Diverse Groups

Genome-wide identification and phylogenetic and syntenic comparison were performed for the genes responsible for phenylalanine ammonia lyase (PAL) and peroxidase A (POX A) enzymes in nine plant species representing very diverse groups like legumes (Glycine maxandMedicago truncatula), fruits (Vitis vinifera), cereals (Sorghum bicolor,Zea mays, andOryza sativa), trees (Populus trichocarpa), and model dicot (Arabidopsis thaliana) and monocot (Brachypodium distachyon) species. A total of 87 and 1045 genes in PAL and POX A gene families, respectively, have been identified in these species. The phylogenetic and syntenic comparison along with motif distributions shows a high degree of conservation of PAL genes, suggesting that these genes may predate monocot/eudicot divergence. The POX A family genes, present in clusters at the subtelomeric regions of chromosomes, might be evolving and expanding with higher rate than the PAL gene family. Our analysis showed that during the expansion of POX A gene family, many groups and subgroups have evolved, resulting in a high level of functional divergence among monocots and dicots. These results will act as a first step toward the understanding of monocot/eudicot evolution and functional characterization of these gene families in the future.

scholarly journals Genome-Wide Analysis of the R2R3-MYB Gene Family in Fragaria × ananassa and Its Function Identification During Anthocyanins Biosynthesis in Pink-Flowered Strawberry

2021 ◽  
Vol 12 ◽  
Author(s):  
Jiaxin Liu ◽  
Jian Wang ◽  
Mingqian Wang ◽  
Jun Zhao ◽  
Yang Zheng ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Developmental Stages ◽  
Anthocyanin Biosynthesis ◽  
Functional Divergence ◽  
Purifying Selection ◽  
Leaf Petiole ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
R2r3 Myb

The strawberry (Fragaria × ananassa) is an economically important fruit throughout the world. The large R2R3-MYB gene family participates in a variety of plant functions, including anthocyanin biosynthesis. The present study is the first genome-wide analysis of the MYB gene family in the octoploid strawberry and describes the identification and characterization of the family members using the recently sequenced F. × ananassa genome. Specifically, we aimed to identify the key MYBs involved in petal coloration in the pink-flowered strawberry, which increases its ornamental value. A comprehensive, genome-wide analysis of F. × ananassa R2R3-FaMYBs was performed, investigating gene structures, phylogenic relationships, promoter regions, chromosomal locations, and collinearity. A total of 393 R2R3-FaMYB genes were identified in the F. × ananassa genome and divided into 36 subgroups based on phylogenetic analysis. Most genes with similar functions in the same subgroup exhibited similar exon-intron structures and motif compositions. These R2R3-FaMYBs were unevenly distributed over 28 chromosomes. The expansion of the R2R3-FaMYB gene family in the F. × ananassa genome was found to be caused mainly by segmental duplication. The Ka/Ks analysis indicated that duplicated R2R3-FaMYBs mostly experienced purifying selection and showed limited functional divergence after the duplication events. To elucidate which R2R3-FaMYB genes were associated with anthocyanin biosynthesis in the petals of the pink-flowered strawberry, we compared transcriptional changes in different flower developmental stages using RNA-seq. There were 131 differentially expressed R2R3-FaMYB genes identified in the petals, of which three genes, FaMYB28, FaMYB54, and FaMYB576, appeared likely, based on the phylogenetic analysis, to regulate anthocyanin biosynthesis. The qRT-PCR showed that these three genes were more highly expressed in petals than in other tissues (fruit, leaf, petiole and stolon) and their expressions were higher in red compared to pink and white petals. These results facilitate the clarification on the roles of the R2R3-FaMYB genes in petal coloration in the pink-flowered strawberry. This work provides useful information for further functional analysis on the R2R3-FaMYB gene family in F. × ananassa.

Sign in / Sign up

Export Citation Format

Share Document