Genome-wide survey of Gγ subunit gene family in eight Rosaceae and expression analysis of PbrGGs in pear (Pyrus bretschneideri)

Abstract Background Heterotrimeric G-proteins, composed of Gα, Gβ and Gγ subunits, are important signal transmitters, mediating the cellular response to multiple stimuli in animals and plants. The Gγ subunit is an essential component of the G-protein, providing appropriate functional specificity to the heterotrimer complex and has been well studied in many species. However, the evolutionary history, expression pattern and functional characteristics of Gγ subunits has not been explored in the Rosaceae, representing many important fruit crops. Results In this study, 35 Gγ subunit genes were identified from the eight species belonging to the Rosaceae family. Based on the structural gene characteristics, conserved protein motifs and phylogenetic analysis of the Gγ subunit genes, the genes were classified into three clades. Purifying selection was shown to play an important role in the evolution of Gγ subunit genes, while a recent whole-genome duplication event was the principal force determining the expansion of the Gγ subunit gene family in the subfamily Maloideae. Gγ subunit genes exhibited diverse spatiotemporal expression patterns in Chinese white pear, including fruit, root, ovary and bud, and under abiotic stress conditions, the relative expression of Gγ subunit genes were up-regulated or down-regulated. In addition, seven of the Gγ subunit proteins in pear were located on the plasma membrane, in the cytoplasm or nucleus. Conclusion Overall, this study of the Gγ subunit gene family in eight Rosaceae species provided useful information to better understand the evolution and expression of these genes and facilitated further exploration of their functions in these important crop plants.

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Slc4 Gene Family in Spotted Sea Bass (Lateolabrax maculatus): Structure, Evolution, and Expression Profiling in Response to Alkalinity Stress and Salinity Changes

Genes ◽

10.3390/genes11111271 ◽

2020 ◽

Vol 11 (11) ◽

pp. 1271

Author(s):

Ling-Yu Wang ◽

Yuan Tian ◽

Hai-Shen Wen ◽

Peng Yu ◽

Yang Liu ◽

...

Keyword(s):

Gene Family ◽

Expression Patterns ◽

Purifying Selection ◽

Sea Bass ◽

Duplication Event ◽

Structure Evolution ◽

Genome Duplication Event ◽

Physiological Processes ◽

Lateolabrax Maculatus ◽

Solute Carrier

The solute carrier 4 (SLC4) family is a class of cell membranes transporters involved in base transport that plays crucial roles in diverse physiological processes. In our study, 15 slc4 genes were identified and annotated in spotted sea bass, including five members of Cl−/HCO3− exchangers, eight genes coding Na+-dependent HCO3− transporters, and two copies of Na+-coupled borate transporters. The gene sequence and structure, chromosomal and syntenic arrangement, phylogenetic and evolution profiles were analyzed. Results showed that the slc4 gene in teleosts obviously expanded compared with higher vertebrates, arising from teleost-specific whole genome duplication event. Most gene sites of slc4 in spotted sea bass were under strong purifying selection during evolution, while positive selection sites were only detected in slc4a1b, slc4a8, and slc4a10b. Additionally, qRT-PCR results showed that different slc4 genes exhibited distinct branchial expression patterns after alkalinity and salinity stresses, of which the strongly responsive members may play essential roles during these physiological processes. Our study provides the systemic overview of the slc4 gene family in spotted sea bass and enables a better understanding for the evolution of this family and further deciphering the biological roles in maintaining ion and acid–base homeostasis in teleosts.

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Genome-wide identification of candidate aquaporins involved in water accumulation of pomegranate outer seed coat

PeerJ ◽

10.7717/peerj.11810 ◽

2021 ◽

Vol 9 ◽

pp. e11810

Author(s):

Jianjian Liu ◽

Gaihua Qin ◽

Chunyan Liu ◽

Xiuli Liu ◽

Jie Zhou ◽

...

Keyword(s):

Seed Coat ◽

Expression Patterns ◽

Purifying Selection ◽

Transcript Abundance ◽

Punica Granatum ◽

Duplication Event ◽

Genome Duplication Event ◽

Specific Expression ◽

Water Accumulation ◽

Seed Coats

Aquaporins (AQPs) are a class of highly conserved integral membrane proteins that facilitate the uptake and transport of water and other small molecules across cell membranes. However, little is known about AQP genes in pomegranate (Punica granatum L.) and their potential role in water accumulation of the outer seed coat. We identified 38 PgrAQP genes in the pomegranate genome and divided them into five subfamilies based on a comparative analysis. Purifying selection played a role in the evolution of PgrAQP genes and a whole-genome duplication event in Myrtales may have contributed to the expansion of PgrTIP, PgrSIP, and PgrXIP genes. Transcriptome data analysis revealed that the PgrAQP genes exhibited different tissue-specific expression patterns. Among them, the transcript abundance of PgrPIPs were significantly higher than that of other subfamilies. The mRNA transcription levels of PgrPIP1.3, PgrPIP2.8, and PgrSIP1.2 showed a significant linear relationship with water accumulation in seed coats, indicating that PgrPIP1.3/PgrPIP2.8 located in the plasma membrane and PgrSIP1.2 proteins located on the tonoplast may be involved in water accumulation and contribute to the cell expansion of the outer seed coat, which then develops into juicy edible flesh. Overall, our results provided not only information on the characteristics and evolution of PgrAQPs, but also insights on the genetic improvement of outer seed coats.

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A new insight into the evolution and functional divergence of FRK genes in Pyrus bretschneideri

Royal Society Open Science ◽

10.1098/rsos.171463 ◽

2018 ◽

Vol 5 (7) ◽

pp. 171463 ◽

Cited By ~ 2

Author(s):

Yunpeng Cao ◽

Shumei Li ◽

Yahui Han ◽

Dandan Meng ◽

Chunyan Jiao ◽

...

Keyword(s):

Gene Family ◽

Gene Structure ◽

Functional Divergence ◽

Sugar Content ◽

Expression Patterns ◽

Evolutionary Relationship ◽

World Market ◽

Pear Fruit ◽

Rosaceae Species ◽

Chinese White

In plants, plant fructokinases (FRKs) are considered to be the main gateway of fructose metabolism as they can phosphorylate fructose to fructose-6-phosphate. Chinese white pears ( Pyrus bretschneideri ) are one of the popular fruits in the world market; sugar content is an important factor affecting the quality of the fruit. We identified 49 FRKs from four Rosaceae species; 20 of these sequences were from Chinese white pear. Subsequently, phylogenic relationship, gene structure and micro-collinearity were analysed. Phylogenetic and exon–intron analysis classified these FRK s into 10 subfamilies, and it was aimed to further reveal the variation of the gene structure and the evolutionary relationship of this gene family. Remarkably, gene expression patterns in different tissues or different development stages of the pear fruit suggested functional redundancy for PbFRKs derived from segmental duplication or genome-wide duplication and sub-functionalization for some of them. Additionally, PbFRK11 , PbFRK13 and PbFRK16 were found to play important roles in regulating the sugar content in the fruit. Overall, this study provided important insights into the evolution of the FRK gene family in four Rosaceae species, and highlighted its roles in both pear tissue and fruits. Results presented here provide the appropriate candidate of PbFRK s that might contribute to fructose efflux in the pear fruit.

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Genome-wide characterization and expression profiling of the MAPKKK genes in Gossypium arboreum L.

Genome ◽

10.1139/gen-2018-0176 ◽

2019 ◽

Vol 62 (9) ◽

pp. 609-622 ◽

Cited By ~ 2

Author(s):

Weidong Zhu ◽

Wei Tan ◽

Qiulin Li ◽

Xiugui Chen ◽

Junjuan Wang ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Expression Patterns ◽

Mitogen Activated Protein Kinase ◽

Gossypium Arboreum ◽

Developmental Processes ◽

Protein Motifs ◽

Genome Wide ◽

A Genome ◽

Salt And Drought Stresses

Mitogen-activated protein kinase kinase kinases (MAPKKKs) are important components of MAPK cascades, which have different functions during developmental processes and stress responses. To date, there has been no systematic investigation of this gene family in the diploid cotton Gossypium arboreum L. In this study, a genome-wide survey was performed that identified 78 MAPKKK genes in G. arboreum. Phylogenetic analysis classified these genes into three subgroups: 14 belonged to ZIK, 20 to MEKK, and 44 to Raf. Chromosome location, phylogeny, and the conserved protein motifs of the MAPKKK gene family in G. arboreum were analyzed. The MAPKKK genes had a scattered genomic distribution across 13 chromosomes. The members in the same subfamily shared similar conserved motifs. The MAPKKK expression patterns were analyzed in mature leaves, stems, roots, and at different ovule developmental stages, as well as under salt and drought stresses. Transcriptome analysis showed that 76 MAPKKK genes had different transcript accumulation patterns in the tested tissues and 38 MAPKKK genes were differentially expressed in response to salt and drought stresses. These results lay the foundation for understanding the complex mechanisms behind MAPKKK-mediated developmental processes and abiotic stress-signaling transduction pathways in cotton.

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Genome-Wide Identification and Characterization of the OPR Gene Family in Wheat (Triticum aestivum L.)

International Journal of Molecular Sciences ◽

10.3390/ijms20081914 ◽

2019 ◽

Vol 20 (8) ◽

pp. 1914 ◽

Cited By ~ 4

Author(s):

Yifei Mou ◽

Yuanyuan Liu ◽

Shujun Tian ◽

Qiping Guo ◽

Chengshe Wang ◽

...

Keyword(s):

Gene Family ◽

Expression Patterns ◽

Triticum Aestivum L ◽

Defense Responses ◽

High Yield ◽

Flavin Mononucleotide ◽

Duplicated Genes ◽

Old Yellow Enzyme ◽

Specific Expression ◽

Protein Motifs

The 12-oxo-phytodienoic acid reductases (OPRs), which belong to the old yellow enzyme (OYE) family, are flavin mononucleotide (FMN)-dependent oxidoreductases with critical functions in plants. Despite the clear characteristics of growth and development, as well as the defense responses in Arabidopsis, tomato, rice, and maize, the potential roles of OPRs in wheat are not fully understood. Here, forty-eight putative OPR genes were found and classified into five subfamilies, with 6 in sub. I, 4 in sub. II, 33 in sub. III, 3 in sub. IV, and 2 in sub. V. Similar gene structures and conserved protein motifs of TaOPRs in wheat were identified in the same subfamilies. An analysis of cis-acting elements in promoters revealed that the functions of OPRs in wheat were mostly related to growth, development, hormones, biotic, and abiotic stresses. A total of 14 wheat OPR genes were identified as tandem duplicated genes, while 37 OPR genes were segmentally duplicated genes. The expression patterns of TaOPRs were tissue- and stress-specific, and the expression of TaOPRs could be regulated or induced by phytohormones and various stresses. Therefore, there were multiple wheat OPR genes, classified into five subfamilies, with functional diversification and specific expression patterns, and to our knowledge, this was the first study to systematically investigate the wheat OPR gene family. The findings not only provide a scientific foundation for the comprehensive understanding of the wheat OPR gene family, but could also be helpful for screening more candidate genes and breeding new varieties of wheat, with a high yield and stress resistance.

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Consequences of Hox gene duplication in the vertebrates: an investigation of the zebrafish Hox paralogue group 1 genes

Development ◽

10.1242/dev.128.13.2471 ◽

2001 ◽

Vol 128 (13) ◽

pp. 2471-2484 ◽

Cited By ~ 3

Author(s):

James M. McClintock ◽

Robin Carlson ◽

Devon M. Mann ◽

Victoria E. Prince

Keyword(s):

Hox Genes ◽

Genome Duplication ◽

Expression Patterns ◽

Detailed Comparison ◽

Duplication Event ◽

Amino Acid Sequences ◽

Functional Domains ◽

Genome Duplication Event ◽

Basic Functions ◽

Functional Capacities

As a result of a whole genome duplication event in the lineage leading to teleosts, the zebrafish has seven clusters of Hox patterning genes, rather than four, as described for tetrapod vertebrates. To investigate the consequences of this genome duplication, we have carried out a detailed comparison of genes from a single Hox paralogue group, paralogue group (PG) 1. We have analyzed the sequences, expression patterns and potential functions of all four of the zebrafish PG1 Hox genes, and compared our data with that available for the three mouse genes. As the basic functions of Hox genes appear to be tightly constrained, comparison with mouse data has allowed us to identify specific changes in the developmental roles of Hox genes that have occurred during vertebrate evolution. We have found variation in expression patterns, amino acid sequences within functional domains, and potential gene functions both within the PG1 genes of zebrafish, and in comparison to mouse PG1 genes. We observed novel expression patterns in the midbrain, such that zebrafish hoxa1a and hoxc1a are expressed anterior to the domain traditionally thought to be under Hox patterning control. The hoxc1a gene shows significant coding sequence changes in known functional domains, which correlate with a reduced capacity to cause posteriorizing transformations. Moreover, the hoxb1 duplicate genes have differing functional capacities, suggesting divergence after duplication. We also find that an intriguing function ‘shuffling’ between paralogues has occurred, such that one of the zebrafish hoxb1 duplicates, hoxb1b, performs the role in hindbrain patterning played in mouse by the non-orthologous Hoxa1 gene.

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Genome-wide identification and analyses of the AHL gene family in cotton (Gossypium)

10.21203/rs.2.10337/v2 ◽

2019 ◽

Author(s):

Lanjie Zhao ◽

Youjun Lu ◽

Wei Chen ◽

Jinbo Yao ◽

Yan Li ◽

...

Keyword(s):

Gene Family ◽

Expression Profiles ◽

Expression Patterns ◽

Purifying Selection ◽

Orthologous Gene ◽

Potential Functions ◽

Pcr Analysis ◽

Type I ◽

Clade B ◽

Genome Wide

Abstract Background: Members of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED ( AHL ) family are involved in various plant biological processes via protein-DNA and protein-protein interaction. However, no the systematic identification and analysis of AHL gene family have been reported in cotton. Results: To investigate the potential functions of AHLs in cotton, genome-wide identification, expressions and structure analysis of the AHL gene family were performed in this study. 48, 51 and 99 AHL genes were identified from the G.raimondii, G.arboreum and G.hirsutum genome, respectively. Phylogenetic analysis revealed that the AHLs in cotton evolved into 2 clades, Clade-A with 4-5 introns and Clade-B with intronless (excluding AHL 20-2). Based on the composition of the AT-hook motif(s) and PPC/DUF 296 domain, AHL proteins were classified into three types (Type-I/-II/-III), with Type-I AHLs forming Clade-B, and the other two types together diversifying in Clade-A. The detection of synteny and collinearity showed that the AHLs expanded with the WGD in cotton, and the sequence structure of AHL20-2 showed the tendency of increasing intron in three different Gossypium spp . The ratios of non-synonymous (Ka) and synonymous (Ks) substitution rates of orthologous gene pairs revealed that the AHL genes of G.hirsutum had undergone through various selection pressures, purifying selection mainly in A-subgenome and positive selection mainly in D-subgenome. Examination of their expression patterns showed most of AHLs of Clade-B expressed predominantly in stem, while those of Clade-A in ovules, suggesting that the AHLs within each clade shared similar expression patterns with each other. qRT-PCR analysis further confirmed that some GhAHLs higher expression in stems and ovules. Conclusion: In this study, 48, 51 and 99 AHL genes were identified from three cotton genomes respectively. AHLs in cotton were classified into two clades by phylogenetic relationship and three type based on the composition of motif and domain. The AHLs expanded with segmental duplication, not tandem duplication. The expression profiles of GhAHLs revealed abundant differences in expression levels in various tissues and at different stages of ovules development. Our study provided significant insights into the potential functions of AHLs in regulating the growth and development in cotton.

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Genome-Wide Analysis of the CCT Gene Family in Chinese White Pear (Pyrus Bretschneideri Rehd.) and Characterization of PbPRR2 in Response to Varying Light Signals

10.21203/rs.3.rs-885482/v1 ◽

2021 ◽

Author(s):

Zheng Liu ◽

Jia-Li Liu ◽

Lin An ◽

Tao Wu ◽

Li Yang ◽

...

Keyword(s):

Gene Family ◽

Expression Profiles ◽

Expression Patterns ◽

Functional Characterization ◽

Light Response ◽

Purifying Selection ◽

Photosynthetic Performance ◽

Negative Regulator ◽

Canopy Architecture ◽

Genome Wide

Abstract Background: Canopy architecture is critical in determining the light environment, and subsequently the photosynthetic productivity of fruit crops. Numerous CCT domain-containing genes are crucial for plant adaptive responses to diverse environmental cues. Due to the biological importance of CCT genes, many researchers have focused on their functional characterization. However, little information was available about the CCT genes (PbCCTs) of pear, an important fruit crop.Results: Genome-wide sequence analysis identified 42 putative PbCCTs in the genome of pear (Pyrus bretschneideri Rehd.). Phylogenetic analysis indicated these genes were divided into five subfamilies, namely, COL (14 members), PRR (8 members), ZIM (6 members), TCR1 (6 members) and ASML2 (8 members). Analysis of exon-intron structures and conserved domains provided support for the classification. Genome duplication analysis indicated that segmental duplication events played a crucial role in the expansion of the CCT family in pear, and that the CCT family evolved under the effect of purifying selection. Expression profiles exhibited diverse expression patterns of PbCCTs in various tissues and in response to varying red and blue light. Additionally, transient overexpression of PbPRR2 in Nicotiana benthamiana leaves resulted in inhibition of photosynthetic performance, suggesting that PbPRR2 may be a negative regulator of photosynthesis. Conclusions:This study provides a comprehensive analysis of the CCT gene family in pear and will facilitate further functional investigations of the PbCCTs to uncover their biological roles in light response.

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Genome-Wide Identification, Expansion Mechanism and Expression Profiling Analysis of GLABROUS1 Enhancer-Binding Protein (GeBP) Gene Family in Gramineae Crops

International Journal of Molecular Sciences ◽

10.3390/ijms22168758 ◽

2021 ◽

Vol 22 (16) ◽

pp. 8758

Author(s):

Jishuai Huang ◽

Qiannan Zhang ◽

Yurong He ◽

Wei Liu ◽

Yanghong Xu ◽

...

Keyword(s):

Gene Family ◽

Profile Analysis ◽

Binding Protein ◽

Expression Patterns ◽

Functional Characterization ◽

Limited Information ◽

Protein Motifs ◽

Biotic Stresses ◽

Enhancer Binding Protein ◽

Gene Structures

The GLABROUS1 enhancer-binding protein (GeBP) gene family encodes a typical transcription factor containing a noncanonical Leucine (Leu-)-zipper motif that plays an essential role in regulating plant growth and development, as well as responding to various stresses. However, limited information on the GeBP gene family is available in the case of the Gramineae crops. Here, 125 GeBP genes from nine Gramineae crops species were phylogenetically classified into four clades using bioinformatics analysis. Evolutionary analyses showed that whole genome duplication (WGD) and segmental duplication play important roles in the expansion of the GeBP gene family. The various gene structures and protein motifs revealed that the GeBP genes play diverse functions in plants. In addition, the expression profile analysis of the GeBP genes showed that 13 genes expressed in all tested organs and stages of development in rice, with especially high levels of expression in the leaf, palea, and lemma. Furthermore, the hormone- and metal-induced expression patterns showed that the expression levels of most genes were affected by various biotic stresses, implying that the GeBP genes had an important function in response to various biotic stresses. Furthermore, we confirmed that OsGeBP11 and OsGeBP12 were localized to the nucleus through transient expression in the rice protoplast, indicating that GeBPs function as transcription factors to regulate the expression of downstream genes. This study provides a comprehensive understanding of the origin and evolutionary history of the GeBP genes family in Gramineae, and will be helpful in a further functional characterization of the GeBP genes.

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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 ◽

10.3390/f12111439 ◽

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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