scholarly journals Genome-Wide Analysis of the D-type Cyclin Gene Family Reveals Differential Expression Patterns and Stem Development in the Woody Plant Prunus mume

Forests ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 147 ◽  
Author(s):  
Tangchun Zheng ◽  
Xiaokang Zhuo ◽  
Lulu Li ◽  
Tangren Cheng ◽  
Qixiang Zhang
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Ornamental Plants ◽  
Prunus Mume ◽  
Specific Expression ◽  
Genome Wide ◽  
Plant Stem ◽  
Stem Development ◽  
Cyclin Gene ◽  
Rate Limiting

Cyclins, a prominent class of cell division regulators, play an extremely important role in plant growth and development. D-type cyclins (CYCDs) are the rate-limiting components of the G1 phase. In plants, studies of CYCDs are mainly concerned with herbaceous plants, yet little information is available about these genes in perennial woody plants, especially ornamental plants. Here, twelve Prunus mume CYCD (PmCYCDs) genes are identified and characterized. The PmCYCDs were named on the basis of orthologues in Arabidopsis thaliana and Oryza sativa. Gene structure and conserved domains of each subgroup CYCDs was similar to that of their orthologues in A. thaliana and O. sativa. However, PmCYCDs exhibited different tissue-specific expression patterns in root, stem, leaf, bud, and fruit organs. The results of qRT-PCR showed that all PmCYCDs, except PmCYCD5;2 and PmCYCD7;1, were primarily highly expressed in leaf buds, shoots, and stems. In addition, the transcript levels of PmCYCD genes were analyzed in roots under different treatments, including exogenous applications of NAA, 6-BA, GA3, ABA, and sucrose. Interestingly, although PmCYCDs were induced by sucrose, the extent of gene induction among PmCYCD subgroups varied. The induction of PmCYCD1;2 by hormones depended on the presence of sucrose. PmCYCD3;1 was stimulated by NAA, and induction was strengthened when sugar and hormones were applied together. Taken together, our study demonstrates that PmCYCDs are functional in plant stem development and provides a basis for selecting members of the cyclin gene family as candidate genes for ornamental plant breeding.

scholarly journals Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon

2019 ◽  
Author(s):  
Yong Zhou ◽  
Yuan Cheng ◽  
Chunpeng Wan ◽  
Youxin Yang ◽  
Jinyin Chen
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Expression Patterns ◽  
Future Research ◽  
Biological Processes ◽  
Biological Functions ◽  
Specific Expression ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Intron Structure

The plant DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors that play vital roles in many biological processes and response to stresses. In the present study, a total of 36 ClDof genes were identified in the watermelon genome, which were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the ClDof proteins could be divided into nine groups, and the members in a particular group had similar motif arrangement and exon-intron structure. We then analyzed the expression patterns of nine selected ClDof genes in eight specific tissues by qRT-PCR, and the results showed that they have tissue-specific expression patterns. We also evaluated the expression levels of the nine selected ClDof genes under salt stress and ABA treatments using qRT-PCR, and they showed differential expression under these treatments, suggesting their important roles in stress response. Taken together, our results provide a basis for future research on the biological functions of Dof genes in watermelon.

scholarly journals Genome-Wide Analysis of Members of the WRKY Gene Family and Their Cold Stress Response in Prunus mume

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 911 ◽  
Author(s):  
Bao ◽  
Ding ◽  
Cheng ◽  
Wang ◽  
Zhang
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Patterns ◽  
Wrky Transcription Factor ◽  
Segmental Duplications ◽  
Wrky Gene ◽  
Prunus Mume ◽  
Spatiotemporal Expression ◽  
Genome Wide ◽  
Transcription Factor Genes

Prunus mume, which is a rosaceous arbor with very high ornamental, edible and medical values, has a distribution that is mainly restricted by low temperature. WRKY transcription factor genes play crucial roles in the growth, development, and stress responses of plants. However, the WRKY gene family has not been characterised in P. mume. There were 58 PmWRKYs identified from genome of P. mume. They were anchored onto eight link groups and categorised into three broad groups. The gene structure and motif composition were reasonably conservative in each group. Investigation of gene duplication indicated that nine and seven PmWRKYs were arranged in tandem and segmental duplications, respectively. PmWRKYs were discriminately expressed in different tissues (i.e., roots, stems, leaves, flowers and fruits) in P. mume. The 17 cold-related candidate genes were selected based on RNA-seq data. Further, to investigate the function of PmWRKYs in low temperatures, the expression patterns under artificial cold treatments were analysed. The results showed that the expression levels of the 12 PmWRKYs genes significantly and 5 genes slightly changed in stems. In particular, the expression level of PmWRKY18 was up-regulated after ABA treatment. In addition, the spatiotemporal expression patterns of 17 PmWRKYs were analysed in winter. These results indicated that 17 PmWRKYs were potential transcription factors regulating cold resistance in P. mume.

scholarly journals The AP2/ERF Gene Family in Triticum durum: Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1464
Author(s):  
Sahar Faraji ◽  
Ertugrul Filiz ◽  
Seyed Kamal Kazemitabar ◽  
Alessandro Vannozzi ◽  
Fabio Palumbo ◽  
...  
Keyword(s):  
Stress Response ◽  
Gene Family ◽  
Durum Wheat ◽  
Triticum Turgidum ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Site Directed Mutagenesis ◽  
Specific Expression ◽  
Docking Simulations ◽  
Genome Wide

Members of the AP2/ERF transcription factor family play critical roles in plant development, biosynthesis of key metabolites, and stress response. A detailed study was performed to identify TtAP2s/ERFs in the durum wheat (Triticum turgidum ssp. durum) genome, which resulted in the identification of 271 genes distributed on chromosomes 1A-7B. By carrying 27 genes, chromosome 6A had the highest number of TtAP2s/ERFs. Furthermore, a duplication assay of TtAP2s/ERFs demonstrated that 70 duplicated gene pairs had undergone purifying selection. According to RNA-seq analysis, the highest expression levels in all tissues and in response to stimuli were associated with DRF and ERF subfamily genes. In addition, the results revealed that TtAP2/ERF genes have tissue-specific expression patterns, and most TtAP2/ERF genes were significantly induced in the root tissue. Additionally, 13 TtAP2/ERF genes (six ERFs, three DREBs, two DRFs, one AP2, and one RAV) were selected for further analysis via qRT-PCR of their potential in coping with drought and salinity stresses. The TtAP2/ERF genes belonging to the DREB subfamily were markedly induced under both drought-stress and salinity-stress conditions. Furthermore, docking simulations revealed several residues in the pocket sites of the proteins associated with the stress response, which may be useful in future site-directed mutagenesis studies to increase the stress tolerance of durum wheat. This study could provide valuable insights for further evolutionary and functional assays of this important gene family in durum wheat.

scholarly journals Genome-wide identification and expression analysis of the NCED family in cotton (Gossypium hirsutum L.)

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246021
Author(s):  
QingHua Li ◽  
XianTao Yu ◽  
Long Chen ◽  
Gang Zhao ◽  
ShiZhou Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Plant Hormone ◽  
Expression Patterns ◽  
Multiple Roles ◽  
Motif Analysis ◽  
Specific Expression ◽  
Genome Wide ◽  
Aba Content ◽  
Aba Synthesis

Abscisic acid (ABA) is an important plant hormone that plays multiple roles in regulating growth and development as well as in stress responses in plants. The NCED gene family includes key genes involved in the process of ABA synthesis. This gene family has been found in many species; however, the function of the NCED gene family in cotton is unclear. Here, a total of 23 NCED genes (designated as GhNCED1 to GhNCED23) were identified in cotton. Phylogenetic analysis indicated that the identified NCED proteins from cotton and Arabidopsis could be classified into 4 subgroups. Conserved motif analysis revealed that the gene structure and motif distribution of proteins within each subgroup were highly conserved. qRT-PCR and ABA content analyses indicated that NCED genes exhibited stage-specific expression patterns at tissue development stages. GhNCED5, GhNCED6 and GhNCED13 expression was similar to the change in ABA content, suggesting that this gene family plays a role in ABA synthesis. These results provide a better understanding of the potential functions of GhNCED genes.

scholarly journals The R2R3-MYB gene family in banana (Musa acuminata): genome-wide identification, classification and expression patterns

2020 ◽  
Author(s):  
Boas Pucker ◽  
Ashutosh Pandey ◽  
Bernd Weisshaar ◽  
Ralf Stracke
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Gene Families ◽  
Defense Responses ◽  
Musa Acuminata ◽  
Specific Expression ◽  
Genome Wide ◽  
A Genome ◽  
Myb Proteins ◽  
R2r3 Myb

AbstractThe R2R3-MYB genes comprise one of the largest transcription factor gene families in plants, playing regulatory roles in plant-specific developmental processes, defense responses and metabolite accumulation. To date MYB family genes have not yet been comprehensively identified in the major staple fruit crop banana. In this study, we present a comprehensive, genome-wide analysis of the MYB genes from Musa acuminata DH-Pahang (A genome). A total of 285 R2R3-MYB genes as well as genes encoding three other classes of MYB proteins containing multiple MYB repeats were identified and characterised with respect to structure and chromosomal organisation. Organ- and development-specific expression patterns were determined from RNA-seq data. For 280 M. acuminata MYB genes for which expression was found in at least one of the analysed samples, a variety of expression patterns were detected. The M. acuminata R2R3-MYB genes were functionally categorised, leading to the identification of seven clades containing only M. acuminata R2R3-MYBs. The encoded proteins may have specialised functions that were acquired or expanded in Musa during genome evolution. This functional classification and expression analysis of the MYB gene family in banana establishes a solid foundation for future comprehensive functional analysis of MaMYBs and can be utilized in banana improvement programmes.

scholarly journals Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8358 ◽  
Author(s):  
Yong Zhou ◽  
Yuan Cheng ◽  
Chunpeng Wan ◽  
Jingwen Li ◽  
Youxin Yang ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Patterns ◽  
Future Research ◽  
Promoter Regions ◽  
Syntenic Relationship ◽  
Specific Expression ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Intron Structure

The plant DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors that play vital roles in many biological processes and stress responses. In the present study, a total of 36 ClDof genes were identified in the watermelon genome, which were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the ClDof proteins could be divided into nine groups, and the members in a particular group had similar motif arrangement and exon–intron structure. Synteny analysis indicated the presence of a large number of syntenic relationship events between watermelon and cucumber. In promoter analysis, five kinds of stress-related and nine kinds of hormone-related cis-elements were identified in the promoter regions of ClDof genes. We then analyzed the expression patterns of nine selected ClDof genes in eight specific tissues by qRT-PCR, and the results showed that they have tissue-specific expression patterns. We also evaluated the expression levels of 12 selected ClDof genes under salt stress and ABA treatments using qRT-PCR. As a result, they showed differential expression under these treatments, suggesting their important roles in stress response. Taken together, our results provide a basis for future research on the biological functions of Dof genes in watermelon.

scholarly journals Genome-Wide Identification and Characterization of the ALOG Domain Genes in Rice

2019 ◽  
Vol 2019 ◽  
pp. 1-13
Author(s):  
Na Li ◽  
Yang Wang ◽  
Jing Lu ◽  
Chuan Liu
Keyword(s):  
Gene Family ◽  
Stem Elongation ◽  
Expression Patterns ◽  
Rice Genome ◽  
Functional Study ◽  
Segmental Duplications ◽  
Specific Expression ◽  
Genome Wide ◽  
A Genome ◽  
Comparative Expression Analysis

The ALOG domain genes, named after the Arabidopsis LSH1 and Oryza G1 (ALOG) proteins, have frequently been reported as key developmental regulators in rice and Arabidopsis. However, the investigation of the ALOG gene family is limited. Here, we conducted a genome-wide investigation of the ALOG gene family in rice and six other species. In total, eighty-four ALOG domain genes were identified from the seven species, of which fourteen ALOG domain genes (OsG1/G1Ls) were identified in the rice genome. The fourteen OsG1/G1Ls were unevenly distributed on eight chromosomes, and we found that eight segmental duplications contributed to the expansion of OsG1/G1Ls in the rice genome. The eighty-four ALOG family genes from seven species were classified into six clusters, and the ALOG domain-defined motifs 1, 2, and 3 were highly conserved across species according to the phylogenetic and structural analysis. However, the newly identified motifs 4 and 5 were only present in monocots, indicating a specified function in monocots. Moreover, OsG1/G1Ls exhibited tissue-specific expression patterns. Coexpression analysis suggested that OsG1 integrates OsMADS50 and the downstream MADS-box genes, such as OsMADS1, to regulate the development of rice inflorescence; OsG1L7 potentially associates with OsMADS22 and OsMADS55 to regulate stem elongation. In addition, comparative expression analysis revealed the conserved biological functions of ALOG family genes among rice, maize, and Arabidopsis. These results have shed light on the functional study of ALOG family genes in rice and other plants.

scholarly journals Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon

2019 ◽  
Author(s):  
Yong Zhou ◽  
Yuan Cheng ◽  
Chunpeng Wan ◽  
Youxin Yang ◽  
Jinyin Chen
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Expression Patterns ◽  
Future Research ◽  
Biological Processes ◽  
Biological Functions ◽  
Specific Expression ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Intron Structure

The plant DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors that play vital roles in many biological processes and response to stresses. In the present study, a total of 36 ClDof genes were identified in the watermelon genome, which were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the ClDof proteins could be divided into nine groups, and the members in a particular group had similar motif arrangement and exon-intron structure. We then analyzed the expression patterns of nine selected ClDof genes in eight specific tissues by qRT-PCR, and the results showed that they have tissue-specific expression patterns. We also evaluated the expression levels of the nine selected ClDof genes under salt stress and ABA treatments using qRT-PCR, and they showed differential expression under these treatments, suggesting their important roles in stress response. Taken together, our results provide a basis for future research on the biological functions of Dof genes in watermelon.

scholarly journals Genome-wide identification and expression profiling of the COBRA-like genes reveal likely roles in stem strength in rapeseed (Brassica napus L.)

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0260268
Author(s):  
Qian Yang ◽  
Shan Wang ◽  
Hao Chen ◽  
Liang You ◽  
Fangying Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Rna Seq ◽  
Brassica Napus L ◽  
Preferential Expression ◽  
Stem Strength ◽  
Genome Wide ◽  
Anisotropic Expansion ◽  
Stem Development ◽  
Genome Triplication

The COBRA-like (COBL) genes play key roles in cell anisotropic expansion and the orientation of microfibrils. Mutations in these genes cause the brittle stem and induce pathogen responsive phenotypes in Arabidopsis and several crop plants. In this study, an in silico genome-wide analysis was performed to identify the COBL family members in Brassica. We identified 44, 20 and 23 COBL genes in B. napus and its diploid progenitor species B. rapa and B. oleracea, respectively. All the predicted COBL genes were phylogenetically clustered into two groups: the AtCOB group and the AtCOBL7 group. The conserved chromosome locations of COBLs in Arabidopsis and Brassica, together with clustering, indicated that the expansion of the COBL gene family in B. napus was primarily attributable to whole-genome triplication. Among the BnaCOBLs, 22 contained all the conserved motifs and derived from 9 of 12 subgroups. RNA-seq analysis was used to determine the tissue preferential expression patterns of various subgroups. BnaCOBL9, BnaCOBL35 and BnaCOBL41 were highly expressed in stem with high-breaking resistance, which implies these AtCOB subgroup members may be involved in stem development and stem breaking resistance of rapeseed. Our results of this study may help to elucidate the molecular properties of the COBRA gene family and provide informative clues for high stem-breaking resistance studies.

scholarly journals Genome-Wide Identification and Expression Profiling Analysis of Wnt Family Genes Affecting Adipocyte Differentiation in Cattle

2021 ◽  
Author(s):  
Cuili Pan ◽  
Shuzhe Wang ◽  
Chaoyun Yang ◽  
Chunli Hu ◽  
Hui Sheng ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Protein Motif ◽  
Chromosomal Distribution ◽  
Specific Expression ◽  
Wnt Proteins ◽  
Genome Wide ◽  
Protein Properties ◽  
Bovine Adipocytes

Abstract Wnt is a family of conserved glycoproteins that functions in a variety of crucial biological processes including tissue regeneration, animal development, and cell proliferation and differentiation. For its functional diversity and importance, Wnt gene family has gained considerable research interest in a variety of species. However, comprehensive identification and analysis of Wnt genes in Bovinae is lacking. In this study, we identified the repertoire of Wnt genes in cattle and seven other species of Bovinae and obtained 19 Wnt genes. Protein properties of these Wnt genes were also described. Phylogenetic analysis showed that the 149 Wnt proteins in Bovinae, together with 38 Wnt proteins from human and mouse, were clustered into 12 major clades. The Wnt genes belonging to the same subfamilies shared similar protein motif compositions and exon-intron patterns. Chromosomal distribution and collinearity analysis of Wnt genes among cattle and five species of Bovinae revealed that this gene family was conservative in evolution. RNA-seq data analysis indicated that Wnt genes exhibited tissue-specific expression patterns in cattle. qPCR analysis of Wnt gene family showed that each gene had a unique expression pattern during bovine adipocytes differentiation. And the comprehensive analysis indicated that Wnt2B may regulate adipose differentiation through activation of FZD5, which is worthy of further study. Our study presents the first genome-wide study of Wnt gene family in Bovinae, and lay the foundation for further functional characterization of the Wnt family in bovine adipocytes differentiation.

Sign in / Sign up

Export Citation Format

Share Document