scholarly journals Characterization and expression analysis of the SPL gene family during floral development and abiotic stress in pecan (Carya illinoinensis)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12490
Author(s):  
Min Wang ◽  
Zhenghai Mo ◽  
Ruozhu Lin ◽  
Cancan Zhu
Keyword(s):  
Fruit Development ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Element Analysis ◽  
Systematic Analysis ◽  
Cis Element ◽  
Gene Pairs ◽  
Spatiotemporal Expression ◽  
Squamosa Promoter Binding Protein ◽  
Flower And Fruit Development

SQUAMOSA promoter binding protein-like (SPL) genes are a type of plant-specific transcription factors that play crucial roles in the regulation of phase transition, floral transformation, fruit development, and various stresses. Although SPLs have been characterized in several model species, no systematic analysis has been studied in pecans, an important woody oil tree species. In this study, a total of 32 SPL genes (CiSPLs) were identified in the pecan genome. After conducting phylogenetic analysis of the conserved SBP proteins from Arabidopsis, rice, and poplar, the CiSPLs were separated into eight subgroups. The CiSPL genes within the same subgroup contained very similar exon-intron structures and conserved motifs. Nine segmentally duplicated gene pairs in the pecan genome and 16 collinear gene pairs between the CiSPL and AtSPL genes were identified. Cis-element analysis showed that CiSPL genes may regulate plant meristem differentiation and seed development, participate in various biological processes, and respond to plant hormones and environmental stresses. Therefore, we focused our study on the expression profiles of CiSPL genes during flower and fruit development. Most of the CiSPL genes were predominantly expressed in buds and/or female flowers. Additionally, quantitative real time PCR (qRT-PCR) analyses confirmed that CiSPL genes showed distinct spatiotemporal expression patterns in response to drought and salt treatments. The study provides foundation for the further exploration of the function and evolution of SPL genes in pecan.

scholarly journals Comprehensive Analysis of the TIFY Gene Family and Its Expression Profiles under Phytohormone Treatment and Abiotic Stresses in Roots of Populus trichocarpa

Forests ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 315
Author(s):  
Hanzeng Wang ◽  
Xue Leng ◽  
Xuemei Xu ◽  
Chenghao Li
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Interaction Network ◽  
Pcr Analysis ◽  
Phylogenetic Tree Analysis ◽  
Element Analysis ◽  
Cis Element

The TIFY gene family is specific to land plants, exerting immense influence on plant growth and development as well as responses to biotic and abiotic stresses. Here, we identify 25 TIFY genes in the poplar (Populus trichocarpa) genome. Phylogenetic tree analysis revealed these PtrTIFY genes were divided into four subfamilies within two groups. Promoter cis-element analysis indicated most PtrTIFY genes possess stress- and phytohormone-related cis-elements. Quantitative real-time reverse transcription polymerase chain reaction (qRT–PCR) analysis showed that PtrTIFY genes displayed different expression patterns in roots under abscisic acid, methyl jasmonate, and salicylic acid treatments, and drought, heat, and cold stresses. The protein interaction network indicated that members of the PtrTIFY family may interact with COI1, MYC2/3, and NINJA. Our results provide important information and new insights into the evolution and functions of TIFY genes in P. trichocarpa.

scholarly journals Comparative and Expression Analysis of Ubiquitin Conjugating Domain-Containing Genes in Two Pyrus Species

Cells ◽  
2018 ◽  
Vol 7 (7) ◽  
pp. 77 ◽  
Author(s):  
Yunpeng Cao ◽  
Dandan Meng ◽  
Yu Chen ◽  
Muhammad Abdullah ◽  
Qing Jin ◽  
...  
Keyword(s):  
Fruit Ripening ◽  
Fruit Development ◽  
Expression Patterns ◽  
Orthologous Gene ◽  
Gene Families ◽  
Pyrus Communis ◽  
Functional Verification ◽  
Systematic Analysis ◽  
Gene Pairs ◽  
Genome Wide

Ripening affects the nutritional contents and quality of fleshy fruits, and it plays an important role during the process of fruit development. Studies have demonstrated that ubiquitin-conjugating (UBC or E2) genes can regulate fruit ripening, but the characterization of UBCs in pear is not well documented. The recently published genome-wide sequences of Pyrus bretschneideri and Pyrus communis have allowed a comprehensive analysis of this important gene family in pear. Using bioinformatics approaches, we identified 83 (PbrUBCs) and 84 (PcpUBCs) genes from P. bretschneideri and P. communis, respectively, which were divided into 13 subfamilies. In total, 198 PbrUBC paralogous, 215 PcpUBC paralogous, and 129 orthologous gene pairs were detected. Some paralogous gene pairs were found to be distributed on the same chromosome, suggesting that these paralogs may be caused by tandem duplications. The expression patterns of most UBC genes were divergent between Pyrus bretschneideri and Pyrus communis during pear fruit development. Remarkably, the transcriptome data showed that UBC genes might play a more important role in fruit ripening for further study. This is the first report on the systematic analysis of two Pyrus UBC gene families, and these data will help further study the role of UBC genes in fruit development and ripening, as well as contribute to the functional verification of UBC genes in pear.

scholarly journals Characterization and Divergence Analysis of Duplicated R2R3-MYB Genes in Watermelon

2020 ◽  
Vol 145 (5) ◽  
pp. 281-288 ◽  
Author(s):  
Jin Wang ◽  
Yue Liu ◽  
Xueliang Chen ◽  
Qiusheng Kong
Keyword(s):  
Fruit Development ◽  
Expression Profiles ◽  
Citrullus Lanatus ◽  
Expression Patterns ◽  
Development Stage ◽  
Duplicated Genes ◽  
Nonsynonymous Mutation ◽  
Gene Pairs ◽  
Duplication Events ◽  
R2r3 Myb

Watermelon (Citrullus lanatus) is an economically important cucurbit (Cucurbitaceae) crop cultivated globally for its nutritional benefits. Fruit development in watermelon is characterized by fast fruit expansion attributed to unique biological processes. Myeloblastosis (MYB) family genes play important roles in plant growth and development, especially R2R3-MYB-type genes. However, the evolution of R2R3-MYB family genes in the watermelon genome and whether they participate in the regulation of watermelon fruit development remain unknown. To address these questions, duplication modes of R2R3-MYB family genes were identified and their expression profiles were investigated during watermelon fruit development. A total of 48 duplicated gene pairs were identified among the 89 R2R3-MYBs in watermelon. Segmental and transposed duplication events play major roles in the R2R3-MYB family gene expansion process. The ratio of nonsynonymous mutation and synonymous mutation analysis indicated that all the duplicated R2R3-MYBs experienced negative selection. Gene structures and cis-element compositions in promoter sequences exhibited abundant divergences between the R2R3-MYB duplicated genes. Transcriptome analyses of seed, rind, and flesh during fruit development showed that only two duplicated gene pairs had significantly similar expression patterns, whereas divergent expression profiles were found between the remaining duplicated gene pairs. Tissue-specific and development stage-specific divergent expression patterns demonstrated that neo-functionalization occurred between watermelon R2R3-MYB duplicated genes. The current study provides valuable information for further functional analyses of R2R3-MYBs in watermelon.

scholarly journals Systematic Analysis of Gibberellin Pathway Components in Medicago truncatula Reveals the Potential Application of Gibberellin in Biomass Improvement

2020 ◽  
Vol 21 (19) ◽  
pp. 7180
Author(s):  
Hongfeng Wang ◽  
Hongjiao Jiang ◽  
Yiteng Xu ◽  
Yan Wang ◽  
Lin Zhu ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Ectopic Expression ◽  
Feedback Regulation ◽  
Specific Expression ◽  
Systematic Analysis ◽  
Model Legume ◽  
Genome Wide ◽  
A Genome

Gibberellins (GAs), a class of phytohormones, act as an essential natural regulator of plant growth and development. Many studies have shown that GA is related to rhizobial infection and nodule organogenesis in legume species. However, thus far, GA metabolism and signaling components are largely unknown in the model legume Medicago truncatula. In this study, a genome-wide analysis of GA metabolism and signaling genes was carried out. In total 29 components, including 8 MtGA20ox genes, 2 MtGA3ox genes, 13 MtGA2ox genes, 3 MtGID1 genes, and 3 MtDELLA genes were identified in M. truncatula genome. Expression profiles revealed that most members of MtGAox, MtGID1, and MtDELLA showed tissue-specific expression patterns. In addition, the GA biosynthesis and deactivation genes displayed a feedback regulation on GA treatment, respectively. Yeast two-hybrid assays showed that all the three MtGID1s interacted with MtDELLA1 and MtDELLA2, suggesting that the MtGID1s are functional GA receptors. More importantly, M. truncatula exhibited increased plant height and biomass by ectopic expression of the MtGA20ox1, suggesting that enhanced GA response has the potential for forage improvement.

scholarly journals Alcohol dehydrogenase (ADH) genes family in wheat (Triticum aestivum): Genome-wide identification, characterization, phylogenetic relationship and expression patterns

2020 ◽  
Author(s):  
Changwei Shen ◽  
Jingping Yuan ◽  
Xingqi Ou
Keyword(s):  
Abiotic Stress ◽  
Alcohol Dehydrogenase ◽  
Expression Patterns ◽  
Rice Genome ◽  
Family Members ◽  
Evolutionary Relationship ◽  
Wheat Genome ◽  
Element Analysis ◽  
Gene Pairs ◽  
Adh Genes

Abstract Background Alcohol dehydrogenase (ADH) plays important roles in plant survival under anaerobic conditions. Although some research has been carried out the functions of ADH in other plants, that of wheat TaADH family genes in response to abiotic stress are unclear. Results A total of 22 ADH genes were obtained from 14 chromosomes of the wheat genome by systematic screening. Multiple sequence alignment and evolutionary relationship show that these genes contain the characteristics of GroES-like domain and Zinc-binding domain, and these belong to Medium-chain -ADH type and can be divided into three subfamilies. There are 17 pairs of fragment replication genes among TaADH family members in the wheat genome, while there are 9 pairs of collinear gene pairs from ADH family members between wheat and rice genome. We speculate that these fragment repetition events may be the main reason for the amplification of TaADH family genes. Ka/Ks analysis indicated that there were 64 repetitive gene pairs, and the Ka/Ks value of these gene pairs was less than 1, which indicated that these sequences of TaADH gene were relatively conservative and did not change greatly in the process of evolution. Promoter element analysis showed that almost all of the upstream promoters of these genes contained the responsive anaerobic inducible element. Tissue localized expression and expression patterns also demonstrated that the TaADH genes responded to abiotic stress and may play an important role in waterlogging stress during the seed germination stage. Conclusions The results of this study may be helpful to further study the function of TaADH genes and determine the candidate gene for wheat stress resistance breeding.

scholarly journals An Actinidia chinensis (kiwifruit) eFP browser and network analysis of transcription factors

2020 ◽  
Author(s):  
Lara Brian ◽  
Ben Warren ◽  
Peter McAtee ◽  
Jessica Rodrigues ◽  
Niels Nieuwenhuizen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Network Analysis ◽  
Fruit Development ◽  
Transcriptional Control ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Actinidia Chinensis ◽  
Knox Gene ◽  
Hub Genes ◽  
Flower And Fruit Development

Abstract BackgroundTranscriptomic studies combined with a well annotated genome have laid the foundations for new understanding of molecular processes. Tools which visualise gene expression patterns have further added to these resources. The manual annotation of the Actinidia chinensis (kiwifruit) genome has resulted in a high quality set of 33,044 genes. Here we investigate gene expression patterns in diverse tissues, visualised in an Electronic Fluorescent Pictograph (eFP) browser, to study the relationship of transcription factor (TF) expression using network analysis. ResultsSixty-one samples covering diverse tissues at different developmental time points were selected for RNAseq analysis and an eFP browser was generated to visualise this dataset. 2,839 TFs representing 57 different classes were identified and named. Network analysis of the TF expression patterns separated TFs into 14 different modules. Two modules consisting of 237 TFs were correlated with floral bud and flower development, a further two modules containing 160 TFs were associated with fruit development and maturation. A single module of 480 TFs was associated with ethylene-induced fruit ripening. Three “hub” genes correlated with flower and fruit development consisted of a HAF-like gene central to gynoecium development, an ERF and a DOF gene. Maturing and ripening hub genes included a KNOX gene that was associated with seed maturation, and a GRAS-like TF.ConclusionsThis study provides an insight into the complexity of the transcriptional control of flower and fruit development, as well as providing a new resource to the plant community. The eFP browser is provided in an accessible format that allows researchers to download and work internally.

scholarly journals Genome-wide investigation of the AP2/ERF gene family in  ginger: evolution and expression profiles during rhizome and inflorescence development

2021 ◽  
Author(s):  
Haitao Xing ◽  
Yusong Jiang ◽  
Xiaoling Long ◽  
Xiaoli Wu ◽  
Yun Ren ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Whole Genome Sequence ◽  
Chromosomal Distribution ◽  
Inflorescence Development ◽  
Systematic Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Erf Transcription Factors

Abstract Background:AP2/ERF transcription factors perform indispensable functions in various biological processes, such as plant growth, development, biotic and abiotic stresses responses. The AP2/ERF transcription factor family has been identified in many plants, and several AP2/ERF transcription factors from Arabidopsis (Arabidopsis thaliana) have been functionally characterized. However, little research has been conducted on the AP2/ERF genes of ginger (Zingiber officinale), which is an important edible and medicinal horticultural plant. The recently published whole genome sequence of ginger allowed us to study the tissue and expression profiles of AP2/ERF genes in ginger on a genome-wide basis.Results:In this study, 163 AP2/ERF genes of ginger (ZoAP2/ERF) were identified and renamed according to the chromosomal distribution of the ZoAP2/ERF genes. According to the number conserved domains and gene structure, the AP2/ERF genes were divided into three subfamilies by phylogenetic analysis, namely, AP2 (35 members), ERF (125 members) and RAV (3 members). A total of 10 motifs were detected in ginger AP2/ERF genes, and some of the unique motifs were found to be important for the function of ZoAP2/ERF genes.Conclusion:A comprehensive analysis of AP2/ERF gene expression patterns in different tissues and rhizome development stages by transcriptom sequence and quantitative real-time PCR (qRT-PCR) showed that they played an important role in the growth and development of ginger, and genes that might regulate rhizome and flower development were preliminarily identified. This systematic analysis establishes a foundation for further studies of the functional characteristics of ZoAP2/ERF genes and improvement of ginger.

scholarly journals Genome-Wide Identification, Characterization and Expression Analysis of TCP Transcription Factors in Petunia

2020 ◽  
Vol 21 (18) ◽  
pp. 6594
Author(s):  
Shuting Zhang ◽  
Qin Zhou ◽  
Feng Chen ◽  
Lan Wu ◽  
Baojun Liu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Leaf Morphogenesis ◽  
Systematic Analysis ◽  
Genome Wide ◽  
A Genome

The plant-specific TCP transcription factors are well-characterized in both monocots and dicots, which have been implicated in multiple aspects of plant biological processes such as leaf morphogenesis and senescence, lateral branching, flower development and hormone crosstalk. However, no systematic analysis of the petunia TCP gene family has been described. In this work, a total of 66 petunia TCP genes (32 PaTCP genes in P. axillaris and 34 PiTCP genes in P. inflata) were identified. Subsequently, a systematic analysis of 32 PaTCP genes was performed. The phylogenetic analysis combined with structural analysis clearly distinguished the 32 PaTCP proteins into two classes—class Ι and class Ⅱ. Class Ⅱ was further divided into two subclades, namely, the CIN-TCP subclade and the CYC/TB1 subclade. Plenty of cis-acting elements responsible for plant growth and development, phytohormone and/or stress responses were identified in the promoter of PaTCPs. Distinct spatial expression patterns were determined among PaTCP genes, suggesting that these genes may have diverse regulatory roles in plant growth development. Furthermore, differential temporal expression patterns were observed between the large- and small-flowered petunia lines for most PaTCP genes, suggesting that these genes are likely to be related to petal development and/or petal size in petunia. The spatiotemporal expression profiles and promoter analysis of PaTCPs indicated that these genes play important roles in petunia diverse developmental processes that may work via multiple hormone pathways. Moreover, three PaTCP-YFP fusion proteins were detected in nuclei through subcellular localization analysis. This is the first comprehensive analysis of the petunia TCP gene family on a genome-wide scale, which provides the basis for further functional characterization of this gene family in petunia.

scholarly journals A gene expression atlas for kiwifruit (Actinidia chinensis) and network analysis of transcription factors

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Lara Brian ◽  
Ben Warren ◽  
Peter McAtee ◽  
Jessica Rodrigues ◽  
Niels Nieuwenhuizen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Network Analysis ◽  
Fruit Development ◽  
Transcriptional Control ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Actinidia Chinensis ◽  
Knox Gene ◽  
Hub Genes ◽  
Flower And Fruit Development

Abstract Background Transcriptomic studies combined with a well annotated genome have laid the foundations for new understanding of molecular processes. Tools which visualise gene expression patterns have further added to these resources. The manual annotation of the Actinidia chinensis (kiwifruit) genome has resulted in a high quality set of 33,044 genes. Here we investigate gene expression patterns in diverse tissues, visualised in an Electronic Fluorescent Pictograph (eFP) browser, to study the relationship of transcription factor (TF) expression using network analysis. Results Sixty-one samples covering diverse tissues at different developmental time points were selected for RNA-seq analysis and an eFP browser was generated to visualise this dataset. 2839 TFs representing 57 different classes were identified and named. Network analysis of the TF expression patterns separated TFs into 14 different modules. Two modules consisting of 237 TFs were correlated with floral bud and flower development, a further two modules containing 160 TFs were associated with fruit development and maturation. A single module of 480 TFs was associated with ethylene-induced fruit ripening. Three “hub” genes correlated with flower and fruit development consisted of a HAF-like gene central to gynoecium development, an ERF and a DOF gene. Maturing and ripening hub genes included a KNOX gene that was associated with seed maturation, and a GRAS-like TF. Conclusions This study provides an insight into the complexity of the transcriptional control of flower and fruit development, as well as providing a new resource to the plant community. The Actinidia eFP browser is provided in an accessible format that allows researchers to download and work internally.

scholarly journals Genome-Wide Investigation of the NF-X1 Gene Family in Populus trichocarpa Expression Profiles during Development and Stress

2021 ◽  
Vol 22 (9) ◽  
pp. 4664
Author(s):  
Fang He ◽  
Yu-Jie Shi ◽  
Jia-Xuan Mi ◽  
Kuang-Ji Zhao ◽  
Xing-Lei Cui ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Molecular Genetic ◽  
Mechanical Damage ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genetic Progress ◽  
Whole Genome Analysis ◽  
Element Analysis

Poplar are planted extensively in reforestation and afforestation. However, their successful establishment largely depends on the environmental conditions of the newly established plantation and their resistance to abiotic as well as biotic stresses. NF-X1, a widespread transcription factor in plants, plays an irreplaceable role in plant growth, development, and stress tolerance. Although the whole genome sequence of Populus trichocarpa has been published for a long time, little is known about the NF-X1 genes in poplar, especially those related to drought stress, mechanical damage, insect feeding, and hormone response at the whole genome level. In this study, whole genome analysis of the poplar NF-X1 family was performed, and 4 PtrNF-X1 genes were identified. Then, bioinformatics analysis and qRT-PCR were applied to analyze the gene structure, phylogeny, chromosomal localization, gene replication, Cis-elements, and expression patterns of PtrNF-X1genes. Sequence analysis revealed that one-quarter of the PtrNF-X1 genes did not contain introns. Phylogenetic analysis revealed that all NF-X1 genes were split into three subfamilies. The number of two pairs of segmented replication genes were detected in poplars. Cis-acting element analysis identified a large number of elements of growth and development and stress-related elements on the promoters of different NF-X1 members. In addition, some PtrNF-X1 could be significantly induced by polyethylene glycol (PEG) and abscisic acid (ABA), thus revealing their potential role in regulating stress response. Comprehensive analysis is helpful in selecting candidate NF-X1 genes for the follow-up study of the biological function, and molecular genetic progress of stress resistance in forest trees provides genetic resources.

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