scholarly journals The Genome-Wide Analysis of RALF-Like Genes in Strawberry (Wild and Cultivated) and Five Other Plant Species (Rosaceae)

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 174
Author(s):  
Hong Zhang ◽  
Xiaotong Jing ◽  
Ying Chen ◽  
Zhe Liu ◽  
Yuting Xin ◽  
...  
Keyword(s):  
Evolutionary Process ◽  
Purifying Selection ◽  
Duplication Event ◽  
Regulatory Elements ◽  
Go Annotation ◽  
Evolution Analysis ◽  
Rosaceae Species ◽  
Genome Wide ◽  
Tandem Duplication Event ◽  
Rapid Alkalinization Factor

The rapid alkalinization factor (RALF) gene family is essential for the plant growth and development. However, there is little known about these genes among Rosaceae species. Here, we identify 124 RALF-like genes from seven Rosaceae species, and 39 genes from Arabidopsis, totally 163 genes, divided into four clades according to the phylogenetic analysis, which includes 45 mature RALF genes from Rosaceae species. The YISY motif and RRXL cleavage site are typical features of true RALF genes, but some variants were detected in our study, such as YISP, YIST, NISY, YINY, YIGY, YVGY, FIGY, YIAY, and RRVM. Motif1 is widely distributed among all the clades. According to screening of cis-regulatory elements, GO annotation, expression sequence tags (EST), RNA-seq, and RT-qPCR, we reported that 24 RALF genes coding mature proteins related to tissue development, fungal infection, and hormone response. Purifying selection may play an important role in the evolutionary process of RALF-like genes among Rosaceae species according to the result from ka/ks. The tandem duplication event just occurs in four gene pairs (Fv-RALF9 and Fv-RALF10, Md-RALF7 and Md-RALF8, Pm-RALF2 and Pm-RALF8, and Pp-RALF11 and Pp-RALF14) from four Rosaceae species. Our research provides a wide overview of RALF-like genes in seven Rosaceae species involved in identification, classification, structure, expression, and evolution analysis.

scholarly journals Genome-Wide Identification of Brassinosteroid Signaling Downstream Genes in Nine Rosaceae Species and Analyses of Their Roles in Stem Growth and Stress Response in Apple

2021 ◽  
Vol 12 ◽  
Author(s):  
Liwei Zheng ◽  
Yingli Yang ◽  
Shengjie Ma ◽  
Wenming Wang ◽  
Jimeng Zhang ◽  
...  
Keyword(s):  
Stress Responses ◽  
Agronomic Traits ◽  
Purifying Selection ◽  
Short Shoot ◽  
Gene Expansion ◽  
Rosaceae Species ◽  
Genome Wide ◽  
Brassinosteroid Signaling ◽  
Stress Signals ◽  
External Signals

Brassinosteroid signaling downstream genes regulate many important agronomic traits in rice. However, information on such genes is limited in Arabidopsis and Rosaceae species. We identified these genes in Arabidopsis and nine Rosaceae species. They were, respectively, named based on chromosomal locations. Segmental duplication and whole-genome duplication under purifying selection, as determined by Ka/Ks analysis, likely contributed to Rosaceae gene expansion. Apple (Malus domestica), Arabidopsis, and rice genes were generally similar, while several Rosaceae genes differed from their rice homologs in various characteristics, such as gene length, subcellular localization, transmembrane topology, conserved domains, secondary structures, and responses to external signals. The brassinosteroid downstream genes in apple were, respectively, induced or repressed by five phytohormones. Furthermore, these apple downstream genes were differentially expressed in different apple grafting combinations (“Nagafu No. 2”/“Malling 9” and “Nagafu No. 2”/“Nagafu No. 2”) and long–short shoot varieties (“Yanfu No. 6” and “Nagafu No. 2”). Responses of the MdBZR genes to diverse stress signals were examined and candidate hub genes were identified. These findings indicated that several brassinosteroid signaling downstream genes in Rosaceae functionally differed from their rice homologs, and certain apple genes may play roles in plant height and stress responses. This study provided valuable information and presented enriched biological theories on brassinosteroid signaling downstream genes in apple. Identification of such genes serve to help expand apple breeding and growth. This study provides useful information for brassinosteroid signaling downstream genes.

scholarly journals Genome-wide survey of sucrose non-fermenting 1-related protein kinase 2 in Rosaceae and expression analysis of PbrSnRK2 in response to ABA stress

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Guodong Chen ◽  
Jizhong Wang ◽  
Xin Qiao ◽  
Cong Jin ◽  
Weike Duan ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Gene Family ◽  
Structural Characteristics ◽  
Purifying Selection ◽  
Related Protein ◽  
Rosaceae Species ◽  
Genome Wide ◽  
A Genome ◽  
Genes Encoding ◽  
Genome Wide Survey

Abstract Background The members of the sucrose non-fermenting 1-related protein kinase 2 (SnRK2) family are specific serine/threonine protein kinases in plants that play important roles in stress signal transduction and adaptation. Because of their positive regulatory roles in response to adverse conditions, the genes encoding thes proteins are considered potential candidates for breeding of plants for disease resistance and genetic improvement. However, there is far less information about this kinase family, and the function of these genes has not been explored in Rosaceae. Results A genome-wide survey and analysis of the genes encoding members of the SnRK2 family were performed in pear (Pyrus bretschneideri) and seven other Rosaceae species. A total of 71 SnRK2 genes were identified from the eight Rosaceae species and classified into three subgroups based on phylogenetic analysis and structural characteristics. Purifying selection played a crucial role in the evolution of SnRK2 genes, and whole-genome duplication and dispersed duplication were the primary forces underlying the characteristics of the SnRK2 gene family in Rosaceae. Transcriptome data and qRT-PCR assay results revealed that the distribution of PbrSnRK2s was very extensive, including across the roots, leaves, pollen, styles, and flowers, although most of them were mainly expressed in leaves. In addition, under stress conditions, the transcript levels of some of the genes were upregulated in leaves in response to ABA treatment. Conclusions This study provides useful information and a theoretical introduction for the study of the evolution, expression, and functions of the SnRK2 gene family in plants.

scholarly journals Molecular Traits and Functional Analysis of the CLAVATA3/Endosperm Surrounding Region-Related Small Signaling Peptides in Three Species of Gossypium Genus

2021 ◽  
Vol 12 ◽  
Author(s):  
Huan Lin ◽  
Wei Wang ◽  
Xiugui Chen ◽  
Zhenting Sun ◽  
Xiulan Han ◽  
...  
Keyword(s):  
Structure Prediction ◽  
Growth And Development ◽  
Developmental Stages ◽  
Evolutionary Process ◽  
Interaction Network ◽  
Purifying Selection ◽  
Regulatory Elements ◽  
Signal Molecules ◽  
Segmental Duplications ◽  
Multiple Sequence

The CLAVATA3/endosperm surrounding region-related (CLE) small peptides are a group of C-terminally encoded and post-translationally modified signal molecules involved in regulating the growth and development of various plants. However, the function and evolution of these peptides have so far remained elusive in cotton. In this study, 55, 56, and 86 CLE genes were identified in the Gossypium raimondii, Gossypium arboreum, and Gossypium hirsutum genomes, respectively, and all members were divided into seven groups. These groups were distinctly different in their protein characteristics, gene structures, conserved motifs, and multiple sequence alignment. Whole genome or segmental duplications played a significant role in the expansion of the CLE family in cotton, and experienced purifying selection during the long evolutionary process in cotton. Cis-acting regulatory elements and transcript profiling revealed that the CLE genes of cotton exist in different tissues, developmental stages, and respond to abiotic stresses. Protein properties, structure prediction, protein interaction network prediction of GhCLE2, GhCLE33.2, and GhCLE28.1 peptides were, respectively, analyzed. In addition, the overexpression of GhCLE2, GhCLE33.2, or GhCLE28.1 in Arabidopsis, respectively, resulted in a distinctive shrub-like dwarf plant, slightly purple leaves, large rosettes with large malformed leaves, and lack of reproductive growth. This study provides important insights into the evolution of cotton CLEs and delineates the functional conservatism and divergence of CLE genes in the growth and development of cotton.

scholarly journals Genome-wide survey of sucrose non-fermenting 1-related protein kinase 2 in Rosaceae and expression analysis of PbrSnRK2 in response to ABA stress

2020 ◽  
Author(s):  
Guodong Chen ◽  
Jizhong Wang ◽  
Xin Qiao ◽  
Cong Jin ◽  
Weike Duan ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Gene Family ◽  
Structural Characteristics ◽  
Purifying Selection ◽  
Related Protein ◽  
Rosaceae Species ◽  
Genome Wide ◽  
A Genome ◽  
Genes Encoding ◽  
Genome Wide Survey

Abstract Background: The members of the sucrose non-fermenting 1-related protein kinase 2 (SnRK2) family are specific serine/threonine protein kinases in plants that play important roles in stress signal transduction and adaptation. Because of their positive regulatory roles in response to adverse conditions, the genes encoding thes proteins are considered potential candidates for breeding of plants for disease resistance and genetic improvement. However, there is far less information about this kinase family, and the function of these genes has not been explored in Rosaceae. Results: A genome-wide survey and analysis of the genes encoding members of the SnRK2 family were performed in pear ( Pyrus bretschneideri ) and seven other Rosaceae species. A total of 71 SnRK2 genes were identified from the eight Rosaceae species and classified into three subgroups based on phylogenetic analysis and structural characteristics. Purifying selection played a crucial role in the evolution of SnRK2 genes, and whole-genome duplication and dispersed duplication were the primary forces underlying the characteristics of the SnRK2 gene family in Rosaceae. Transcriptome data and qRT-PCR assay results revealed that the distribution of PbrSnRK2s was very extensive, including across the roots, leaves, pollen, styles, and flowers, although most of them were mainly expressed in leaves. In addition, under stress conditions, the transcript levels of some of the genes were upregulated in leaves in response to ABA treatment. Conclusions: This study provides useful information and a theoretical introduction for the study of the evolution, expression, and functions of the SnRK2 gene family in plants.

scholarly journals Genome-wide identification of PIP5K in wheat and its relationship with anther male sterility induced by high temperature

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Hongzhan Liu ◽  
Zhongke Sun ◽  
Lizong Hu ◽  
Zonghao Yue
Keyword(s):  
Gene Family ◽  
Male Sterility ◽  
Stress Responses ◽  
Evolutionary Process ◽  
Regulatory Elements ◽  
Genome Wide ◽  
Genes Expression ◽  
Key Enzyme ◽  
Gene Structures ◽  
Phosphatidylinositol 4

Abstract Background Phosphatidylinositol 4 phosphate 5-kinase (PIP5K) plays a key enzyme role in the inositol signal transduction system and has essential functions in plants in terms of growth, development, and stress responses. However, systematic studies on the wheat PIP5K gene family and its relation to male sterility have not been reported yet. Results Sixty-four TaPIP5K genes were identified. The TaPIP5K genes contained similar gene structures and conserved motifs on the same branches of the evolutionary tree, and their cis-regulatory elements were related to MeJA-responsiveness. Furthermore, 49 pairs of collinearity genes were identified and mainly subjected to purification selection during evolution. Synteny analyses showed that some PIP5K genes in wheat and the other four species shared a relatively conserved evolutionary process. The expression levels of many conservative TaPIP5K genes in HT-ms anthers were significantly lower than that in Normal anthers. In addition, HT-ms anthers have no dehiscence, and levels of OPDA and JA-ILE are significantly lower at the trinucleus stage. Conclusion These results indicate that the PIP5K gene family may be associated with male sterility induced by HT, and the reduction of JA-ILE levels and the abnormal levels of these genes expression may be one reason for the HT-ms anthers having no dehiscence, ultimately leading to the abortion of the anthers.

scholarly journals Genome-wide survey of sucrose non-fermenting 1-related protein kinase 2 in Rosaceae and expression analysis of PbrSnRK2 in response to ABA stress

2020 ◽  
Author(s):  
Guodong Chen ◽  
Jizhong Wang ◽  
Xin Qiao ◽  
Cong Jin ◽  
Weike Duan ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Gene Family ◽  
Structural Characteristics ◽  
Purifying Selection ◽  
Related Protein ◽  
Rosaceae Species ◽  
Genome Wide ◽  
A Genome ◽  
Genes Encoding ◽  
Genome Wide Survey

Abstract Background The members of the sucrose non-fermenting 1-related protein kinase 2 (SnRK2) family are specific serine/threonine protein kinases in plants, which play important roles in stress signal transduction and adaptation. Because of these positive regulatory roles in response to adversity, the genes encoding them are considered potential candidates for breeding of plants for disease resistance and genetic improvement. However, there is far less information about this kinase family and the function of these genes has not been explored in Rosaceae. Results A genome-wide survey and analysis of the genes encoding members of the SnRK2 family were performed in pear (Pyrus bretschneideri) and seven other Rosaceae species. A total of 71 SnRK2 genes were identified from the eight Rosaceae species and classified into three subgroups based on phylogenetic analysis and structural characteristics. Purifying selection played a crucial role in the evolution of SnRK2 genes, and whole-genome duplication and dispersed duplication were the main forces underlying the characteristics of the SnRK2 gene family in Rosaceae. Transcriptome data and qRT-PCR assays revealed that the distribution of PbrSnRK2s was very extensive including across the roots, leaves, pollen, styles, and flowers, although most of them were mainly expressed in leaves. In addition, under stress conditions, the transcript levels of some of the genes were upregulated in leaves in response to ABA treatments. Conclusions This study provides useful information and a theoretical introduction for the study of the evolution, expression, and functions of the SnRK2 gene family in plants.

scholarly journals Genome-Wide Identification and Characterization of Pectin Methylesterase Inhibitor Genes in Brassica oleracea

2018 ◽  
Vol 19 (11) ◽  
pp. 3338 ◽  
Author(s):  
Tingting Liu ◽  
Hui Yu ◽  
Xingpeng Xiong ◽  
Youjian Yu ◽  
Xiaoyan Yue ◽  
...  
Keyword(s):  
Brassica Oleracea ◽  
Evolutionary Process ◽  
Purifying Selection ◽  
Pectin Methylesterase ◽  
Homologous Gene ◽  
Functional Conservation ◽  
Functional Studies ◽  
Genome Wide ◽  
Inhibitor Genes

The activities of pectin methylesterases (PMEs) are regulated by pectin methylesterase inhibitors (PMEIs), which consequently control the pectin methylesterification status. However, the role of PMEI genes in Brassica oleracea, an economically important vegetable crop, is poorly understood. In this study, 95 B. oleracea PMEI (BoPMEI) genes were identified. A total of 77 syntenic ortholog pairs and 10 tandemly duplicated clusters were detected, suggesting that the expansion of BoPMEI genes was mainly attributed to whole-genome triplication (WGT) and tandem duplication (TD). During diploidization after WGT, BoPMEI genes were preferentially retained in accordance with the gene balance hypothesis. Most homologous gene pairs experienced purifying selection with ω (Ka/Ks) ratios lower than 1 in evolution. Five stamen-specific BoPMEI genes were identified by expression pattern analysis. By combining the analyses of expression and evolution, we speculated that nonfunctionalization, subfunctionalization, neofunctionalization, and functional conservation can occur in the long evolutionary process. This work provides insights into the characterization of PMEI genes in B. oleracea and contributes to the further functional studies of BoPMEI genes.

scholarly journals Genome-wide Identification and Evolution of the PP2C Gene Family in Eight Rosaceae Species and Expression Analysis Under Stress in Pyrus bretschneideri

2021 ◽  
Vol 12 ◽  
Author(s):  
Guoming Wang ◽  
Xun Sun ◽  
Zhihua Guo ◽  
Dirk Joldersma ◽  
Lei Guo ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Expression Analysis ◽  
Protein Phosphatase ◽  
Purifying Selection ◽  
Japanese Apricot ◽  
Rosaceae Species ◽  
Chinese White ◽  
Genome Wide ◽  
Organ Specific ◽  
Pp2c Gene

Type 2C protein phosphatase (PP2C) plays an essential role in abscisic acid (ABA) signaling transduction processes. In the current study, we identify 719 putative PP2C genes in eight Rosaceae species, including 118 in Chinese white pear, 110 in European pear, 73 in Japanese apricot, 128 in apple, 74 in peach, 65 in strawberry, 78 in sweet cherry, and 73 in black raspberry. Further, the phylogenetic analysis categorized PbrPP2C genes of Chinese white pear into twelve subgroups based on the phylogenic analysis. We observed that whole-genome duplication (WGD) and dispersed gene duplication (DSD) have expanded the Rosaceae PP2C family despite simultaneous purifying selection. Expression analysis finds that PbrPP2C genes have organ-specific functions. QRT-PCR validation of nine PbrPP2C genes of subgroup A indicates a role in ABA-mediated response to abiotic stress. Finally, we find that five PbrPP2C genes of subgroup A function in the nucleus. In summary, our research suggests that the PP2C family functions to modulate ABA signals and responds to abiotic stress.

scholarly journals Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data

2020 ◽  
Author(s):  
Tingting Qin ◽  
Christopher Lee ◽  
Raymond Cavalcante ◽  
Peter Orchard ◽  
Heming Yao ◽  
...  
Keyword(s):  
Target Genes ◽  
Cell Types ◽  
Regulatory Elements ◽  
Systematic Evaluation ◽  
Cell Type ◽  
Gene Set ◽  
Go Annotation ◽  
Genome Wide ◽  
Comparable Performance ◽  
Tf Gene

AbstractRevealing the gene targets of distal regulatory elements is challenging yet critical for interpreting regulome data. Experiment-derived enhancer-gene links are restricted to a small set of enhancers and/or cell types, while the accuracy of genome-wide approaches remains elusive due to the lack of a systematic evaluation. We combined multiple spatial and in silico approaches for defining enhancer locations and linking them to their target genes aggregated across >500 cell types, generating 1,860 human genome-wide distal Enhancer to Target gene Definitions (EnTDefs). To evaluate performance, we used gene set enrichment testing on 87 independent ENCODE ChIP-seq datasets of 34 transcription factors (TFs) and assessed concordance of results with known TF Gene Ontology (GO) annotations., assuming that greater concordance with TF-GO annotation signifies better enrichment results and thus more accurate enhancer-to-gene assignments. Notably, the top ranked 741 (40%) EnTDefs significantly outperformed the common, naïve approach of linking distal regions to the nearest genes (FDR < 0.05), and the top 10 ranked EnTDefs performed well when applied to ChIP-seq data of other cell types. These general EnTDefs also showed comparable performance to EnTDefs generated using cell-type-specific data. Our findings illustrate the power of our approach to provide genome-wide interpretation regardless of cell type.

scholarly journals DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

2021 ◽  
Author(s):  
Yanrong Ji ◽  
Zhihan Zhou ◽  
Han Liu ◽  
Ramana V Davuluri
Keyword(s):  
Dna Sequences ◽  
Regulatory Elements ◽  
Ease Of Use ◽  
Fine Tuning ◽  
Supplementary Information ◽  
Sequence Motifs ◽  
Semantic Relationship ◽  
Accurate Identification ◽  
Conserved Sequence ◽  
Genome Wide

Abstract Motivation Deciphering the language of non-coding DNA is one of the fundamental problems in genome research. Gene regulatory code is highly complex due to the existence of polysemy and distant semantic relationship, which previous informatics methods often fail to capture especially in data-scarce scenarios. Results To address this challenge, we developed a novel pre-trained bidirectional encoder representation, named DNABERT, to capture global and transferrable understanding of genomic DNA sequences based on up and downstream nucleotide contexts. We compared DNABERT to the most widely used programs for genome-wide regulatory elements prediction and demonstrate its ease of use, accuracy and efficiency. We show that the single pre-trained transformers model can simultaneously achieve state-of-the-art performance on prediction of promoters, splice sites and transcription factor binding sites, after easy fine-tuning using small task-specific labeled data. Further, DNABERT enables direct visualization of nucleotide-level importance and semantic relationship within input sequences for better interpretability and accurate identification of conserved sequence motifs and functional genetic variant candidates. Finally, we demonstrate that pre-trained DNABERT with human genome can even be readily applied to other organisms with exceptional performance. We anticipate that the pre-trained DNABERT model can be fined tuned to many other sequence analyses tasks. Availability and implementation The source code, pretrained and finetuned model for DNABERT are available at GitHub (https://github.com/jerryji1993/DNABERT). Supplementary information Supplementary data are available at Bioinformatics online.

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