scholarly journals Automatic identification and annotation of MYB gene family members in plants

2021 ◽  
Author(s):  
Boas Pucker
Keyword(s):  
Gene Family ◽  
Functional Annotation ◽  
Sequence Data ◽  
Transcriptome Assembly ◽  
Automatic Identification ◽  
Data Set ◽  
Body Of Knowledge ◽  
Myb Gene ◽  
Genome Wide ◽  
Croton Tiglium

Background: MYBs are among the largest transcription factor families in plants. Consequently, members of this family are involved in a plethora of processes including development and specialized metabolism. The MYB families of many plant species were investigated in the last two decades since the first investigation looked at Arabidopsis thaliana. This body of knowledge and characterized sequences provide the basis for the identification, classification, and functional annotation of candidate sequences in new genome and transcriptome assemblies. Results: A pipeline for the automatic identification and functional annotation of MYBs in a given sequence data set was implemented in Python. MYB candidates are identified, screened for the presence of a MYB domain and other motifs, and finally placed in a phylogenetic context with well characterized sequences. In addition to technical benchmarking based on existing annotation, the transcriptome assembly of Croton tiglium and the annotated genome sequence of Castanea crenata were screened for MYBs. Results of both analyses are presented in this study to illustrate the potential of this application. The analysis of one species takes only a few minutes depending on the number of predicted sequences and the size of the MYB gene family. This pipeline, the required bait sequences, and reference sequences for a classification are freely available on github: https://github.com/bpucker/MYB_annotator. Conclusions: This automatic annotation of the MYB gene family in novel assemblies makes genome-wide investigations consistent and paves the way for comparative studies in the future. Candidate genes for in-depth analyses are presented based on their orthology to previously characterized sequences which allows the functional annotation of the newly identified MYBs with high confidence. The identification of orthologs can also be harnessed to detect duplication and deletion events.

scholarly journals Automatic Identification of Players in the Flavonoid Biosynthesis with Application on the Biomedicinal Plant Croton tiglium

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1103
Author(s):  
Boas Pucker ◽  
Franziska Reiher ◽  
Hanna Marie Schilbert
Keyword(s):  
Sequence Similarity ◽  
Transcriptome Assembly ◽  
Flavonoid Biosynthesis ◽  
Automatic Identification ◽  
Amino Acid Residues ◽  
Proof Of Concept ◽  
Pollinator Attraction ◽  
Biotechnological Potential ◽  
Knowledge Based ◽  
Croton Tiglium

The flavonoid biosynthesis is a well-characterised model system for specialised metabolism and transcriptional regulation in plants. Flavonoids have numerous biological functions such as UV protection and pollinator attraction, but also biotechnological potential. Here, we present Knowledge-based Identification of Pathway Enzymes (KIPEs) as an automatic approach for the identification of players in the flavonoid biosynthesis. KIPEs combines comprehensive sequence similarity analyses with the inspection of functionally relevant amino acid residues and domains in subjected peptide sequences. Comprehensive sequence sets of flavonoid biosynthesis enzymes and knowledge about functionally relevant amino acids were collected. As a proof of concept, KIPEs was applied to investigate the flavonoid biosynthesis of the medicinal plant Croton tiglium on the basis of a transcriptome assembly. Enzyme candidates for all steps in the biosynthesis network were identified and matched to previous reports of corresponding metabolites in Croton species.

scholarly journals Genome-Wide, Integrative Analysis Implicates Exosome-Derived MicroRNA Dysregulation in Schizophrenia

2019 ◽  
Vol 45 (6) ◽  
pp. 1257-1266 ◽  
Author(s):  
Yang Du ◽  
Yun Yu ◽  
Yang Hu ◽  
Xiao-Wan Li ◽  
Ze-Xu Wei ◽  
...  
Keyword(s):  
Target Genes ◽  
Sequence Data ◽  
Protein Glycosylation ◽  
Mirna Sequence ◽  
First Episode ◽  
Data Set ◽  
Protein Levels ◽  
Genome Wide ◽  
Exosomal Mirnas ◽  
Mirna Expression Profiling

Abstract Genetic variants conferring risk for schizophrenia (SCZ) have been extensively studied, but the role of posttranscriptional mechanisms in SCZ is not well studied. Here we performed the first genome-wide microRNA (miRNA) expression profiling in serum-derived exosome from 49 first-episode, drug-free SCZ patients and 46 controls and identified miRNAs and co-regulated modules that were perturbed in SCZ. Putative targets of these SCZ-affected miRNAs were enriched strongly for genes that have been implicated in protein glycosylation and were also related to neurotransmitter receptor and dendrite (spine) development. We validated several differentially expressed blood exosomal miRNAs in 100 SCZ patients as compared with 100 controls by quantitative reverse transcription-polymerase chain reaction. The potential regulatory relationships between several SCZ-affected miRNAs and their putative target genes were also validated. These include hsa-miR-206, which is the most upregulated miRNA in the blood exosomes of SCZ patients and that previously reported to regulate brain-derived neurotrophic factor expression, which we showed reduced mRNA and protein levels in the blood of SCZ patients. In addition, we found 11 miRNAs in blood exosomes from the miRNA sequence data that can be used to classify samples from SCZ patients and control subjects with close to 90% accuracy in the training samples, and approximately 75% accuracy in the testing samples. Our findings support a role for exosomal miRNA dysregulation in SCZ pathophysiology and provide a rich data set and framework for future analyses of miRNAs in the disease, and our data also suggest that blood exosomal miRNAs are promising biomarkers for SCZ.

scholarly journals  Genome-Wide Analysis of R2R3-MYB Transcription Factors Family in The Autopolyploid Saccharum Spontaneum: An Exploration of Dominance Expression and Stress Response 

2021 ◽  
Author(s):  
Yuan Yuan ◽  
Xiping Yang ◽  
Mengfang Feng ◽  
Hongyan Ding ◽  
Khan Muhammad Tahir ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Response ◽  
Gene Family ◽  
Expression Analysis ◽  
Expression Profiling ◽  
Saccharum Spontaneum ◽  
Myb Gene ◽  
Genome Wide ◽  
Myb Genes ◽  
R2r3 Myb

Abstract Background: Sugarcane (Saccharum) is the most important sugar crop in the world. As one of the most enriched transcription factor families in plants, MYB genes display a great potential to contribute to sugarcane improvement by trait modification. We have identified the sugarcane MYB gene family at a whole-genome level through systematic evolution analyses and expression profiling. R2R3-MYB is a large subfamily involved in many plant-specific processes. Results: A total of 202 R2R3-MYB genes (356 alleles) were identified in the polyploid Saccharum spontaneum genome and classified into 15 subgroups by phylogenetic analysis. The sugarcane MYB family had more members by a comparative analysis in sorghum and significant advantages among most plants, especially grasses. Collinearity analysis revealed that 70% of the SsR2R3-MYB genes had experienced duplication events, logically suggesting the contributors to the MYB gene family expansion. Functional characterization was performed to identify 56 SsR2R3-MYB genes involved in various plant bioprocesses with expression profiling analysis on 60 RNA-seq databases. We identified 22 MYB genes specifically expressed in the stem, of which MYB43, MYB53, MYB65, MYB78, and MYB99 were validated by qPCR. Allelic expression dominance in the stem was more significant than that in the leaf, implying the differential expression of alleles may be responsible for the high expression of MYB in the stem. MYB169, MYB181, MYB192 were identified as candidate C4 photosynthetic regulators by C4 expression pattern and robust circadian oscillations. Furthermore, stress expression analysis showed that MYB36, MYB48, MYB54, MYB61 actively responded to drought treatment; 19 and 10 MYB genes were involved in response to the sugarcane pokkah boeng and mosaic disease, respectively. Conclusions: A Genome-wide expression analysis demonstrated that SsMYB genes were involved in stem development and stress response. This study largely contributed to understanding the extent to which MYB transcription factors investigate regulatory mechanisms and functional divergence in sugarcane.

scholarly journals MYB Gene Family in Potato (Solanum tuberosum L.): Genome-Wide Identification of Hormone-Responsive Reveals Their Potential Functions in Growth and Development

2019 ◽  
Vol 20 (19) ◽  
pp. 4847 ◽  
Author(s):  
Wenjun Sun ◽  
Zhaotang Ma ◽  
Hui Chen ◽  
Moyang Liu
Keyword(s):  
Solanum Tuberosum ◽  
Gene Family ◽  
Stress Responses ◽  
Growth And Development ◽  
Solanum Tuberosum L ◽  
Potential Functions ◽  
Anthocyanin Synthesis ◽  
Myb Gene ◽  
Genome Wide ◽  
R2r3 Myb

As an important nongrain crop, the growth and yield of potato (Solanum tuberosum L.) is often affected by an unfavorable external environment in the process of cultivation. The MYB family is one of the largest and most important gene families, participating in the regulation of plant growth and development and response to abiotic stresses. Several MYB genes in potato that regulate anthocyanin synthesis and participate in abiotic stress responses have been identified. To identify all Solanum tuberosum L. MYB (StMYB) genes involved in hormone or stress responses to potentially regulate potato growth and development, we identified the MYB gene family at the genome-wide level. In this work, 158 StMYB genes were found in the potato genome. According to the amino acid sequence of the MYB domain and gene structure, the StMYB genes were divided into R2R3-MYB and R1R2R3-MYB families, and the R2R3-MYB family was divided into 20 subgroups (SGs). The expression of 21 StMYB genes from different SGs in roots, stems, leaves, flowers, shoots, stolons, young tubers, and mature tubers was determined by quantitative real-time polymerase chain reaction (qRT-PCR). The expression patterns of StMYB genes in potatoes treated with abscisic acid (ABA), indole-3-acetic acid (IAA), gibberellin acid 3 (GA3), NaCl, mannitol, and heat were also measured. We have identified several potential candidate genes that regulate the synthesis of potato flavonoids or participate in hormone or stress responses. This work provides a comprehensive understanding of the MYB family in potato and will lay a foundation for the future investigation of the potential functions of StMYB genes in the growth and development of potato.

scholarly journals Genome-Wide Comparative Analysis of R2R3 MYB Gene Family in Populus and Salix and Identification of Male Flower Bud Development-Related Genes

2021 ◽  
Vol 12 ◽  
Author(s):  
Fangwei Zhou ◽  
Yingnan Chen ◽  
Huaitong Wu ◽  
Tongming Yin
Keyword(s):  
Transcription Factor ◽  
Comparative Analysis ◽  
Gene Family ◽  
Pollen Development ◽  
Male Flower ◽  
Flower Bud ◽  
Myb Gene ◽  
Genome Wide ◽  
Myb Genes ◽  
R2r3 Myb

The MYB transcription factor (TF) family is one of the largest plant transcription factor gene family playing vital roles in plant growth and development, including defense, cell differentiation, secondary metabolism, and responses to biotic and abiotic stresses. As a model tree species of woody plants, in recent years, the identification and functional prediction of certain MYB family members in the poplar genome have been reported. However, to date, the characterization of the gene family in the genome of the poplar’s sister species willow has not been done, nor are the differences and similarities between the poplar and willow genomes understood. In this study, we conducted the first genome-wide investigation of the R2R3 MYB subfamily in the willow, identifying 216 R2R3 MYB gene members, and combined with the poplar R2R3 MYB genes, performed the first comparative analysis of R2R3 MYB genes between the poplar and willow. We identified 81 and 86 pairs of R2R3 MYB paralogs in the poplar and willow, respectively. There were 17 pairs of tandem repeat genes in the willow, indicating active duplication of willow R2R3 MYB genes. A further 166 pairs of poplar and willow orthologs were identified by collinear and synonymous analysis. The findings support the duplication of R2R3 MYB genes in the ancestral species, with most of the R2R3 MYB genes being retained during the evolutionary process. The phylogenetic trees of the R2R3 MYB genes of 10 different species were drawn. The functions of the poplar and willow R2R3 MYB genes were predicted using reported functional groupings and clustering by OrthoFinder. Identified 5 subgroups in general expanded in woody species, three subgroups were predicted to be related to lignin synthesis, and we further speculate that the other two subgroups also play a role in wood formation. We analyzed the expression patterns of the GAMYB gene of subgroup 18 (S18) related to pollen development in the male flower buds of poplar and willow at different developmental stages by qRT-PCR. The results showed that the GAMYB gene was specifically expressed in the male flower bud from pollen formation to maturity, and that the expression first increased and then decreased. Both the specificity of tissue expression specificity and conservation indicated that GAMYB played an important role in pollen development in both poplar and willow and was an ideal candidate gene for the analysis of male flower development-related functions of the two species.

scholarly journals Genome-Wide Analysis of MYB Gene Family in Chinese Bayberry (Morella rubra) and Identification of Members Regulating Flavonoid Biosynthesis

2021 ◽  
Vol 12 ◽  
Author(s):  
Yunlin Cao ◽  
Huimin Jia ◽  
Mengyun Xing ◽  
Rong Jin ◽  
Donald Grierson ◽  
...  
Keyword(s):  
Gene Family ◽  
Anthocyanin Biosynthesis ◽  
Expression Patterns ◽  
Flavonoid Biosynthesis ◽  
Structure Evolution ◽  
Chinese Bayberry ◽  
Genome Wide Analysis ◽  
Myb Gene ◽  
Genome Wide ◽  
Family Analysis

Chinese bayberry (Morella rubra), the most economically important fruit tree in the Myricaceae family, is a rich source of natural flavonoids. Recently the Chinese bayberry genome has been sequenced, and this provides an opportunity to investigate the organization and evolutionary characteristics of MrMYB genes from a whole genome view. In the present study, we performed the genome-wide analysis of MYB genes in Chinese bayberry and identified 174 MrMYB transcription factors (TFs), including 122 R2R3-MYBs, 43 1R-MYBs, two 3R-MYBs, one 4R-MYB, and six atypical MYBs. Collinearity analysis indicated that both syntenic and tandem duplications contributed to expansion of the MrMYB gene family. Analysis of transcript levels revealed the distinct expression patterns of different MrMYB genes, and those which may play important roles in leaf and flower development. Through phylogenetic analysis and correlation analyses, nine MrMYB TFs were selected as candidates regulating flavonoid biosynthesis. By using dual-luciferase assays, MrMYB12 was shown to trans-activate the MrFLS1 promoter, and MrMYB39 and MrMYB58a trans-activated the MrLAR1 promoter. In addition, overexpression of 35S:MrMYB12 caused a significant increase in flavonol contents and induced the expression of NtCHS, NtF3H, and NtFLS in transgenic tobacco leaves and flowers and significantly reduced anthocyanin accumulation, resulting in pale-pink or pure white flowers. This indicates that MrMYB12 redirected the flux away from anthocyanin biosynthesis resulting in higher flavonol content. The present study provides valuable information for understanding the classification, gene and motif structure, evolution and predicted functions of the MrMYB gene family and identifies MYBs regulating different aspects of flavonoid biosynthesis in Chinese bayberry.

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

PLoS ONE ◽  
2020 ◽  
Vol 15 (10) ◽  
pp. e0239275
Author(s):  
Boas Pucker ◽  
Ashutosh Pandey ◽  
Bernd Weisshaar ◽  
Ralf Stracke
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Musa Acuminata ◽  
Myb Gene ◽  
Genome Wide ◽  
R2r3 Myb
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