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Temporally distinct regulatory pathways coordinate thermo-responsive storage organ formation in potato. Cell Rep 2022; 38:110579. [PMID: 35354037 DOI: 10.1016/j.celrep.2022.110579] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/14/2021] [Accepted: 03/04/2022] [Indexed: 11/23/2022] Open
Abstract
Tuberization is an important developmental process in potatoes, but it is highly affected by environmental conditions. Temperature is a major environmental factor affecting tuberization, with high temperatures suppressing tuber development. However, the temporal aspects of thermo-responsive tuberization remain elusive. In this study, we show that FT homolog StSP6A is suppressed by temporally distinct regulatory pathways. Experiments using StSP6A-overexpressing plants show that post-transcriptional regulation plays a major role at the early stage, while transcriptional regulation is an important late-stage factor, suppressing StSP6A at high temperatures in leaves. Overexpression of StSP6A in leaves restores tuber formation but does not recover tuber yield at the late stage, possibly because of suppressed sugar transport at high temperatures. Transcriptome analyses lead to the identification of potential regulators that may be involved in thermo-responsive tuberization at different stages. Our work shows that potato has temporally distinct molecular mechanisms that finely control tuber development at high temperatures.
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2
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Zhang G, Tang R, Niu S, Si H, Yang Q, Rajora OP, Li XQ. Heat-stress-induced sprouting and differential gene expression in growing potato tubers: Comparative transcriptomics with that induced by postharvest sprouting. HORTICULTURE RESEARCH 2021; 8:226. [PMID: 34654802 PMCID: PMC8519922 DOI: 10.1038/s41438-021-00680-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 08/08/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Crops face increased risk from heat stress due to climate change. Potato (Solanum tuberosum L.) tubers grown in hot summers often have defects including pre-harvest sprouting ("heat sprouts"). We have used 18 potato cultivars to investigate whether heat stress (HS) conditions alone could cause heat sprouting and dormancy changes in tubers. We also examined transcriptomic responses of potato to HS and whether these responses are like those induced by postharvest sprouting. We demonstrated that HS alone caused heat sprouts and shortened postharvest dormancy period, heat-sprouted tubers became dormant after harvest, and cultivars varied substantially for producing heat spouts but there was no clear association with cultivar maturity earliness. Cultivar Innovator did not show any heat sprouts and still had long dormancy. Dormancy-associated genes (DOG1 and SLP) were downregulated in HS tubers like in postharvest sprouting tubers. We have identified 1201 differentially expressed genes, 14 enriched GO terms and 12 enriched KEGG pathways in response to HS in growing tubers of 'Russet Burbank'. Transcriptomic response of 'Russet Burbank' to HS showed significant similarities to that of postharvest non-HS sprouted tubers. Gibberellin biosynthesis pathway was enriched in heat-stressed tubers and was likely involved in heat sprouting and dormancy release. Heat sprouting and postharvest sprouting shared common candidate genes and had significant similarity in gene expression. Our study has significance for selecting potato cultivars for farming, planning storage and utilization of heat-stressed tubers, identifying sprouting-related genes, understanding heat-stress biology, and breeding heat-tolerant potato cultivars, especially for sustainable potato production under climate change.
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Affiliation(s)
- Guodong Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, Fredericton, New Brunswick, Canada
| | - Ruimin Tang
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, Fredericton, New Brunswick, Canada
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Suyan Niu
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, Fredericton, New Brunswick, Canada
- Institute of Bioengineering, Zhengzhou Normal University, Zhengzhou, China
| | - Huaijun Si
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China.
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China.
| | - Qing Yang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China.
| | - Om P Rajora
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, Canada.
| | - Xiu-Qing Li
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, Fredericton, New Brunswick, Canada.
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3
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Wimalanathan K, Lawrence-Dill CJ. Gene Ontology Meta Annotator for Plants (GOMAP). PLANT METHODS 2021; 17:54. [PMID: 34034755 PMCID: PMC8146647 DOI: 10.1186/s13007-021-00754-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/10/2021] [Indexed: 05/03/2023]
Abstract
Annotating gene structures and functions to genome assemblies is necessary to make assembly resources useful for biological inference. Gene Ontology (GO) term assignment is the most used functional annotation system, and new methods for GO assignment have improved the quality of GO-based function predictions. The Gene Ontology Meta Annotator for Plants (GOMAP) is an optimized, high-throughput, and reproducible pipeline for genome-scale GO annotation of plants. We containerized GOMAP to increase portability and reproducibility and also optimized its performance for HPC environments. Here we report on the pipeline's availability and performance for annotating large, repetitive plant genomes and describe how GOMAP was used to annotate multiple maize genomes as a test case. Assessment shows that GOMAP expands and improves the number of genes annotated and annotations assigned per gene as well as the quality (based on [Formula: see text]) of GO assignments in maize. GOMAP has been deployed to annotate other species including wheat, rice, barley, cotton, and soy. Instructions and access to the GOMAP Singularity container are freely available online at https://bioinformapping.com/gomap/ . A list of annotated genomes and links to data is maintained at https://dill-picl.org/projects/gomap/ .
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Affiliation(s)
- Kokulapalan Wimalanathan
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, 50010, USA.
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA, 50010, USA.
- Greenlight Biosciences Inc., Medford, MA, 02155, USA.
| | - Carolyn J Lawrence-Dill
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, 50010, USA.
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA, 50010, USA.
- Department of Agronomy, Iowa State University, Ames, IA, 50010, USA.
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Mora-Márquez F, Chano V, Vázquez-Poletti JL, López de Heredia U. TOA: A software package for automated functional annotation in non-model plant species. Mol Ecol Resour 2020; 21:621-636. [PMID: 33070442 DOI: 10.1111/1755-0998.13285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 10/01/2020] [Accepted: 10/13/2020] [Indexed: 01/05/2023]
Abstract
The increase of sequencing capacity provided by high-throughput platforms has made it possible to routinely obtain large sets of genomic and transcriptomic sequences from model and non-model organisms. Subsequent genomic analysis and gene discovery in next-generation sequencing experiments are, however, bottlenecked by functional annotation. One common way to perform functional annotation of sets of sequences obtained from next-generation sequencing experiments, is by searching for homologous sequences and accessing the related functional information deposited in genomic databases. Functional annotation is especially challenging for non-model organisms, like many plant species. In such cases, existing free and commercial general-purpose applications may not offer complete and accurate results. We present TOA (Taxonomy-oriented annotation), a Python-based user-friendly open source application designed to establish functional annotation pipelines geared towards non-model plant species that can run in Linux/Mac computers, HPCs and cloud servers. TOA performs homology searches against proteins stored in the PLAZA databases, NCBI RefSeq Plant, Nucleotide Database and Non-Redundant Protein Sequence Database, and outputs functional information from several ontology systems: Gene Ontology, InterPro, EC, KEGG, Mapman and MetaCyc. The software performance was validated by comparing the runtimes, total number of annotated sequences and accuracy of the functional information obtained for several plant benchmark data sets with TOA and other functional annotation solutions. TOA outperformed the other software in terms of number of annotated sequences and accuracy of the annotation and constitutes a good alternative to improve functional annotation in plants. TOA is especially recommended for gymnosperms or for low quality sequence data sets of non-model plants.
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Affiliation(s)
- Fernando Mora-Márquez
- GI Sistemas Naturales e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
| | - Víctor Chano
- GI Sistemas Naturales e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
| | - José Luis Vázquez-Poletti
- GI Arquitectura de Sistemas Distribuidos, Dpto. Arquitectura de Computadores y Automática, Facultad de Informática, Universidad Complutense de Madrid, Madrid, Spain
| | - Unai López de Heredia
- GI Sistemas Naturales e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
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5
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Alexandersson E, Kushwaha S, Subedi A, Weighill D, Climer S, Jacobson D, Andreasson E. Linking crop traits to transcriptome differences in a progeny population of tetraploid potato. BMC PLANT BIOLOGY 2020; 20:120. [PMID: 32183694 PMCID: PMC7079428 DOI: 10.1186/s12870-020-2305-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/24/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Potato is the third most consumed crop in the world. Breeding for traits such as yield, product quality and pathogen resistance are main priorities. Identifying molecular signatures of these and other important traits is important in future breeding efforts. In this study, a progeny population from a cross between a breeding line, SW93-1015, and a cultivar, Désirée, was studied by trait analysis and RNA-seq in order to develop understanding of segregating traits at the molecular level and identify transcripts with expressional correlation to these traits. Transcript markers with predictive value for field performance applicable under controlled environments would be of great value for plant breeding. RESULTS A total of 34 progeny lines from SW93-1015 and Désirée were phenotyped for 17 different traits in a field in Nordic climate conditions and controlled climate settings. A master transcriptome was constructed with all 34 progeny lines and the parents through a de novo assembly of RNA-seq reads. Gene expression data obtained in a controlled environment from the 34 lines was correlated to traits by different similarity indices, including Pearson and Spearman, as well as DUO, which calculates the co-occurrence between high and low values for gene expression and trait. Our study linked transcripts to traits such as yield, growth rate, high laying tubers, late and tuber blight, tuber greening and early flowering. We found several transcripts associated to late blight resistance and transcripts encoding receptors were associated to Dickeya solani susceptibility. Transcript levels of a UBX-domain protein was negatively associated to yield and a GLABRA2 expression modulator was negatively associated to growth rate. CONCLUSION In our study, we identify 100's of transcripts, putatively linked based on expression with 17 traits of potato, representing both well-known and novel associations. This approach can be used to link the transcriptome to traits. We explore the possibility of associating the level of transcript expression from controlled, optimal environments to traits in a progeny population with different methods introducing the application of DUO for the first time on transcriptome data. We verify the expression pattern for five of the putative transcript markers in another progeny population.
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Affiliation(s)
- Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Sundsvägen 10, Alnarp, Sweden.
- Present address: Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
| | - Sandeep Kushwaha
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Uppsala, Sweden
- National Institute of Animal Biotechnology, Hyderabad, India
| | - Aastha Subedi
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Sundsvägen 10, Alnarp, Sweden
| | - Deborah Weighill
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Knoxville, TN, USA
| | | | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Knoxville, TN, USA
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Sundsvägen 10, Alnarp, Sweden
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Bebane PSA, Hunt BJ, Pegoraro M, Jones ARC, Marshall H, Rosato E, Mallon EB. The effects of the neonicotinoid imidacloprid on gene expression and DNA methylation in the buff-tailed bumblebee Bombus terrestris. Proc Biol Sci 2019; 286:20190718. [PMID: 31213186 PMCID: PMC6599982 DOI: 10.1098/rspb.2019.0718] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/27/2019] [Indexed: 02/07/2023] Open
Abstract
Neonicotinoids are effective insecticides used on many important arable and horticultural crops. They are nicotinic acetylcholine receptor agonists which disrupt the function of insect neurons and cause paralysis and death. In addition to direct mortality, there are numerous sublethal effects of low doses of neonicotinoids on bees. We hypothesize that some of these large array of effects could be a consequence of epigenetic changes in bees induced by neonicotinoids. We compared whole methylome (BS-seq) and RNA-seq libraries of the brains of buff-tailed bumblebee Bombus terrestris workers exposed to field-realistic doses of the neonicotinoid imidacloprid to libraries from control workers. We found numerous genes which show differential expression between neonicotinoid-treated bees and control bees, but no differentially methylated cytosines in any context. We found CpG methylation to be focused mainly in exons and associated with highly expressed genes. We discuss the implications of our results for future legislation.
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Affiliation(s)
- P. S. A. Bebane
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - B. J. Hunt
- School of Natural Sciences and Psychology, John Moores University Liverpool, Liverpool L3 3AF, UK
| | - M. Pegoraro
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - A. R. C Jones
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - H. Marshall
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - E. Rosato
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - E. B. Mallon
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
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7
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Bolger ME, Arsova B, Usadel B. Plant genome and transcriptome annotations: from misconceptions to simple solutions. Brief Bioinform 2018; 19:437-449. [PMID: 28062412 PMCID: PMC5952960 DOI: 10.1093/bib/bbw135] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/29/2016] [Indexed: 12/14/2022] Open
Abstract
Next-generation sequencing has triggered an explosion of available genomic and transcriptomic resources in the plant sciences. Although genome and transcriptome sequencing has become orders of magnitudes cheaper and more efficient, often the functional annotation process is lagging behind. This might be hampered by the lack of a comprehensive enumeration of simple-to-use tools available to the plant researcher. In this comprehensive review, we present (i) typical ontologies to be used in the plant sciences, (ii) useful databases and resources used for functional annotation, (iii) what to expect from an annotated plant genome, (iv) an automated annotation pipeline and (v) a recipe and reference chart outlining typical steps used to annotate plant genomes/transcriptomes using publicly available resources.
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Affiliation(s)
- Marie E Bolger
- Forschungszentrum Jülich, Wilhelm Johnen Str, Jülich, Germany
| | - Borjana Arsova
- Forschungszentrum Jülich, Wilhelm Johnen Str, Jülich, Germany
- FRS-FNRS Chargé de Recherches, Functional Genomics and Plant Molecular Imaging Center for Protein Engineering (CIP), Dpt of Life Sciences, University of Liège, Quartier de la Vallée, 1, Chemin de la Vallée, 4 - Bât B22, 4000 LIEGE, Belgium
| | - Björn Usadel
- Forschungszentrum Jülich, Wilhelm Johnen Str, Jülich, Germany
- RWTH Aachen University, Institute for Biology I Botany, BioSC, Worringer Weg 3, Aachen, Germany
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8
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Song H, Lin K, Hu J, Pang E. An Updated Functional Annotation of Protein-Coding Genes in the Cucumber Genome. FRONTIERS IN PLANT SCIENCE 2018; 9:325. [PMID: 29599790 PMCID: PMC5863696 DOI: 10.3389/fpls.2018.00325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/27/2018] [Indexed: 06/08/2023]
Abstract
Background: Although the cucumber reference genome and its annotation were published several years ago, the functional annotation of predicted genes, particularly protein-coding genes, still requires further improvement. In general, accurately determining orthologous relationships between genes allows for better and more robust functional assignments of predicted genes. As one of the most reliable strategies, the determination of collinearity information may facilitate reliable orthology inferences among genes from multiple related genomes. Currently, the identification of collinear segments has mainly been based on conservation of gene order and orientation. Over the course of plant genome evolution, various evolutionary events have disrupted or distorted the order of genes along chromosomes, making it difficult to use those genes as genome-wide markers for plant genome comparisons. Results: Using the localized LASTZ/MULTIZ analysis pipeline, we aligned 15 genomes, including cucumber and other related angiosperm plants, and identified a set of genomic segments that are short in length, stable in structure, uniform in distribution and highly conserved across all 15 plants. Compared with protein-coding genes, these conserved segments were more suitable for use as genomic markers for detecting collinear segments among distantly divergent plants. Guided by this set of identified collinear genomic segments, we inferred 94,486 orthologous protein-coding gene pairs (OPPs) between cucumber and 14 other angiosperm species, which were used as proxies for transferring functional terms to cucumber genes from the annotations of the other 14 genomes. In total, 10,885 protein-coding genes were assigned Gene Ontology (GO) terms which was nearly 1,300 more than results collected in Uniprot-proteomic database. Our results showed that annotation accuracy would been improved compared with other existing approaches. Conclusions: In this study, we provided an alternative resource for the functional annotation of predicted cucumber protein-coding genes, which we expect will be beneficial for the cucumber's biological study, accessible from http://cmb.bnu.edu.cn/functional_annotation. Meanwhile, using the cucumber reference genome as a case study, we presented an efficient strategy for transferring gene functional information from previously well-characterized protein-coding genes in model species to newly sequenced or "non-model" plant species.
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Affiliation(s)
- Hongtao Song
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Kui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Jinglu Hu
- Graduate School of Information, Production and Systems, Waseda University, Kitakyushu-shi, Japan
| | - Erli Pang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
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Zwaenepoel A, Diels T, Amar D, Van Parys T, Shamir R, Van de Peer Y, Tzfadia O. MorphDB: Prioritizing Genes for Specialized Metabolism Pathways and Gene Ontology Categories in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:352. [PMID: 29616063 PMCID: PMC5867296 DOI: 10.3389/fpls.2018.00352] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/02/2018] [Indexed: 05/20/2023]
Abstract
Recent times have seen an enormous growth of "omics" data, of which high-throughput gene expression data are arguably the most important from a functional perspective. Despite huge improvements in computational techniques for the functional classification of gene sequences, common similarity-based methods often fall short of providing full and reliable functional information. Recently, the combination of comparative genomics with approaches in functional genomics has received considerable interest for gene function analysis, leveraging both gene expression based guilt-by-association methods and annotation efforts in closely related model organisms. Besides the identification of missing genes in pathways, these methods also typically enable the discovery of biological regulators (i.e., transcription factors or signaling genes). A previously built guilt-by-association method is MORPH, which was proven to be an efficient algorithm that performs particularly well in identifying and prioritizing missing genes in plant metabolic pathways. Here, we present MorphDB, a resource where MORPH-based candidate genes for large-scale functional annotations (Gene Ontology, MapMan bins) are integrated across multiple plant species. Besides a gene centric query utility, we present a comparative network approach that enables researchers to efficiently browse MORPH predictions across functional gene sets and species, facilitating efficient gene discovery and candidate gene prioritization. MorphDB is available at http://bioinformatics.psb.ugent.be/webtools/morphdb/morphDB/index/. We also provide a toolkit, named "MORPH bulk" (https://github.com/arzwa/morph-bulk), for running MORPH in bulk mode on novel data sets, enabling researchers to apply MORPH to their own species of interest.
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Affiliation(s)
- Arthur Zwaenepoel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Tim Diels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - David Amar
- Stanford Center for Inherited Cardiovascular Disease, Stanford University, Stanford, CA, United States
| | - Thomas Van Parys
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
- Genomics Research Institute, University of Pretoria, Pretoria, South Africa
- *Correspondence: Yves Van de Peer
| | - Oren Tzfadia
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
- Oren Tzfadia
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10
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Van Dyke MW, Beyer MD, Clay E, Hiam KJ, McMurry JL, Xie Y. Identification of Preferred DNA-Binding Sites for the Thermus thermophilus Transcriptional Regulator SbtR by the Combinatorial Approach REPSA. PLoS One 2016; 11:e0159408. [PMID: 27428627 PMCID: PMC4948773 DOI: 10.1371/journal.pone.0159408] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 07/02/2016] [Indexed: 01/04/2023] Open
Abstract
One of the first steps towards elucidating the biological function of a putative transcriptional regulator is to ascertain its preferred DNA-binding sequences. This may be rapidly and effectively achieved through the application of a combinatorial approach, one involving very large numbers of randomized oligonucleotides and reiterative selection and amplification steps to enrich for high-affinity nucleic acid-binding sequences. Previously, we had developed the novel combinatorial approach Restriction Endonuclease Protection, Selection and Amplification (REPSA), which relies not on the physical separation of ligand-nucleic acid complexes but instead selects on the basis of ligand-dependent inhibition of enzymatic template inactivation, specifically cleavage by type IIS restriction endonucleases. Thus, no prior knowledge of the ligand is required for REPSA, making it more amenable for discovery purposes. Here we describe using REPSA, massively parallel sequencing, and bioinformatics to identify the preferred DNA-binding sites for the transcriptional regulator SbtR, encoded by the TTHA0167 gene from the model extreme thermophile Thermus thermophilus HB8. From the resulting position weight matrix, we can identify multiple operons potentially regulated by SbtR and postulate a biological role for this protein in regulating extracellular transport processes. Our study provides a proof-of-concept for the application of REPSA for the identification of preferred DNA-binding sites for orphan transcriptional regulators and a first step towards determining their possible biological roles.
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Affiliation(s)
- Michael W. Van Dyke
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
- * E-mail:
| | - Matthew D. Beyer
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Emily Clay
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Kamir J. Hiam
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Jonathan L. McMurry
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Ying Xie
- Department of Computer Science, Kennesaw State University, Kennesaw, Georgia, United States of America
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11
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The nitrogen responsive transcriptome in potato (Solanum tuberosum L.) reveals significant gene regulatory motifs. Sci Rep 2016; 6:26090. [PMID: 27193058 PMCID: PMC4872257 DOI: 10.1038/srep26090] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/25/2016] [Indexed: 12/18/2022] Open
Abstract
Nitrogen (N) is the most important nutrient for the growth of potato (Solanum tuberosum L.). Foliar gene expression in potato plants with and without N supplementation at 180 kg N ha(-1) was compared at mid-season. Genes with consistent differences in foliar expression due to N supplementation over three cultivars and two developmental time points were examined. In total, thirty genes were found to be over-expressed and nine genes were found to be under-expressed with supplemented N. Functional relationships between over-expressed genes were found. The main metabolic pathway represented among differentially expressed genes was amino acid metabolism. The 1000 bp upstream flanking regions of the differentially expressed genes were analysed and nine overrepresented motifs were found using three motif discovery algorithms (Seeder, Weeder and MEME). These results point to coordinated gene regulation at the transcriptional level controlling steady state potato responses to N sufficiency.
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12
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Seibt KM, Wenke T, Muders K, Truberg B, Schmidt T. Short interspersed nuclear elements (SINEs) are abundant in Solanaceae and have a family-specific impact on gene structure and genome organization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:268-285. [PMID: 26996788 DOI: 10.1111/tpj.13170] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 03/11/2016] [Accepted: 03/14/2016] [Indexed: 06/05/2023]
Abstract
Short interspersed nuclear elements (SINEs) are highly abundant non-autonomous retrotransposons that are widespread in plants. They are short in size, non-coding, show high sequence diversity, and are therefore mostly not or not correctly annotated in plant genome sequences. Hence, comparative studies on genomic SINE populations are rare. To explore the structural organization and impact of SINEs, we comparatively investigated the genome sequences of the Solanaceae species potato (Solanum tuberosum), tomato (Solanum lycopersicum), wild tomato (Solanum pennellii), and two pepper cultivars (Capsicum annuum). Based on 8.5 Gbp sequence data, we annotated 82 983 SINE copies belonging to 10 families and subfamilies on a base pair level. Solanaceae SINEs are dispersed over all chromosomes with enrichments in distal regions. Depending on the genome assemblies and gene predictions, 30% of all SINE copies are associated with genes, particularly frequent in introns and untranslated regions (UTRs). The close association with genes is family specific. More than 10% of all genes annotated in the Solanaceae species investigated contain at least one SINE insertion, and we found genes harbouring up to 16 SINE copies. We demonstrate the involvement of SINEs in gene and genome evolution including the donation of splice sites, start and stop codons and exons to genes, enlargement of introns and UTRs, generation of tandem-like duplications and transduction of adjacent sequence regions.
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Affiliation(s)
- Kathrin M Seibt
- Institute of Botany, Technische Universität Dresden, 01062, Dresden, Germany
| | - Torsten Wenke
- Institute of Botany, Technische Universität Dresden, 01062, Dresden, Germany
| | | | | | - Thomas Schmidt
- Institute of Botany, Technische Universität Dresden, 01062, Dresden, Germany
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Tzfadia O, Diels T, De Meyer S, Vandepoele K, Aharoni A, Van de Peer Y. CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool. FRONTIERS IN PLANT SCIENCE 2016; 6:1194. [PMID: 26779228 PMCID: PMC4700130 DOI: 10.3389/fpls.2015.01194] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 12/11/2015] [Indexed: 05/23/2023]
Abstract
MOTIVATION Comparative transcriptomics is a common approach in functional gene discovery efforts. It allows for finding conserved co-expression patterns between orthologous genes in closely related plant species, suggesting that these genes potentially share similar function and regulation. Several efficient co-expression-based tools have been commonly used in plant research but most of these pipelines are limited to data from model systems, which greatly limit their utility. Moreover, in addition, none of the existing pipelines allow plant researchers to make use of their own unpublished gene expression data for performing a comparative co-expression analysis and generate multi-species co-expression networks. RESULTS We introduce CoExpNetViz, a computational tool that uses a set of query or "bait" genes as an input (chosen by the user) and a minimum of one pre-processed gene expression dataset. The CoExpNetViz algorithm proceeds in three main steps; (i) for every bait gene submitted, co-expression values are calculated using mutual information and Pearson correlation coefficients, (ii) non-bait (or target) genes are grouped based on cross-species orthology, and (iii) output files are generated and results can be visualized as network graphs in Cytoscape. AVAILABILITY The CoExpNetViz tool is freely available both as a PHP web server (link: http://bioinformatics.psb.ugent.be/webtools/coexpr/) (implemented in C++) and as a Cytoscape plugin (implemented in Java). Both versions of the CoExpNetViz tool support LINUX and Windows platforms.
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Affiliation(s)
- Oren Tzfadia
- Department of Plant Systems Biology, Vlaams Instituut voor BiotechnologieGhent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
- Bioinformatics Institute Ghent, Ghent UniversityGhent, Belgium
| | - Tim Diels
- Department of Plant Systems Biology, Vlaams Instituut voor BiotechnologieGhent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
- Bioinformatics Institute Ghent, Ghent UniversityGhent, Belgium
| | - Sam De Meyer
- Department of Plant Systems Biology, Vlaams Instituut voor BiotechnologieGhent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
| | - Klaas Vandepoele
- Department of Plant Systems Biology, Vlaams Instituut voor BiotechnologieGhent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
- Bioinformatics Institute Ghent, Ghent UniversityGhent, Belgium
| | - Asaph Aharoni
- Department of Plant Sciences and the Environment, Weizmann Institute of ScienceRehovot, Israel
| | - Yves Van de Peer
- Department of Plant Systems Biology, Vlaams Instituut voor BiotechnologieGhent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
- Bioinformatics Institute Ghent, Ghent UniversityGhent, Belgium
- Genomics Research Institute, University of PretoriaPretoria, South Africa
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Frades I, Abreha KB, Proux-Wéra E, Lankinen Å, Andreasson E, Alexandersson E. A novel workflow correlating RNA-seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones. FRONTIERS IN PLANT SCIENCE 2015; 6:718. [PMID: 26442032 PMCID: PMC4585127 DOI: 10.3389/fpls.2015.00718] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 08/27/2015] [Indexed: 05/18/2023]
Abstract
Comparative transcriptomics between species can provide valuable understanding of plant-pathogen interactions. Here, we focus on wild Solanum species and potato clones with varying degree of resistance against Phytophthora infestans, which causes the devastating late blight disease in potato. The transcriptomes of three wild Solanum species native to Southern Sweden, Solanum dulcamara, Solanum nigrum, and Solanum physalifolium were compared to three potato clones, Desiree (cv.), SW93-1015 and Sarpo Mira. Desiree and S. physalifolium are susceptible to P. infestans whereas the other four have different degrees of resistance. By building transcript families based on de novo assembled RNA-seq across species and clones and correlating these to resistance phenotypes, we created a novel workflow to identify families with expanded or depleted number of transcripts in relation to the P. infestans resistance level. Analysis was facilitated by inferring functional annotations based on the family structure and semantic clustering. More transcript families were expanded in the resistant clones and species and the enriched functions of these were associated to expected gene ontology (GO) terms for resistance mechanisms such as hypersensitive response, host programmed cell death and endopeptidase activity. However, a number of unexpected functions and transcripts were also identified, for example transmembrane transport and protein acylation expanded in the susceptible group and a cluster of Zinc knuckle family proteins expanded in the resistant group. Over 400 expressed putative resistance (R-)genes were identified and resistant clones Sarpo Mira and SW93-1015 had ca 25% more expressed putative R-genes than susceptible cultivar Desiree. However, no differences in numbers of susceptibility (S-)gene homologs were seen between species and clones. In addition, we identified P. infestans transcripts including effectors in the early stages of P. infestans-Solanum interactions.
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Affiliation(s)
| | | | | | | | | | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural SciencesAlnarp, Sweden
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