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Mannapperuma, Chanaka
Publications (10 of 10) Show all publications
Wegrzyn, J. L., Staton, M. A., Street, N. R., Main, D., Grau, E., Herndon, N., . . . Ficklin, S. (2019). Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment. Frontiers in Plant Science, 10, Article ID 813.
Open this publication in new window or tab >>Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment
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2019 (English)In: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 10, article id 813Article, review/survey (Refereed) Published
Abstract [en]

Despite tremendous advancements in high throughput sequencing, the vast majority of tree genomes, and in particular, forest trees, remain elusive. Although primary databases store genetic resources for just over 2,000 forest tree species, these are largely focused on sequence storage, basic genome assemblies, and functional assignment through existing pipelines. The tree databases reviewed here serve as secondary repositories for community data. They vary in their focal species, the data they curate, and the analytics provided, but they are united in moving toward a goal of centralizing both data access and analysis. They provide frameworks to view and update annotations for complex genomes, interrogate systems level expression profiles, curate data for comparative genomics, and perform real-time analysis with genotype and phenotype data. The organism databases of today are no longer simply catalogs or containers of genetic information. These repositories represent integrated cyberinfrastructure that support cross-site queries and analysis in web-based environments. These resources are striving to integrate across diverse experimental designs, sequence types, and related measures through ontologies, community standards, and web services. Efficient, simple, and robust platforms that enhance the data generated by the research community, contribute to improving forest health and productivity.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2019
Keywords
database, content management system, forest tree, bioinformatics, web services
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:umu:diva-161586 (URN)10.3389/fpls.2019.00813 (DOI)000473047200001 ()
Available from: 2019-07-22 Created: 2019-07-22 Last updated: 2019-07-22Bibliographically approved
Mannapperuma, C., Street, N. & Waterworth, J. (2019). Designing Usable Bioinformatics Tools for Specialized Users. In: Rocha Á., Ferrás C., Paredes M. (Ed.), Information Technology and Systems: Proceedings of ICITS 2019. Paper presented at ICITS'19 - The 2019 International Conference on Information Technology & Systems (pp. 649-670). Paper presented at ICITS'19 - The 2019 International Conference on Information Technology & Systems. Cham: Springer
Open this publication in new window or tab >>Designing Usable Bioinformatics Tools for Specialized Users
2019 (English)In: Information Technology and Systems: Proceedings of ICITS 2019 / [ed] Rocha Á., Ferrás C., Paredes M., Cham: Springer, 2019, p. 649-670Chapter in book (Refereed)
Abstract [en]

Visualization - the process of interpreting data into visual forms -  is increasingly important in science as data grows rapidly in volume and complexity. A common challenge faced by many biologists is how to benefit from this data deluge without being overwhelmed by it. Here, our main interest is in the visualization of genomes, sequence alignments, phylogenies and systems biology data. Bringing together new technologies, including design theory, and applying them into the above three areas in biology will improve the usability and user interaction.

The main goal of this paper is to apply design principles to make bioinformatics resources, evaluate them using different usability methods, and provide recommended steps to design usable tools.

Place, publisher, year, edition, pages
Cham: Springer, 2019
Series
Advances in Intelligent Systems and Computing ; 918
Keywords
User Experience Designing, Participatory Design, Bioinformatics
National Category
Media and Communications Human Computer Interaction
Research subject
media and communication studies; human-computer interaction
Identifiers
urn:nbn:se:umu:diva-153032 (URN)10.1007/978-3-030-11890-7_62 (DOI)978-3-030-11889-1 (ISBN)978-3-030-11890-7 (ISBN)
Conference
ICITS'19 - The 2019 International Conference on Information Technology & Systems
Available from: 2018-11-02 Created: 2018-11-02 Last updated: 2020-01-13Bibliographically approved
Kumar, V., Hainaut, M., Delhomme, N., Mannapperuma, C., Immerzeel, P., Street, N., . . . Mellerowicz, E. J. (2019). Poplar carbohydrate-active enzymes: whole-genome annotation and functional analyses based on RNA expression data. The Plant Journal, 99(4), 589-609
Open this publication in new window or tab >>Poplar carbohydrate-active enzymes: whole-genome annotation and functional analyses based on RNA expression data
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2019 (English)In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 99, no 4, p. 589-609Article in journal (Refereed) Published
Abstract [en]

Carbohydrate-active enzymes (CAZymes) catalyze the formation and modification of glycoproteins, glycolipids, starch, secondary metabolites and cell wall biopolymers. They are key enzymes for the biosynthesis of food and renewable biomass. Woody biomass is particularly important for long-term carbon storage and as an abundant renewable natural resource for many industrial applications. This study presents a re-annotation of CAZyme genes in the current Populus trichocarpa genome assembly and in silico functional characterization, based on high-resolution RNA-Seq data sets. Altogether, 1914 CAZyme and expansin genes were annotated in 101 families. About 1797 of these genes were found expressed in at least one Populus organ. We identified genes involved in the biosynthesis of different cell wall polymers and their paralogs. Whereas similar families exist in poplar and Arabidopsis thaliana (with the exception of CBM13 found only in poplar), a few families had significantly different copy numbers between the two species. To identify the transcriptional coordination and functional relatedness within the CAZymes and other proteins, we performed co-expression network analysis of CAZymes in wood-forming tissues using the AspWood database () for Populus tremula. This provided an overview of the transcriptional changes in CAZymes during the transition from primary to secondary wall formation, and the clustering of transcripts into potential regulons. Candidate enzymes involved in the biosynthesis of polysaccharides were identified along with many tissue-specific uncharacterized genes and transcription factors. These collections offer a rich source of targets for the modification of secondary cell wall biosynthesis and other developmental processes in woody plants.

Place, publisher, year, edition, pages
John Wiley & Sons, 2019
Keywords
carbohydrate metabolism, cell wall, comparative genomics, genome sequencing, vegetative development, wood formation
National Category
Plant Biotechnology Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-161701 (URN)10.1111/tpj.14417 (DOI)000473849600001 ()31111606 (PubMedID)
Funder
Swedish Research CouncilSwedish Research Council FormasSwedish Foundation for Strategic Research , RBP14-0011VinnovaKnut and Alice Wallenberg FoundationThe Kempe Foundations
Available from: 2019-08-05 Created: 2019-08-05 Last updated: 2019-10-14Bibliographically approved
Lin, Y.-C., Wang, J., Delhomme, N., Schiffthaler, B., Sundström, G., Zuccolo, A., . . . Street, N. R. (2018). Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen. Proceedings of the National Academy of Sciences of the United States of America, 115(46), E10970-E10978
Open this publication in new window or tab >>Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen
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2018 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 46, p. E10970-E10978Article in journal (Refereed) Published
Abstract [en]

The Populus genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily Populus trichocarpa (Torr. & Gray), which was the first tree with a whole-genome assembly. To further advance evolutionary and functional genomic analyses in Populus, we produced genome assemblies and population genetics resources of two aspen species, Populus tremula L. and Populus tremuloides Michx. The two aspen species have distributions spanning the Northern Hemisphere, where they are keystone species supporting a wide variety of dependent communities and produce a diverse array of secondary metabolites. Our analyses show that the two aspens share a similar genome structure and a highly conserved gene content with P. trichocarpa but display substantially higher levels of heterozygosity. Based on population resequencing data, we observed widespread positive and negative selection acting on both coding and noncoding regions. Furthermore, patterns of genetic diversity and molecular evolution in aspen are influenced by a number of features, such as expression level, coexpression network connectivity, and regulatory variation. To maximize the community utility of these resources, we have integrated all presented data within the PopGenIE web resource (PopGenIE.org).

Place, publisher, year, edition, pages
NATL ACAD SCIENCES, 2018
Keywords
genome assembly, natural selection, coexpression, population genetics, Populus
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-154950 (URN)10.1073/pnas.1801437115 (DOI)000449934400020 ()30373829 (PubMedID)2-s2.0-85056516875 (Scopus ID)
Available from: 2019-01-07 Created: 2019-01-07 Last updated: 2019-01-07Bibliographically approved
Jokipii-Lukkari, S., Delhomme, N., Schiffthaler, B., Mannapperuma, C., Prestele, J., Nilsson, O., . . . Tuominen, H. (2018). Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce. Plant Physiology, 176(4), 2851-2870
Open this publication in new window or tab >>Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce
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2018 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 176, no 4, p. 2851-2870Article in journal (Refereed) Published
Abstract [en]

Seasonal cues influence several aspects of the secondary growth of tree stems, including cambial activity, wood chemistry, and transition to latewood formation. We investigated seasonal changes in cambial activity, secondary cell wall formation, and tracheid cell death in woody tissues of Norway spruce (Picea abies) throughout one seasonal cycle. RNA sequencing was performed simultaneously in both the xylem and cambium/phloem tissues of the stem. Principal component analysis revealed gradual shifts in the transcriptomes that followed a chronological order throughout the season. A notable remodeling of the transcriptome was observed in the winter, with many genes having maximal expression during the coldest months of the year. A highly coexpressed set of monolignol biosynthesis genes showed high expression during the period of secondary cell wall formation as well as a second peak in midwinter. This midwinter peak in expression did not trigger lignin deposition, as determined by pyrolysis-gas chromatography/mass spectrometry. Coexpression consensus network analyses suggested the involvement of transcription factors belonging to the ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES and MYELOBLASTOSIS-HOMEOBOX families in the seasonal control of secondary cell wall formation of tracheids. Interestingly, the lifetime of the latewood tracheids stretched beyond the winter dormancy period, correlating with a lack of cell death-related gene expression. Our transcriptomic analyses combined with phylogenetic and microscopic analyses also identified the cellulose and lignin biosynthetic genes and putative regulators for latewood formation and tracheid cell death in Norway spruce, providing a toolbox for further physiological and functional assays of these important phase transitions.

Place, publisher, year, edition, pages
American Society of Plant Biologists, 2018
National Category
Cell Biology
Identifiers
urn:nbn:se:umu:diva-148642 (URN)10.1104/pp.17.01590 (DOI)000429089100021 ()29487121 (PubMedID)
Projects
Bio4Energy
Funder
Knut and Alice Wallenberg Foundation, KAW 2013.0305The Kempe Foundations, SMK-1340Swedish Research Council, 621-2013-4949Vinnova, 2015-02290
Available from: 2018-06-21 Created: 2018-06-21 Last updated: 2019-08-30Bibliographically approved
Sundell, D., Street, N. R., Kumar, M., Mellerowicz, E. J., Kucukoglu, M., Johnsson, C., . . . Hvidsten, T. R. (2017). AspWood: High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in Populus tremula. The Plant Cell, 29(7), 1585-1604
Open this publication in new window or tab >>AspWood: High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in Populus tremula
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2017 (English)In: The Plant Cell, ISSN 1040-4651, E-ISSN 1532-298X, Vol. 29, no 7, p. 1585-1604Article in journal (Refereed) Published
Abstract [en]

Trees represent the largest terrestrial carbon sink and a renewable source of ligno-cellulose. There is significant scope for yield and quality improvement in these largely undomesticated species, and efforts to engineer elite varieties will benefit from improved understanding of the transcriptional network underlying cambial growth and wood formation. We generated high-spatial-resolution RNA sequencing data spanning the secondary phloem, vascular cambium, and wood-forming tissues of Populus tremula. The transcriptome comprised 28,294 expressed, annotated genes, 78 novel protein-coding genes, and 567 putative long intergenic noncoding RNAs. Most paralogs originating from the Salicaceae whole-genome duplication had diverged expression, with the exception of those highly expressed during secondary cell wall deposition. Coexpression network analyses revealed that regulation of the transcriptome underlying cambial growth and wood formation comprises numerous modules forming a continuum of active processes across the tissues. A comparative analysis revealed that a majority of these modules are conserved in Picea abies. The high spatial resolution of our data enabled identification of novel roles for characterized genes involved in xylan and cellulose biosynthesis, regulators of xylem vessel and fiber differentiation and lignification. An associated web resource (AspWood, http://aspwood.popgenie.org) provides interactive tools for exploring the expression profiles and coexpression network.

National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:umu:diva-139016 (URN)10.1105/tpc.17.00153 (DOI)000407495000008 ()
Projects
Bio4Energy
Available from: 2017-09-06 Created: 2017-09-06 Last updated: 2019-08-30Bibliographically approved
Giacomello, S., Salmen, F., Terebieniec, B. K., Vickovic, S., Navarro, J. F., Alexeyenko, A., . . . Lundeberg, J. (2017). Spatially resolved transcriptome profiling in model plant species. Nature Plants, 3(6), Article ID 17061.
Open this publication in new window or tab >>Spatially resolved transcriptome profiling in model plant species
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2017 (English)In: Nature Plants, ISSN 2055-026X, Vol. 3, no 6, article id 17061Article in journal (Refereed) Published
Abstract [en]

Understanding complex biological systems requires functional characterization of specialized tissue domains. However, existing strategies for generating and analysing high-throughput spatial expression profiles were developed for a limited range of organisms, primarily mammals. Here we present the first available approach to generate and study highresolution, spatially resolved functional profiles in a broad range of model plant systems. Our process includes highthroughput spatial transcriptome profiling followed by spatial gene and pathway analyses. We first demonstrate the feasibility of the technique by generating spatial transcriptome profiles from model angiosperms and gymnosperms microsections. In Arabidopsis thaliana we use the spatial data to identify differences in expression levels of 141 genes and 189 pathways in eight inflorescence tissue domains. Our combined approach of spatial transcriptomics and functional profiling offers a powerful new strategy that can be applied to a broad range of plant species, and is an approach that will be pivotal to answering fundamental questions in developmental and evolutionary biology.

Place, publisher, year, edition, pages
Nature Publishing Group, 2017
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:umu:diva-138048 (URN)10.1038/nplants.2017.61 (DOI)000406036800002 ()28481330 (PubMedID)
Available from: 2017-08-10 Created: 2017-08-10 Last updated: 2019-02-19Bibliographically approved
Sundell, D., Street, N. R., Kumar, M., Mellerowicz, E. J., Kucukoglu, M., Johnsson, C., . . . Hvidsten, T. R. (2016). High-spatial-resolution transcriptome profiling reveals uncharacterized regulatory complexity underlying cambial growth and wood formation in Populus tremula.
Open this publication in new window or tab >>High-spatial-resolution transcriptome profiling reveals uncharacterized regulatory complexity underlying cambial growth and wood formation in Populus tremula
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2016 (English)Manuscript (preprint) (Other academic)
Abstract [en]

Trees represent the largest terrestrial carbon sink and a renewable source of ligno-cellulose. There is significant scope for yield and quality improvement in these largely undomesticated species, however, efforts to engineer new, elite varieties are constrained by the lack of a comprehensive understanding of the transcriptional network underlying cambial growth and wood formation. We generated RNA Sequencing transcriptome data for four mature, wild-growing aspens (Populus tremula) from high-spatial-resolution tangential cryosection series spanning the secondary phloem, vascular cambium, expanding and secondary cell wall forming xylem cells, cell death zone and the previous years annual ring. The transcriptome comprised 28,294 expressed, previously annotated protein-coding genes, 78 novel protein-coding genes and 567 long intergenic non-coding RNAs. Most paralogs originating from the Salicaceae whole genome duplication had diverged expression, with the notable exception of those with high expression during secondary cell wall deposition. We performed co-expression network analysis to identify central transcriptional modules and associated several of these with known biological processes. This revealed previously uncharacterized complexity underlying the regulation of cambial growth and wood formation, with modules forming a continuum of activated processes across the tissues. The high spatial resolution suggested novel roles for known genes involved in xylan and cellulose biosynthesis, regulators of xylem vessel and fiber differentiation and components of lignification. The associated web resource (AspWood, http://aspwood.popgenie.org) integrates the data within a set of interactive tools for exploring the co-expression network of cambial growth and wood formation.

National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:umu:diva-133999 (URN)10.1101/094060 (DOI)
Available from: 2017-04-26 Created: 2017-04-26 Last updated: 2018-06-09
Sundell, D., Mannapperuma, C., Netotea, S., Delhomme, N., Lin, Y.-C., Sjödin, A., . . . Street, N. R. (2015). The Plant Genome Integrative Explorer Resource: PlantGenIE.org. New Phytologist, 208(4), 1149-1156
Open this publication in new window or tab >>The Plant Genome Integrative Explorer Resource: PlantGenIE.org
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2015 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 208, no 4, p. 1149-1156Article in journal (Refereed) Published
Abstract [en]

Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, BLAST homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the COMPLEX resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.

Keywords
annotation, coexpression, conifer, database, genome browser, Populus, transcriptomics, web source
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-113426 (URN)10.1111/nph.13557 (DOI)000365393000016 ()26192091 (PubMedID)
Available from: 2015-12-18 Created: 2015-12-18 Last updated: 2018-06-07Bibliographically approved
Schiffthaler, B., Terebieniec, B. K., Mähler, N., Robinson, K. M., Mannapperuma, C., Jansson, S. & Street, N. R.An integrated functional genomics and systems genetics analysis of leaf shape in Populus tremula .
Open this publication in new window or tab >>An integrated functional genomics and systems genetics analysis of leaf shape in Populus tremula 
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Leaf shape is an important component of our relationship with the living world, representing a defining feature of how we recognise and classify plant species. There is extensive variation in the form and function of leaves within and between species. In the current study we utilised variation in leaf shape represented among individuals of a collection of Eurasian aspen (Populus tremula L.) sampled across Sweden and the remarkable extent of heterophylly present to establish morphological, cellular and transcriptional developmental time lines. We performed gene expression network and phenotypical regression analyses to identify genes of central importance or that were highly predictive of shape and size phenotypes during leaf development using a systems biology approach. We complemented this developmental study with a genome wide association study of leaf shape variation to identify single nucleotide polymorphisms associated with leaf shape and size, their genomic context and the biological role of associated genes. We then compared these association candidate genes to differentially expressed genes between groups of genotypes with highly contrasting leaf shapes, also considering whether there were expression quantitative trait loci associated with the genes. We demonstrate that our developmental gene expression series captured known biology for homologs of functionally characterised Arabidopsis thaliana genes and biological processes of importance during leaf development. We identified genes of high importance from the developmental series and natural variation analyses. These included genes with characterised functions in leaf development in addition to many novel candidates. Our systems genetics approach identified numerous genes supported by the developmental time series, phenotypic and expression association mapping and differential expression between phenotypic extremes. As such, we describe a rich resource for directing future functional characterisation studies and a comprehensive data resource characterising the role of gene expression during leaf development in aspen.

Keywords
leaf shape, RNA-Sequencing, expression network, Populus tremula, natural variation, GWAS
National Category
Bioinformatics and Systems Biology Biochemistry and Molecular Biology
Research subject
Molecular Biology; Genetics
Identifiers
urn:nbn:se:umu:diva-156461 (URN)
Available from: 2019-02-15 Created: 2019-02-15 Last updated: 2019-02-19
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