Chanaka Mannapperuma
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View article: An Improved Chromosome‐scale Genome Assembly and Population Genetics resource for <i>Populus tremula</i>.
An Improved Chromosome‐scale Genome Assembly and Population Genetics resource for <i>Populus tremula</i>. Open
Aspen ( Populus tremula L.) is a keystone species and a model system for forest tree genomics. We present an updated resource comprising a chromosome‐scale assembly, population genetics and genomics data. Using the resource, we explore the…
View article: NAC domain transcription factors VNI2 and ATAF2 form protein complexes and regulate leaf senescence
NAC domain transcription factors VNI2 and ATAF2 form protein complexes and regulate leaf senescence Open
The NAM, ATAF1/2, and CUC2 (NAC) domain transcription factor VND‐INTERACTING2 (VNI2) negatively regulates xylem vessel formation by interacting with another NAC domain transcription factor, VASCULAR‐RELATED NAC‐DOMAIN7 (VND7), a master reg…
View article: Identification of growth regulators using cross-species network analysis in plants
Identification of growth regulators using cross-species network analysis in plants Open
With the need to increase plant productivity, one of the challenges plant scientists are facing is to identify genes that play a role in beneficial plant traits. Moreover, even when such genes are found, it is generally not trivial to tran…
View article: qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE)
qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE) Open
Background Affordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits. The availability of…
View article: Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance
Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance Open
In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequenc…
View article: Identification of new growth regulators using cross-species network analysis in plants
Identification of new growth regulators using cross-species network analysis in plants Open
With the need to increase plant productivity, one of the challenges plant scientists are facing is to identify genes playing a role in beneficial plant traits. Moreover, even when such genes are found, it is generally not trivial to transf…
View article: The BOP‐type co‐transcriptional regulator NODULE ROOT1 promotes stem secondary growth of the tropical Cannabaceae tree <i>Parasponia andersonii</i>
The BOP‐type co‐transcriptional regulator NODULE ROOT1 promotes stem secondary growth of the tropical Cannabaceae tree <i>Parasponia andersonii</i> Open
Summary Tree stems undergo a massive secondary growth in which secondary xylem and phloem tissues arise from the vascular cambium. Vascular cambium activity is driven by endogenous developmental signalling cues and environmental stimuli. C…
View article: Additional file 1 of qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE)
Additional file 1 of qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE) Open
Additional file 1: Table S1. Metadata for RNA-seq datasets integrated in EucGenIE. In total 355 transcriptome datasets were integrated: 42 exAtlas datasets, 30 biotic interactions datasets and 283 transcriptomes from different F2 backcross…
View article: Genome-Wide Identification of Populus Malectin/Malectin-Like Domain-Containing Proteins and Expression Analyses Reveal Novel Candidates for Signaling and Regulation of Wood Development
Genome-Wide Identification of Populus Malectin/Malectin-Like Domain-Containing Proteins and Expression Analyses Reveal Novel Candidates for Signaling and Regulation of Wood Development Open
Malectin domain (MD) is a ligand-binding protein motif of pro- and eukaryotes. It is particularly abundant in Viridiplantae, where it occurs as either a single (MD, PF11721) or tandemly duplicated domain (PF12819) called malectin-like doma…
View article: Leaf shape in <i>Populus tremula</i> is a complex, omnigenic trait
Leaf shape in <i>Populus tremula</i> is a complex, omnigenic trait Open
Leaf shape is a defining feature of how we recognize and classify plant species. Although there is extensive variation in leaf shape within many species, few studies have disentangled the underlying genetic architecture. We characterized t…
View article: GenIE-Sys: Genome Integrative Explorer System
GenIE-Sys: Genome Integrative Explorer System Open
There are an ever-increasing number of genomes being sequenced, many of which have associated RNA sequencing and other genomics data. The availability of user-friendly web-accessible mining tools ensures that these data repositories provid…
View article: An Improved Chromosome-scale Genome Assembly and Population Genetics resource for<i>Populus tremula</i>
An Improved Chromosome-scale Genome Assembly and Population Genetics resource for<i>Populus tremula</i> Open
Aspen ( Populus tremula L.) is a widely distributed keystone species and a model system for forest tree genomics, with extensive resources developed for population genetics and genomics. Here we present an updated resource comprising a chr…
View article: Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment
Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment Open
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, …
View article: Poplar carbohydrate‐active enzymes: whole‐genome annotation and functional analyses based on <scp>RNA</scp> expression data
Poplar carbohydrate‐active enzymes: whole‐genome annotation and functional analyses based on <span>RNA</span> expression data Open
Summary Carbohydrate‐active enzymes ( CAZ ymes) 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…
View article: Functional and evolutionary genomic inferences in <i>Populus</i> through genome and population sequencing of American and European aspen
Functional and evolutionary genomic inferences in <i>Populus</i> through genome and population sequencing of American and European aspen Open
Significance We performed de novo, full-genome sequence analysis of two Populus species, North American quaking and Eurasian trembling aspen, that contain striking levels of genetic variation. Our results showed that positive and negative …
View article: Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce
Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce Open
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 form…
View article: AspWood: High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in <i>Populus tremula</i>
AspWood: High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in <i>Populus tremula</i> Open
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 wi…