43 results on '"Mannapperuma, Chanaka"'
Search Results
2. Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen
- Author
-
Lin, Yao-Cheng, Wang, Jing, Delhomme, Nicolas, Schiffthaler, Bastian, Sundström, Görel, Zuccolo, Andrea, Nystedt, Björn, Hvidsten, Torgeir R., de la Torre, Amanda, Cossu, Rosa M., Hoeppner, Marc P., Lantz, Henrik, Scofield, Douglas G., Zamani, Neda, Johansson, Anna, Mannapperuma, Chanaka, Robinson, Kathryn M., Mähler, Niklas, Leitch, Ilia J., Pellicer, Jaume, Park, Eung-Jun, Van Montagu, Marc, Van de Peer, Yves, Grabherr, Manfred, Jansson, Stefan, Ingvarsson, Pär K., and Street, Nathaniel R.
- Published
- 2018
3. qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE)
- Author
-
Christie, Nanette, Mannapperuma, Chanaka, Ployet, Raphael, van der Merwe, Karen, Mähler, Niklas, Delhomme, Nicolas, Naidoo, Sanushka, Mizrachi, Eshchar, Street, Nathaniel R., and Myburg, Alexander A.
- Published
- 2021
- Full Text
- View/download PDF
4. NAC domain transcription factors VNI2 and ATAF2 form protein complexes and regulate leaf senescence
- Author
-
Nagahage, Isura Sumeda Priyadarshana, primary, Matsuda, Kohei, additional, Miyashita, Kyoko, additional, Fujiwara, Sumire, additional, Mannapperuma, Chanaka, additional, Yamada, Takuya, additional, Sakamoto, Shingo, additional, Ishikawa, Toshiki, additional, Nagano, Minoru, additional, Ohtani, Misato, additional, Kato, Ko, additional, Uchimiya, Hirofumi, additional, Mitsuda, Nobutaka, additional, Kawai‐Yamada, Maki, additional, Demura, Taku, additional, and Yamaguchi, Masatoshi, additional
- Published
- 2023
- Full Text
- View/download PDF
5. Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce
- Author
-
Jokipii-Lukkari, Soile, Delhomme, Nicolas, Schiffthaler, Bastian, Mannapperuma, Chanaka, Prestele, Jakob, Nilsson, Ove, Street, Nathaniel R., and Tuominen, Hannele
- Published
- 2018
6. AspWood : High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in Populus tremula
- Author
-
Sundell, David, Street, Nathaniel R., Kumar, Manoj, Mellerowicz, Ewa J., Kucukoglu, Melis, Johnsson, Christoffer, Kumar, Vikash, Mannapperuma, Chanaka, Delhomme, Nicolas, Nilsson, Ove, Tuominen, Hannele, Pesquet, Edouard, Fischer, Urs, Niittylä, Totte, Sundberg, Björn, and Hvidsten, Torgeir R.
- Published
- 2017
7. Chromosome-level genome assembly of a parent species of widely cultivated azaleas
- Author
-
Yang, Fu-Sheng, Nie, Shuai, Liu, Hui, Shi, Tian-Le, Tian, Xue-Chan, Zhou, Shan-Shan, Bao, Yu-Tao, Jia, Kai-Hua, Guo, Jing-Fang, Zhao, Wei, An, Na, Zhang, Ren-Gang, Yun, Quan-Zheng, Wang, Xin-Zhu, Mannapperuma, Chanaka, Porth, Ilga, El-Kassaby, Yousry Aly, Street, Nathaniel Robert, Wang, Xiao-Ru, Van de Peer, Yves, and Mao, Jian-Feng
- Published
- 2020
- Full Text
- View/download PDF
8. NAC domain transcription factors VNI2 and ATAF2 form protein complexes and regulate leaf senescence
- Author
-
Nagahage, Isura Sumeda Priyadarshana, Matsuda, Kohei, Miyashita, Kyoko, Fujiwara, Sumire, Mannapperuma, Chanaka, Yamada, Takuya, Sakamoto, Shingo, Ishikawa, Toshiki, Nagano, Minoru, Ohtani, Misato, Kato, Ko, Uchimiya, Hirofumi, Mitsuda, Nobutaka, Kawai-Yamada, Maki, Demura, Taku, Yamaguchi, Masatoshi, Nagahage, Isura Sumeda Priyadarshana, Matsuda, Kohei, Miyashita, Kyoko, Fujiwara, Sumire, Mannapperuma, Chanaka, Yamada, Takuya, Sakamoto, Shingo, Ishikawa, Toshiki, Nagano, Minoru, Ohtani, Misato, Kato, Ko, Uchimiya, Hirofumi, Mitsuda, Nobutaka, Kawai-Yamada, Maki, Demura, Taku, and Yamaguchi, Masatoshi
- Abstract
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 regulator of xylem vessel formation. Here, we screened interacting proteins with VNI2 using yeast two-hybrid assay and isolated two NAC domain transcription factors, Arabidopsis thaliana ACTIVATION FACTOR 2 (ATAF2) and NAC DOMAIN CONTAINING PROTEIN 102 (ANAC102). A transient gene expression assay showed that ATAF2 upregulates the expression of genes involved in leaf senescence, and VNI2 effectively inhibits the transcriptional activation activity of ATAF2. vni2 mutants accelerate leaf senescence, whereas ataf2 mutants delay leaf senescence. In addition, the accelerated leaf senescence phenotype of the vni2 mutant is recovered by simultaneous mutation of ATAF2. Our findings strongly suggest that VNI2 interacts with and inhibits ATAF2, resulting in negatively regulating leaf senescence.
- Published
- 2023
- Full Text
- View/download PDF
9. Identification of growth regulators using cross-species network analysis in plants
- Author
-
Curci, Pasquale Luca, primary, Zhang, Jie, additional, Mähler, Niklas, additional, Seyfferth, Carolin, additional, Mannapperuma, Chanaka, additional, Diels, Tim, additional, Van Hautegem, Tom, additional, Jonsen, David, additional, Street, Nathaniel, additional, Hvidsten, Torgeir R, additional, Hertzberg, Magnus, additional, Nilsson, Ove, additional, Inzé, Dirk, additional, Nelissen, Hilde, additional, and Vandepoele, Klaas, additional
- Published
- 2022
- Full Text
- View/download PDF
10. Identification of growth regulators using cross-species network analysis in plants
- Author
-
Curci, Pasquale Luca, Zhang, Jie, Mähler, Niklas, Seyfferth, Carolin, Mannapperuma, Chanaka, Diels, Tim, Van Hautegem, Tom, Jonsen, David, Street, Nathaniel, Hvidsten, Torgeir R., Hertzberg, Magnus, Nilsson, Ove, Inzé, Dirk, Nelissen, Hilde, Vandepoele, Klaas, Curci, Pasquale Luca, Zhang, Jie, Mähler, Niklas, Seyfferth, Carolin, Mannapperuma, Chanaka, Diels, Tim, Van Hautegem, Tom, Jonsen, David, Street, Nathaniel, Hvidsten, Torgeir R., Hertzberg, Magnus, Nilsson, Ove, Inzé, Dirk, Nelissen, Hilde, and Vandepoele, Klaas
- Abstract
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 transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on the leaf to study plant growth. First, we built leaf growth transcriptional networks in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and aspen (Populus tremula). Next, known growth regulators, here defined as genes that when mutated or ectopically expressed alter plant growth, together with cross-species conserved networks, were used as guides to predict novel Arabidopsis growth regulators. Using an in-depth literature screening, 34 out of 100 top predicted growth regulators were confirmed to affect leaf phenotype when mutated or overexpressed and thus represent novel potential growth regulators. Globally, these growth regulators were involved in cell cycle, plant defense responses, gibberellin, auxin, and brassinosteroid signaling. Phenotypic characterization of loss-of-function lines confirmed two predicted growth regulators to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). In conclusion, the presented network approach offers an integrative cross-species strategy to identify genes involved in plant growth and development.
- Published
- 2022
- Full Text
- View/download PDF
11. Spatially resolved transcriptome profiling in model plant species
- Author
-
Giacomello, Stefania, Salmén, Fredrik, Terebieniec, Barbara K., Vickovic, Sanja, Navarro, José Fernandez, Alexeyenko, Andrey, Reimegård, Johan, McKee, Lauren S., Mannapperuma, Chanaka, Bulone, Vincent, Ståhl, Patrik L., Sundström, Jens F., Street, Nathaniel R., and Lundeberg, Joakim
- Published
- 2017
- Full Text
- View/download PDF
12. 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
- Author
-
Liu, Hui, primary, Yan, Xue-Mei, additional, Wang, Xin-rui, additional, Zhang, Dong-Xu, additional, Zhou, Qingyuan, additional, Shi, Tian-Le, additional, Jia, Kai-Hua, additional, Tian, Xue-Chan, additional, Zhou, Shan-Shan, additional, Zhang, Ren-Gang, additional, Yun, Quan-Zheng, additional, Wang, Qing, additional, Xiang, Qiuhong, additional, Mannapperuma, Chanaka, additional, Van Zalen, Elena, additional, Street, Nathaniel R., additional, Porth, Ilga, additional, El-Kassaby, Yousry A., additional, Zhao, Wei, additional, Wang, Xiao-Ru, additional, Guan, Wenbin, additional, and Mao, Jian-Feng, additional
- Published
- 2021
- Full Text
- View/download PDF
13. Identification of new growth regulators using cross-species network analysis in plants
- Author
-
Curci, Pasquale Luca, primary, Zhang, Jie, additional, Mähler, Niklas, additional, Seyfferth, Carolin, additional, Mannapperuma, Chanaka, additional, Diels, Tim, additional, Hautegem, Tom Van, additional, Jonsen, David, additional, Street, Nathaniel, additional, Hvidsten, Torgeir R., additional, Hertzberg, Magnus, additional, Nilsson, Ove, additional, Inze, Dirk, additional, Nelissen, Hilde, additional, and Vandepoele, Klaas, additional
- Published
- 2021
- Full Text
- View/download PDF
14. Additional file 2 of qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE)
- Author
-
Christie, Nanette, Mannapperuma, Chanaka, Ployet, Raphael, van der Merwe, Karen, M��hler, Niklas, Delhomme, Nicolas, Naidoo, Sanushka, Mizrachi, Eshchar, Street, Nathaniel R., and Myburg, Alexander A.
- Abstract
Additional file 2: Method S1. Expression profiling of RNA-seq datasets. Method S2. QTL and eQTL analysis of data in qtlXplorer. Method S3. Overview of the EucGenIE tools. Method S4. Translating genes between species within PlantGenIE. Method S5. Case study: Laccases and peroxidases.
- Published
- 2021
- Full Text
- View/download PDF
15. Additional file 3 of qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE)
- Author
-
Christie, Nanette, Mannapperuma, Chanaka, Ployet, Raphael, van der Merwe, Karen, M��hler, Niklas, Delhomme, Nicolas, Naidoo, Sanushka, Mizrachi, Eshchar, Street, Nathaniel R., and Myburg, Alexander A.
- Abstract
Additional file 3: Figure S1. Co-expression analysis of 137 LAC/PRX genes using exNet in EucGenIE. (a) Correlation network representing 62 correlations between 42 (out of a total of 137) LAC/PRX genes, filtered at threshold 5. (b) Correlation network representing 1877 correlations between 90 LAC/PRX and 1043 other correlated genes, obtained after expanding at threshold 6. Correlation networks are based on 72 transcriptomic datasets (all exAtlas and biotic interactions datasets; sample collections 2���4 in Table 1) in EucGenIE and were visualized using the exNet tool.
- Published
- 2021
- Full Text
- View/download PDF
16. Additional file 4 of qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE)
- Author
-
Christie, Nanette, Mannapperuma, Chanaka, Ployet, Raphael, van der Merwe, Karen, M��hler, Niklas, Delhomme, Nicolas, Naidoo, Sanushka, Mizrachi, Eshchar, Street, Nathaniel R., and Myburg, Alexander A.
- Abstract
Additional file 4: Figure S2. Systems genetics analysis of the eight LAC/PRX genes associated with secondary cell wall (SCW) biosynthesis in Eucalyptus xylem formation. The network was built from data exported from qtlXplorer and follows the same structure as presented in Fig. 6. Cis- and trans-eQTL associations connecting candidate genes (blue nodes) or cell wall-related genes (green nodes) to eQTL peak positions (turquoise triangles) are represented by red and blue edges, respectively. Transcription factors (TFs) underlying eQTL peak positions are represented by grey or green squares and connected to eQTL peak positions via grey dashed line edges. Gene expression profile correlations are represented by grey solid edges, with thickness proportional to the absolute value of the correlation. Physical overlap of trait QTLs (purple nodes) with candidate gene or eQTL peak positions are represented by green dashed lines. eQTL peak position node size is proportional to the number of genes having eQTLs (cis or trans) mapped at that genomic position. Underlying TF node size is proportional to the number and average value of the correlations of TFs with genes having cis- or trans-eQTLs mapped at that position (underlying TF score; Additional file 1: Table S8). Candidate gene node size is proportional to its score for prioritization (see Additional file 2: Methods S5; Additional file 1: Table S9), taking into account (i) their correlations (number and average value) with SCW genes across the population-wide transcriptomic data, (ii) the number of physical overlaps with candidate gene/SCW-related QTLs, (iii) the number of eQTLs mapped at SCW-enriched eQTL positions, (iv) the number of overlaps of their eQTL positions with SCW-related trait QTLs, and (v) the number of SCW-related TFs in the top 10 best candidate TFs underlying their eQTL positions.
- Published
- 2021
- Full Text
- View/download PDF
17. The BOP-type co-transcriptional regulator NODULE ROOT1 promotes stem secondary growth of the tropical Cannabaceae tree Parasponia andersonii
- Author
-
Shen, Defeng, Holmer, Rens, Kulikova, Olga, Mannapperuma, Chanaka, Street, Nathaniel, Yan, Zhichun, van der Maden, Thomas, Bu, Fengjiao, Zhang, Yuanyuan, Geurts, Rene, Magne, Kévin, Shen, Defeng, Holmer, Rens, Kulikova, Olga, Mannapperuma, Chanaka, Street, Nathaniel, Yan, Zhichun, van der Maden, Thomas, Bu, Fengjiao, Zhang, Yuanyuan, Geurts, Rene, and Magne, Kévin
- Abstract
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. Current knowledge regarding the genetic regulation of cambium activity and secondary growth is still far from complete. The tropical Cannabaceae tree Parasponia andersonii is a non-legume research model of nitrogen-fixing root nodulation. Parasponia andersonii can be transformed efficiently, making it amenable for CRISPR-Cas9-mediated reverse genetics. We considered whether P. andersonii also could be used as a complementary research system to investigate tree-related traits, including secondary growth. We established a developmental map of stem secondary growth in P. andersonii plantlets. Subsequently, we showed that the expression of the co-transcriptional regulator PanNODULE ROOT1 (PanNOOT1) is essential for controlling this process. PanNOOT1 is orthologous to Arabidopsis thaliana BLADE-ON-PETIOLE1 (AtBOP1) and AtBOP2, which are involved in the meristem-to-organ-boundary maintenance. Moreover, in species forming nitrogen-fixing root nodules, NOOT1 is known to function as a key nodule identity gene. Parasponia andersonii CRISPR-Cas9 loss-of-function Pannoot1 mutants are altered in the development of the xylem and phloem tissues without apparent disturbance of the cambium organization and size. Transcriptomic analysis showed that the expression of key secondary growth-related genes is significantly down-regulated in Pannoot1 mutants. This allows us to conclude that PanNOOT1 positively contributes to the regulation of stem secondary growth. Our work also demonstrates that P. andersonii can serve as a tree research system.
- Published
- 2021
- Full Text
- View/download PDF
18. Reverse genetics using CRISPR-Cas9 in the tropical tree Parasponia andersonii revealed a promotive role for PanNODULE ROOT1 in stem secondary growth
- Author
-
Shen, Defeng, Holmer, Rens, Kulikova, Olga, Mannapperuma, Chanaka, Street, Nathaniel R., Yan, Zhichun, van der Maden, Thomas, Bu, Fengjiao, Zhang, Yuanyuan, Geurts, Rene, Magne, Kévin, Shen, Defeng, Holmer, Rens, Kulikova, Olga, Mannapperuma, Chanaka, Street, Nathaniel R., Yan, Zhichun, van der Maden, Thomas, Bu, Fengjiao, Zhang, Yuanyuan, Geurts, Rene, and Magne, Kévin
- Abstract
NODULE ROOT (NOOT), BLADE-ON-PETIOLE (BOP), COCHLEATA (COCH)-LIKE (NBCL) are plant-specific developmental regulator participating in many developmental process of the primary growth. NBCL contribute to the meristem-to-organ-boundaries maintenance by inhibiting meristematic activities and promoting adjacent tissues initiation, development and determinacy. To determine if NBCL contribute to the regulation of tree secondary growth, we studied the impact of the PanNODULE ROOT1 (PanNOOT1) gene loss-of-function on the secondary growth of Parasponia andersonii (P. andersonii).
- Published
- 2021
19. The BOP‐type co‐transcriptional regulator NODULE ROOT1 promotes stem secondary growth of the tropical Cannabaceae tree Parasponia andersonii
- Author
-
Shen, Defeng, primary, Holmer, Rens, additional, Kulikova, Olga, additional, Mannapperuma, Chanaka, additional, Street, Nathaniel R., additional, Yan, Zhichun, additional, van der Maden, Thomas, additional, Bu, Fengjiao, additional, Zhang, Yuanyuan, additional, Geurts, Rene, additional, and Magne, Kévin, additional
- Published
- 2021
- Full Text
- View/download PDF
20. Genome-Wide Identification of Populus Malectin/Malectin-Like Domain-Containing Proteins and Expression Analyses Reveal Novel Candidates for Signaling and Regulation of Wood Development
- Author
-
Kumar, Vikash, Donev, Evgeniy N., Barbut, Felix R., Kushwah, Sunita, Mannapperuma, Chanaka, Urbancsok, Janos, and Mellerowicz, Ewa J.
- Subjects
fungi ,cell wall integrity ,Botany ,Plant Science ,Botanik ,lcsh:Plant culture ,malectin domain ,Populus ,malectin-like domain ,CrRLK1L ,lcsh:SB1-1110 ,CBM57 ,Agricultural Science ,Original Research ,receptor-like protein kinases - Abstract
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 domain (MLD). In herbaceous plants, MD- or MLD-containing proteins (MD proteins) are known to regulate development, reproduction, and resistance to various stresses. However, their functions in woody plants have not yet been studied. To unravel their potential role in wood development, we carried out genome-wide identification of MD proteins in the model tree species black cottonwood (Populus trichocarpa), and analyzed their expression and co-expression networks. P. trichocarpa had 146 MD genes assigned to 14 different clades, two of which were specific to the genus Populus. 87% of these genes were located on chromosomes, the rest being associated with scaffolds. Based on their protein domain organization, and in agreement with the exon-intron structures, the MD genes identified here could be classified into five superclades having the following domains: leucine-rich repeat (LRR)-MD-protein kinase (PK), MLD-LRR-PK, MLD-PK (CrRLK1L), MLD-LRR, and MD-Kinesin. Whereas the majority of MD genes were highly expressed in leaves, particularly under stress conditions, eighteen showed a peak of expression during secondary wall formation in the xylem and their co-expression networks suggested signaling functions in cell wall integrity, pathogen-associated molecular patterns, calcium, ROS, and hormone pathways. Thus, P. trichocarpa MD genes having different domain organizations comprise many genes with putative foliar defense functions, some of which could be specific to Populus and related species, as well as genes with potential involvement in signaling pathways in other tissues including developing wood.
- Published
- 2020
21. Mänskliga-datorinteraktion principer för utveckling av webb-baserade resurser för genomik
- Author
-
Mannapperuma, Chanaka
- Subjects
Bioinformatics and Systems Biology ,Genetics ,Bioinformatik och systembiologi ,Genetik ,Human Computer Interaction ,Människa-datorinteraktion (interaktionsdesign) - Abstract
Genomics projects, including genome sequencing, transcriptomics, genome-wide association mapping and epigenetics assays, producevast quantities of data. Extracting the required information from such complex datasets is a significant challenge and even where software tools do exist, these are often not intuitive or designed fornon-specialist users. This dissertation details how I have applied design principles from the field of Human-Computer Interaction (HCI) to the development of intuitive bioinformatics web-based resources for exploring genomics data. In the first part of the thesis I detail the development of a specialised genomics resource that enables non specialists who lack bioinformatics skills to access, explore and extract new knowledge from a variety of genomics data types. These tools were developed in collaboration with wet lab biologists and bioinformaticians who represent typical end-users. The tools developed have been integrated within the PlantGenIE (Plant Genome IntegrativeExplorer) web resource, which has been established as a platform for exploring genomics data for Populus, conifer, Eucalyptus and Arabidopsisgenomics data. Even though the ability to collect, store and manage data is increasing faster due to new technologies and science, our ability to understand it remains constant. To help address this, in the second part of this dissertation I focus on the usability enhancement of tools based on the HCI and User Experience (UX) practices. To achieve this, I utilised visualisation techniques and design principles in the design process for the improvement of the PlantGenIEUser Interface (UI), and applied usability methods to evaluate the UX of PlantGenIE tools. These results were then used to inform adaptations and fine-tuning of those. I show that utilisation of these research methods and practices with the development life cycle represents a framework for designing usable bioinformatics tools. Wider-scale use of these methods by future designers and developers will enable the creation of more usable bioinformatics resources.
- Published
- 2020
22. Leaf shape in Populus tremula is a complex, omnigenic trait
- Author
-
Mähler, Niklas, Schiffthaler, Bastian, Robinson, Kathryn M., Terebieniec, Barbara K., Vucak, Matej, Mannapperuma, Chanaka, Bailey, Mark, Jansson, Stefan, Hvidsten, Torgeir, Street, Nathaniel R., Mähler, Niklas, Schiffthaler, Bastian, Robinson, Kathryn M., Terebieniec, Barbara K., Vucak, Matej, Mannapperuma, Chanaka, Bailey, Mark, Jansson, Stefan, Hvidsten, Torgeir, and Street, Nathaniel R.
- Abstract
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 the genetic architecture of leaf shape variation in Eurasian aspen (Populus tremula L.) by performing genome‐wide association study (GWAS) for physiognomy traits. To ascertain the roles of identified GWAS candidate genes within the leaf development transcriptional program, we generated RNA‐Seq data that we used to perform gene co‐expression network analyses from a developmental series, which is publicly available within the PlantGenIE resource. We additionally used existing gene expression measurements across the population to analyze GWAS candidate genes in the context of a population‐wide co‐expression network and to identify genes that were differentially expressed between groups of individuals with contrasting leaf shapes. These data were integrated with expression GWAS (eQTL) results to define a set of candidate genes associated with leaf shape variation. Our results identified no clear adaptive link to leaf shape variation and indicate that leaf shape traits are genetically complex, likely determined by numerous small‐effect variations in gene expression. Genes associated with shape variation were peripheral within the population‐wide co‐expression network, were not highly connected within the leaf development co‐expression network, and exhibited signatures of relaxed selection. As such, our results are consistent with the omnigenic model., Originally included in thesis in manuscript form.
- Published
- 2020
- Full Text
- View/download PDF
23. Human-computer interaction principles for developing web-based genomics resources
- Author
-
Mannapperuma, Chanaka and Mannapperuma, Chanaka
- Abstract
Genomics projects, including genome sequencing, transcriptomics, genome-wide association mapping and epigenetics assays, producevast quantities of data. Extracting the required information from such complex datasets is a significant challenge and even where software tools do exist, these are often not intuitive or designed fornon-specialist users. This dissertation details how I have applied design principles from the field of Human-Computer Interaction (HCI) to the development of intuitive bioinformatics web-based resources for exploring genomics data. In the first part of the thesis I detail the development of a specialised genomics resource that enables non specialists who lack bioinformatics skills to access, explore and extract new knowledge from a variety of genomics data types. These tools were developed in collaboration with wet lab biologists and bioinformaticians who represent typical end-users. The tools developed have been integrated within the PlantGenIE (Plant Genome IntegrativeExplorer) web resource, which has been established as a platform for exploring genomics data for Populus, conifer, Eucalyptus and Arabidopsisgenomics data. Even though the ability to collect, store and manage data is increasing faster due to new technologies and science, our ability to understand it remains constant. To help address this, in the second part of this dissertation I focus on the usability enhancement of tools based on the HCI and User Experience (UX) practices. To achieve this, I utilised visualisation techniques and design principles in the design process for the improvement of the PlantGenIEUser Interface (UI), and applied usability methods to evaluate the UX of PlantGenIE tools. These results were then used to inform adaptations and fine-tuning of those. I show that utilisation of these research methods and practices with the development life cycle represents a framework for designing usable bioinformatics tools. Wider-scale use of these methods by future design
- Published
- 2020
24. PlantGenIE-PLAZA : integrating orthology into the PlantGenIE.org resource using the PLAZA pipeline
- Author
-
Mannapperuma, Chanaka, Liu, H., Bel, M., Delhomme, Nicolas, Serrano, A., Schiffthaler, Bastian, Hvidsten, Torgeir R., Vandepoele, K., Ayllón-Benítez, A., Street, Nathaniel, Mannapperuma, Chanaka, Liu, H., Bel, M., Delhomme, Nicolas, Serrano, A., Schiffthaler, Bastian, Hvidsten, Torgeir R., Vandepoele, K., Ayllón-Benítez, A., and Street, Nathaniel
- Published
- 2020
25. The Eucalyptus Genome Integrative Explorer : an online resource for systems genetics in forest tree species
- Author
-
Christie, N., Mannapperuma, Chanaka, Ployet, R., Merwe, K. van der, Mähler, Niklas, Delhomme, Nicolas, Naidoo, S., Mizrachi, E., Street, Nathaniel, Myburg, A. A., Christie, N., Mannapperuma, Chanaka, Ployet, R., Merwe, K. van der, Mähler, Niklas, Delhomme, Nicolas, Naidoo, S., Mizrachi, E., Street, Nathaniel, and Myburg, A. A.
- Published
- 2020
26. Genome-Wide Identification of Populus Malectin/Malectin-Like Domain-Containing Proteins and Expression Analyses Reveal Novel Candidates for Signaling and Regulation of Wood Development
- Author
-
Kumar, Vikash, primary, Donev, Evgeniy N., additional, Barbut, Félix R., additional, Kushwah, Sunita, additional, Mannapperuma, Chanaka, additional, Urbancsok, János, additional, and Mellerowicz, Ewa J., additional
- Published
- 2020
- Full Text
- View/download PDF
27. Leaf shape in Populus tremula is a complex, omnigenic trait
- Author
-
Mähler, Niklas, primary, Schiffthaler, Bastian, additional, Robinson, Kathryn M., additional, Terebieniec, Barbara K., additional, Vučak, Matej, additional, Mannapperuma, Chanaka, additional, Bailey, Mark E. S., additional, Jansson, Stefan, additional, Hvidsten, Torgeir R., additional, and Street, Nathaniel R., additional
- Published
- 2020
- Full Text
- View/download PDF
28. Poplar carbohydrate-active enzymes : whole-genome annotation and functional analyses based on RNA expression data
- Author
-
Kumar, Vikash, Hainaut, Matthieu, Delhomme, Nicolas, Mannapperuma, Chanaka, Immerzeel, Peter, Street, Nathaniel R., Henrissat, Bernard, Mellerowicz, Ewa J., Swedish University of Agricultural Sciences (SLU), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Umeå University, Svenska Forskningsrådet Formas, Knut och Alice Wallenbergs Stiftelse,VR, Kempestiftelserna,VINNOVA, Stiftelsen för Strategisk Forskning. Grant Number: ValueTree RBP14‐0011, Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Karlstad University [Sweden], Umea Plant Science Center (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU)-Swedish University of Agricultural Sciences (SLU), SSF project ValueTree RBP14-0011, and Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Resource ,Whole Genome Sequencing ,[SDV]Life Sciences [q-bio] ,fungi ,Carbohydrates ,Biochemistry and Molecular Biology ,Genomics ,comparative genomics ,Chemical Engineering ,Wood ,genome sequencing ,vegetative development ,Populus ,Gene Expression Regulation, Plant ,Kemiteknik ,RNA ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,cell wall ,wood formation ,carbohydrate metabolism ,Plant Biotechnology ,Växtbioteknologi ,Biokemi och molekylärbiologi ,Plant Proteins - Abstract
Summary 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 (http://aspwood.popgenie.org/aspwood-v3.0/) 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., Significance Statement Re‐annotation of carbohydrate‐active enzymes in poplar and their transcript analyses reveal genes and gene families involved in wood cell wall biosynthesis.
- Published
- 2019
29. Cyberinfrastructure to Improve Forest Health and Productivity : The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment
- Author
-
Wegrzyn, Jill L., Staton, Margaret A., Street, Nathaniel R., Main, Dorrie, Grau, Emily, Herndon, Nic, Buehler, Sean, Falk, Taylor, Zaman, Sumaira, Ramnath, Risharde, Richter, Peter, Sun, Lang, Condon, Bradford, Almsaeed, Abdullah, Chen, Ming, Mannapperuma, Chanaka, Jung, Sook, Ficklin, Stephen, Wegrzyn, Jill L., Staton, Margaret A., Street, Nathaniel R., Main, Dorrie, Grau, Emily, Herndon, Nic, Buehler, Sean, Falk, Taylor, Zaman, Sumaira, Ramnath, Risharde, Richter, Peter, Sun, Lang, Condon, Bradford, Almsaeed, Abdullah, Chen, Ming, Mannapperuma, Chanaka, Jung, Sook, and Ficklin, Stephen
- Abstract
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.
- Published
- 2019
- Full Text
- View/download PDF
30. GenIE-Sys: Genome Integrative Explorer System
- Author
-
Mannapperuma, Chanaka, primary, Waterworth, John, additional, and Street, Nathaniel, additional
- Published
- 2019
- Full Text
- View/download PDF
31. Poplar carbohydrate‐active enzymes: whole‐genome annotation and functional analyses based onRNAexpression data
- Author
-
Kumar, Vikash, primary, Hainaut, Matthieu, additional, Delhomme, Nicolas, additional, Mannapperuma, Chanaka, additional, Immerzeel, Peter, additional, Street, Nathaniel R., additional, Henrissat, Bernard, additional, and Mellerowicz, Ewa J., additional
- Published
- 2019
- Full Text
- View/download PDF
32. Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment
- Author
-
Wegrzyn, Jill L., primary, Staton, Margaret A., additional, Street, Nathaniel R., additional, Main, Dorrie, additional, Grau, Emily, additional, Herndon, Nic, additional, Buehler, Sean, additional, Falk, Taylor, additional, Zaman, Sumaira, additional, Ramnath, Risharde, additional, Richter, Peter, additional, Sun, Lang, additional, Condon, Bradford, additional, Almsaeed, Abdullah, additional, Chen, Ming, additional, Mannapperuma, Chanaka, additional, Jung, Sook, additional, and Ficklin, Stephen, additional
- Published
- 2019
- Full Text
- View/download PDF
33. AspWood: High-spatial-resolution transcriptome profiles reveal uncharacterized modularity of wood formation in Populus tremula
- Author
-
Sundell, David, primary, Street, Nathaniel R., additional, Kumar, Manoj, additional, Mellerowicz, Ewa J., additional, Kucukoglu, Melis, additional, Johnsson, Christoffer, additional, Kumar, Vikash, additional, Mannapperuma, Chanaka, additional, Delhomme, Nicolas, additional, Nilsson, Ove, additional, Tuominen, Hannele, additional, Pesquet, Edouard, additional, Fischer, Urs, additional, Niittylä, Totte, additional, Sundberg, Bjöern, additional, and Hvidsten, Torgeir R., additional
- Published
- 2016
- Full Text
- View/download PDF
34. Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen.
- Author
-
Yao-Cheng Lin, Jing Wang, Delhomme, Nicolas, Schiffthaler, Bastian, Sundström, Görel, Zuccolo, Andrea, Nystedt, Björn, Hvidsten, Torgeir R., de la Torre, Amanda, Cossu, Rosa M., Hoeppner, Marc P., Lantz, Henrik, Scofield, Douglas G., Zamani, Neda, Johansson, Anna, Mannapperuma, Chanaka, Robinson, Kathryn M., Mähler, Niklas, Leitch, Ilia J., and Pellicer, Jaume
- Subjects
POPLARS ,ASPEN (Trees) ,HETEROZYGOSITY ,GENE expression ,NUCLEOTIDE sequencing ,PLANTS - Abstract
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). [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
35. High-spatial-resolution transcriptome profiling reveals uncharacterized regulatory complexity underlying cambial growth and wood formation in Populus tremula
- Author
-
Sundell, David, Street, Nathaniel R, Kumar, Manoj, Mellerowicz, Ewa J, Kucukoglu, Melis, Johnsson, Christoffer, Kumar, Vikash, Mannapperuma, Chanaka, Nilsson, Ove, Tuominen, Hannele, Pesquet, Edouard, Fischer, Urs, Niittyla, Totte, Sundberg, Bjoern, Hvidsten, Torgeir R, Sundell, David, Street, Nathaniel R, Kumar, Manoj, Mellerowicz, Ewa J, Kucukoglu, Melis, Johnsson, Christoffer, Kumar, Vikash, Mannapperuma, Chanaka, Nilsson, Ove, Tuominen, Hannele, Pesquet, Edouard, Fischer, Urs, Niittyla, Totte, Sundberg, Bjoern, and Hvidsten, Torgeir R
- Abstract
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.
- Published
- 2016
- Full Text
- View/download PDF
36. The Plant Genome Integrative Explorer Resource : PlantGenIE.org
- Author
-
Sundell, David, Mannapperuma, Chanaka, Netotea, Sergiu, Delhomme, Nicolas, Lin, Yao-Cheng, Sjödin, Andreas, Van de Peer, Yves, Jansson, Stefan, Hvidsten, Torgeir R., Street, Nathaniel R., Sundell, David, Mannapperuma, Chanaka, Netotea, Sergiu, Delhomme, Nicolas, Lin, Yao-Cheng, Sjödin, Andreas, Van de Peer, Yves, Jansson, Stefan, Hvidsten, Torgeir R., and Street, Nathaniel R.
- Abstract
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.
- Published
- 2015
- Full Text
- View/download PDF
37. The Plant Genome Integrative Explorer Resource: PlantGen IE .org
- Author
-
Sundell, David, primary, Mannapperuma, Chanaka, additional, Netotea, Sergiu, additional, Delhomme, Nicolas, additional, Lin, Yao‐Cheng, additional, Sjödin, Andreas, additional, Van de Peer, Yves, additional, Jansson, Stefan, additional, Hvidsten, Torgeir R., additional, and Street, Nathaniel R., additional
- Published
- 2015
- Full Text
- View/download PDF
38. Tangible Social Network System : Visual Markers for Social Network
- Author
-
Mannapperuma, Chanaka
- Subjects
AGNES project ,design and development ,social networking ,usability evaluation ,social network and ageing ,ubiquitous computing ,elderly ,tangible social network ,data flow diagram ,flowchart ,social network system for older people ,embodied interaction ,Systemvetenskap, informationssystem och informatik ,Information Systems - Abstract
Tangible social network system is a home-based communication solution specifically designed for elders. Former researches indicate that insufficient communication among elders cause several challenges in their daily activities such as social isolation, loneliness, depression and decreased appetite. In addition, lack of social participation increases the risk of Alzheimer´s (Ligt Enid, 1990). The major cause of these challenges are that elders are increasingly removed from communication technology using emails, text messaging, interact with social network systems and mobile phones due to cognitive and physical difficulties. To overcome this problem, new suggested social network system incorporates photo frame and photo album based interaction which allows instantaneous participation to the social network. By designing the new social network system, I tried to create an easier venue for more active cross-generational communication between elders and younger family members.This paper discusses the early results of the marker based social networking system aiming to propose digital technologies to enhance the social life of older people, who live alone their home. A prototype combining a touch screen, photo frame and a camera are described. It allows the older people to manage their participation to the social network system and get in touch with their loved ones. This paper demonstrates a User Sensitive inclusive Design (USID) process from the generation of user needs to the evaluation prototype. A key theme of tangible social network system shows how usable and emotional design derived from a user inclusive design process can encourage elders to adopt new modern technology. A first evaluation has shown the usability as well as the good acceptance of this system. AGNES
- Published
- 2010
39. Try to Understand Design and Design Process
- Author
-
Mannapperuma, Chanaka
- Subjects
design process ,interaction design triangle ,new design circle ,design ,understand design ,understand design process - Abstract
It is difficult for designers to explain what they do. In addition,those unfamiliar with design do not understand the rigor and logic of design thinking and process .We can’t formulate pre defined model for design process because every design situation is unique and new situation. But I tried to formulate my own model for design process as common with Inspirations from my supervisors/Lectures. I tried to describe what is design? And what is design process? In this paper.This personal position paper explores the personal improvement throughout the course work and what I learnt though out the course work.
- Published
- 2010
40. AspWood: High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in Populus tremula</em>
- Author
-
Sundell, David, Street, Nathaniel R., Kumar, Manoj, Mellerowicz, Ewa J., Kucukoglu, Melis, Johnsson, Christoffer, Kumar, Vikash, Mannapperuma, Chanaka, Delhomme, Nicolas, Nilsson, Ove, Hannele Tuominen, Pesquet, Edouard, Fischer, Urs, Niittylä, Totte, Sundberg, Björn, and Hvidsten, Torgeir R.
41. An integrated functional genomics and systems genetics analysis of leaf shape in Populus tremula
- Author
-
Schiffthaler, Bastian, Terebieniec, Barbara K, Mähler, Niklas, Robinson, Kathryn M, Mannapperuma, Chanaka, Jansson, Stefan, Street, Nathaniel R, Schiffthaler, Bastian, Terebieniec, Barbara K, Mähler, Niklas, Robinson, Kathryn M, Mannapperuma, Chanaka, Jansson, Stefan, and Street, Nathaniel R
- Abstract
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 studi
42. GenIE-Sys : Genome Integrative Explorer System
- Author
-
Mannapperuma, Chanaka, Waterworth, John, Street, Nathaniel, Mannapperuma, Chanaka, Waterworth, John, and Street, Nathaniel
- Abstract
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 provide maximum benefit to the community. However, there are relatively few options available for setting up such standalone frameworks. We developed the Genome Integrative Explorer System (GenIE-Sys) to set up web resources to enable search, visualization and exploration of genomics data typically generated by a genome project. GenIE-Sys is implemented in PHP, JavaScript and Python and is freely available under the GNU GPL 3 public license. All source code is freely available at the GenIE-Sys website (https://geniesys.org) or GitHub (http://github.com/plantgenie/geniesys.git). Documentation is available at http://geniesys.readthedocs.io.
- Full Text
- View/download PDF
43. An Improved Chromosome-scale Genome Assembly and Population Genetics resource for Populus tremula.
- Author
-
Robinson KM, Schiffthaler B, Liu H, Rydman SM, Rendón-Anaya M, Kalman TA, Kumar V, Canovi C, Bernhardsson C, Delhomme N, Jenkins J, Wang J, Mähler N, Richau KH, Stokes V, A'Hara S, Cottrell J, Coeck K, Diels T, Vandepoele K, Mannapperuma C, Park EJ, Plaisance S, Jansson S, Ingvarsson PK, and Street NR
- Subjects
- Chromosomes, Plant genetics, Phenotype, Plant Leaves genetics, Genomics methods, Chromosome Mapping, Populus genetics, Genome, Plant genetics, Polymorphism, Single Nucleotide genetics, Genome-Wide Association Study, Genetics, Population
- Abstract
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 genetic basis of natural variation in leaf size and shape, traits with complex genetic architecture. We generated the genome assembly using long-read sequencing, optical and high-density genetic maps. We conducted whole-genome resequencing of the Umeå Aspen (UmAsp) collection. Using the assembly and re-sequencing data from the UmAsp, Swedish Aspen (SwAsp) and Scottish Aspen (ScotAsp) collections we performed genome-wide association analyses (GWAS) using Single Nucleotide Polymorphisms (SNPs) for 26 leaf physiognomy phenotypes. We conducted Assay of Transposase Accessible Chromatin sequencing (ATAC-Seq), identified genomic regions of accessible chromatin, and subset SNPs to these regions, improving the GWAS detection rate. We identified candidate long non-coding RNAs in leaf samples, quantified their expression in an updated co-expression network, and used this to explore the functions of candidate genes identified from the GWAS. A GWAS found SNP associations for seven traits. The associated SNPs were in or near genes annotated with developmental functions, which represent candidates for further study. Of particular interest was a ~177-kbp region harbouring associations with several leaf phenotypes in ScotAsp. We have incorporated the assembly, population genetics, genomics, and GWAS data into the PlantGenIE.org web resource, including updating existing genomics data to the new genome version, to enable easy exploration and visualisation. We provide all raw and processed data to facilitate reuse in future studies., (© 2024 The Author(s). Physiologia Plantarum published by John Wiley & Sons Ltd on behalf of Scandinavian Plant Physiology Society.)
- Published
- 2024
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.