Accelerating structure‐function mapping using the ViVa webtool to mine natural variation
Abstract Thousands of sequenced genomes are now publicly available capturing a significant amount of natural variation within plant species; yet, much of these data remain inaccessible to researchers without significant bioinformatics experience. Here, we present a webtool called ViVa (Visualizing V...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2019-07-01
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| Series: | Plant Direct |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/pld3.147 |
| _version_ | 1818617697671315456 |
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| author | Morgan O. Hamm Britney L. Moss Alexander R. Leydon Hardik P. Gala Amy Lanctot Román Ramos Hannah Klaeser Andrew C. Lemmex Mollye L. Zahler Jennifer L. Nemhauser R. Clay Wright |
| author_facet | Morgan O. Hamm Britney L. Moss Alexander R. Leydon Hardik P. Gala Amy Lanctot Román Ramos Hannah Klaeser Andrew C. Lemmex Mollye L. Zahler Jennifer L. Nemhauser R. Clay Wright |
| author_sort | Morgan O. Hamm |
| collection | DOAJ |
| description | Abstract Thousands of sequenced genomes are now publicly available capturing a significant amount of natural variation within plant species; yet, much of these data remain inaccessible to researchers without significant bioinformatics experience. Here, we present a webtool called ViVa (Visualizing Variation) which aims to empower any researcher to take advantage of the amazing genetic resource collected in the Arabidopsis thaliana 1001 Genomes Project (http://1001genomes.org). ViVa facilitates data mining on the gene, gene family, or gene network level. To test the utility and accessibility of ViVa, we assembled a team with a range of expertise within biology and bioinformatics to analyze the natural variation within the well‐studied nuclear auxin signaling pathway. Our analysis has provided further confirmation of existing knowledge and has also helped generate new hypotheses regarding this well‐studied pathway. These results highlight how natural variation could be used to generate and test hypotheses about less‐studied gene families and networks, especially when paired with biochemical and genetic characterization. ViVa is also readily extensible to databases of interspecific genetic variation in plants as well as other organisms, such as the 3,000 Rice Genomes Project ( http://snp-seek.irri.org/) and human genetic variation ( https://www.ncbi.nlm.nih.gov/clinvar/). |
| first_indexed | 2024-12-16T17:09:49Z |
| format | Article |
| id | doaj.art-1b8f987d4642459f99be3f1ace67bf8a |
| institution | Directory Open Access Journal |
| issn | 2475-4455 |
| language | English |
| last_indexed | 2024-12-16T17:09:49Z |
| publishDate | 2019-07-01 |
| publisher | Wiley |
| record_format | Article |
| series | Plant Direct |
| spelling | doaj.art-1b8f987d4642459f99be3f1ace67bf8a2022-12-21T22:23:27ZengWileyPlant Direct2475-44552019-07-0137n/an/a10.1002/pld3.147Accelerating structure‐function mapping using the ViVa webtool to mine natural variationMorgan O. Hamm0Britney L. Moss1Alexander R. Leydon2Hardik P. Gala3Amy Lanctot4Román Ramos5Hannah Klaeser6Andrew C. Lemmex7Mollye L. Zahler8Jennifer L. Nemhauser9R. Clay Wright10Department of Biology University of Washington Seattle WashingtonDepartment of Biology Whitman College Walla Walla WashingtonDepartment of Biology University of Washington Seattle WashingtonDepartment of Biology University of Washington Seattle WashingtonDepartment of Biology University of Washington Seattle WashingtonDepartment of Biology University of Washington Seattle WashingtonDepartment of Biology Whitman College Walla Walla WashingtonDepartment of Biology University of Washington Seattle WashingtonDepartment of Biology University of Washington Seattle WashingtonDepartment of Biology University of Washington Seattle WashingtonBiological Systems Engineering Virginia Tech Blacksburg VirginiaAbstract Thousands of sequenced genomes are now publicly available capturing a significant amount of natural variation within plant species; yet, much of these data remain inaccessible to researchers without significant bioinformatics experience. Here, we present a webtool called ViVa (Visualizing Variation) which aims to empower any researcher to take advantage of the amazing genetic resource collected in the Arabidopsis thaliana 1001 Genomes Project (http://1001genomes.org). ViVa facilitates data mining on the gene, gene family, or gene network level. To test the utility and accessibility of ViVa, we assembled a team with a range of expertise within biology and bioinformatics to analyze the natural variation within the well‐studied nuclear auxin signaling pathway. Our analysis has provided further confirmation of existing knowledge and has also helped generate new hypotheses regarding this well‐studied pathway. These results highlight how natural variation could be used to generate and test hypotheses about less‐studied gene families and networks, especially when paired with biochemical and genetic characterization. ViVa is also readily extensible to databases of interspecific genetic variation in plants as well as other organisms, such as the 3,000 Rice Genomes Project ( http://snp-seek.irri.org/) and human genetic variation ( https://www.ncbi.nlm.nih.gov/clinvar/).https://doi.org/10.1002/pld3.147accessibilityArabidopsis thalianagenome diversitygenotype‐phenotypenatural variationstructure‐function |
| spellingShingle | Morgan O. Hamm Britney L. Moss Alexander R. Leydon Hardik P. Gala Amy Lanctot Román Ramos Hannah Klaeser Andrew C. Lemmex Mollye L. Zahler Jennifer L. Nemhauser R. Clay Wright Accelerating structure‐function mapping using the ViVa webtool to mine natural variation Plant Direct accessibility Arabidopsis thaliana genome diversity genotype‐phenotype natural variation structure‐function |
| title | Accelerating structure‐function mapping using the ViVa webtool to mine natural variation |
| title_full | Accelerating structure‐function mapping using the ViVa webtool to mine natural variation |
| title_fullStr | Accelerating structure‐function mapping using the ViVa webtool to mine natural variation |
| title_full_unstemmed | Accelerating structure‐function mapping using the ViVa webtool to mine natural variation |
| title_short | Accelerating structure‐function mapping using the ViVa webtool to mine natural variation |
| title_sort | accelerating structure function mapping using the viva webtool to mine natural variation |
| topic | accessibility Arabidopsis thaliana genome diversity genotype‐phenotype natural variation structure‐function |
| url | https://doi.org/10.1002/pld3.147 |
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