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Reference Genome for the Highly Transformable Setaria viridis ME034V
Setaria viridis (green foxtail) is an important model system for improving cereal crops due to its diploid genome, ease of cultivation, and use of C(4) photosynthesis. The S. viridis accession ME034V is exceptionally transformable, but the lack of a sequenced genome for this accession has limited it...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Genetics Society of America
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7534418/ https://www.ncbi.nlm.nih.gov/pubmed/32694197 http://dx.doi.org/10.1534/g3.120.401345 |
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author | Thielen, Peter M. Pendleton, Amanda L. Player, Robert A. Bowden, Kenneth V. Lawton, Thomas J. Wisecaver, Jennifer H. |
author_facet | Thielen, Peter M. Pendleton, Amanda L. Player, Robert A. Bowden, Kenneth V. Lawton, Thomas J. Wisecaver, Jennifer H. |
author_sort | Thielen, Peter M. |
collection | PubMed |
description | Setaria viridis (green foxtail) is an important model system for improving cereal crops due to its diploid genome, ease of cultivation, and use of C(4) photosynthesis. The S. viridis accession ME034V is exceptionally transformable, but the lack of a sequenced genome for this accession has limited its utility. We present a 397 Mb highly contiguous de novo assembly of ME034V using ultra-long nanopore sequencing technology (read N50 = 41kb). We estimate that this genome is largely complete based on our updated k-mer based genome size estimate of 401 Mb for S. viridis. Genome annotation identified 37,908 protein-coding genes and >300k repetitive elements comprising 46% of the genome. We compared the ME034V assembly with two other previously sequenced Setaria genomes as well as to a diversity panel of 235 S. viridis accessions. We found the genome assemblies to be largely syntenic, but numerous unique polymorphic structural variants were discovered. Several ME034V deletions may be associated with recent retrotransposition of copia and gypsy LTR repeat families, as evidenced by their low genotype frequencies in the sampled population. Lastly, we performed a phylogenomic analysis to identify gene families that have expanded in Setaria, including those involved in specialized metabolism and plant defense response. The high continuity of the ME034V genome assembly validates the utility of ultra-long DNA sequencing to improve genetic resources for emerging model organisms. Structural variation present in Setaria illustrates the importance of obtaining the proper genome reference for genetic experiments. Thus, we anticipate that the ME034V genome will be of significant utility for the Setaria research community. |
format | Online Article Text |
id | pubmed-7534418 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Genetics Society of America |
record_format | MEDLINE/PubMed |
spelling | pubmed-75344182020-10-13 Reference Genome for the Highly Transformable Setaria viridis ME034V Thielen, Peter M. Pendleton, Amanda L. Player, Robert A. Bowden, Kenneth V. Lawton, Thomas J. Wisecaver, Jennifer H. G3 (Bethesda) Genome Report Setaria viridis (green foxtail) is an important model system for improving cereal crops due to its diploid genome, ease of cultivation, and use of C(4) photosynthesis. The S. viridis accession ME034V is exceptionally transformable, but the lack of a sequenced genome for this accession has limited its utility. We present a 397 Mb highly contiguous de novo assembly of ME034V using ultra-long nanopore sequencing technology (read N50 = 41kb). We estimate that this genome is largely complete based on our updated k-mer based genome size estimate of 401 Mb for S. viridis. Genome annotation identified 37,908 protein-coding genes and >300k repetitive elements comprising 46% of the genome. We compared the ME034V assembly with two other previously sequenced Setaria genomes as well as to a diversity panel of 235 S. viridis accessions. We found the genome assemblies to be largely syntenic, but numerous unique polymorphic structural variants were discovered. Several ME034V deletions may be associated with recent retrotransposition of copia and gypsy LTR repeat families, as evidenced by their low genotype frequencies in the sampled population. Lastly, we performed a phylogenomic analysis to identify gene families that have expanded in Setaria, including those involved in specialized metabolism and plant defense response. The high continuity of the ME034V genome assembly validates the utility of ultra-long DNA sequencing to improve genetic resources for emerging model organisms. Structural variation present in Setaria illustrates the importance of obtaining the proper genome reference for genetic experiments. Thus, we anticipate that the ME034V genome will be of significant utility for the Setaria research community. Genetics Society of America 2020-07-21 /pmc/articles/PMC7534418/ /pubmed/32694197 http://dx.doi.org/10.1534/g3.120.401345 Text en Copyright © 2020 Thielen et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Genome Report Thielen, Peter M. Pendleton, Amanda L. Player, Robert A. Bowden, Kenneth V. Lawton, Thomas J. Wisecaver, Jennifer H. Reference Genome for the Highly Transformable Setaria viridis ME034V |
title | Reference Genome for the Highly Transformable Setaria viridis ME034V |
title_full | Reference Genome for the Highly Transformable Setaria viridis ME034V |
title_fullStr | Reference Genome for the Highly Transformable Setaria viridis ME034V |
title_full_unstemmed | Reference Genome for the Highly Transformable Setaria viridis ME034V |
title_short | Reference Genome for the Highly Transformable Setaria viridis ME034V |
title_sort | reference genome for the highly transformable setaria viridis me034v |
topic | Genome Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7534418/ https://www.ncbi.nlm.nih.gov/pubmed/32694197 http://dx.doi.org/10.1534/g3.120.401345 |
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