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Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance

The diploid C(4) plant foxtail millet (Setaria italica L. Beauv.) is an important crop in many parts of Africa and Asia for the vast consumption of its grain and ability to grow in harsh environments, but remains understudied in terms of complete genomic architecture. To date, there have been only t...

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Autores principales: Tsai, Kevin J., Lu, Mei-Yeh Jade, Yang, Kai-Jung, Li, Mengyun, Teng, Yuchuan, Chen, Shihmay, Ku, Maurice S. B., Li, Wen-Hsiung
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062080/
https://www.ncbi.nlm.nih.gov/pubmed/27734962
http://dx.doi.org/10.1038/srep35076
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author Tsai, Kevin J.
Lu, Mei-Yeh Jade
Yang, Kai-Jung
Li, Mengyun
Teng, Yuchuan
Chen, Shihmay
Ku, Maurice S. B.
Li, Wen-Hsiung
author_facet Tsai, Kevin J.
Lu, Mei-Yeh Jade
Yang, Kai-Jung
Li, Mengyun
Teng, Yuchuan
Chen, Shihmay
Ku, Maurice S. B.
Li, Wen-Hsiung
author_sort Tsai, Kevin J.
collection PubMed
description The diploid C(4) plant foxtail millet (Setaria italica L. Beauv.) is an important crop in many parts of Africa and Asia for the vast consumption of its grain and ability to grow in harsh environments, but remains understudied in terms of complete genomic architecture. To date, there have been only two genome assembly and annotation efforts with neither assembly reaching over 86% of the estimated genome size. We have combined de novo assembly with custom reference-guided improvements on a popular cultivar of foxtail millet and have achieved a genome assembly of 477 Mbp in length, which represents over 97% of the estimated 490 Mbp. The assembly anchors over 98% of the predicted genes to the nine assembled nuclear chromosomes and contains more functional annotation gene models than previous assemblies. Our annotation has identified a large number of unique gene ontology terms related to metabolic activities, a region of chromosome 9 with several growth factor proteins, and regions syntenic with pearl millet or maize genomic regions that have been previously shown to affect growth. The new assembly and annotation for this important species can be used for detailed investigation and future innovations in growth for millet and other grains.
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spelling pubmed-50620802016-10-24 Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance Tsai, Kevin J. Lu, Mei-Yeh Jade Yang, Kai-Jung Li, Mengyun Teng, Yuchuan Chen, Shihmay Ku, Maurice S. B. Li, Wen-Hsiung Sci Rep Article The diploid C(4) plant foxtail millet (Setaria italica L. Beauv.) is an important crop in many parts of Africa and Asia for the vast consumption of its grain and ability to grow in harsh environments, but remains understudied in terms of complete genomic architecture. To date, there have been only two genome assembly and annotation efforts with neither assembly reaching over 86% of the estimated genome size. We have combined de novo assembly with custom reference-guided improvements on a popular cultivar of foxtail millet and have achieved a genome assembly of 477 Mbp in length, which represents over 97% of the estimated 490 Mbp. The assembly anchors over 98% of the predicted genes to the nine assembled nuclear chromosomes and contains more functional annotation gene models than previous assemblies. Our annotation has identified a large number of unique gene ontology terms related to metabolic activities, a region of chromosome 9 with several growth factor proteins, and regions syntenic with pearl millet or maize genomic regions that have been previously shown to affect growth. The new assembly and annotation for this important species can be used for detailed investigation and future innovations in growth for millet and other grains. Nature Publishing Group 2016-10-13 /pmc/articles/PMC5062080/ /pubmed/27734962 http://dx.doi.org/10.1038/srep35076 Text en Copyright © 2016, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Tsai, Kevin J.
Lu, Mei-Yeh Jade
Yang, Kai-Jung
Li, Mengyun
Teng, Yuchuan
Chen, Shihmay
Ku, Maurice S. B.
Li, Wen-Hsiung
Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance
title Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance
title_full Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance
title_fullStr Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance
title_full_unstemmed Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance
title_short Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance
title_sort assembling the setaria italica l. beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062080/
https://www.ncbi.nlm.nih.gov/pubmed/27734962
http://dx.doi.org/10.1038/srep35076
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