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Chromosome-level genome assembly of Japanese chestnut (Castanea crenata Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids

Japanese chestnut (Castanea crenata Sieb. et Zucc.), unlike other Castanea species, is resistant to most diseases and wasps. However, genomic data of Japanese chestnut that could be used to determine its biotic stress resistance mechanisms have not been reported to date. In this study, we employed l...

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Autores principales: Shirasawa, Kenta, Nishio, Sogo, Terakami, Shingo, Botta, Roberto, Marinoni, Daniela Torello, Isobe, Sachiko
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8435554/
https://www.ncbi.nlm.nih.gov/pubmed/34424280
http://dx.doi.org/10.1093/dnares/dsab016
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author Shirasawa, Kenta
Nishio, Sogo
Terakami, Shingo
Botta, Roberto
Marinoni, Daniela Torello
Isobe, Sachiko
author_facet Shirasawa, Kenta
Nishio, Sogo
Terakami, Shingo
Botta, Roberto
Marinoni, Daniela Torello
Isobe, Sachiko
author_sort Shirasawa, Kenta
collection PubMed
description Japanese chestnut (Castanea crenata Sieb. et Zucc.), unlike other Castanea species, is resistant to most diseases and wasps. However, genomic data of Japanese chestnut that could be used to determine its biotic stress resistance mechanisms have not been reported to date. In this study, we employed long-read sequencing and genetic mapping to generate genome sequences of Japanese chestnut at the chromosome level. Long reads (47.7 Gb; 71.6× genome coverage) were assembled into 781 contigs, with a total length of 721.2 Mb and a contig N50 length of 1.6 Mb. Genome sequences were anchored to the chestnut genetic map, comprising 14,973 single nucleotide polymorphisms (SNPs) and covering 1,807.8 cM map distance, to establish a chromosome-level genome assembly (683.8 Mb), with 69,980 potential protein-encoding genes and 425.5 Mb repetitive sequences. Furthermore, comparative genome structure analysis revealed that Japanese chestnut shares conserved chromosomal segments with woody plants, but not with herbaceous plants, of rosids. Overall, the genome sequence data of Japanese chestnut generated in this study is expected to enhance not only its genetics and genomics but also the evolutionary genomics of woody rosids.
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spelling pubmed-84355542021-09-14 Chromosome-level genome assembly of Japanese chestnut (Castanea crenata Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids Shirasawa, Kenta Nishio, Sogo Terakami, Shingo Botta, Roberto Marinoni, Daniela Torello Isobe, Sachiko DNA Res Resource Article: Genomes Explored Japanese chestnut (Castanea crenata Sieb. et Zucc.), unlike other Castanea species, is resistant to most diseases and wasps. However, genomic data of Japanese chestnut that could be used to determine its biotic stress resistance mechanisms have not been reported to date. In this study, we employed long-read sequencing and genetic mapping to generate genome sequences of Japanese chestnut at the chromosome level. Long reads (47.7 Gb; 71.6× genome coverage) were assembled into 781 contigs, with a total length of 721.2 Mb and a contig N50 length of 1.6 Mb. Genome sequences were anchored to the chestnut genetic map, comprising 14,973 single nucleotide polymorphisms (SNPs) and covering 1,807.8 cM map distance, to establish a chromosome-level genome assembly (683.8 Mb), with 69,980 potential protein-encoding genes and 425.5 Mb repetitive sequences. Furthermore, comparative genome structure analysis revealed that Japanese chestnut shares conserved chromosomal segments with woody plants, but not with herbaceous plants, of rosids. Overall, the genome sequence data of Japanese chestnut generated in this study is expected to enhance not only its genetics and genomics but also the evolutionary genomics of woody rosids. Oxford University Press 2021-08-23 /pmc/articles/PMC8435554/ /pubmed/34424280 http://dx.doi.org/10.1093/dnares/dsab016 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Resource Article: Genomes Explored
Shirasawa, Kenta
Nishio, Sogo
Terakami, Shingo
Botta, Roberto
Marinoni, Daniela Torello
Isobe, Sachiko
Chromosome-level genome assembly of Japanese chestnut (Castanea crenata Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids
title Chromosome-level genome assembly of Japanese chestnut (Castanea crenata Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids
title_full Chromosome-level genome assembly of Japanese chestnut (Castanea crenata Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids
title_fullStr Chromosome-level genome assembly of Japanese chestnut (Castanea crenata Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids
title_full_unstemmed Chromosome-level genome assembly of Japanese chestnut (Castanea crenata Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids
title_short Chromosome-level genome assembly of Japanese chestnut (Castanea crenata Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids
title_sort chromosome-level genome assembly of japanese chestnut (castanea crenata sieb. et zucc.) reveals conserved chromosomal segments in woody rosids
topic Resource Article: Genomes Explored
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8435554/
https://www.ncbi.nlm.nih.gov/pubmed/34424280
http://dx.doi.org/10.1093/dnares/dsab016
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