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Whole-genome sequence and methylome profiling of the almond [Prunus dulcis (Mill.) D.A. Webb] cultivar ‘Nonpareil’

Almond [Prunus dulcis (Mill.) D.A. Webb] is an economically important, specialty nut crop grown almost exclusively in the United States. Breeding and improvement efforts worldwide have led to the development of key, productive cultivars, including ‘Nonpareil,’ which is the most widely grown almond c...

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Autores principales: D’Amico-Willman, Katherine M, Ouma, Wilberforce Z, Meulia, Tea, Sideli, Gina M, Gradziel, Thomas M, Fresnedo-Ramírez, Jonathan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9073694/
https://www.ncbi.nlm.nih.gov/pubmed/35325123
http://dx.doi.org/10.1093/g3journal/jkac065
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author D’Amico-Willman, Katherine M
Ouma, Wilberforce Z
Meulia, Tea
Sideli, Gina M
Gradziel, Thomas M
Fresnedo-Ramírez, Jonathan
author_facet D’Amico-Willman, Katherine M
Ouma, Wilberforce Z
Meulia, Tea
Sideli, Gina M
Gradziel, Thomas M
Fresnedo-Ramírez, Jonathan
author_sort D’Amico-Willman, Katherine M
collection PubMed
description Almond [Prunus dulcis (Mill.) D.A. Webb] is an economically important, specialty nut crop grown almost exclusively in the United States. Breeding and improvement efforts worldwide have led to the development of key, productive cultivars, including ‘Nonpareil,’ which is the most widely grown almond cultivar. Thus far, genomic resources for this species have been limited, and a whole-genome assembly for ‘Nonpareil’ is not currently available despite its economic importance and use in almond breeding worldwide. We generated a 571X coverage genome sequence using Illumina, PacBio, and optical mapping technologies. Gene prediction revealed 49,321 putative genes using MinION Oxford nanopore and Illumina RNA sequencing, and genome annotation found that 68% of predicted models are associated with at least one biological function. Furthermore, epigenetic signatures of almond, namely DNA cytosine methylation, have been implicated in a variety of phenotypes including self-compatibility, bud dormancy, and development of noninfectious bud failure. In addition to the genome sequence and annotation, this report also provides the complete methylome of several almond tissues, including leaf, flower, endocarp, mesocarp, exocarp, and seed coat. Comparisons between methylation profiles in these tissues revealed differences in genome-wide weighted % methylation and chromosome-level methylation enrichment.
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spelling pubmed-90736942022-05-06 Whole-genome sequence and methylome profiling of the almond [Prunus dulcis (Mill.) D.A. Webb] cultivar ‘Nonpareil’ D’Amico-Willman, Katherine M Ouma, Wilberforce Z Meulia, Tea Sideli, Gina M Gradziel, Thomas M Fresnedo-Ramírez, Jonathan G3 (Bethesda) Genome Report Almond [Prunus dulcis (Mill.) D.A. Webb] is an economically important, specialty nut crop grown almost exclusively in the United States. Breeding and improvement efforts worldwide have led to the development of key, productive cultivars, including ‘Nonpareil,’ which is the most widely grown almond cultivar. Thus far, genomic resources for this species have been limited, and a whole-genome assembly for ‘Nonpareil’ is not currently available despite its economic importance and use in almond breeding worldwide. We generated a 571X coverage genome sequence using Illumina, PacBio, and optical mapping technologies. Gene prediction revealed 49,321 putative genes using MinION Oxford nanopore and Illumina RNA sequencing, and genome annotation found that 68% of predicted models are associated with at least one biological function. Furthermore, epigenetic signatures of almond, namely DNA cytosine methylation, have been implicated in a variety of phenotypes including self-compatibility, bud dormancy, and development of noninfectious bud failure. In addition to the genome sequence and annotation, this report also provides the complete methylome of several almond tissues, including leaf, flower, endocarp, mesocarp, exocarp, and seed coat. Comparisons between methylation profiles in these tissues revealed differences in genome-wide weighted % methylation and chromosome-level methylation enrichment. Oxford University Press 2022-03-23 /pmc/articles/PMC9073694/ /pubmed/35325123 http://dx.doi.org/10.1093/g3journal/jkac065 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Genome Report
D’Amico-Willman, Katherine M
Ouma, Wilberforce Z
Meulia, Tea
Sideli, Gina M
Gradziel, Thomas M
Fresnedo-Ramírez, Jonathan
Whole-genome sequence and methylome profiling of the almond [Prunus dulcis (Mill.) D.A. Webb] cultivar ‘Nonpareil’
title Whole-genome sequence and methylome profiling of the almond [Prunus dulcis (Mill.) D.A. Webb] cultivar ‘Nonpareil’
title_full Whole-genome sequence and methylome profiling of the almond [Prunus dulcis (Mill.) D.A. Webb] cultivar ‘Nonpareil’
title_fullStr Whole-genome sequence and methylome profiling of the almond [Prunus dulcis (Mill.) D.A. Webb] cultivar ‘Nonpareil’
title_full_unstemmed Whole-genome sequence and methylome profiling of the almond [Prunus dulcis (Mill.) D.A. Webb] cultivar ‘Nonpareil’
title_short Whole-genome sequence and methylome profiling of the almond [Prunus dulcis (Mill.) D.A. Webb] cultivar ‘Nonpareil’
title_sort whole-genome sequence and methylome profiling of the almond [prunus dulcis (mill.) d.a. webb] cultivar ‘nonpareil’
topic Genome Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9073694/
https://www.ncbi.nlm.nih.gov/pubmed/35325123
http://dx.doi.org/10.1093/g3journal/jkac065
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