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

Publication Overview
TitleWhole-genome sequence and methylome profiling of the almond (Prunus dulcis [Mill.] D.A.Webb) cultivar 'Nonpareil'.
AuthorsD'Amico-Willman KM, Ouma WZ, Meulia T, Sideli GM, Gradziel TM, Fresnedo-Ramírez J
TypeJournal Article
Journal NameG3 (Bethesda, Md.)
Year2022
CitationD'Amico-Willman KM, Ouma WZ, Meulia T, Sideli GM, Gradziel TM, Fresnedo-Ramírez J. Whole-genome sequence and methylome profiling of the almond (Prunus dulcis [Mill.] D.A.Webb) cultivar 'Nonpareil'.. G3 (Bethesda, Md.). 2022 Mar 23.

Abstract

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. Further, epigenetic signatures of almond, namely DNA cytosine methylation, have been implicated in a variety of phenotypes including self-compatibility, bud dormancy, and development of non-infectious 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 percent methylation and chromosome-level methylation enrichment.