Prunus dulcis Nonpareil Genome v1.0 Assembly & Annotation

Publication

D'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). 2022 May 6;12(5):jkac065. doi: 10.1093/g3journal/jkac065. (GDR | Journal)

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. 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.

Funding

This work was supported through the Ohio State University CFAES-SEEDS program grant 2019-125, the Almond Board of California Grant HORT35, the Translational Plant Sciences Graduate Fellowship, the Cancer Center Support Grant (CCSG) P30CA016058, the AFRI-EWD Predoctoral Fellowship 2019-67011-29558 from the USDA National Institute of Food and Agriculture.