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Hortic Res. 2019 Mar 25;6:55. doi: 10.1038/s41438-019-0139-1. eCollection 2019.

Sequencing a Juglans regia × J. microcarpa hybrid yields high-quality genome assemblies of parental species.

Author information

1
1Department of Plant Sciences, University of California, Davis, CA 95616 USA.
2
2Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6 Canada.
3
3Genome Center, University of California, Davis, CA 95616 USA.
4
4Crops Pathology and Genetics Research Unit, USDA-ARS, Davis, CA 95616 USA.
5
5National Clonal Germplasm Repository, USDA-ARS, Davis, CA 95616 USA.
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Contributed equally

Abstract

Members of the genus Juglans are monecious wind-pollinated trees in the family Juglandaceae with highly heterozygous genomes, which greatly complicates genome sequence assembly. The genomes of interspecific hybrids are usually comprised of haploid genomes of parental species. We exploited this attribute of interspecific hybrids to avoid heterozygosity and sequenced an interspecific hybrid Juglans microcarpa × J. regia using a novel combination of single-molecule sequencing and optical genome mapping technologies. The resulting assemblies of both genomes were remarkably complete including chromosome termini and centromere regions. Chromosome termini consisted of arrays of telomeric repeats about 8 kb long and heterochromatic subtelomeric regions about 10 kb long. The centromeres consisted of arrays of a centromere-specific Gypsy retrotransposon and most contained genes, many of them transcribed. Juglans genomes evolved by a whole-genome-duplication dating back to the Cretaceous-Paleogene boundary and consist of two subgenomes, which were fractionated by numerous short gene deletions evenly distributed along the length of the chromosomes. Fractionation was shown to be asymmetric with one subgenome exhibiting greater gene loss than the other. The asymmetry of the process is ongoing and mirrors an asymmetry in gene expression between the subgenomes. Given the importance of J. microcarpa × J. regia hybrids as potential walnut rootstocks, we catalogued disease resistance genes in the parental genomes and studied their chromosomal distribution. We also estimated the molecular clock rates for woody perennials and deployed them in estimating divergence times of Juglans genomes and those of other woody perennials.

Conflict of interest statement

The authors declare that they have no conflict of interest.

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