Sequencing a Juglans regia\u2009\xd7\u2009J. microcarpa hybrid yields high-quality genome assemblies of parental species

Tingting Zhu,Jie Li,Karin R Deal,Ming-Cheng Luo,Daniel Kluepfel,Jan Dvorak,Sandeep Chakraborty,Abhaya M Dandekar,Le Wang,Cai-Zhong Jiang,Frank M You,Mallikarjuna K Aradhya,Juan C Rodriguez,Patrick J Brown,Patrick E Mcguire,Bipin Balan,Charles A Leslie,Limin Chen

doi:10.1038/s41438-019-0139-1

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.

Highlights

Haplotype phasing[1] and navigating between allelic and nonallelic variation are the major challenges in assembling genomes of outcrossing species with high levels of heterozygosity such as found in members of the genus Juglans
The parental maps consisted of ‘haploid’ regions, in which the haplotypes were similar enough to collapse into a single contig, and ‘diploid’ regions, in which the haplotypes were dissimilar enough to be assembled into separate contigs
Similar results were previously obtained for other outcrossing woody perennials with the Sanger sequencing technology[18,35,36,37], which is often considered as the gold standard of DNA sequencing

Summary

Introduction

Haplotype phasing[1] and navigating between allelic and nonallelic variation are the major challenges in assembling genomes of outcrossing species with high levels of heterozygosity such as found in members of the genus Juglans. Interspecific hybrids offer another strategy to avoid heterozygosity. Using an interspecific hybrid between cultivated walnut and its wild relative J. microcarpa, we describe here a novel approach to sequencing hybrid genomes which results in. The cultivated Persian/English walnut, Juglans regia, is native to Asia whereas J. microcarpa is native to North America, where it occurs in riparian areas in the southwestern USA. Both species are wind-pollinated, highly heterozygous, and intolerant of inbreeding.

Methods

Results

Conclusion