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

Authors: ZHU, TINGTING - University Of California; WANG, LE - University Of California; YOU, FRANK - Agriculture And Agri-Food Canada; RODRIGUEZ, JUAN - University Of California; DEAL, KARIN - University Of California; CHEN, LIMIN - University Of California; LI, JIE - University Of California; CHAKRABORTY, SANDEEP - University Of California; BALAN, BIPIN - University Of California; Jiang, Cai-Zhong; BROWNE, PATRICK - University Of California; LESLIE, CHARLES - University Of California; Aradhya, Mallikarjuna; DANDEKAR, ABHAYA - University Of California; MCGUIRE, PATRICK - University Of California; Kluepfel, Daniel; DVORAK, JAN - University Of California; MING-CHEN, LUO - University Of California

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/10/2019
Publication Date: 3/25/2019
Citation: Zhu, T., Wang, L., You, F.M., Rodriguez, J., Deal, K., Chen, L., Li, J., Chakraborty, S., Balan, B., Jiang, C., Browne, P.J., Leslie, C., Aradhya, M.K., Dandekar, A., McGuire, P.E., Kluepfel, D.A., Dvorak, J., Ming-Chen, L. 2019. Sequencing a Juglans regia × J. microcarpa hybrid yields high-quality genome assemblies of parental species. Horticulture Research. 6:55. https://doi.org/10.1038/s41438-019-0139-1.
DOI: https://doi.org/10.1038/s41438-019-0139-1

Interpretive Summary: High levels of heterozygosity pose a serious problem and assemble woody perennial specie genomes. We describe a novel strategy that circumvents this difficulty to efficiently and accurately assemble genomes of parental species of dihaploid interspecific genomes. We illustrate this approach by sequencing a hybrid Juglans species, native to Asia, with J. microcarpa, native to North America. We analyze the resulting genome assemblies for accuracy and completeness of assembly. We use sequences for comparative genome analysis, genome evolution in view of the ancient whole genome duplication, and analyze the structure of telomeres and centromeres.

Technical 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 CretaceousPaleogene 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.