Genomic variation among and within six Juglans species

Authors: STEVENS, KRISTIAN - University Of California; WOESTE, KEITH - Purdue University; CHAKRABORTY, SANDEEP - University Of California; CREPEAU, MARC - University Of California; LESLIE, CHARLES - University Of California; MARTINEZ-GARCIA, PEDRO - University Of California; PUIU, DANIELA - Johns Hopkins University; ROMERO-SEVERSON, JEANNE - University Of Notre Dame; COGGESHALL, MARK - Purdue University; DANDEKAR, ABHAYA - University Of California; Kluepfel, Daniel; NEALE, DAVID - University Of California; SALZBERG, STEVEN - Johns Hopkins University; LANGLEY, CHARLES - University Of California

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/25/2018
Publication Date: 7/1/2018
Citation: Stevens, K.A., Woeste, K., Chakraborty, S., Crepeau, M.W., Leslie, C.A., Martinez-Garcia, P.J., Puiu, D., Romero-Severson, J., Coggeshall, M., Dandekar, A.M., Kluepfel, D.A., Neale, D.B., Salzberg, S.L., Langley, C.H. 2018. Genomic variation among and within six Juglans species. G3, Genes/Genomes/Genetics. 8(7):2153-2165. https://doi.org/10.1534/g3.118.200030.
DOI: https://doi.org/10.1534/g3.118.200030

Interpretive Summary: We report here the sequencing and assembly of the genomes of five additional Juglans species. Secondly, we provide accessible pairwise alignments of these genomes annotating micro synteny and between- species divergence. Finally, an important adjunct to the genome structures and divergences revealed in these resources are surveys of the within species genomic polymorphisms for four species. Beyond the obvious value of detected SNPs as a resource for the development of genotyping tools, genomic variants can be annotated with respect to their potential phenotypic consequences (Cingolani et al 2012; McLaren et al. 2016), thus serving as a readily accessible source of candidates in functional genomic analyses and gene-oriented breeding and biotechnology. We report the resequencing of samples of independent accessions of two Juglans species with scion breeding programs, J. regia and nigra, as well as two species involved in rootstock development, J. hindsii and J. microcarpa. Species differences in the overall levels of genomic polymorphism are documented. Polymorphism is used in conjunction with divergence to infer recent selection possibly associated with domestication. Finally, we demonstrate how these genomic resources can be visualized in support of gene-oriented analyses by employing the widely used and well-supported JBrowse software (Skinner et al. 2009).

Technical Abstract: Genomic analysis in Juglans (walnuts) is expected to transform the breeding and agricultural production of both nuts and lumber. To that end, we report here the determination of reference sequences for six additional relatives of Juglans regia: Juglans sigillata (also from section Dioscaryon), Juglans nigra, Juglans microcarpa, Juglans hindsii (from section Rhysocaryon), Juglans cathayensis (from section Cardiocaryon), and the closely related Pterocarya stenoptera. While these are ‘draft’ genomes, ranging in size between 640Mbp and 990Mbp, their contiguities and accuracies can support powerful annotations of genomic variation that are often the foundation of new avenues of research and breeding. To facilely leverage these new resources we created complete pairwise alignments of the each reference genome to the remaining six. In addition, we have re-sequenced a sample of accessions from four Juglans species (including regia). The variation discovered in these surveys comprises a critical resource for experimentation and breeding, as well as a solid complementary annotation. To demonstrate the potential of these resources the structural and sequence variation in and around the polyphenol oxidases loci, PPO1 and PPO2 were investigated. As reported for other seed crops variation in this gene is implicated the domestication of walnuts. The apparently Juglandaceae specific PPO1 duplicate shows accelerated divergence and an excess of amino acid replacement on the lineage leading to accessions of the domesticated nut crop species, Juglans regia and sigillata.