TY - JOUR
T1 - Genomic variation among and within six Juglans species
AU - Stevens, Kristian A.
AU - Woeste, Keith
AU - Chakraborty, Sandeep
AU - Crepeau, Marc W.
AU - Leslie, Charles A.
AU - Martínez-García, Pedro J.
AU - Puiu, Daniela
AU - Romero-Severson, Jeanne
AU - Coggeshall, Mark
AU - Dandekar, Abhaya M.
AU - Kluepfel, Daniel
AU - Neale, David B.
AU - Salzberg, Steven L.
AU - Langley, Charles H.
N1 - Funding Information:
This project was supported by the California Walnut Board, USDA NIFA SCRI-Award no. 2012-51181-20027 and USDA ARS CRIS project no. 5306-22000-015-00D. We would also like to thank Mallikarjuna Aradhya and Daniel Potter for thoughtful discussions.
Publisher Copyright:
© 2018 Stevens et al.
PY - 2018/7/1
Y1 - 2018/7/1
N2 - 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. We annotated nucleotide divergence and synteny by creating complete pairwise alignments of 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 oxidase loci, PPO1 and PPO2 were investigated. As reported for other seed crops variation in this gene is implicated in 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.
AB - 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. We annotated nucleotide divergence and synteny by creating complete pairwise alignments of 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 oxidase loci, PPO1 and PPO2 were investigated. As reported for other seed crops variation in this gene is implicated in 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.
KW - Genomic variation
KW - Juglans
KW - Polyphenol oxidase
KW - Reference genomes
KW - Walnut
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U2 - 10.1534/g3.118.200030
DO - 10.1534/g3.118.200030
M3 - Article
C2 - 29792315
AN - SCOPUS:85049409718
SN - 2160-1836
VL - 8
SP - 2153
EP - 2165
JO - G3: Genes, Genomes, Genetics
JF - G3: Genes, Genomes, Genetics
IS - 7
ER -