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Chromosome-scale assembly and annotation of the macadamia genome (Macadamia integrifolia HAES 741)

View ORCID ProfileCatherine J. Nock, View ORCID ProfileAbdul Baten, View ORCID ProfileRamil Mauleon, View ORCID ProfileKirsty S. Langdon, View ORCID ProfileBruce Topp, View ORCID ProfileCraig Hardner, View ORCID ProfileAgnelo Furtado, View ORCID ProfileRobert J. Henry, View ORCID ProfileGraham J. King
doi: https://doi.org/10.1101/2020.05.25.114009
Catherine J. Nock
1Southern Cross Plant Science, Southern Cross University, Lismore NSW 2480, Australia
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  • For correspondence: cathy.nock@scu.edu.au
Abdul Baten
1Southern Cross Plant Science, Southern Cross University, Lismore NSW 2480, Australia
2AgResearch NZ, Grasslands Research Centre, Palmerston North 4442, New Zealand
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Ramil Mauleon
1Southern Cross Plant Science, Southern Cross University, Lismore NSW 2480, Australia
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Kirsty S. Langdon
1Southern Cross Plant Science, Southern Cross University, Lismore NSW 2480, Australia
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Bruce Topp
3Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia QLD 4069, Australia
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Craig Hardner
3Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia QLD 4069, Australia
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Agnelo Furtado
3Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia QLD 4069, Australia
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  • ORCID record for Agnelo Furtado
Robert J. Henry
3Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia QLD 4069, Australia
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Graham J. King
1Southern Cross Plant Science, Southern Cross University, Lismore NSW 2480, Australia
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Abstract

Macadamia integrifolia is a representative of the large basal eudicot family Proteaceae and the main progenitor species of the Australian native nut crop macadamia. Since its commercialisation in Hawaii fewer than 100 years ago, global production has expanded rapidly. However, genomic resources are limited in comparison to other horticultural crops. The first draft assembly of M. integrifolia had good coverage of the functional gene space but its high fragmentation has restricted its use in comparative genomics and association studies. Here we have generated an improved assembly of cultivar HAES 741 (4,094 scaffolds, 745 Mb, N50 413 kb) using a combination of Illumina paired and PacBio long read sequences. Scaffolds were anchored to 14 pseudo-chromosomes using seven genetic linkage maps. This assembly has improved contiguity and coverage, with >120 Gb of additional sequence. Following annotation, 34,274 protein-coding genes were predicted, representing 92% of the expected gene content. Our results indicate that the macadamia genome is repetitive and heterozygous. The total repeat content was 55% and genome-wide heterozygosity, estimated by read mapping, was 0.98% or one SNP per 102 bp. This is the first chromosome-scale genome assembly for macadamia and the Proteaceae. It is expected to be a valuable resource for breeding, gene discovery, conservation and evolutionary genomics.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 27, 2020.
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Chromosome-scale assembly and annotation of the macadamia genome (Macadamia integrifolia HAES 741)
Catherine J. Nock, Abdul Baten, Ramil Mauleon, Kirsty S. Langdon, Bruce Topp, Craig Hardner, Agnelo Furtado, Robert J. Henry, Graham J. King
bioRxiv 2020.05.25.114009; doi: https://doi.org/10.1101/2020.05.25.114009
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Chromosome-scale assembly and annotation of the macadamia genome (Macadamia integrifolia HAES 741)
Catherine J. Nock, Abdul Baten, Ramil Mauleon, Kirsty S. Langdon, Bruce Topp, Craig Hardner, Agnelo Furtado, Robert J. Henry, Graham J. King
bioRxiv 2020.05.25.114009; doi: https://doi.org/10.1101/2020.05.25.114009

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