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Journal article
Chromosome-Scale Assembly and Annotation of the Macadamia Genome (Macadamia integrifolia HAES 741)
G3 : genes - genomes - genetics, Vol.10(10), pp.3497-3504
2020
PMID: 32747341
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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 90% 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 an average of 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.
Details
- Title
- Chromosome-Scale Assembly and Annotation of the Macadamia Genome (Macadamia integrifolia HAES 741)
- Creators
- Catherine J Nock - Southern Cross UniversityAbdul Baten - Southern Cross UniversityRamil Mauleon - Southern Cross UniversityKirsty S Langdon - Southern Cross UniversityBruce Topp - University of QueenslandCraig Hardner - University of QueenslandAgnelo Furtado - University of QueenslandRobert J Henry - University of QueenslandGraham J King - Southern Cross University
- Publication Details
- G3 : genes - genomes - genetics, Vol.10(10), pp.3497-3504
- Publisher
- Genetics Society of America
- Grant note
- MC15008 / Horticulture Innovation Australia
- Identifiers
- 991012896297202368
- Academic Unit
- Faculty of Science and Engineering; Science; Southern Cross Plant Science
- Language
- English
- Resource Type
- Journal article