Summary
Publication
Nock, C. J., Baten, A., Barkla, B. J., Furtado, A., Henry, R. J., & King, G. J. (2016). Genome and transcriptome sequencing characterises the gene space of Macadamia integrifolia (Proteaceae). BMC genomics, 17(1), 937.
Name
Macadamia integrofolia - Reference Genome
Resource Type
Genome Assembly
Organism
Details
Program, Pipeline, Workflow or Method Name
De novo assembly using CLC Genomics Workbench (CLC)
Program Version
6.5
Date Performed
Thursday, February 7, 2019 - 16:50
Data Source
Description and Download
Fresh plant tissue was collected from a Macadamia integrifolia and stored at -80 °C. Prior to DNA and RNA extraction, leaf tissue was frozen in liquid nitrogen and ground using a tissue lyser. Total genomic DNA was extracted using a DNeasy Plant Maxi kit for all DNA sequencing with the exception of mate pair (MP) library sequencing where DNA was extracted using a CTAB-based method developed for next-generation sequencing. Paired-end libraries (PE) with average insert sizes of 480 and 700 bp and an 8 kb MP library were prepared using Illumina TruSeq DNA Sample Preparation kit v2 following manufacturer’s instructions. Paired-end sequence reads were trimmed to remove low quality bases and adapter sequences and de novo assembled using CLC Genomics Workbench (CLC) version 6.5 (CLC Bio, Aarhus, Denmark). MP reads were also trimmed to remove low quality bases and adapter sequences. Genome assembly was performed in the following two steps: preliminary contig assembly using PE reads in CLC, followed by assembly of sequence contigs and filtered high quality MP reads using the scaffolding program SSPACE to obtain a final set of scaffolds. Putative repetitive sequences were identified using the RepeatModeler program with default parameters. In parallel, known repetitive sequences were identified using the RepeatMasker program with the latest release of RepBase curated repeat libraries. Annotation of gene models was conducted using MAKER (version 2.31.8) which combines the power of protein and Expressed Sequence Tag (EST) based homology with ab initio gene predictions to produce polished gene annotations. To obtain the homology based genes MAKER aligned reference ESTs and proteins using Blastx and exonerate against the macadamia scaffolds.

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Genomic scaffolds
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