[Coral-List] Coral genome sequence assembled
david.miller at jcu.edu.au
Wed Jul 6 02:55:54 EDT 2011
A preliminary assembly of the genome of the coral Acropora millepora has been generated, and is made available to the community under certain conditions via the coralbase.org website. The genome assembly is the result of a collaboration between the Australian Genome Research Facility (AGRF) and The ARC Centre of Excellence for Coral Reef Studies at James Cook University (JCU) but also involved some of the brightest and best of the Australian bioinformatics community.
The sequencing was carried out by the AGRF on DNA extracted from the sperm of a single colony of A. millepora from Magnetic Island, Queensland, Australia. This assembly is based exclusively on short (75-100bp) Illumina reads (GA IIx and HiSeq) from paired end (160 to 580 bp) and mate pair (2200 to 10000 bp) libraries. A variety of tools were used for the assembly, including libngs (https://github.com/sylvainforet/libngs), Nesoni (http://bioinformatics.net.au/software.nesoni.shtml), and a modified Velvet assembler (https://github.com/sylvainforet/velvet). The genome is approximately 400 Mb and contains around 25,000 genes. The N50 of the assembly is about 170 kb, and coverage about 80x.
To access the genome assembly hosted at coralbase.org, you will need to agree to the terms and conditions of release, become a registered user and then log in to the server using a link that will be emailed to you.
This is an important first for Australian science – it is the first fully “home-grown” genome sequence for a complex organism – as well as a milestone for coral biology.
Prof David J Miller
ARC Centre of Excellence for Coral Reef Studies and
School of Pharmacy and Molecular Sciences
James Cook University
email: david.miller at jcu.edu.au
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