[Coral-List] Coral genome sequence assembled

Keven Reed reedkc at comcast.net
Thu Jul 7 07:19:52 EDT 2011

Congratulations to Australian Science.  Fantastic!  Bravo-Zulu.

As our minds race ahead, may I remind everyone of some interesting comparisons/implications:

about 31,000 genes in the water flea, freshwater crustacean Daphnia pulex

about 23,000 genes in humans

about 25,000 genes in a reef building scleractinian, Acropora millepora

Warmest regards,

Dr. Keven Reed, Orange Park Eye Center

mobile:  904-505-7277
office:  904-264-1206
  ----- Original Message ----- 
  From: Miller, David 
  To: coral-list at coral.aoml.noaa.gov 
  Sent: Wednesday, July 06, 2011 2:55 AM
  Subject: [Coral-List] Coral genome sequence assembled

  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
  Townsville 4811

  Phone: ++61-(0)747-814473
  Fax: ++61-(0)747-816078
  email: david.miller at jcu.edu.au
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  Coral-List at coral.aoml.noaa.gov

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