[Coral-List] Coral genome sequence assembled

[UT]

Our estimate (based on RNA-seq experiments) is that the total number of genes that are actually expressed in A.millepora larva is about 18,000 (Meyer et al, Molecular Ecology in press), which is similar to the total number of genes stated for the sea anemone Nematostella - although of course there must be quite a few adult-specific genes on top of that, so it seems to me that we are in agreement here

Question to David Miller: would you allow the use the genome data as a reference to map next-gen sequencing reads? This is where the genome would be by far the most useful for the future progress of coral biology.  Please reply to all, I am more than sure that there are quite a few people on the coral-list with the same question...

Cheers 

Misha Matz

Sent from my iPhone

On Jul 8, 2011, at 6:19 AM, "Keven Reed" <reedkc at comcast.net> wrote:

> Concur.  For me, however, the implications have to do with gene drop out during evolution, and the philosophical discussions of animals more recently evolved perhaps not being more complex but just different.  I've always admired the lessons we learn about immunology from invertebrate models who don't have a thymus gland or bone marrow like the Homo sapiens model.
> 
> Cheers,
> Keven
>  ----- Original Message ----- 
>  From: Craig Bingman 
>  To: Keven Reed 
>  Cc: Miller, David ; coral-list at coral.aoml.noaa.gov 
>  Sent: Thursday, July 07, 2011 11:47 PM
>  Subject: Re: [Coral-List] Coral genome sequence assembled
> 
> 
>  This isn't an apples to apples comparison.  Immediately after the human 
>  genome was completed, people were claiming numbers almost 2x higher than 
>  the (somewhat) accepted number for humans today.  I suspect that most of 
>  these gene calls have been made automatically, and that the number of 
>  actual genes in Acropora will be somewhat lower than is currently claimed... 
>  Ditto for Daphnia.
> 
>  However, I am very happy that a coral genome has been sequenced.
> 
>  -- 
>  cbingman at panix.com
> 
> 
>  On Thu, 7 Jul 2011, Keven Reed wrote:
> 
>> 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,
>> Keven
>> 
>> Dr. Keven Reed, Orange Park Eye Center
>> Florida
>> 
>> 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
>> Australia
>> 
>> Phone: ++61-(0)747-814473
>> Fax: ++61-(0)747-816078
>> email: david.miller at jcu.edu.au
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