By Monica Heger
This article, originally published Nov. 24, has been updated from a previous version to include additional information about the project.
The Turkey Genome Sequencing Consortium has sequenced 90 percent of the domesticated turkey (Meleagris gallopavo) genome, and under a new two-year $908,280 grant from the United States Department of Agriculture plans to complete the genome to a standard that it hopes will allow it to be the new reference genome for avian genomics.
The project began as a pilot study last year (see In Sequence 12/2/2008), with the goal of applying for the USDA grant to complete the genome. The original group, involving Virginia Tech, Michigan State University, the University of Minnesota, Utah State University, and the University of Edinburgh’s Roslin Institute, was using the Roche GS-FLX platform with Titanium reagents, and planned to sequence the genome at about two-fold coverage. But at the beginning of the year, the group joined forces with two additional teams: researchers at the USDA's Agricultural Research Center who are using the Illumina platform, and a bioinformatics group at the University of Maryland.
They now have 90 percent of the genome sequenced at several-fold higher coverage than anticipated, said consortium member Otto Folkerts from the Virginia Bioinformatics Institute at Virginia Tech. The team has already submitted data to GenBank, and Folkerts said it will likely be available by December or January.
"The combination of 454 and Illumina data proved to be really important," Folkerts said. "Both platforms are independent technologies, so there were areas that were really complementary to each other." He added that the total cost for the project, when completed, should be just over $1 million, including the USDA grant.
The GS-FLX platform provided longer reads, which helped build scaffolds and contigs, and the Illumina platform yielded shorter reads, which helped to fill in the gaps. Using the 454 technology, Folkerts said they achieved 5.5- to 6-fold coverage, and with the Illumina data about 25-fold coverage.
About half the coverage came from Illumina unpaired reads, about a quarter from Illumina paired-end sequencing, around 16 percent from Roche shotgun sequencing, and less than 3 percent and 0.1 percent from 454 paired-end sequencing and BAC end sequencing, respectively. While Roche's 3-kilobase and 20-kilobase paired end reads and the BAC-end sequences contributed little to the overall coverage, "they contribute tremendously to building contigs and scaffolds," Folkerts said.
The genome is being assembled using the Celera assembler and the team has so far mapped about 900 to 910 megabases of the 1-gigabase haploid genome to chromosomes.
The chicken genome was sequenced about five years ago using Sanger technology, and is the current avian reference genome. But Folkerts said there are many gaps in the chicken genome because it was done through a clone-based approach. Folkerts said that he and his colleagues are sequencing the turkey genome solely through de novo next-generation sequencing.
Over the next two years, the consortium plans to complete the sequencing so it has 97 to 98 percent of the genome sequenced with very few holes. Right now, "there are a lot of gaps," said Folkerts. "They're not particularly large gaps, but we do want to close the gaps. And, some regions of the genome are poorly represented." In particular, the sex chromosomes Z and W, the centromeres and also avian microchromosomes — very small chromosomes that are unique to birds — are areas that Folkerts said they will try to improve. The avian microchromosomes especially are difficult to sequence because many of them do not have genetic markers.
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"With a lot of the next-gen sequencing platforms, people sequence large genomes routinely, but there are still large gaps or areas that are poorly covered," said Folkerts. "Our goal is to complete the genome to reference genome status so it can become the new reference for avian genomic studies."
Moving forward, the group will primarily use Roche 3-kilobase and 20-kilobase paired end sequencing. They may use limited Roche shotgun sequencing and Illumina sequencing to fill in a few more gaps, and will use BAC-end sequencing for areas of low coverage, as well as transcriptome sequencing.
Aside from providing a reference avian genome, having a complete turkey genome will serve as a starting point for many other research projects, according to the consortium. Industry will be particularly interested in determining which genes are related to disease, fertility, and higher quality meat yields, in order to improve commercial breeds of turkey. Academic researchers will be able to use the genome to study the biology of turkeys and compare it to other birds.
"The work funded by this grant will take us a long way towards our longer-term goal of discovering ways to improve the immune competence of the turkey. It will also provide invaluable information that will help develop new, more effective strategies for disease prevention," said Virginia Tech researcher Rami Dalloul in a statement.