NEW YORK (GenomeWeb News) – An international research group led by investigators at Virginia Tech, the University of Minnesota, the US Department of Agriculture, and the University of Maryland reported online Tuesday in PLoS Biology that they have sequenced a draft version of the turkey genome.
The team used a combination of Roche 454 and Illumina sequencing to tackle the genome of the domestic turkey, Meleagris gallopavo. By comparing the newly generated sequence with the genomes of the chicken, zebra finch, and several non-avian species, the researchers have now started uncovering new clues about the evolutionary history of birds and other vertebrates. In addition, they explained, a better understanding of turkey genetics is expected to help those involved in breeding and producing the economically important bird.
"In the short term, the genome sequence will provide scientists with knowledge of specific genes that are important in meat yield and quality, health and disease resistance, fertility, and reproduction," co-lead author Rami Dalloul, a poultry researcher at Virginia Tech, said in a statement, noting that "producers may be able to use the knowledge we gain from the genome sequence to grow turkeys faster and healthier."
The turkey genome sequencing project started in 2008, with researchers at Virginia Tech and the University of Minnesota securing more than $900,000 in funding from the USDA the following year to support the sequencing effort.
By the end of 2009, members of the team announced that they had sequenced some 90 percent of the turkey genome. And as GenomeWeb Daily News sister publication In Sequence reported at the time, those involved in the project expressed hope that the burgeoning turkey genome would eventually serve as a key reference sequence for those studying other avian species.
Now, the team is reporting on that sequencing effort as well as their analyses of the turkey genome.
Consortium members used Roche 454 GS-FLX Titanium and Illumina Genome Analyzer II platforms to sequence the roughly 1.1 billion base pair, heterozygous genome of a female Nicholas Inbred turkey nicknamed Nici, generating about five times genome coverage with the Roche 454 approach and 25 times coverage with the Genome Analyzer.
They then aligned and assembled this sequence using a turkey genetic map, bacterial artificial chromosome-based maps, and information from the chicken genome. So far, the team has been able to place 917 million bases of sequence to turkey chromosomes.
Based on their analyses, the researchers estimate that the turkey genome contains 15,093 protein-coding genes and 611 non-coding RNAs. They also identified 601,490 high confidence SNPs and another 920,126 potential SNPs.
In general, they found that the turkey genome was quite similar to that of chicken, with just 30 or so rearrangements turning up between the two. Their analysis suggests the turkey and the chicken share some 881 gene families with one another and 271 gene families with other birds but not with mammals.
While the turkey, chicken, and zebra finch genomes housed comparable copy numbers for many gene families, the team noted, they did detect differences in some families, including those involved in processes such as transcription, metabolism, and cell signaling, differentiation, and development.
Meanwhile, comparisons between the turkey genomes and those of non-avian animals provided new insights about which gene families are shared between vertebrates and which show up exclusively in birds or mammals. For instance, researchers explained, birds lack specific gene families thought to contribute to processes such as scent detection and tooth formation in mammals.
Beyond the findings from and potential applications of the turkey genome sequence, the team also touted the advantages of their combined high-throughput sequencing method, particularly in terms of price. The cost of sequencing the turkey genome reportedly came in at around $250,000 — far less than the estimated $10 million or more spent on the chicken genome just a few years ago.
"This genome project is a first where the majority of the production cost was invested in analysis and interpretation rather than generating sequence," the authors argued, noting that "the assembly is comparable in genome coverage to the predominantly Sanger-based sequences of the chicken and zebra finch."