Abstract
Author SummaryIn contrast to the compact sequence of viruses and bacteria, determining the complete genome sequence of complex vertebrate genomes can be a daunting task. With the advent of “next-generation” sequencing platforms, it is now possible to rapidly sequence and assemble a vertebrate genome, especially for species for which genomic resources—genetic maps and markers—are currently available. We used a combination of two next-generation sequencing platforms, Roche 454 and Illumina GAII, and unique assembly tools to sequence the genome of the agriculturally important turkey, Meleagris gallopavo. Our draft assembly comprises approximately 1.1 gigabases of which 917 megabytes are assigned to specific chromosomes. Comparisons of the turkey genome sequence with those of the chicken, Gallus gallus, and the zebra finch, Taeniopygia guttata, provide insights into the evolution of the avian lineage. This genome sequence will facilitate discovery of agriculturally important genetic variants.
Highlights
The rapid and continuing development of next-generation sequencing (NGS) technologies has made it feasible to contemplate sequencing the genomes of hundreds—if not thousands—of species of agronomic, evolutionary, and ecological importance, as well as biomedical interest [1]
With the exception of the bacterial artificial chromosome (BAC) end sequences (BES) used only for chromosome alignment, the sequence data used for this assembly came solely from two sequencing platforms: the Roche/ 454 GS-FLX Titanium platform (454 Life Sciences/Roche Diagnostics, Branford, CT) and the Illumina Genome Analyzer II (GAII; Illumina, Inc., San Diego, CA)
The 454 data were generated using the latest ‘‘Titanium’’ protocol at Roche and the Virginia Bioinformatics Institute (Virginia Tech) and included both unpaired shotgun reads and paired-end reads produced from two libraries with estimated 3 kilobase pair (Kbp) and 20 Kbp fragment sizes
Summary
The rapid and continuing development of next-generation sequencing (NGS) technologies has made it feasible to contemplate sequencing the genomes of hundreds—if not thousands—of species of agronomic, evolutionary, and ecological importance, as well as biomedical interest [1]. We describe the genome sequence of the turkey (Meleagris gallopavo) determined using primarily NGS platforms In this case, a combination of Roche 454 and Illumina GAII sequencing was employed. Unlike the case for the panda, this novel approach allowed us to use a BAC contig-based physical and comparative map, along with the turkey genetic map [3] and the chicken genome sequence [4], to align the turkey sequence contigs and scaffolds to most of the turkey chromosomes. Such an alignment is essential for making long range evolutionary comparisons and employing the sequence to improve breeding practices using, for example, genome-based selection approaches, where chromosome locations are critical
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