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Turkey Genome Leftovers

11/24/2011
Andrew S. Wiecek

Last year, researchers reported that 90% of the turkey genome had been sequenced and assembled. A year later, they are still working on the leftovers.

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Last year, an international consortium of researchers reported that 90% of the turkey genome had been sequenced and assembled (1). Since then, they have been working on trying to improve that draft by digesting the leftovers of the turkey genome, which may prove to be more insightful than the rest.

“You see this with all genomes. The percent that’s problematic or poorly assembled often points in the direction of the more interesting regions,” says Kent Reed, a professor in the University of Minnesota’s College of Veterinary Medicine who participated in the Turkey Genome Consortium.

To improve the initial turkey genome draft, Reed’s group at the University of Minnesota is attacking on two fronts: scaffold size and coverage. Source: Wikimedia Commons, Lupin







For one thing, gaps in genome assemblies often represent regions where gene families reside. Assembly programs do not efficiently process sequence data with multiple loci. Furthermore, regions with biased DNA content and high-GC content are also underrepresented.

Specifically, the major histocompatibility complex (MHC)—a region of the genome that plays an important role in immunity—is underrepresented in the turkey genome draft as well as other poultry genomes. This is because the MHC region is full of repeat elements, high-GC content, and gene families.

“You put together all these problems that you have with the assembling genomes into one grab bag in the MHC region,” says Reed. “It’s one of the smallest scaffolds that we have put together, but we know there are problems with it.”

In addition, the consortium could not assemble 10% of the genome because they lacked the genetic markers to assign these sequences to a chromosome. Most of these markers with poor depth are on the turkey’s microchromosomes, small chromosomes less than 20 Mb in size that account for about half of the turkey’s 80 chromosomes.

To improve the initial draft, Reed’s group at the University of Minnesota is attacking on two fronts: scaffold size and coverage. To increase scaffold size, his team is adding more sequences from libraries with larger insert clones. To improve coverage, they are adding more short Illumina reads for low-coverage regions, for example, from the unassigned regions.

To better annotate the genome, Reed’s group is sequencing the transcriptome using RNAseq. The goal is to gather as much information as possible about which genes are actually expressed in the turkey and what their possible function is within the avian.

At the University of Maryland, Reed’s colleague Aleksey Zimin is improving the assembly software. One of the novel aspects of the turkey genome draft was that it used sequence data from multiple platforms. Since then, Zimin has refined this multiplatform assembly tool and has already put together another build of the genome with another build on the way.

Other groups have already begun analyzing the turkey genome for sequence variants in the genome, identifying SNPs to be used for genetic selection. In addition, other labs have already doing comparative genomics of the turkey genome and other organisms, including the chicken and other avians.

“Now that we have more bird sequences—the duck is out or close—we learn more about what makes a bird genome as opposed to a mammalian genome. But there’s a development pipeline that needs to be in place before you see a lot of these studies.”

References

  1. Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, et al. Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis. PLoS Biology, 2010; 8(9): e1000475