Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): Genome assembly and analysis

Dalloul, R. A., Long, J. A., Zimin, A. V., Aslam, L., Beal, K., Blomberg, L. A., Bouffard, P., Burt, D. W., Crasta, O., Crooijmans, R. P. M. A., Cooper, K., Coulombe, R. A., De, S., Delany, M. E., Dodgson, J. B., Dong, J. J., Evans, C., Frederickson, K. M., Flicek, P., Florea, L., Folkerts, O., Groenen, M. A. M., Harkins, T. T., Herrero, J., Hoffmann, S., Megens, H. J., Jiang, A., de Jong, P., Kaiser, P., Kim, H., Kim, K. W., Kim, S., Langenberger, D., Lee, M. K., Lee, T., Mane, S., Marcais, G., Marz, M., McElroy, A. P., Modise, T., Nefedov, M., Notredame, C., Paton, I. R., Payne, W. S., Pertea, G., Prickett, D., Puiu, D., Qioa, D., Raineri, E., Ruffier, M., Salzberg, S. L., Schatz, M. C., Scheuring, C., Schmidt, C. J., Schroeder, S., Searle, S. M. J., Smith, E. J., Smith, J., Sonstegard, T. S., Stadler, P. F., Tafer, H., Tu, Z., van Tassell, C. P., Vilella, A. J., Williams, K. P., Yorke, J. A., Zhang, L., Zhang, H. B., Zhang, X., Zhang, Y., Reed, K. M. (2010) Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): Genome assembly and analysis. PLoS Biology, 8 (9). ISSN 1544-9173

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URL: http://www.ncbi.nlm.nih.gov/pubmed/20838655
DOI: 10.1371/journal.pbio.1000475

Abstract

A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (~1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.

Item Type: Paper
Additional Information:
Uncontrolled Keywords: nucleotide untranslated RNA article bacterial artificial chromosome bird chicken contig mapping controlled study domestic fowl fowl gene identification gene loss gene sequence genetic variability genome analysis genome assembly genomic instability heterozygosity immune system mammal meleagris gallopavo molecular genetics nonhuman poultry quantitative trait RNA gene species comparison turkey (bird) vertebrate Animals Base Sequence Chromosome Mapping DNA Genome Polymorphism, Single Nucleotide Sequence Analysis, DNA Sequence Homology, Nucleic Acid Species Specificity Turkeys Aves Mammalia Taeniopygia guttata Vertebrata
Subjects: bioinformatics > genomics and proteomics > annotation > map annotation
bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > Mapping and Rendering > Sequence Rendering
CSHL Authors:
Communities: CSHL labs > Schatz lab
Depositing User: CSHL Librarian
Date: 2010
Date Deposited: 16 Mar 2012 14:54
Last Modified: 15 Mar 2013 19:06
PMCID: PMC2935454
Related URLs:
URI: http://repository.cshl.edu/id/eprint/25364

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