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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT OF NEW TECHNOLOGIES AND METHODS TO ENHANCE THE UTILIZATION AND LONG-TERM STORAGE OF POULTRY, SWINE AND FISH GERMPLASM Title: Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo) genome assembly and analysis

Authors
item Dalloul, Rami -
item Long, Julie
item Zimin, Aleksey -
item Reed, Kent -
item Blomberg, Le Ann
item Van Tassell, Curtis
item Schroeder, Steven
item Sonstegard, Tad
item Aslam, Luqman -
item Beal, Kathryn -
item Biedler, Jim -
item Burt, David -
item Crasta, Oswald -
item Crooijmans, Richard -
item Cooper, Kristal -
item Coulombe, Roger -
item De, Supriyo -
item Delany, Mary -
item Dodgson, Jerry -
item Dong, Jennifer -
item Evans, Clive -
item Flicek, Paul -
item Florea, Liliana -
item Folkerts, Otto -
item Groenen, Martien -
item Harkins, Tim -
item Herrero, Javier -
item Hoffmann, Steve -
item Megens, Hendrik-Jan -
item Jiang, Andrew -
item Jong, Pieter DE -
item Kaiser, Pete -
item Kim, Heebal -
item Kim, Kyu-Won -
item Kim, Sungwon -
item Langenberger, David -
item Lee, Mi-Kyung -
item Lee, Taeheon -
item Mane, Shrinivasrao -
item Marcais, Guillaume -
item Marz, Manja -
item Mcelroy, Audrey -
item Modise, Thero -
item Nefedov, Mikhail -
item Notredame, Cedric -
item Paton, Ian -
item Payne, William -
item Pertea, Geo -
item Prickett, Dennis -
item Puiu, Daniela -
item Qioa, Dan -
item Raineri, Emanuele -
item Salzberg, Steven -
item Schatz, Michael -
item Scheuring, Chantel -
item Schmidt, Carl -
item Schroeder, Steven -
item Smith, Ed -
item Smith, Jacqueline -
item Sonstegard, Tad -
item Stadler, Peter -
item Tafer, Hakim -
item Tu, Zhijian Jake -
item Van Tassell, Curtis -
item Vilella, Albert -
item Williams, Kelly -
item Yorke, James -
item Zhang, Liqing -
item Zhang, Hongbin -
item Zhang, Ziaojun -
item Zhang, Yang -

Submitted to: PLoS Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 5, 2010
Publication Date: September 7, 2010
Citation: Dalloul, R.A., Long, J.A., Zimin, A.V., Reed, K.M., Blomberg, L., Van Tassell, C.P., Schroeder, S.G., Sonstegard, T.S., Aslam, L., Beal, K., Biedler, J., Burt, D.W., Crasta, O., Crooijmans, R.P., Cooper, K., Coulombe, R.A., De, S., Delany, M.E., Dodgson, J.B., Dong, J.J., Evans, C., Flicek, P., Florea, L., Folkerts, O., Groenen, M.A., Harkins, T.T., Herrero, J., Hoffmann, S., Megens, H., Jiang, A., Jong, P., Kaiser, P., Kim, H., Kim, K., Kim, S., Langenberger, D., Lee, M., 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., Salzberg, S.L., Schatz, M.C., Scheuring, C., Schmidt, C.J., Schroeder, S.G., Smith, E.J., Smith, J., Sonstegard, T.S., Stadler, P.F., Tafer, H., Tu, Z., Van Tassell, C.P., Vilella, A.J., Williams, K., Yorke, J.A., Zhang, L., Zhang, H., Zhang, Z., Zhang, Y. 2010. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo) genome assembly and analysis. PLoS Biology. 8(9):e1000475.

Interpretive Summary: Sequencing: 1. First non-human genome completely sequenced and assembled with a combination of Roche-454 and Illumina-GAII NGS technologies; 2. The high throughput and low cost of NGS technologies facilitated cost effective production of the reference genome assembly through whole genome shotgun sequencing; 3. The first genome project where most of the funding was used for analyzing and interpreting the data rather than generating sequence. Genetic variation: 1. Nucleotide diversity is similar for macro- and microchromosomes, and is only about 50% of autosomal nucleotide diversity for chromosome Z; 2. In many chromosomes, extended regions of low nucleotide diversity seem to coincide with centromeric regions. Genome conservation: 1. Despite an estimated divergence of 30-40 M years ago, conservation of the chromosome architecture and transposon sequences between the turkey and chicken genomes is indicative of remarkable stability in avian genomes. Rearrangements that differentiate the two genomes show a trend towards turkey chromosomes being more frequently acrocentric; 2. Purifying selection on microchromosomes is greater than macrochromosomes and is greatest for Z-chromosome. Protein encoding genes 1. Gene families found only in birds give a big picture on what makes a bird a bird; 2. Copy number variation between birds and an egg-laying mammal (platypus) show gene functions that are shared by egg-laying animals in general and also genes that are unique to egg-laying birds. RNA genes 1. The Y1 gene, lost in the chicken, still exists in turkey; 2. Evolutionary analysis reveals a major difference between snoRNA and miRNA, the latter being much more species-specific. Evolution 1. 9.87% of the turkey genome bases are under constraint while the fraction of conserved regions in mammals is around 5%; 2. Re-examination of Galliform phylogeny, confirms that turkey is a sister taxa to the grouses. Comparison of Avian Immune Elements 1. Turkey and chickens show differences in rates of evolution of specific sets of genes; 2. Immune gene families in birds are smaller than in mammals.

Technical Abstract: Next-generation sequencing technologies were used to rapidly and efficiently sequence the genome of the domestic turkey (Meleagris gallopavo). The current genome assembly (~1.1 Gb) includes 917 Mb of sequence assigned to chromosomes. Innate heterozygosity of the sequenced bird allowed discovery of 0.6 M strongly supported single nucleotide variants. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 RNA genes. Comparative analysis of the turkey, chicken and zebra finch genomes, and comparison of these to mammals, supports the notable stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the immune system where expansions and novel genes are less frequent in birds than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and to discover genetic variations underlying economically important quantitative traits.

Last Modified: 4/19/2014
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