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United States Department of Agriculture

Agricultural Research Service

Title: Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo) genome assembly and analysis

item Dalloul, Rami
item Long, Julie
item Zimin, Aleksey
item Reed, Kent
item Blomberg, Le Ann
item Van Tassell, Curtis - Curt
item Schroeder, Steven - Steve
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: 7/5/2010
Publication Date: 9/7/2010
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: 07/26/2017
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