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

Authors: DALLOUL, RAMI - Virginia Polytechnic Institution & State University; Long, Julie; ZIMIN, ALEKSEY - University Of Maryland; REED, KENT - University Of Minnesota; Blomberg, Le Ann; Van Tassell, Curtis - Curt; Schroeder, Steven - Steve; Sonstegard, Tad; ASLAM, LUQMAN - Wageningen Agricultural University; BEAL, KATHRYN - European Bioinformatics Institute; BIEDLER, JIM - Virginia Polytechnic Institution & State University; BURT, DAVID - Roslin Institute; CRASTA, OSWALD - Virginia Polytechnic Institution & State University; CROOIJMANS, RICHARD - Wageningen Agricultural University; COOPER, KRISTAL - Virginia Polytechnic Institution & State University; COULOMBE, ROGER - Utah State University; DE, SUPRIYO - National Institutes Of Health (NIH); DELANY, MARY - University Of California; DODGSON, JERRY - Michigan State University; DONG, JENNIFER - Texas A&M University; EVANS, CLIVE - Virginia Polytechnic Institution & State University; FLICEK, PAUL - European Bioinformatics Institute; FLOREA, LILIANA - University Of Maryland; FOLKERTS, OTTO - Virginia Polytechnic Institution & State University; GROENEN, MARTIEN - Wageningen Agricultural University; HARKINS, TIM - Roche Applied Science; HERRERO, JAVIER - European Bioinformatics Institute; HOFFMANN, STEVE - University Of Leipzig; MEGENS, HENDRIK-JAN - Wageningen Agricultural University; JIANG, ANDREW - University Of California; JONG, PIETER DE - Children'S Hospital Oakland Research Institute; KAISER, PETE - Institute For Animal Health; KIM, HEEBAL - Seoul National University; KIM, KYU-WON - Seoul National University; KIM, SUNGWON - Virginia Polytechnic Institution & State University; LANGENBERGER, DAVID - University Of Leipzig; LEE, MI-KYUNG - Texas A&M University Health Science Center; LEE, TAEHEON - Seoul National University; MANE, SHRINIVASRAO - Virginia Polytechnic Institution & State University; MARCAIS, GUILLAUME - University Of Maryland; MARZ, MANJA - University Of Leipzig; MCELROY, AUDREY - Virginia Polytechnic Institution & State University; MODISE, THERO - Virginia Polytechnic Institution & State University; NEFEDOV, MIKHAIL - Children'S Hospital Oakland Research Institute; NOTREDAME, CEDRIC - Center For Genomic Regulation (CRG); PATON, IAN - Roslin Institute; PAYNE, WILLIAM - Michigan State University; PERTEA, GEO - University Of Maryland; PRICKETT, DENNIS - Institute For Animal Health; PUIU, DANIELA - University Of Maryland; QIOA, DAN - Virginia Polytechnic Institution & State University; RAINERI, EMANUELE - Center For Genomic Regulation (CRG); SALZBERG, STEVEN - University Of Maryland; SCHATZ, MICHAEL - University Of Maryland; SCHEURING, CHANTEL - Texas A&M University; SCHMIDT, CARL - University Of Delaware; SCHROEDER, STEVEN - US Department Of Agriculture (USDA); SMITH, ED - Virginia Polytechnic Institution & State University; SMITH, JACQUELINE - Roslin Institute; SONSTEGARD, TAD - US Department Of Agriculture (USDA); STADLER, PETER - University Of Leipzig; TAFER, HAKIM - University Of Leipzig; TU, ZHIJIAN JAKE - Virginia Polytechnic Institution & State University; VAN TASSELL, CURTIS - US Department Of Agriculture (USDA); VILELLA, ALBERT - European Bioinformatics Institute; WILLIAMS, KELLY - Virginia Polytechnic Institution & State University; YORKE, JAMES - University Of Maryland; ZHANG, LIQING - Virginia Polytechnic Institution & State University; ZHANG, HONGBIN - Texas A&M University; ZHANG, ZIAOJUN - Texas A&M University; ZHANG, YANG - Texas A&M University

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.