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

Author
item DALLOUL, RAMI - VIRGINIA POLYTECHNIC INSTITUTION & STATE UNIVERSITY
item Long, Julie
item ZIMIN, ALEKSEY - UNIVERSITY OF MARYLAND
item REED, KENT - UNIVERSITY OF MINNESOTA
item Blomberg, Le Ann
item Van Tassell, Curtis - Curt
item Schroeder, Steven - Steve
item SONSTEGARD, TAD
item ASLAM, LUQMAN - WAGENINGEN AGRICULTURAL UNIVERSITY
item BEAL, KATHRYN - EUROPEAN BIOINFORMATICS INSTITUTE
item BIEDLER, JIM - VIRGINIA POLYTECHNIC INSTITUTION & STATE UNIVERSITY
item BURT, DAVID - ROSLIN INSTITUTE
item CRASTA, OSWALD - VIRGINIA POLYTECHNIC INSTITUTION & STATE UNIVERSITY
item CROOIJMANS, RICHARD - WAGENINGEN AGRICULTURAL UNIVERSITY
item COOPER, KRISTAL - VIRGINIA POLYTECHNIC INSTITUTION & STATE UNIVERSITY
item COULOMBE, ROGER - UTAH STATE UNIVERSITY
item DE, SUPRIYO - NATIONAL INSTITUTES OF HEALTH (NIH)
item DELANY, MARY - UNIVERSITY OF CALIFORNIA
item DODGSON, JERRY - MICHIGAN STATE UNIVERSITY
item DONG, JENNIFER - TEXAS A&M UNIVERSITY
item EVANS, CLIVE - VIRGINIA POLYTECHNIC INSTITUTION & STATE UNIVERSITY
item FLICEK, PAUL - EUROPEAN BIOINFORMATICS INSTITUTE
item FLOREA, LILIANA - UNIVERSITY OF MARYLAND
item FOLKERTS, OTTO - VIRGINIA POLYTECHNIC INSTITUTION & STATE UNIVERSITY
item GROENEN, MARTIEN - WAGENINGEN AGRICULTURAL UNIVERSITY
item HARKINS, TIM - ROCHE APPLIED SCIENCE
item HERRERO, JAVIER - EUROPEAN BIOINFORMATICS INSTITUTE
item HOFFMANN, STEVE - UNIVERSITY OF LEIPZIG
item MEGENS, HENDRIK-JAN - WAGENINGEN AGRICULTURAL UNIVERSITY
item JIANG, ANDREW - UNIVERSITY OF CALIFORNIA
item JONG, PIETER DE - CHILDREN'S HOSPITAL OAKLAND RESEARCH INSTITUTE
item KAISER, PETE - INSTITUTE FOR ANIMAL HEALTH
item KIM, HEEBAL - SEOUL NATIONAL UNIVERSITY
item KIM, KYU-WON - SEOUL NATIONAL UNIVERSITY
item KIM, SUNGWON - VIRGINIA POLYTECHNIC INSTITUTION & STATE UNIVERSITY
item LANGENBERGER, DAVID - UNIVERSITY OF LEIPZIG
item LEE, MI-KYUNG - TEXAS A&M UNIVERSITY HEALTH SCIENCE CENTER
item LEE, TAEHEON - SEOUL NATIONAL UNIVERSITY
item MANE, SHRINIVASRAO - VIRGINIA POLYTECHNIC INSTITUTION & STATE UNIVERSITY
item MARCAIS, GUILLAUME - UNIVERSITY OF MARYLAND
item MARZ, MANJA - UNIVERSITY OF LEIPZIG
item MCELROY, AUDREY - VIRGINIA POLYTECHNIC INSTITUTION & STATE UNIVERSITY
item MODISE, THERO - VIRGINIA POLYTECHNIC INSTITUTION & STATE UNIVERSITY
item NEFEDOV, MIKHAIL - CHILDREN'S HOSPITAL OAKLAND RESEARCH INSTITUTE
item NOTREDAME, CEDRIC - CENTER FOR GENOMIC REGULATION (CRG)
item PATON, IAN - ROSLIN INSTITUTE
item PAYNE, WILLIAM - MICHIGAN STATE UNIVERSITY
item PERTEA, GEO - UNIVERSITY OF MARYLAND
item PRICKETT, DENNIS - INSTITUTE FOR ANIMAL HEALTH
item PUIU, DANIELA - UNIVERSITY OF MARYLAND
item QIOA, DAN - VIRGINIA POLYTECHNIC INSTITUTION & STATE UNIVERSITY
item RAINERI, EMANUELE - CENTER FOR GENOMIC REGULATION (CRG)
item SALZBERG, STEVEN - UNIVERSITY OF MARYLAND
item SCHATZ, MICHAEL - UNIVERSITY OF MARYLAND
item SCHEURING, CHANTEL - TEXAS A&M UNIVERSITY
item SCHMIDT, CARL - UNIVERSITY OF DELAWARE
item SCHROEDER, STEVEN - U.S. DEPARTMENT OF AGRICULTURE (USDA)
item SMITH, ED - VIRGINIA POLYTECHNIC INSTITUTION & STATE UNIVERSITY
item SMITH, JACQUELINE - ROSLIN INSTITUTE
item SONSTEGARD, TAD - U.S. DEPARTMENT OF AGRICULTURE (USDA)
item STADLER, PETER - UNIVERSITY OF LEIPZIG
item TAFER, HAKIM - UNIVERSITY OF LEIPZIG
item TU, ZHIJIAN JAKE - VIRGINIA POLYTECHNIC INSTITUTION & STATE UNIVERSITY
item VAN TASSELL, CURTIS - U.S. DEPARTMENT OF AGRICULTURE (USDA)
item VILELLA, ALBERT - EUROPEAN BIOINFORMATICS INSTITUTE
item WILLIAMS, KELLY - VIRGINIA POLYTECHNIC INSTITUTION & STATE UNIVERSITY
item YORKE, JAMES - UNIVERSITY OF MARYLAND
item ZHANG, LIQING - VIRGINIA POLYTECHNIC INSTITUTION & STATE UNIVERSITY
item ZHANG, HONGBIN - TEXAS A&M UNIVERSITY
item ZHANG, ZIAOJUN - TEXAS A&M UNIVERSITY
item 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.