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

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.

SUBMITTER: Dalloul RA

PROVIDER: S-EPMC2935454 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature

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

Dalloul Rami A RA Long Julie A JA Zimin Aleksey V AV Aslam Luqman L Beal Kathryn K Blomberg Le Ann Le Ann Bouffard Pascal P Burt David W DW Crasta Oswald O Crooijmans Richard P M A RP Cooper Kristal K Coulombe Roger A RA De Supriyo S Delany Mary E ME Dodgson Jerry B JB Dong Jennifer J JJ Evans Clive C Frederickson Karin M KM Flicek Paul P Florea Liliana L Folkerts Otto O Groenen Martien A M MA Harkins Tim T TT Herrero Javier J Hoffmann Steve S Megens Hendrik-Jan HJ Jiang Andrew A de Jong Pieter P Kaiser Pete P Kim Heebal H Kim Kyu-Won KW Kim Sungwon S Langenberger David D Lee Mi-Kyung MK Lee Taeheon T Mane Shrinivasrao S Marcais Guillaume G Marz Manja M McElroy Audrey P AP Modise Thero T Nefedov Mikhail M Notredame Cédric C Paton Ian R IR Payne William S WS Pertea Geo G Prickett Dennis D Puiu Daniela D Qioa Dan D Raineri Emanuele E Ruffier Magali M Salzberg Steven L SL Schatz Michael C MC Scheuring Chantel C Schmidt Carl J CJ Schroeder Steven S Searle Stephen M J SM Smith Edward J EJ Smith Jacqueline J Sonstegard Tad S TS Stadler Peter F PF Tafer Hakim H Tu Zhijian Jake ZJ Van Tassell Curtis P CP Vilella Albert J AJ Williams Kelly P KP Yorke James A JA Zhang Liqing L Zhang Hong-Bin HB Zhang Xiaojun X Zhang Yang Y Reed Kent M KM

PLoS biology 20100907 9

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 i ...[more]

PMID: 20838655

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Project description:BackgroundThe turkey (Meleagris gallopavo) is an important agricultural species and the second largest contributor to the world's poultry meat production. Genetic improvement is attributed largely to selective breeding programs that rely on highly heritable phenotypic traits, such as body size and breast muscle development. Commercial breeding with small effective population sizes and epistasis can result in loss of genetic diversity, which in turn can lead to reduced individual fitness and reduced response to selection. The presence of genomic diversity in domestic livestock species therefore, is of great importance and a prerequisite for rapid and accurate genetic improvement of selected breeds in various environments, as well as to facilitate rapid adaptation to potential changes in breeding goals. Genomic selection requires a large number of genetic markers such as e.g. single nucleotide polymorphisms (SNPs) the most abundant source of genetic variation within the genome.ResultsAlignment of next generation sequencing data of 32 individual turkeys from different populations was used for the discovery of 5.49 million SNPs, which subsequently were used for the analysis of genetic diversity among the different populations. All of the commercial lines branched from a single node relative to the heritage varieties and the South Mexican turkey population. Heterozygosity of all individuals from the different turkey populations ranged from 0.17-2.73 SNPs/Kb, while heterozygosity of populations ranged from 0.73-1.64 SNPs/Kb. The average frequency of heterozygous SNPs in individual turkeys was 1.07 SNPs/Kb. Five genomic regions with very low nucleotide variation were identified in domestic turkeys that showed state of fixation towards alleles different than wild alleles.ConclusionThe turkey genome is much less diverse with a relatively low frequency of heterozygous SNPs as compared to other livestock species like chicken and pig. The whole genome SNP discovery study in turkey resulted in the detection of 5.49 million putative SNPs compared to the reference genome. All commercial lines appear to share a common origin. Presence of different alleles/haplotypes in the SM population highlights that specific haplotypes have been selected in the modern domesticated turkey.

Dataset Information

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

Publications

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

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