Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2010 Sep 7;8(9):e1000475.
doi: 10.1371/journal.pbio.1000475.

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

Rami A Dalloul  1 , Julie A Long, Aleksey V Zimin, Luqman Aslam, Kathryn Beal, Le Ann Blomberg, Pascal Bouffard, David W Burt, Oswald Crasta, Richard P M A Crooijmans, Kristal Cooper, Roger A Coulombe, Supriyo De, Mary E Delany, Jerry B Dodgson, Jennifer J Dong, Clive Evans, Karin M Frederickson, Paul Flicek, Liliana Florea, Otto Folkerts, Martien A M Groenen, Tim T Harkins, Javier Herrero, Steve Hoffmann, Hendrik-Jan Megens, Andrew Jiang, Pieter de Jong, Pete Kaiser, Heebal Kim, Kyu-Won Kim, Sungwon Kim, David Langenberger, Mi-Kyung Lee, Taeheon Lee, Shrinivasrao Mane, Guillaume Marcais, Manja Marz, Audrey P McElroy, Thero Modise, Mikhail Nefedov, Cédric Notredame, Ian R Paton, William S Payne, Geo Pertea, Dennis Prickett, Daniela Puiu, Dan Qioa, Emanuele Raineri, Magali Ruffier, Steven L Salzberg, Michael C Schatz, Chantel Scheuring, Carl J Schmidt, Steven Schroeder, Stephen M J Searle, Edward J Smith, Jacqueline Smith, Tad S Sonstegard, Peter F Stadler, Hakim Tafer, Zhijian Jake Tu, Curtis P Van Tassell, Albert J Vilella, Kelly P Williams, James A Yorke, Liqing Zhang, Hong-Bin Zhang, Xiaojun Zhang, Yang Zhang, Kent M Reed
Affiliations

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

Rami A Dalloul et al. PLoS Biol. .

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.

PubMed Disclaimer

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Synteny map of chicken (left) and turkey (right).
Each chromosome is assigned a color in the chicken chromosome, ranging from red (Chr 1) through the spectrum to yellow, green, and blue. Turkey chromosomes are shown using the same colors, indicating differences due to chromosome numbering; e.g., turkey Chr 8 matches chicken Chr 6. The figure shows that there have been no large-scale chromosomal rearrangements in either species since their divergence.
Figure 2
Figure 2. Venn diagram showing the amount of sequence (in Mbp) aligned among the three avian genomes.
Numbers in brackets refer to the amount of sequence that is part of the alignments, but as species-specific insertions. For instance, out of the 142 Mbp of the turkey genome not aligned to the other two genomes, 105 Mbp are included in the alignments as turkey-specific insertions. The lower panel shows an example alignment. Regions where all three species are aligned are highlighted with a black line, and species-specific sequence is shown with an arrow.
Figure 3
Figure 3. Top 20 most expanded and contracted gene families in turkey genome assembly as compared to the chicken.
The axis is the log ratio of copy number in turkey versus copy number in chicken.
Figure 4
Figure 4. Lineage events in the turkey: variation of (a) synonymous (dS), (b) non-synonymous (dN), and (c) dN/dS ratios based on chromosome sizes.
The chromosome lengths are expressed as log base2 (nucleotide lengths in base pairs).
Figure 5
Figure 5. Rapid evolution of sex-linked genes in birds.
Figure 6
Figure 6. Significant GO terms in the accelerated genes in: (a) turkey compared with chicken and (b) chicken compared with turkey.
Number in parenthesis indicates non-redundant number of genes in each group. The representative term in each group was selected manually.
Figure 7
Figure 7. Comparison of the dN/dS ratios between innate immune related genes and other genes.
Error bars indicate 95% standard error of the mean dN/dS ratios. Significance tests were performed using Wilcoxon rank sum test since the dN/dS ratios did not follow normal assumptions (Table S9).
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Genome 10K Community of Scientists. Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered. 2009;100:659–674. - PMC - PubMed
    1. Li R, Fan W, Tian G, Zhu H, He L, et al. The sequence and de novo assembly of the giant panda genome. Nature. 2010;463:311–317. - PMC - PubMed
    1. Reed K. M, Chaves L. D, Mendoza K. M. An integrated and comparative genetic map of the turkey genome. Cytogenet Genome Res. 2007;119:113–126. - PubMed
    1. Hillier L. W, Miller W, Birney E, Warren W, Hardison R. C, et al. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004;432:695–716. - PubMed
    1. Elsik C. G, Tellam R. L, Worley K. C The Bovine Genome Sequencing Analysis Consortium. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science. 2009;324:522–528. - PMC - PubMed

Publication types

LinkOut - more resources