Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.
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.
Dalloul
Rami A
RA
Avian Immunobiology Laboratory, Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia, United States of America.
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
D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D004247:DNA / Q000235:genetics; D016678:Genome; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D014422:Turkeys / Q000235:genetics*
D004247:DNA