The sequence and analysis of duplication-rich human chromosome 16.
Human chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes. We report here the 78,884,754 base pairs of finished chromosome 16 sequence, representing over 99.9% of its euchromatin. Manual annotation revealed 880 protein-coding genes confirmed by 1,670 aligned transcripts, 19 transfer RNA genes, 341 pseudogenes and three RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukaemia. Several large-scale structural polymorphisms spanning hundreds of kilobase pairs were identified and result in gene content differences among humans. Whereas the segmental duplications of chromosome 16 are enriched in the relatively gene-poor pericentromere of the p arm, some are involved in recent gene duplication and conversion events that are likely to have had an impact on the evolution of primates and human disease susceptibility.
Martin
Joel
J
DOE Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, California 94598, USA.
Han
Cliff
C
Gordon
Laurie A
LA
Terry
Astrid
A
Prabhakar
Shyam
S
She
Xinwei
X
Xie
Gary
G
Hellsten
Uffe
U
Chan
Yee Man
YM
Altherr
Michael
M
Couronne
Olivier
O
Aerts
Andrea
A
Bajorek
Eva
E
Black
Stacey
S
Blumer
Heather
H
Branscomb
Elbert
E
Brown
Nancy C
NC
Bruno
William J
WJ
Buckingham
Judith M
JM
Callen
David F
DF
Campbell
Connie S
CS
Campbell
Mary L
ML
Campbell
Evelyn W
EW
Caoile
Chenier
C
Challacombe
Jean F
JF
Chasteen
Leslie A
LA
Chertkov
Olga
O
Chi
Han C
HC
Christensen
Mari
M
Clark
Lynn M
LM
Cohn
Judith D
JD
Denys
Mirian
M
Detter
John C
JC
Dickson
Mark
M
Dimitrijevic-Bussod
Mira
M
Escobar
Julio
J
Fawcett
Joseph J
JJ
Flowers
Dave
D
Fotopulos
Dea
D
Glavina
Tijana
T
Gomez
Maria
M
Gonzales
Eidelyn
E
Goodstein
David
D
Goodwin
Lynne A
LA
Grady
Deborah L
DL
Grigoriev
Igor
I
Groza
Matthew
M
Hammon
Nancy
N
Hawkins
Trevor
T
Haydu
Lauren
L
Hildebrand
Carl E
CE
Huang
Wayne
W
Israni
Sanjay
S
Jett
Jamie
J
Jewett
Phillip B
PB
Kadner
Kristen
K
Kimball
Heather
H
Kobayashi
Arthur
A
Krawczyk
Marie-Claude
MC
Leyba
Tina
T
Longmire
Jonathan L
JL
Lopez
Frederick
F
Lou
Yunian
Y
Lowry
Steve
S
Ludeman
Thom
T
Manohar
Chitra F
CF
Mark
Graham A
GA
McMurray
Kimberly L
KL
Meincke
Linda J
LJ
Morgan
Jenna
J
Moyzis
Robert K
RK
Mundt
Mark O
MO
Munk
A Christine
AC
Nandkeshwar
Richard D
RD
Pitluck
Sam
S
Pollard
Martin
M
Predki
Paul
P
Parson-Quintana
Beverly
B
Ramirez
Lucia
L
Rash
Sam
S
Retterer
James
J
Ricke
Darryl O
DO
Robinson
Donna L
DL
Rodriguez
Alex
A
Salamov
Asaf
A
Saunders
Elizabeth H
EH
Scott
Duncan
D
Shough
Timothy
T
Stallings
Raymond L
RL
Stalvey
Malinda
M
Sutherland
Robert D
RD
Tapia
Roxanne
R
Tesmer
Judith G
JG
Thayer
Nina
N
Thompson
Linda S
LS
Tice
Hope
H
Torney
David C
DC
Tran-Gyamfi
Mary
M
Tsai
Ming
M
Ulanovsky
Levy E
LE
Ustaszewska
Anna
A
Vo
Nu
N
White
P Scott
PS
Williams
Albert L
AL
Wills
Patricia L
PL
Wu
Jung-Rung
JR
Wu
Kevin
K
Yang
Joan
J
Dejong
Pieter
P
Bruce
David
D
Doggett
Norman A
NA
Deaven
Larry
L
Schmutz
Jeremy
J
Grimwood
Jane
J
Richardson
Paul
P
Rokhsar
Daniel S
DS
Eichler
Evan E
EE
Gilna
Paul
P
Lucas
Susan M
SM
Myers
Richard M
RM
Rubin
Edward M
EM
Pennacchio
Len A
LA
D000818:Animals; D002885:Chromosomes, Human, Pair 16 / Q000235:genetics*; D020440:Gene Duplication; D005796:Genes / Q000235:genetics; D023281:Genomics; D006570:Heterochromatin / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D020161:Physical Chromosome Mapping; D011110:Polymorphism, Genetic / Q000235:genetics; D017422:Sequence Analysis, DNA; D026801:Synteny / Q000235:genetics
D006570:Heterochromatin