Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species.
Rice (Oryza sativa L.) chromosome 3 is evolutionarily conserved across the cultivated cereals and shares large blocks of synteny with maize and sorghum, which diverged from rice more than 50 million years ago. To begin to completely understand this chromosome, we sequenced, finished, and annotated 36.1 Mb ( approximately 97%) from O. sativa subsp. japonica cv Nipponbare. Annotation features of the chromosome include 5915 genes, of which 913 are related to transposable elements. A putative function could be assigned to 3064 genes, with another 757 genes annotated as expressed, leaving 2094 that encode hypothetical proteins. Similarity searches against the proteome of Arabidopsis thaliana revealed putative homologs for 67% of the chromosome 3 proteins. Further searches of a nonredundant amino acid database, the Pfam domain database, plant Expressed Sequence Tags, and genomic assemblies from sorghum and maize revealed only 853 nontransposable element related proteins from chromosome 3 that lacked similarity to other known sequences. Interestingly, 426 of these have a paralog within the rice genome. A comparative physical map of the wild progenitor species, Oryza nivara, with japonica chromosome 3 revealed a high degree of sequence identity and synteny between these two species, which diverged approximately 10,000 years ago. Although no major rearrangements were detected, the deduced size of the O. nivara chromosome 3 was 21% smaller than that of japonica. Synteny between rice and other cereals using an integrated maize physical map and wheat genetic map was strikingly high, further supporting the use of rice and, in particular, chromosome 3, as a model for comparative studies among the cereals.
Buell
C Robin
CR
The Institute for Genomic Research, Rockville, Maryland 20850, USA. rbuell@tigr.org
Yuan
Qiaoping
Q
Ouyang
Shu
S
Liu
Jia
J
Zhu
Wei
W
Wang
Aihui
A
Maiti
Rama
R
Haas
Brian
B
Wortman
Jennifer
J
Pertea
Mihaela
M
Jones
Kristine M
KM
Kim
Mary
M
Overton
Larry
L
Tsitrin
Tamara
T
Fadrosh
Douglas
D
Bera
Jayati
J
Weaver
Bruce
B
Jin
Shaohua
S
Johri
Shivani
S
Reardon
Matt
M
Webb
Kristen
K
Hill
Jessica
J
Moffat
Kelly
K
Tallon
Luke
L
Van Aken
Susan
S
Lewis
Matthew
M
Utterback
Teresa
T
Feldblyum
Tamara
T
Zismann
Victoria
V
Iobst
Stacey
S
Hsiao
Joseph
J
de Vazeille
Aymeric R
AR
Salzberg
Steven L
SL
White
Owen
O
Fraser
Claire
C
Yu
Yeisoo
Y
Kim
HeyRan
H
Rambo
Teri
T
Currie
Jennifer
J
Collura
Kristi
K
Kernodle-Thompson
Shelly
S
Wei
Fusheng
F
Kudrna
Kudrna
K
Ammiraju
Jetty Siva S
JS
Luo
Meizhong
M
Goicoechea
Jose Luis
JL
Wing
Rod A
RA
Henry
David
D
Oates
Ryan
R
Palmer
Michael
M
Pries
Gina
G
Saski
Christopher
C
Simmons
Jessica
J
Soderlund
Carol
C
Nelson
William
W
de la Bastide
Melissa
M
Spiegel
Lori
L
Nascimento
Lidia
L
Huang
Emily
E
Preston
Raymond
R
Zutavern
Theresa
T
Palmer
Lance
L
O'Shaughnessy
Andrew
A
Dike
Sujit
S
McCombie
W Richard
WR
Minx
Pat
P
Cordum
Holly
H
Wilson
Richard
R
Jin
Weiwei
W
Lee
Hye-Ran
HR
Jiang
Jiming
J
Jackson
Scott
S
D017360:Arabidopsis / Q000235:genetics; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics*; D017343:Genes, Plant; D018598:Minisatellite Repeats; D008969:Molecular Sequence Data; D012275:Oryza / Q000145:classification / Q000235:genetics*; D020161:Physical Chromosome Mapping; D006109:Poaceae / Q000145:classification / Q000235:genetics*; D020543:Proteome; D013045:Species Specificity; D003313:Zea mays / Q000145:classification / Q000235:genetics
D020543:Proteome