title: Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species.
abstract: 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.
authors.affiliation: The Institute for Genomic Research, Rockville, Maryland 20850, USA. rbuell@tigr.org
authors.forename: C Robin
authors.initials: CR
authors.lastname: Buell
authors.forename: Qiaoping
authors.initials: Q
authors.lastname: Yuan
authors.forename: Shu
authors.initials: S
authors.lastname: Ouyang
authors.forename: Jia
authors.initials: J
authors.lastname: Liu
authors.forename: Wei
authors.initials: W
authors.lastname: Zhu
authors.forename: Aihui
authors.initials: A
authors.lastname: Wang
authors.forename: Rama
authors.initials: R
authors.lastname: Maiti
authors.forename: Brian
authors.initials: B
authors.lastname: Haas
authors.forename: Jennifer
authors.initials: J
authors.lastname: Wortman
authors.forename: Mihaela
authors.initials: M
authors.lastname: Pertea
authors.forename: Kristine M
authors.initials: KM
authors.lastname: Jones
authors.forename: Mary
authors.initials: M
authors.lastname: Kim
authors.forename: Larry
authors.initials: L
authors.lastname: Overton
authors.forename: Tamara
authors.initials: T
authors.lastname: Tsitrin
authors.forename: Douglas
authors.initials: D
authors.lastname: Fadrosh
authors.forename: Jayati
authors.initials: J
authors.lastname: Bera
authors.forename: Bruce
authors.initials: B
authors.lastname: Weaver
authors.forename: Shaohua
authors.initials: S
authors.lastname: Jin
authors.forename: Shivani
authors.initials: S
authors.lastname: Johri
authors.forename: Matt
authors.initials: M
authors.lastname: Reardon
authors.forename: Kristen
authors.initials: K
authors.lastname: Webb
authors.forename: Jessica
authors.initials: J
authors.lastname: Hill
authors.forename: Kelly
authors.initials: K
authors.lastname: Moffat
authors.forename: Luke
authors.initials: L
authors.lastname: Tallon
authors.forename: Susan
authors.initials: S
authors.lastname: Van Aken
authors.forename: Matthew
authors.initials: M
authors.lastname: Lewis
authors.forename: Teresa
authors.initials: T
authors.lastname: Utterback
authors.forename: Tamara
authors.initials: T
authors.lastname: Feldblyum
authors.forename: Victoria
authors.initials: V
authors.lastname: Zismann
authors.forename: Stacey
authors.initials: S
authors.lastname: Iobst
authors.forename: Joseph
authors.initials: J
authors.lastname: Hsiao
authors.forename: Aymeric R
authors.initials: AR
authors.lastname: de Vazeille
authors.forename: Steven L
authors.initials: SL
authors.lastname: Salzberg
authors.forename: Owen
authors.initials: O
authors.lastname: White
authors.forename: Claire
authors.initials: C
authors.lastname: Fraser
authors.forename: Yeisoo
authors.initials: Y
authors.lastname: Yu
authors.forename: HeyRan
authors.initials: H
authors.lastname: Kim
authors.forename: Teri
authors.initials: T
authors.lastname: Rambo
authors.forename: Jennifer
authors.initials: J
authors.lastname: Currie
authors.forename: Kristi
authors.initials: K
authors.lastname: Collura
authors.forename: Shelly
authors.initials: S
authors.lastname: Kernodle-Thompson
authors.forename: Fusheng
authors.initials: F
authors.lastname: Wei
authors.forename: Kudrna
authors.initials: K
authors.lastname: Kudrna
authors.forename: Jetty Siva S
authors.initials: JS
authors.lastname: Ammiraju
authors.forename: Meizhong
authors.initials: M
authors.lastname: Luo
authors.forename: Jose Luis
authors.initials: JL
authors.lastname: Goicoechea
authors.forename: Rod A
authors.initials: RA
authors.lastname: Wing
authors.forename: David
authors.initials: D
authors.lastname: Henry
authors.forename: Ryan
authors.initials: R
authors.lastname: Oates
authors.forename: Michael
authors.initials: M
authors.lastname: Palmer
authors.forename: Gina
authors.initials: G
authors.lastname: Pries
authors.forename: Christopher
authors.initials: C
authors.lastname: Saski
authors.forename: Jessica
authors.initials: J
authors.lastname: Simmons
authors.forename: Carol
authors.initials: C
authors.lastname: Soderlund
authors.forename: William
authors.initials: W
authors.lastname: Nelson
authors.forename: Melissa
authors.initials: M
authors.lastname: de la Bastide
authors.forename: Lori
authors.initials: L
authors.lastname: Spiegel
authors.forename: Lidia
authors.initials: L
authors.lastname: Nascimento
authors.forename: Emily
authors.initials: E
authors.lastname: Huang
authors.forename: Raymond
authors.initials: R
authors.lastname: Preston
authors.forename: Theresa
authors.initials: T
authors.lastname: Zutavern
authors.forename: Lance
authors.initials: L
authors.lastname: Palmer
authors.forename: Andrew
authors.initials: A
authors.lastname: O'Shaughnessy
authors.forename: Sujit
authors.initials: S
authors.lastname: Dike
authors.forename: W Richard
authors.initials: WR
authors.lastname: McCombie
authors.forename: Pat
authors.initials: P
authors.lastname: Minx
authors.forename: Holly
authors.initials: H
authors.lastname: Cordum
authors.forename: Richard
authors.initials: R
authors.lastname: Wilson
authors.forename: Weiwei
authors.initials: W
authors.lastname: Jin
authors.forename: Hye-Ran
authors.initials: HR
authors.lastname: Lee
authors.forename: Jiming
authors.initials: J
authors.lastname: Jiang
authors.forename: Scott
authors.initials: S
authors.lastname: Jackson
mesh_terms: 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
chemical_list: D020543:Proteome