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Comparative Study
. 2007 Feb;17(2):175-83.
doi: 10.1101/gr.5509507. Epub 2007 Jan 8.

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

Rice Annotation Project  1 ; Takeshi Itoh, Tsuyoshi Tanaka, Roberto A Barrero, Chisato Yamasaki, Yasuyuki Fujii, Phillip B Hilton, Baltazar A Antonio, Hideo Aono, Rolf Apweiler, Richard Bruskiewich, Thomas Bureau, Frances Burr, Antonio Costa de Oliveira, Galina Fuks, Takuya Habara, Georg Haberer, Bin Han, Erimi Harada, Aiko T Hiraki, Hirohiko Hirochika, Douglas Hoen, Hiroki Hokari, Satomi Hosokawa, Yue-ie Hsing, Hiroshi Ikawa, Kazuho Ikeo, Tadashi Imanishi, Yukiyo Ito, Pankaj Jaiswal, Masako Kanno, Yoshihiro Kawahara, Toshiyuki Kawamura, Hiroaki Kawashima, Jitendra P Khurana, Shoshi Kikuchi, Setsuko Komatsu, Kanako O Koyanagi, Hiromi Kubooka, Damien Lieberherr, Yao-Cheng Lin, David Lonsdale, Takashi Matsumoto, Akihiro Matsuya, W Richard McCombie, Joachim Messing, Akio Miyao, Nicola Mulder, Yoshiaki Nagamura, Jongmin Nam, Nobukazu Namiki, Hisataka Numa, Shin Nurimoto, Claire O'Donovan, Hajime Ohyanagi, Toshihisa Okido, Satoshi Oota, Naoki Osato, Lance E Palmer, Francis Quetier, Saurabh Raghuvanshi, Naomi Saichi, Hiroaki Sakai, Yasumichi Sakai, Katsumi Sakata, Tetsuya Sakurai, Fumihiko Sato, Yoshiharu Sato, Heiko Schoof, Motoaki Seki, Michie Shibata, Yuji Shimizu, Kazuo Shinozaki, Yuji Shinso, Nagendra K Singh, Brian Smith-White, Jun-ichi Takeda, Motohiko Tanino, Tatiana Tatusova, Supat Thongjuea, Fusano Todokoro, Mika Tsugane, Akhilesh K Tyagi, Apichart Vanavichit, Aihui Wang, Rod A Wing, Kaori Yamaguchi, Mayu Yamamoto, Naoyuki Yamamoto, Yeisoo Yu, Hao Zhang, Qiang Zhao, Kenichi Higo, Benjamin Burr, Takashi Gojobori, Takuji Sasaki
Affiliations
Comparative Study

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

Rice Annotation Project et al. Genome Res. 2007 Feb.

Abstract

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is approximately 32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene.

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Figures

Figure 1.
Figure 1.
Correlation between the number of tRNA gene copies and occurrence frequency of amino acids in (A) O. sativa and (B) A. thaliana. The horizontal axis indicates the occurrence frequency (%), and the vertical axis indicates the copy number. R2 values were 0.41 and 0.16 in O. sativa and A. thaliana, respectively.
Figure 2.
Figure 2.
Number of orthologous clusters created by duplication after the speciation of O. sativa and A. thaliana. The vertical axis indicates the log-scaled number of orthologs (clusters), and the horizontal axis indicates the number of paralog members in a cluster. Black bars represent O. sativa, and white bars represent A. thaliana.
Figure 3.
Figure 3.
Number of functional domains based on InterProScan and Gene Ontology. Note that the numbers do not correspond to the numbers of the proteins because a single protein can contain multiple domains.
Figure 4.
Figure 4.
Result of similarity search of the O. sativa and A. thaliana proteins against the protein databases. The proteins were classified into five groups: homologous to nonplant, (nonflowering) plant, (nonmonocot/eudicot) flowering plant, (non-Oryzeae/Arabidopsis) monocot/eudicot, and Oryzeae/Arabidopsis-specific proteins.
See this image and copyright information in PMC

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