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Open Access Research article

Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis

Hiroaki Sakai and Takeshi Itoh*

Author Affiliations

Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan

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BMC Genomics 2010, 11:121  doi:10.1186/1471-2164-11-121

Published: 19 February 2010

Additional files

Additional file 1:

Phylogenetic tree of the five Oryza species used in this study: Oj, O. sativa L. ssp. japonica; Oi, O. sativa L. ssp. indica; On, O. nivara; Or, O. rufipogon; and Og, O. glaberrima. We used (A) the neighbour-joining and (B) the maximum-likelihood methods using the third positions of 15,053 codons. We used Kimura's two-parameter method for the neighbour-joining tree. Bootstrap values are shown above the internal branches. The scale indicates the branch length.

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Additional file 2:

Statistics of simulated BESs of O. sativa: Oj, O. sativa L. ssp. japonica; Oi, O. sativa L. ssp. indica.

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Additional file 3:

Fraction of repetitive elements in the genomic sequences of five species: Oj, O. sativa L. ssp. japonica; Oi, O. sativa L. ssp. indica; On, O. nivara; Or, O. rufipogon; Og, O. glaberrima. The classification of repetitive elements was based on the MIPS Repeat Element Database.

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Additional file 4:

Distributions of interval sizes of paired BESs along the Oj genome.

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Additional file 5:

Shared and unique genomic portions in Oj and Oi. Although the Oj-specific portion is unknown, the size of the shared region in Oj is expected to be nearly equal to that in Oi.

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Additional file 6:

Rates of BESs that overlap with RAP2 proteins of more than 50 bp. Gene densities of On, Or, and Og were estimated by counting the numbers of BESs that overlapped with protein-coding regions on the Oj genome of more than 50 bp, and calculating the ratios of BESs of each species to simulated BESs of Oj.

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Additional file 7:

Estimation of the numbers of species-specific genes. In contrast to Table 2, the ambiguous BESs were regarded as unmapped BESs.

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Additional file 8:

Estimates of unique genes in the genomes of close relatives under three different criteria: hu, the number of unmapped BESs that matched nr database proteins; hm, the number of mapped BESs that matched nr database proteins; nu, the number of genes in the close relative-specific regions. Because the numbers of unique genes depend on the ratio of hu to hm, we examined two other thresholds for similarity searches against the nr database, an E-value of < 1.0 × 10-20 and < 1.0 × 10-50, in addition to an E-value of < 1.0 × 10-10. Although the ratios slightly decreased with stringent thresholds, the numbers of unique genes did not drastically change, suggesting that the three close relatives possess ~1,000 unique genes that are missing from the genomes of Oj and Oi.

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Additional file 9:

Functional classifications of the proteins of Oj and two close relatives, On and Og. The classifications of mapped and unmapped BESs of On and Og were derived from the nr database proteins that were homologous to the mapped and unmapped BESs. Protein categories were based on the molecular functions of the Gene Ontology (GO) hierarchy.

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Additional file 10:

Functional classifications of the proteins of Oj and three close relatives, On, Or, and Og. All BESs were mapped to the genome of O. sativa L. ssp. indica (Oi). The classifications of mapped and unmapped BESs of the close relatives were derived from the nr database proteins that were homologous to the mapped and unmapped BESs. Protein categories were based on the molecular functions of the Gene Ontology (GO) hierarchy.

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Additional file 11:

Functional classifications of the proteins of Oj and of simulated BESs of Oj and Oi. Simulated BESs of Oj were mapped to the genome of Oi, and vice versa. The classifications of mapped and unmapped BESs were derived from nr database proteins that were homologous to the mapped and unmapped BESs. Protein categories were based on the molecular functions of the GO hierarchy.

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Additional file 12:

The ten most frequent domains among the unmapped BESs of On and Og. For each domain, the numbers of genes with or without the domain are listed for the mapped and unmapped BESs. P values were calculated using Fisher's exact test.

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Additional file 13:

List of 83 disease resistance-related genes that matched the unmapped BESs of On, Or, and Og. BESs that had internal stop codons within the aligned regions are presented in parentheses.

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Additional file 14:

Amino acid alignment between the On-specific disease resistance gene, CL716448, and its homologues. Amino acid sequences with black backgrounds indicate leucine-rich repeat domains predicted by InterProScan searches.

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Additional file 15:

Phylogenetic tree of possible disease resistance proteins. CL619881 is a newly found homologue from On. Accession numbers and species names are shown. The tree was reconstructed by the neighbour-joining method. The interior branches were tested by 1,000 bootstrap replicates, and bootstrap values of 50% or greater are shown above the branches. The scale indicates the branch length.

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Additional file 16:

Density of the BESs throughout the Oj genome. Numbers of the BESs were counted by using a sliding window of 1 Mbp width with a step size of 500 Kbp.

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Additional file 17:

Length distributions of BESs of three close relatives

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Additional file 18:

Distributions of the amino acid identities of mapped BESs against the top-hit nr database proteins with a threshold of 10-10

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Additional file 19:

Indirect functional classifications of the genes of Oj. We obtained protein-coding nucleotide sequences of representative sequences for each gene of Oj from RAP-DB and conducted BLASTX searches against the nr database with a threshold of 10-10. Indirect classifications were facilitated using four sets of the nr database proteins: Top-hit, top-hit genes; ID = 90%, nr database proteins with amino acid identities over 90%; ID = 80%, nr database proteins with amino acid identities over 80%; ID = 70%, nr database proteins with amino acid identities over 70%. As a comparison, the functional classification of the representative sequences of the Oj genes (Rep) is shown on the right.

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