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Zou XH
Zhang FM
Zhang JG
Zang LL
Tang L
Wang J
Sang T
Ge S

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Ge S
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Research

Analysis of 142 genes resolves the rapid diversification of the rice genus

Xin-Hui Zou^*¹ , Fu-Min Zhang^*¹ , Jian-Guo Zhang^*² , Li-Li Zang¹ , Liang Tang¹ , Jun Wang² , Tao Sang³ and Song Ge¹^,4

¹State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China

²Beijing Genomics Institute, Beijing, 101300, China

³Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA

⁴The Graduate School, Chinese Academy of Sciences, Beijing, 100039, China

author email corresponding author email* Contributed equally

Genome Biology 2008, 9:R49doi:10.1186/gb-2008-9-3-r49


Published:	3 March 2008

Subject areas: Bioinformatics, Evolution, Plant biology

Additional files

Additional data file 1:

The relative location on rice chromosomes of the 142 genes sampled in this study.

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Additional data file 2:

Detailed information on each of 142 loci.

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Additional data file 3:

GC content variation among lineages and the result of Chi-square test for the concatenated data set.

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Additional data file 4:

Summary of the Tajima's relative rate test for concatenated sequences using Leersia as outgroup, with estimates of the ratio of substitution rate between lineages.

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Additional data file 5:

Results of testing the effect of rate bias caused by the fast-evolving genes of the F-genome.

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Additional data file 6:

The 14 alternative models used in BI analyses.

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Additional data file 7:

The effect of model components on model fit judged by Bayes factor comparisons of competing models

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Additional data file 8:

Consensus networks of a collection of 106 optimal ML trees from the 106 genes with the complete set of seven species, applying thresholds of 0.05, 0.1, 0.15, 0.2, 0.25 and 0.3, respectively.

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Additional data file 9:

Results of the ILD test for pairwise comparisons of process partitions.

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Additional data file 10:

The number of genes that failed the ILD test with the target gene at P < 0.01 for total, intron, exon and the third codon sites, respectively, and the P value of the ILD test between the target gene and all the rest of genes.

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Additional data file 11:

Topologies of bootstrap 75% majority-rule consensus trees by different methods of analyses for each gene.

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Additional data file 12:

Saturation analyses in the concatenated datasets of total, intron, exon, and third codon positions, respectively.

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Additional data file 13:

Proportions of topology (or clades) identical to those shown in Figure 1 inferred from randomly sampled genes or sites in 500 replicates.

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Additional data file 14:

Primers for PCR amplification and the GenBank accession numbers of the sequences of 142 loci sampled.

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