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Differentiation of the two rice subspecies indica and japonica: a Gene Ontology perspective

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Abstract

Cultivated rice (Oryza sativa) is comprised of two subspecies: japonica and indica. Polymorphism levels between putative homologues were determined for genes whose japonica homologue had been classified into functional categories using the Gene Ontology (GO) system. Genes were partitioned into below-average and above-average polymorphism groups, and then the set of genes having each GO term was checked for the randomness of its distribution into these polymorphism groups using a series of False Discovery Rate (FDR) tests. The robustness of the conclusions was enhanced by employing different cutoff values and sequence samplings in the FDR tests. Significant nonrandom polymorphism distributions were found for protein-coding sequences in many GO categories. In contrast, a random distribution for nearly all GO terms was seen with intron sequences. These results were extended by measuring the nonsynonymous to synonymous codon usage ratio (dN/dS) using a permutation test, which showed that some above-average polymorphism GO categories also had a high proportion of genes with a dN/dS ratio greater than one, suggesting positive selection on these GO categories during indica–japonica differentiation. An analysis of predominant gene names in the significant GO categories divided them into four functional classes: production of defense-related compounds, cell wall, cell signaling, and transcription factors.

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Acknowledgment

This work was supported in part by The National Institutes of Health, grant number 1 R15 GM069408-01. We thank Jacqueline E. Roach for editorial and coaching services.

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  1. Department of Biological Sciences, Northern Illinois University, DeKalb, IL, 60115, USA

    Mitrick A. Johns & Long Mao

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Correspondence to Mitrick A. Johns.

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Supplementary Fig. 1

Summary of FDR experiments for CDS data. GO term numbers and their corresponding names can be found in Table 2. A + above the bar indicates a significant (q-value < = 0.05) excess of genes in the above-average polymorphism group; a - indicates an excess of genes in the below-average- polymorphism group; a 0 indicates a random distribution of genes; a blank symbol indicates that this GO category did not exist or had fewer than 10 genes for the given FDR experiment. Height of bar is proportional to the rank of the q-value for that GO term. Bar shading indicates q-value: solid: q-value <.001; diagonal lines: q-value <.01; vertical lines: q-value <.05; empty: q-value <=.05. From left to right: Bar 1: third level terms: cutoff = mean polymorphisms for CDS (3.49/kb); Bar 2: SWAT-aligned genes, third level terms: cutoff = mean polymorphisms for CDS (3.28/kb); Bar 3: cDNA-derived genes: cutoff = mean polymorphisms for CDS (3.19/kb); Bar 4: complete GO terms: cutoff = mean polymorphisms for CDS (3.49/kb); Bar 5: original plant GO_slim terms: cutoff = mean polymorphisms for CDS (3.49/kb); Bar 6: cutoff = 1.00 polymorphisms/kb; Bar 7: cutoff = 3.00 polymorphisms/kb; Bar 8: cutoff = 5.00 polymorphisms/kb; Bar 9: cutoff = 10.00 polymorphisms/kb ; Bar 10: all CDS (including those without introns); cutoff = 3.49; Bar 11: gene families reduced to 1 member; cutoff = 3.49; Bar 12: all gene family members removed; cutoff = 3.49 (GIF 46 867 kb)

10142_2006_36_Fig1_ESM.png

Supplementary Fig. 2

Summary of FDR experiments for intron data. GO term numbers and their corresponding names can be found in Table 2. A + above the bar indicates a significant (q-value <=0.05) excess of genes in the above-average -polymorphism group; a - indicates an excess of genes in the below-average- polymorphism group; a 0 indicates a random distribution of genes; a blank symbol indicates that this GO category did not exist or had fewer than 10 genes for the given FDR experiment. Height of bar is proportional to the rank of the q-value for that GO term. Bar shading indicates q-value: solid: q-value <.001; diagonal lines: q-value <.01; vertical lines: q-value <.05; empty: q-value >=.05. From left to right: Bar 1: third level terms: cutoff = mean polymorphisms for introns (3.49/kb); Bar 2: SWAT-aligned genes, third level terms: cutoff = mean polymorphisms for introns (4.82/kb); Bar 3: cDNA-derived genes: cutoff = mean polymorphisms for introns (3.88/kb); Bar 4: complete GO terms: cutoff = mean polymorphisms for introns (3.11/kb); Bar 5: original plant GO_slim terms: cutoff = mean polymorphisms for introns (3.11/kb); Bar 6: cutoff = 1.00 polymorphisms/kb; Bar 7: cutoff = 3.00 polymorphisms/kb; Bar 8: cutoff = 5.00 polymorphisms/kb; Bar 9: cutoff = 10.00 polymorphisms/kb ; Bar 10: all CDS (including those without introns); cutoff = 3.11; Bar 11: gene families reduced to 1 member; cutoff = 3.11; Bar 12: all gene family members removed; cutoff = 3.11 (GIF 47 239 kb)

10142_2006_36_Fig2_ESM.png

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Johns, M.A., Mao, L. Differentiation of the two rice subspecies indica and japonica: a Gene Ontology perspective. Funct Integr Genomics 7, 135–151 (2007). https://doi.org/10.1007/s10142-006-0036-1

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