Positive selection of yeast nonhomologous end-joining genes and a retrotransposon conflict hypothesis

Sawyer and Malik 1010.1073/pnas.0605468103

Supporting Information

Files in this Data Supplement:

Supporting Figure 4
Supporting Table 2
Supporting Table 3




Supporting Figure 4

Fig. 4. Multiple alignments of NEJ1 and XRS2 used for PAML analysis. Gapped regions have been pruned from the alignments.

References

1. Kellis M, Patterson N, Endrizzi M, Birren, B, Lander ES (2003) Nature 423:241-254.

2. Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G (2004) Bioinformatics 20:3710-3715.

3. Bustamante CD, Fledel-Alon A, Williamson S, Nielsen R, Hubisz MT, Glanowski S, Tanenbaum DM, White TJ, Sninsky JJ, Hernandez RD, et al. (2005) Nature 437:1153-1157.

4. Clark AG, Glanowski S, Nielsen R, Thomas PD, Kejariwal A, Todd MA, Tanenbaum DM, Civello D, Lu F, Murphy B, et al. (2003) Science 302:1960-1963.

5. Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, Hubisz MJ, Fledel-Alon A, Tanenbaum DM, Civello D, White TJ, et al. (2005) PLoS Biol 3:e170.

6. Voight BF, Kudaravalli S, Wen, X, Pritchard JK (2006) PLoS Biol 4:e72.

7. Wang ET, Kodama G, Baldi, P, Moyzis RK (2006) Proc Natl Acad Sci USA 103:135-140.

Table 2. Reexamination of genes with whole-gene values of dN/dS > 1 (based on the analysis of Kellis et al.)

Previous analysis (1) of the S. cerevisiae-S. paradoxus genomes found nine genes with whole-gene values of dN/dS greater than one. We find that eight of these genes are now annotated as "dubious" ORFs on the Saccharomyces Genome Database (SGD), and all but three overlap significantly with another ORF on the same or opposite strand. Our reanalysis suggests that there are no S. cerevisiae-S. paradoxus orthologous gene pairs with a whole-gene value of dN/dS > 1. Furthermore, most of the genes identified as having dN/dS = 1 actually have no replacement changes, with one exception being YNL326C.

* Overlaps a gene on the same strand, but the two ORFs are in different reading frames.

^a dN/dS values reported are as calculated by Kellis et al. [Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003) Nature 423:241-254]. "R" and "S" are actual numbers of replacement and synonymous changes calculated in the present study. This indicates a consistent problem in the calculation of dN/dS ratios when there are no R changes.

^b This column reports instances where the gene in question overlaps another ORF, either on the same or opposite strand. "C" and "W" at the end of gene names indicate Watson or Crick strand.

^{c Listed by the Saccharomyces Genome Database (SGD) at Stanford. SGD defines a dubious ORF as follows: ORFs which are not conserved in other Saccharomyces species and for which there is no experimental evidence that a gene product is produced in S. cerevisiae. Many ORFs classified as "Dubious" are small and overlap a larger ORF of the class "Verified" or "Uncharacterized"; however, overlap with another ORF does not mandate that an ORF be classified as "Dubious."}

^{d No unambiguous S. paradoxus orthologs have been identified by the Fungal Alignment tool at SGD.}

^e YNL326C is also called PFA3. The SGD description for this gene is: "Palmitoyltransferase for Vac8p, required for vacuolar membrane fusion; contains an Asp-His-His-Cys-cysteine rich (DHHC-CRD) domain; autoacylates; required for vacuolar integrity under stress conditions"

^f There are multiple S. paradoxus orthologs for this gene identified by the Fungal Alignment tool at SGD.

• Early Edition
• Archives
• Online Submission

• Feature Articles

  (Expanded research articles of exceptional breadth)

• Commentaries

  (Expert commentary on leading research)

• Letters

  (Online-only letters to the editor)

• Inaugural Articles

  (Articles by recently elected NAS members)

• PNAS Profiles

  (Biographical profiles of Academy members)

• Sustainability Science

  (Interactions of human and environmental systems)

• Collected Papers

  (Editorials, Perspectives, Reviews, Colloquia, etc.)

• Special Features

  (Solicited articles on exceptional research topics)

• Sackler Colloquia

  (Scientific reports held under NAS auspices)

• Podcasts

  Brief podcasts with leading scientists