Molecular evolution of sex-biased genes in the Drosophila ananassae subgroup

Sonja Grath, John F Baines, John Parsch

Department of Biology, University of Munich (LMU), Munich, Germany

Additional Material

Microarrays

Gene selection and PCR primers

Our D. ananassae microarrays contained PCR-amplified exon probes to 148 genes, with each probe spotted in 8 replicates. 136 of these genes are comprised of 91 autosomal genes reported by Pröschel et al. (2006) and 45 X-linked genes reported by Baines et al. (2008). For these genes, polymorphism data from 12 African D. melanogaster strains and divergence data to D. simulans are available. We used the D. ananassae (Assembly August 2005; http://genome.ucsc.edu/) genome to design polymerase chain reaction (PCR) primers flanking single exons of all of the above genes.

Additional File 1 - Primers for PCR-amplicon microarrays
Download

Sex-biased gene expression

Additional File 2 - Sex-biased gene expression in D. ananassae compared to D. melanogaster and D. pseudoobscura
Download

Raw data

Raw data for all microarrays can be downloaded below. For the strain KK1 (Kota Kinabalu, Borneo), we performed four biological replicates. For the strain KK2, we performed two biological replicates. Each biological replicate included a technical (dye-swap) replicate, leading to a total of 12 microarrays.

Array Description Data
KK1_1 D. ananassae strain KK1, biological replicate 1 Download
KK1_1_ds D. ananassae strain KK1, biological replicate 1, dye-swap Download
KK1_2 D. ananassae strain KK1, biological replicate 2 Download
KK1_2_ds D. ananassae strain KK1, biological replicate 2, dye-swap Download
KK1_3 D. ananassae strain KK1, biological replicate 3 Download
KK1_3_ds D. ananassae strain KK1, biological replicate 3, dye-swap Download
KK1_4 D. ananassae strain KK1, biological replicate 4 Download
KK1_4_ds D. ananassae strain KK1, biological replicate 4, dye-swap Download
KK2_1 D. ananassae strain KK2, biological replicate 1 Download
KK2_1_ds D. ananassae strain KK2, biological replicate 1, dye-swap Download
KK2_2 D. ananassae strain KK2, biological replicate 2 Download
KK2_2_ds D. ananassae strain KK2, biological replicate 2, dye-swap Download

Analysis of polymorphism and divergence

Comparison D. ananassae/D. melanogaster

For 43 genes, we have polymorphism data for both D. melanogaster (Zimbabwe, Africa) and D. ananassae (Bangkok, Thailand). For D. melanogaster, divergence was determined to D. simulans. For D. ananassae, divergence was determined to D. atripex and/or D. phaeopleura.

Additional File 3 - Comparison D. ananassae/D. melanogaster
Download

Ancestral state of sex-biased gene expression

For genes that differed in their sex-bias classification between D. melanogaster and D. ananassae, we inferred the ancestral expression state using D. pseudoobscura as an outgroup and published microarray data from Zhang et al. (2007).

Additional File 4 - Inference of ancestral sex-biased expression state of genes differing in expression between D. melanogaster (Dmel) and D. ananassae (Dana), using D. pseudoobscura (Dpse) as the outgroup
Download

PCR and sequencing primers

We designed PCR primers flanking the coding regions of each target gene. PCR primers were used for both PCR and sequencing. For some genes, additional internal (Int) primers were used for sequencing.

Additional File 5 - PCR and sequencing primers
Download

References

Baines JF, Sawyer SA, Hartl DL, Parsch J: Effects of X-linkage and sex-biased gene expression on the rate of adaptive protein evolution in Drosophila. Mol Biol Evol. 2008, 25:1639-1650.
Gibson G, Riley-Berger R, Harshman L, Kopp A, Vacha S, Nuzhdin S, Wayne M: Extensive sex-specific non-additivity of gene expression in Drosophila melanogaster. Genetics 2004, 167:1791-1799.
Parisi M, Nuttall R, Naiman D, Bouffard G, Malley J, Andrews J, Eastman S, Oliver B: Paucity of genes on the Drosophila X chromosome showing male-biased expression. Science 2003, 299:697-700.
Pröschel M, Zhang Z, Parsch J: Widespread adaptive evolution of Drosophila genes with sex-biased expression. Genetics 2006, 174:893-900.
Ranz JM, Castillo-Davis CI, Meiklejohn CD, Hartl DL: Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 2003, 300:1742-1745.
Zhang Y, Sturgill D, Parisi M, Kumar S, Oliver B: Constraint and turnover in sex-biased gene expression in the genus Drosophila. Nature 2007, 450:233-238.