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.

Sex-biased gene expression

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.

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.

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).

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.

References