dpse expression and annotation

We mapped RNA-seq reads to our assembly using Tophat v2.0.13 and estimated expression level with cufflinks v2.2.2. We then searched for homologous genes using the predicted transcripts as BLAST queries to all D. melanogaster translations and transposon sequences (r6.07) with NCBIblast

dpse_falcon gtf

We identified exon-introns junctions by mapping annotated transcripts (r3.03; Flybase) and transcripts of Y-linked genes from NCBI (gi|295126506|gb|GU937420.1|, gi|255764727|gb|EU595397.2|, gi|295126512|gb|GU937423.1|) to our assembly using exonerate 2.4.0. To complement these data, we mapped RNA-seq reads to our assembly using Tophat v2.0.13. We annotated transcripts, eliminated small redundant isoforms with cufflinks v2.2.2

dpse_falcon assembly

We downloaded raw PacBio reads from ftp://ftp.hgsc.bcm.edu/Dpseudoobscura/Towards_finishing_the_D.pseudoobscura_genome/PacBio_Data/FastQ_files/ (these reads was generously granted by Drs. Stephen Schaeffer and Stephen Richards). We used the Falcon assembler v0.3.0 (https://github.com/PacificBiosciences/FALCON-integrate) to filter, correct and assemble reads. Then we polished the assembly using Quiver (SMRT Analysis v2.3.0

A negative correlation between the weekly offspring numbers by parthenogenesis and by sexual reproduction in mated KKU119-bo females of the single mating group.

<p>Spearman's <i>ρ</i> = −0.58, <i>P</i> = 4.99×10⁻¹⁰.</p

Weekly offspring numbers of single virgin KKU119 (A), mated KKU119 (B), and mated #55.1 (C) females of <i>Drosophila albomicans</i>.

<p>The X-axis denotes weeks after mating. The Y-axis denotes offspring numbers. Sample size: A  =  34, B  =  41, C  =  18. Error bars indicate standard errors. Different letters indicate that the values are significantly different between weeks at <i>P</i><0.05 by Friedman's test and an additional post hoc analysis of Bonferroni-corrected Wilcoxon signed-rank test.</p

Percentages of various diploidization mechanisms of parthenogenesis in <i>Drosophila albomicans.</i>

<p>* See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113275#pone-0113275-g001" target="_blank">Figure 1</a> for the inference of diploidization mechanisms by different genotypes.</p><p>Percentages of various diploidization mechanisms of parthenogenesis in <i>Drosophila albomicans.</i></p

Female mating propensities of the parthenogenetic and sexual strains of <i>Drosophila albomicans.</i>

a.<p>One female from each strain was paired with one male from #55.1.</p><p>Female mating propensities of the parthenogenetic and sexual strains of <i>Drosophila albomicans.</i></p

The percentage of virgin females capable of producing progeny and the fertility of virgin females from three strains of <i>Drosophila albomicans</i> and their sexually produced F₁ progeny.

<p>The percentage of virgin females capable of producing progeny and the fertility of virgin females from three strains of <i>Drosophila albomicans</i> and their sexually produced F₁ progeny.</p

Possible genotypes based on different diploidization mechanisms in parthenogenesis in <i>Drosophila albomicans</i>.

<p>The three possible diploidization mechanisms are illustrated in the left column. The four nuclei produced after meiosis are indicated by colored circles. Central fusion is the fusion of two nuclei derived from different meiosis I nuclei (“dark blue fusion with pink or red circles” or “light blue fusion with pink or red circles”), whereas terminal fusion is derived from the same meiosis I nucleus (“dark blue fusion with light blue circles” or “pink fusion with red circles”). Gamete duplication is the fusion of two nuclei duplicated from one of four nuclei. All possible genotypes of two linked markers are listed under three mechanisms with (A) no recombination, (B) one recombination event between two markers and the centromere, (C) one recombination event between two markers, and (D) double crossover. The chromosomes from parthenogenetic and sexual strains are labeled by blue and red, respectively. The alleles of each locus are labeled as <i>P</i> for parthenogenetic strain and <i>S</i> for the two sexual strains. Because the double-crossover rate was extremely low, recombinant F₂ offspring arising from double crossover are not considered in this analysis. Genotypes that can have come from only one of the three mechanisms are labeled in blue, the genotypes in black (i.e., <i>PS</i>,<i>PS</i>) are from central fusion or terminal fusion, and genotypes that are shared by the three mechanisms are labeled in gray.</p