CO frequencies in <i>dl-49</i> heterozygotes from cross 1 and cross 2 (Fig 2).

These distributions are not significantly different from each other and were combined into one dataset (Kolmogorov-Smirnov test, p = 0.61). (DOCX)</p

PCR primers used to detect the <i>dl-49</i> breakpoints.

PCR results show that primer sets fail to amplify a specific band in Oregon-RM, but do amplify specific bands of the expected sizes in dl-49, confirming that the expected breakpoints are present. (DOCX)</p

Crossover frequencies in the specified genetic intervals for the full-sibling wildtype Oregon-RM and the <i>dl-49</i> inversion.

Number of recovered offspring are shown, and the corresponding cM is shown in parentheses below.</p

Crosses used to generate full sibling Oregon-RM and <i>dl-49</i> stocks.

A) We previously isogenized dl-49 and crossed in an isogenized chr2 from Oregon-RM. This stock was used for cross 1 in Fig 2. The next several generations were needed to create a stock that was heterozygous for dl-49 and chrX from Oregon-RM and that shared genetic background on chr3. Full-sibling stocks were created at generation 10 by crossing dl-49 heterozygotes to either dl-49 males (B) or Oregon-RM males (C). This cross scheme did not result in isogenized 3rd chromosome but did create a shared genetic background. (DOCX)</p

S5 Fig -

A) Raw counts of CO frequencies in Oregon-RM. 96 COs between y and cv or wy and f were sequenced. COs that occur between cv and wy were from samples that had more than one CO on the chromosome. These COs were not included in any analysis. B) Raw counts of CO frequencies from dl-49 heterozygotes. 145 COs between y and f were sequenced. (DOCX)</p

Fig 1 -

A) Canonical recombination pathways used in meiosis. 1) Meiosis is initiated by an enzymatically mediated DSB. 2) The DSB is resected into single-stranded ends, one of which invades the homologous chromosome and primes DNA synthesis. This forms a displacement loop (D-loop) and during synthesis dependent strand annealing (SDSA), this structure can be unwound by a helicase into a NCO. 3) If the second end of the DSB is captured by the D-loop, it also primes synthesis. 4) The second-end capture intermediate is ligated into a double Holliday Junction, which is cleaved by a meiosis-specific endonuclease to form mostly COs, although some NCOs can occasionally form. B) Predicted pairing arrangement between an inversion and a standard arrangement homologous chromosome. Single COs within the inversion breakpoints lead to acentric and dicentric chromosomes with deletions and duplications. If these COs occur, they are not recovered in the offspring (the so-called transmission distortion effect). COs are also suppressed in the collinear regions outside of the inversion breakpoints, even though COs in these regions would not lead to chromosome rearrangements. This suggests that COs are prevented from forming, as opposed to being suppressed due to transmission distortion.</p

Complete dataset for number of H2AV foci per nucleus in Fig 5.

Complete dataset for number of H2AV foci per nucleus in Fig 5.</p

Detailed information on all CO and NCOGC events, including precise locations, genotype information, 95% confidence intervals.

Detailed information on all CO and NCOGC events, including precise locations, genotype information, 95% confidence intervals.</p

Sequencing confirmation of pre-meiotic NCOGC events.

Table lists the location of NCOGC, primers used for PCR and sequencing, expected PCR product size, and the samples sequenced. Sanger sequencing traces are shown for each sample and are in the same order as in the table. (DOCX)</p

Location and frequencies of NCOGCs recovered from Oregon-RM and <i>dl-49</i> heterozygotes.

Location and frequencies of NCOGCs recovered from Oregon-RM and dl-49 heterozygotes.</p