Table 1 The mapping coverage of mitogenomes and genomes of Wolbachia strains obtained from three Rhagoletis cerasi individuals and one Ceratitis capitata individual. Genomes of wCer1, wCer2 and wCer4 were assembled from libraries of individuals which only had one strain. Then these reference genomes were used to competitively map reads of RcerAS to wCer1, wCer2 and wCer5, and reads of RcerIZ to wCer1 and wCer5; all other libraries (and sampled libraries) were mapped to a single Wolbachia strain. Subsampling of total reads was selectively applied to normalise the number of mapped reads for comparison between libraries. Mapping parameters were 97% similarity over 97% length, keeping only properly paired reads
Host Species | Rhagoletis cerasi | C. capitata | ||
|---|---|---|---|---|
Population | RcerHB; Bajna, Hungary | RcerIZ; Zafferana, Italy | RcerAS; Stillfried, Austria | Ccap10.3 (WolMed S10.3) |
Tissue source (DNA extraction) | single pupa (whole individual) | single larva (whole individual) | single pupa (whole individual) | single adult (abdomen) |
Wolbachia strain detected by MLST markers | wCer1 | wCer1; wCer5 | wCer1; wCer2; wCer5 | wCer4 |
No. of paired reads after QC | 125,415,852 | 147,147,772 | 131,385,710 | 130,835,872 |
No. paired reads mapped to mtDNA (full library) | 19,390,560 | 1,053,116 | 39,939,364 | 31,839,758 |
Percentage mapped to mtDNA | 15.46% | 0.72% | 30.40% | 24.34% |
No. paired reads mapped to mtDNA (no. subsampled) | 81,548 (530,000) | 85,244 (12million) | 81,608 (270,000) | na |
Percentage mapped to mtDNA | 15.46% | 0.71%% | 30.23%% | na |
No. paired reads mapped to wCer1 (full library) | 3,586,116 | 258,194 | 1,411,170 | na |
Percentage mapped to wCer1 | 2.86% | 0.18% | 1.08% | na |
No. paired reads mapped to wCer1 (no. subsampled) | 286,212 (10million) | na | 278,582 (26million) | na |
Percentage mapped to wCer1 | 2.86% | na | 1.07% | na |
No. paired reads mapped to wCer2 (full library) | na | na | 2,561,484 | na |
Percentage mapped to wCer2 | na | na | 1.95% | na |
No. paired reads mapped to wCer2 (no. subsampled) | na | na | 1,697,166 (87million) | na |
Percentage mapped to wCer2 | na | na | 1.95% | na |
No. paired reads mapped to wCer4 (full library) | na | na | na | 1,701,414 |
Percentage mapped to wCer4 | na | na | na | 1.30% |
No. paired reads mapped to wCer5 (full library) | na | 51,402 | 191,892 | na |
Percentage mapped to wCer5 | na | 0.03% | 0.15% | na |