Fig. 3

Improved mappability of RNA and gDNA sequencing data to the new assembly for Cx. quinquefasciatus. A Mapping of short genomic reads from field-caught Cx. quinquefasciatus mosquitoes to the chromosomal scaffolds of the new (J5) and old (J3) assemblies. Percentages of reads that mapped in various ways. Each set of paired dots with connecting line represents the reads from a single individual. **P < 0.01 (Paired Wilcoxon singed-rank tests). B–C Analysis of genomic regions harboring “assembly-specific” reads, which mapped to only J5 or only J3. Panel B shows the genic and repeat content of such regions in the J5 assembly. Each dot represents a non-overlapping 10 Mb, and the y-axis shows the fraction of bases within the given window covered by reads that did not map to J3. Panel C shows the distribution along chromosomes of J5-specific (top) or J3-specific (bottom) reads. J3 chromosomes are 5–10% shorter than their J5 counterparts but plotted proportionally to take up the same total space in the panel. Vertical, colored, dotted lines show the locations of odorant receptors (ORs) and odorant-binding proteins (OBPs) that were new or unplaced in J5. Note that only 17 of 19 unplaced ORs were located on the chromosomal scaffolds of J3 and are thus plotted at the bottom. Numbers above the lines indicate that the given number of new or unplaced genes is present at that location. D Mapping of RNAseq reads from embryo [51] and adult brain [52] to the new and old assemblies. Each set of paired dots with connecting line represents the reads from a single sample. Embryonic samples include 2 from the anterior pole and 3 from the posterior pole. Brain samples include 3 females and 3 males