These three genomic regions harbor the breakpoints of the paracentric inversions 3R(7) and 3R(8), also known as In(3R)84F1;93F6–7, and have been reconstructed by BLAST analysis, in situ hybridization, resequencing, and whole-genome alignments at UCSC (http://genome.ucsc.edu/). According to the information in D. erecta and different outgroup species (), D. simulans (S) is the species that best represents the ancestral (A) configuration for all three regions. Reference genes at the different breakpoint regions have been colored red, blue, and orange. Between some of the reference genes, putatively expressed genes (green and yellow; []) and repetitive sequences (pink) are also present. Other surrounding genes are indicated in brown. Top, cytological coordinates of the regions in D. melanogaster (M). Long horizontal lines indicate chromosomes; solid pattern indicates key region; and dashed pattern indicates chromosomal stretch separating key regions. Cen, centromere; Tel, telomere. The head of each colored horizontal arrow represents the 3′ end of each gene or putative gene. Chromosomal segments included in the inversion 3R(7) and 3R(8) are indicated by dotted lines. For both inversions, the sequences between paired staggered breakpoints are indicated by short horizontal solid lines. Roman numerals indicate different chromosomal stretches spanning inversion breakpoints that were sequenced as a control. Vertical arrows indicate the localization in the ancestor (D. simulans) of the four breakpoints (a, b, c, and d) that are necessary to explain the inversion 3R(8) and the duplication of HDC14862, pfd800, and HDC12400 at 84E9 (3R:3862326–3867817; 3R:3874931–3876653) and 93F6–7 (3R:17554739–17562483) of D. melanogaster (see ). The gene configuration CG7918-CG34034-CG5849 has been disrupted independently in the lineages of D. melanogaster and D. yakuba (Y) by the inversions 3R(8) and 3R(7), respectively. In D. melanogaster, the gene pair CG2708 (Tom34)-CG31176 is also disrupted, whereas in D. yakuba, CG31286-CG1315 is disrupted. Inversion 3R(8) and its associated duplication event generate an apparently full copy of the putative expressed gene HDC14862 in 3R:93E10-F2 of D. melanogaster. This contains 56–59 bp from the 3′ UTR of the gene CG2708 (blue triangle) within one of its putative introns. HDC14862 is present as two different fragments both in D. simulans and D. yakuba (see main text for details). Further, the inversion 3R(7) has disrupted the antisense overlap of CG31286 and CG1315 in D. yakuba: the antisense configuration is conserved at 84A1 of D. melanogaster and D. simulans, as well as in other species (). Inversion 3R(7) was accompanied by a duplication of CG34034 and a complex pattern of rearrangement that also involved a fragment of the 5′ region of HDC14862. The two open reading frames (ORFs) of CG34034 are functional according to GENSCAN (http://genes.mit.edu/GENSCAN.html), although the putative protein sequences they encode differ substantially from that of their orthologs in D. melanogaster and D. erecta. Some stretches with significant homology with CG31286 are also detected adjacent to CG1315 in D. yakuba. The reference gene CG31286 is also tandemly duplicated and adjacent to CG34034. In D. yakuba, there are three copies of CG31286, two of them being pseudogenes (denoted as a red gradient). Only the copy immediately distal to HDC12143 is functional, although it apparently codes for only one of the two isoforms of its D. melanogaster ortholog. Genes and distances between them are not represented proportionally.