Figure 1.
Experimental strategy used for mapping the distal (left) and proximal (right) breakpoints of inversion 2z3.
The segments depicted in each column are ordered from top to bottom in four successive steps with increasing mapping resolution. The distance between consecutive bars stands for 10 Mb, 100 kb, 10 kb and 1 kb, in the four steps, respectively. Line 1: Relative position of the contigs on the physical map of D. buzzatii standard chromosome 2. Line 2: Relative position of the BAC clones encompassing the distal breakpoint (left) and the proximal breakpoint (right). Line 3: Position of the PCR probes used to pinpoint the breakpoints within the overlapping segment of BAC clones. Line 4: Genes located in the breakpoint regions of the non-inverted chromosome (designated as AB and CD) are represented by dark grey rectangles with a pointed end indicating the direction of transcription and TEs by light grey rectangles. Short numbered segments under the genes in the distal breakpoint region (left) represent intergenic regions amplified by PCR and grey bars below the genes in the proximal breakpoint column (right) correspond to plasmid subclones of BAC 40C11. Line 5: Genes located in the breakpoint region of the inverted chromosome (designated as AC and BD). Thick lines above the inverted chromosome represent the lambda clones isolated during the cloning of the 2z3 breakpoints. Small horizontal arrows represent PCR primers (e.g. AF, NR, …). Vertical arrows mark the location of the breakpoints. Note that there is a reversal of orientation between lines 1 and 2 in the distal breakpoint (left). The reason is inversion 2z3 took place in a 2j chromosome and not in the standard chromosome 2 represented in line 1. See Materials and Methods for details.
Figure 2.
Schematic representation of the structures found at the distal and proximal breakpoint of inversion 2z3 in D. buzzatii.
Thick lines represent the single-copy A, B, C and D sequences. Coding regions of genes are represented as grey boxes with an arrow that indicates their orientation. Transposable elements are represented as coloured boxes with pointed ends. The different copies of GalileoN have been numbered sequentially following the order of the copies previously described [61]. Vertical arrows indicate the location of the breakpoints. Target site duplications flanking TE insertions are shown in boxes above them.
Figure 3.
Nucleotide polymorphism at the breakpoints of inversion 2z3 in inverted and non-inverted chromosomes.
For each region, nucleotide positions are numbered taking the breakpoint as start points. The sequence of line st-1 is taken as reference for the A, B, C and D regions, and the BuT5-8 insertion. Positions with nucleotides identical to the reference sequence are indicated by a dot. The nucleotide substitution generating a premature stop codon in Dlh exon 2 is shown underlined. Insertions and deletions are represented by minus and plus signs in the reference sequence, respectively, and a number in the line with the insertion or deletion indicating its size in nucleotides. In the case of deletions in st-1, a plus sign was added is in the rest of lines, indicating that this sequence is present. Deletions including more than one position of the reference line are included in rectangles. Exons, introns and intergenic regions are not drawn to scale. Variation in the BuT5-8 insertion is represented separately from region D.
Figure 4.
Neighbour-joining phylogenetic tree of the ABCD breakpoint sequences excluding the (AT)16–24 microsatellite and the TE insertions.
Table 1.
Transposable elements found at the breakpoint regions of inversion 2z3 in D. buzzatii.
Figure 5.
Chimeric structure of the two GalileoN copies (GalileoN-4 and GalileoN-5) observed at the breakpoints of inversion 2z3.
GalileoN-1 and GalileoN-2 were found in a previous study [60]. Top: Nucleotides present in the four GalileoN copies at 53 variable sites are shown. Bottom: Neighbor-joining phylogenetic trees of the GalileoN sequences built separately for the two portions of the sequence: sites 1–824 (left) and sites 966–1567 (right).
Table 2.
Nucleotide divergence between the TIRs of four GalileoN copies.
Table 3.
Number of TE copies found in the breakpoint regions of three D. buzzatii polymorphic inversions.