Schematic representation of the PtC25 and PtC75 recombinant loci. LTR-RT of the CoDi5.3 (orange) and CoDi2.3 (blue) groups are drawn with their LTRs (flanking arrows). Gene family 1 (green) and gene family 2 (purple) and other genes (grey) are drawn as arrows. Gene family 1 is further distinguished by red and/or blue bar on top and similar colors indicate similar sequences (see Additional file 4). Black or grey boxes with identical numbers indicate similar intergenic regions. Grey parallelograms project large duplicated regions from chromosome to chromosome. The blue parallelogram indicates the high similarity between the PtC25 and PtC75 elements. We indicate a 30 bp gap found in the CoDi5.3 segment flanking PtC75. We also indicate that the PtC25-associated CoDi5.3 entity contains a 5' truncated LTR which starts precisely where the gap described on chromosome 31 ends, further consolidating the historical link between these two loci. Bd 31.35 indicates a scaffold that could not be successfully mapped during P. tricornutum genome assembly.