Our RT domain alignment and were used to build a phylogenetic
Our RT domain alignment and were used to build a phylogenetic tree in which we also incorporated RT sequences from the green algae Chlamydomonas reinhardtii and Ostreococcus tauri, the brown alga Aureococcus anophagefferens, and the RT domain from the PyRE10G element found in the red alga Porphyra yezoensis [31] (Figure 10). As expected, we observed an enormous diversity within GOS sequences. It was found that GOS RT domains clustered with all the LTR-RT lineages described here, including the CoDiI and CoDiII lineages. However, RT domains belonging to the Ty3/gypsy, Copia, and the recently iden-tified red/aquatic species (RAS) lineage [32] are the most abundant in the dataset analyzed. We also noticed that the RAS-like lineage appears to be quite a diverse assemblage (Figure 10). These RAS-like elements appear to be the most abundant in the Sargasso Sea samples, especially from the 0.22-0.8 m filters (data not shown).DiscussionIn this work, we have identified seven groups of Ty1/copialike LTR-retrotransposons in diatom genomes. Four groups (CoDi1-2-3 and CoDi7) were found only in the P. tricornutum genome whereas elements belonging to the CoDi4-5-6 groups were detected in both diatom genomes. The presence of both classes suggests either that they were present in the diatom common ancestor and that the CoDi1-3 groups became extinct in the lineage leading to the centric species T. pseudonana, or that representatives of each group have been separately introduced horizontally in pennate and centric diatoms. The topology of the treePage 10 of(page number not for citation purposes)BMC Genomics 2009, 10:http://www.biomedcentral.com/1471-2164/10/Figure 8 Schematic get OPC-8212 representation of the PtC25 and PtC75 recombinant loci 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 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/25957400 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. presented in Figure 2 shows that CoDi3 and CoDi4 are bootstrap-supported sister groups that share a common ancestor after the separation from CoDi1 and CoDi2. This, together with the fact that we could not detect traces of diverged remnant copies from the CoDi1-3 groups in the T. pseudonana genome by BLAST searches (data not shown) PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26024392 favors the horizontal transfer hypothesis to explain the presence of CoDi4 elements in the T. pseudonana genome. Ty3/gypsy-like elements were found in the T. pseudonana genome but not in the P. tricornutum genome. We also identified RT sequences corresponding to Ty3/gypsy-like elements from the pennate diatoms P. multiseries and P. multistriata which clearly cluster wi.