Additional file 6 of DNA methylation atlas and machinery in the developing and regenerating annelid Platynereis dumerilii
Creators: name: Planques, Anabelle
name: Kerner, Pierre
name: Ferry, Laure
name: Grunau, Christoph
name: Gazave, Eve
name: Vervoort, Michel
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 6: Figure S4. Phylogenetic trees of 5mC and NuRD toolkit proteins. Maximum likelihood (ML) trees constructed with PhyML are shown. Statistical supports (aLRT values) for all nodes are indicated with a color code provided in the inset. Terminal branches are colored using the shown color code also used in Fig. 2. P. dumerilii sequences are in bold and indicated by arrows. (A) DNMT proteins. The three subfamilies DNMT1, 2 and 3 are indicated. In the DNMT3 subfamily, the vertebrate-specific groups DNMT3A, B and -like are also shown. We used a distantly related sequence (Dnmt5) from Acanthamoeba castellanii (Acas, an amoeba) as outgroup to root the phylogenetic tree. We also retrieved Dnmt sequences from two choanoflagellates species, Monosiga brevicollis (Mbre) and Salpingoeca rosetta (Sros), which all belong to the DNMT2 subfamily. (B) TET proteins. The three vertebrate-specific groups TET1, 2 and 3 are indicated. We used midpoint rooting for this tree as we were unable to find Tet genes in choanoflagellates or another suitable outgroup. (C) TDG. The phylogenetic tree is rooted using choanoflagellate sequences as outgroup. (D) UHRF. The two vertebrate-specific groups UHRF1 and 2 are indicated. We used midpoint rooting for this tree as we were unable to find Uhrf genes in choanoflagellates or another suitable outgroup. (E) MBD proteins. The two subfamilies MBD1/2/3 and MBD4 subfamilies are indicated. Vertebrate-specific groups are also shown. While not found in S. rosetta and M. brevicollis, a single Mbd gene was found in three other choanoflagellates (Helgoeca nana (Hnan), Salpingoeca urceolata (Surc), and Acanthoeca spectabilis (Aspe)) for which extensive transcriptomic data have been produced. Two of these choanoflagellate Mbd sequences (Hnan and Aspe) form a monophyletic group that was used as outgroup to root the tree, while the third one (Surc) clusters with MBD 4 proteins. (F) CHD proteins. The three subfamilies CHD1/2, CHD3/4/5 and CHD6/7/8/9 are indicated. Vertebrate-specific groups are also shown. We used the distantly related SNF2L1 sequence from Human as outgroup to root the phylogenetic tree. (G) Class I HDAC proteins. The three subfamilies HDAC1/2, HDAC3 and HDAC8 are indicated. Vertebrate-specific HDAC1 and 2 groups are also shown. Class II and IV HDACs from Human were used as outgroup to root the phylogenetic tree. We also retrieved HDACs from choanoflagellates, three of which clustering with the outgroup, two with HDAC3 proteins, and two with HDAC1/2 proteins. (H) RBBP4/7 proteins. Vertebrate-specific RBBP4 and 7 groups are shown. The phylogenetic tree is rooted using choanoflagellate sequences as outgroup. (I) MTA1/2/3 proteins. Vertebrate-specific MTA1, 2 and 3 groups are shown. (J) GATAD2 proteins. Vertebrate-specific GATAD2-alpha and GATAD2-beta groups are shown. For (I) and (J), midpoint rooting has been used in the absence of choanoflagellate members of these two gene families and the absence of other suitable outgroups.