The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes
Figure 10
Telomere end-binding protein-α paralogs in ciliates.
The phylogeny is an ML tree generated by PhyML [123] with a single substitution rate category and the JTT substitution model, optimized for tree topology and branch length. Bootstrap percentages for 1,000 replicates are indicated at the tree nodes. The multiple sequence alignments underlying the phylogeny were produced with MAFFT (v 6.418b [124]) (default parameters; BLOSUM 62 substitution matrix) and were trimmed with trimal1.2 [125] with the “-automated1” parameter to remove excess gaps and poorly aligned regions. GenBank accessions are provided for the taxa unless otherwise indicated. Euplotes crassus is indicated in blue (Q06184 and Q06183), and an additional match from our preliminary Euplotes genome assembly is EUP_contig393834_f1_1. Perkinsus marinus is purple (EER00428) and Oxytricha nova is light green (P29549). Tetrahymena thermophila (salmon color) accessions are from the Tetrahymena genome database [126]—TTHERM_00378980 and TTHERM_00378990; Paramecium tetraurelia's TeBP-α protein (pink) is from ParameciumDB [127] (GSPATP00001065001). All the nodes beginning with “Contig” are Oxytricha trifallax TeBP-α paralogs (dark green) and Contig22209.0.g66 is TeBP-α1, the original TeBP-α. The tree is rooted at the midpoint of the branch between Arabidopsis thaliana (Pot1a—AAX78213 and Pot1b—AAS99712) and Homo sapiens (Pot1—EAW83616; black) and the rest of the phylogeny. Gene expression levels are normalized RNA-seq counts (see Text S1; Supporting Materials and Methods) before (“fed”) and during conjugation (0–60 h) are shown for the Oxytricha trifallax TeBP-α paralogs; coding sequence lengths are also indicated (in bp) for each of these paralogs.