DOI: 10.5061/dryad.b5mkkwhjz
title: Supplementary data for: Encyclopaedia of family A DNA polymerases localized in organelles: Evolutionary contribution of bacteria including the proto-mitochondrion

description: DNA polymerases (DNAPs) synthesize DNA from deoxyribonucleotides in a
 semi-conservative manner and serve as the core of DNA replication and
 repair machinery. In eukaryotic cells, there are two genome-containing
 organelles, mitochondria and plastids, that were derived from an
 α-proteobacterium and a cyanobacterium, respectively. Except for rare
 cases of genome-lacking mitochondria and plastids, both organelles must be
 served by nucleus-encoded DNAPs that localize and work in them to maintain
 their genomes. The evolution of organellar DNAPs has yet to be fully
 understood because of two unsettled issues. First, the diversity of
 organellar DNAPs has not been elucidated in the full spectrum of
 eukaryotes. Second, it is unclear when the DNAPs that were used originally
 in the endosymbiotic bacteria giving rise to mitochondria and plastids
 were discarded, as the organellar DNAPs known to date show no phylogenetic
 affinity to those of the extant α-proteobacteria or cyanobacteria. In this
 study, we identified from diverse eukaryotes 134 family A DNAP sequences,
 which were classified into 10 novel types, and explored their evolutionary
 origins. The subcellular localizations of selected DNAPs were further
 examined experimentally. The results presented here suggest that the
 diversity of organellar DNAPs has been shaped by multiple transfers of the
 PolI gene from phylogenetically broad bacteria, and their occurrence in
 eukaryotes was additionally impacted by secondary plastid endosymbioses.
 Finally, we propose that the last eukaryotic common ancestor may have
 possessed two mitochondrial DNAPs, POP and a candidate of the direct
 descendant of the proto-mitochondrial DNAP, rdxPolA, identified in this
 study.
description: # Supplemetanry data for Harada et al. "Encyclopaedia of family A DNA
 polymerases localized in organelles: Evolutionary contribution of bacteria
 including the proto-mitochondrion." ## Description of the data and
 file structure When you extract "sup_data_20231129.zip" file,
 you will see four sub-folders, "DNAP_phylogeny,"
 "Euk_340_genes," "SRA_assemblies," and
 "Tsukubamonas_Fabomonas_assemblies." In
 "DNAP_phylogeny," 20 alignments of DNA polymerases (DNAPs) and
 19 treefiles inferred from the alignments are stored in
 "alignments" and "treefiles," respectively. The trees
 inferred by the maximum likelihood method are named as
 "(DNAP_name)_ML.treefile." Likewise, those inferred by Bayesian
 method are named as "(DNAP_name)_pb.treefile." In
 "Euk_340_genes," you can find a phylogenomic alignment composed
 of 340 genes (340_genes_97_OTU.fasta), the ML tree inferred from the
 340-gene alignment (340_genes_97_OTU.treefile), and coverage for each 340
 genes and species (coverage.tsv). In addition, the 340 single-gene
 alignments are provided in "single_genes_fasta" folder. The
 treefiles used for AU test and result of AU test are provided in
 "AU_test" folder. "SRA_assemblies" contains 13
 assembled data in the fasta format. The 13 transcriptome data deposited in
 the GenBank SRA database were assembled by ourselves using Trinity.
 DRR036721; Polyblepharides amylifera DRR036722; Pyramimonas parkeae
 ERR558152; Vitrella brassicaformis CCMP3155 PRJNA301448; Pharyngomonas
 kirbyi PRJNA310762; Euglena gracilis PRJNA471257; Euglena longa
 SRR1294408; Eutreptiella gymnastica SRR1617398; Nutomonas longa
 strain:CCAP 1958/5 SRR5996795; Gefionella okellyi (strain 249) SRR5997436;
 Ancyromonas sigmoides CCAP 1958/3 SRR6175506; Ancoracysta twista TD-1
 SRR9888042; Digyalum oweni SRR10384242; Chromera velia
 "Tsukubamonas_Fabomonas_assemblies" contains two assemble data
 in the fasta format. The two transcriptome data of Tsukubamonas globosa
 NIES-1390 and Fabomonas tropica SRT902 were generated in this study and
 assembled by Trinity. The two transcriptome data were deposited in
 GenBank/EMBL/DDBJ Sequence Read Archive under accession no. PRJNA932580.