DOI: 10.5061/dryad.m0cfxpp9m
title: Data from: Whole mitochondrial genome phylogeny of the family Drosophilidae

description: A total of 241 mitochondrial genomes were assembled and annotated from the
 SRA database to reconstruct a mtDNA genome phylogeny for the genus
 Drosophila, the family Drosophilidae, and close relatives. The resulting
 mtDNA genome phylogeny is largely congruent with previous higher-level
 analyses of Drosophila species with the exception of the relationships
 between the melanogaster, montium, anannassae, saltans and obscura groups.
 Although relationships within these species groups are congruent between
 nuclear and mtDNA studies, the mtDNA genome phylogeny of the groups is
 different when compared to earlier studies. Monophyly of known species
 groups within the genus Drosophila are highly supported and, as in
 previous work, the genera Lordiphosa, Hirtodrosophila, Zaprionus and
 Scaptomya are all imbedded within the genus Drosophila. Incongruence and
 partitioned support analyses indicate that DNA sequences are better at
 resolving the phylogeny than their translated protein sequences. Such
 analyses also indicate that genes on the minus strand of the circular
 molecule (Lrrna, Srrna, ND4, ND4L and ND5) provide most of the support for
 the overall phylogenetic hypothesis.
description: There were four basic ways we obtained the sequences for this
 study. First, about 40 of the genomes were present in the NIH Organelle
 Genome database (https://www.ncbi.nlm.nih.gov/genome/organelle/). These were simply downloaded from the database. Second, the NCBI assembly database (https://www.ncbi.nlm.nih.gov/assembly/) contains contigs that can be assembled into more contiguous sequences and then fully annotated. These contigs were mostly deposited by the authors of several recent large genome studies of drosophilid flies. Contigs containing mtDNA sequences were extracted and partially assembled using MitoZ  with final assembly in MitoS.  The initial assemblies relied on several methods of assembly and the quality of these draft mtDNA genomes was highly variable. Third, the assembly libraries were reassembled with a single  assembly program (SPAdes v3.11.1). Assembly with this program appeared to be more consistent and complete than with other approaches. The fourth approach was to reassemble the SRA reads (https://www.ncbi.nlm.nih.gov/sra) directly to the <em>Drosophila melanogaster</em> reference  mtDNA genome using Geneious software with the “map to reference” function; the genomes thus obtained were then annotated using MitoS.  The last approach ended up being the most efficient and accurate, so we repeated many of the previously assembled genome assemblies using the Geneious-MitoS approach. A few of the genomes assembled this final way were generated from RNA-Seq data, but the majority were from WGS SRA sequences.
description: # Data from: Whole mitochondrial genome phylogeny of the family
 Drosophilidae 1. Drosophila_mt.cat: A txt file holding 199 assembled
 drosophilid mtDNA genomes. These assembled genomes are described in
 DeSalle, Rob, Sara Oppenheim, and Patrick M. O’Grady. "Whole
 mitochondrial genome phylogeny of Drosophilidae." *Mitochondrial DNA
 Part A* 33, no. 1-8 (2022): 1-9. 2. Assemblies_Dros_mtDNA.txt: A text file
 holding mtDNA genome assemblies, annotations and accession lists of
 species used in the study. 3. Accession numbers.docx: A microsoft word
 file holding all of the accession information for the drosophilid species
 in the study. 4. 241_mtDNA_B.txt: A txt file holding the aligned
 assemblies for 241 drosophilid species in NEXUS format, fully partitioned
 into genes, proteins, tRNA's, rRNAs and clusters of
 tRNAs.Sharing/Access information.