Journal: BMC Evolutionary Biology

Article Title: Evolutionary dynamics of origin and loss in the deep history of phospholipase D toxin genes

doi: 10.1186/s12862-018-1302-2

Figure Lengend Snippet: Subtree for Aquatic clade, color-coded by organismal classification. Asterisks indicate lower confidence sequences from organisms with transcriptome-only support, when these occur within sparsely or weakly represented phyla. These include Euphausia superba and Meganyctiphanes norvegica as representatives of the class Malacostraca, respectively, within the sparsely represented phylum Arthropoda; as well as the two representatives from the phylum Mollusca . Taxon names include genus and species labels (e.g. Rota_ta for Rotaria tardigrada ) as well as specific protein or nucleotide database identifiers

Article Snippet: Within the Aquatic group, several sequences putatively belonging to Oreochromis niloticus (a fish commonly known as tilapia) proved to be identical to confirmed genome and transcriptome sequences from Amoebidium parasiticum , a microorganism that is not found in association with tilapia but which had been sequenced at the same institute (Broad Institute).

Techniques:

Journal: BMC Evolutionary Biology

Article Title: Evolutionary dynamics of origin and loss in the deep history of phospholipase D toxin genes

doi: 10.1186/s12862-018-1302-2

Figure Lengend Snippet: Partial eukaryotic organism tree showing widespread losses of ST-like and/or Aquatic GDPD-like SMaseD/PLD genes, according to a model of ancient duplication followed by vertical descent. Colors indicate nodes and branches retaining both paralogs (purple), ST-like only (red), Aquatic only (blue), or neither (black). Branch labels indicate important clades: M, Metazoa; C, Cnidaria; D, Deuterostomia; P, Protostomia; S, Spiralia; E, Ecdysozoa; A, Arthropoda; H, Hexapoda (see Materials and Methods). Each taxon (phylum or class in most cases) is annotated with the number of genomes containing a PLD gene, divided by the total number of NCBI representative genomes assembled at scaffold level or higher (May 2018). Taxa marked with * also include additional genomes in which PLD genes were detected in unassembled (or assembled but not NCBI-deposited) genomic data. Taxa marked with ^ showed no PLD genes in NCBI representative genomes but did have hits in transcriptomes from multiple genera. Taxa marked with ~ showed one or several hits but with contamination suspected. This tree topology and evolutionary model imply 15 losses of ST-like and 18 losses of Aquatic genes, and additional losses would be necessary to explain incomplete conservation within certain taxa. While such extensive loss seems unlikely, the insets (dashed boxes) show distributions within Anthozoa and Rotifera that are consistent with at least three ST-like or Aquatic gene loss events in these phyla alone. The Anthozoan tree includes genera with transcriptome data only (italicized). The presence of scattered proteobacterial homologs in the Aquatic clade supports a role for lateral gene transfer in contributing to the observed sparse species distribution

Article Snippet: Within the Aquatic group, several sequences putatively belonging to Oreochromis niloticus (a fish commonly known as tilapia) proved to be identical to confirmed genome and transcriptome sequences from Amoebidium parasiticum , a microorganism that is not found in association with tilapia but which had been sequenced at the same institute (Broad Institute).

Techniques: