Molecular-assisted alpha taxonomy of the genus <i>Rhodymenia</i> (Rhodymeniaceae, Rhodymeniales) from Australia reveals overlooked species diversity

<p>A previously published DNA barcode survey of red macroalgae in Australia revealed significant cryptic and overlooked diversity for the genus <i>Rhodymenia</i> with recognition of <i>R. novahollandica, R. prolificans, R. stenoglossa, R. wilsonis</i> and an additional four uncharacterized genetic species groups. Since that study, increased sampling effort in Australia has warranted reassessment and reinvestigation of the number of genetic species groups attributed to <i>Rhodymenia</i> and their respective taxonomic affiliations. Using molecular-assisted alpha taxonomy employing the DNA barcode (COI-5P), the present study resolved 188 Australian specimens in 12 genetic species groups assignable to the genus <i>Rhodymenia</i>. Four of these groups were attributed to the previously recognized species (above), whereas some collections from Lord Howe Island were attributed to the New Zealand species <i>R. novazelandica</i>, expanding its biogeographic range. The following seven genetic groups were inconsistent with existing species of <i>Rhodymenia</i> and established as novel taxa: <i>R. compressa</i> sp. nov., <i>R. contortuplicata</i> sp. nov., <i>R. gladiata</i> sp. nov., <i>R. insularis</i> sp. nov., <i>R. lociperonica</i> sp. nov., <i>R. norfolkensis</i> sp. nov. and <i>R. womersleyi</i> sp. nov. Although morphological and biogeographic features were adequate for distinguishing some species of <i>Rhodymenia</i> from Australia, DNA sequencing in combination with morphology and biogeography provided the most reliable means of identification.</p

Ubiquitin fusion proteins in algae: implications for cell biology and the spread of photosynthesis

Abstract Background The process of gene fusion involves the formation of a single chimeric gene from multiple complete or partial gene sequences. Gene fusion is recognized as an important mechanism by which genes and their protein products can evolve new functions. The presence-absence of gene fusions can also be useful characters for inferring evolutionary relationships between organisms. Results Here we show that the nuclear genomes of two unrelated single-celled algae, the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans, possess an unexpected diversity of genes for ubiquitin fusion proteins, including novel arrangements in which ubiquitin occupies amino-terminal, carboxyl-terminal, and internal positions relative to its fusion partners. We explore the evolution of the ubiquitin multigene family in both genomes, and show that both algae possess a gene encoding an ubiquitin-nickel superoxide dismutase fusion protein (Ubiq-NiSOD) that is widely but patchily distributed across the eukaryotic tree of life – almost exclusively in phototrophs. Conclusion Our results suggest that ubiquitin fusion proteins are more common than currently appreciated; because of its small size, the ubiquitin coding region can go undetected when gene predictions are carried out in an automated fashion. The punctate distribution of the Ubiq-NiSOD fusion across the eukaryotic tree could serve as a beacon for the spread of plastids from eukaryote to eukaryote by secondary and/or tertiary endosymbiosis

TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets

International audienceVarious bioinformatics protocols have been developed for trimming the number of operational taxonomic units (OTUs) in phylogenetic datasets, but they typically require significant manual intervention. Here we present TreeTuner, a semi-automated pipeline that allows both coarse and fine-scale tuning of large protein sequence phylogenetic datasets via the minimization of OTU redundancy. TreeTuner facilitates preliminary investigation of such datasets as well as more rigorous downstream analysis of specific subsets of OTUs

The protist Aurantiochytrium has universal subtelomeric rDNAs and is a host for mirusviruses

Viruses are the most abundant biological entities in the world's oceans, where they play important ecological and biogeochemical roles. Metagenomics is revealing new groups of eukaryotic viruses, although disconnected from known hosts. Among these are the recently described mirusviruses, which share some similarities with herpesviruses.1 50 years ago, "herpes-type" viral particles2 were found in a thraustochytrid member of the labyrinthulomycetes, a diverse group of abundant and ecologically important marine eukaryotes,3,4 but could not be further characterized by methods then available. Long-read sequencing has allowed us to connect the biology of mirusviruses and thraustochytrids. We sequenced the genome of the genetically tractable model thraustochytrid Aurantiochytrium limacinum ATCC MYA-1381 and found that its 26 linear chromosomes have an extraordinary configuration. Subtelomeric ribosomal DNAs (rDNAs) found at all chromosome ends are interspersed with long repeated sequence elements denoted as long repeated-telomere and rDNA spacers (LORE-TEARS). We identified two genomic elements that are related to mirusvirus genomes. The first is a ∼300-kbp episome (circular element 1 [CE1]) present at a high copy number. Strikingly, the second, distinct, mirusvirus-like element is integrated between two sets of rDNAs and LORE-TEARS at the left end of chromosome 15 (LE-Chr15). Similar to metagenomically derived mirusviruses, these putative A.&nbsp;limacinum mirusviruses have a virion module related to that of herpesviruses along with an informational module related to nucleocytoplasmic large DNA viruses (NCLDVs). CE1 and LE-Chr15 bear striking similarities to episomal and endogenous latent forms of herpesviruses, respectively, and open new avenues of research into marine virus-host interactions