Biology subjects

Plese, B.

Publications and source records attributed to Plese, B..

2 recordsLinked to original sources

bioRxiv2018

Freshwater Adaptation at the Molecular Scale in the Unique Sponges of Lake Baikal

Freshwater sponges (Spongillida) are a unique lineage of demosponges that secondarily colonized lakes and rivers and are now found ubiquitously in these ecosystems. They developed specific adaptations to freshwater systems, including the ability to survive extreme thermal ranges, long-lasting dessication, anoxia, and resistance to a variety of pollutants. While spongillids have colonized all freshwater systems, the family Lubomirskiidae is endemic to Lake Baikal, and plays a range of key roles in this ecosystem. Our work compares the genomic content and microbiome of individuals of three species of the Lubomirskiidae, providing hypotheses for how molecular evolution has allowed them to adapt to their unique environments. We have sequenced deep (>92% of the metazoan Benchmarking Universal Single-Copy Orthologs (BUSCO) set) transcriptomes from three species of Lubomirskiidae and a draft genome resource for Lubomirskia baikalensis. We note Baikal sponges contain unicellular algal and bacterial symbionts, as well as the dinoflagellate Gyrodinium. We investigated molecular evolution, gene duplication and novelty in freshwater sponges compared to marine lineages. Sixty one orthogroups have consilient evidence of positive selection. Transporters (e.g. zinc transporter-2), transcription factors (aristaless-related homeobox) and structural proteins (for example actin-3), alongside other genes, are under strong evolutionary pressure in freshwater, with duplication driving novelty across the Spongillida, but especially in the Lubomirskiidae. This addition to knowledge of freshwater sponge genetics provides a range of tools for understanding the molecular biology and, in the future, the ecology (for example, colonization and migration patterns) of these key species.

zoology↗

bioRxiv2018

Trimitomics: An efficient pipeline for mitochondrial assembly from transcriptomic reads in non-model species

Mitochondrial resources are of known utility to many fields of phylogenetic, population and molecular biology. Their combination of faster and slower-evolving regions and high copy number enables them to be used in many situations where other loci are unsuitable, with degraded samples and after recent speciation events.\n\nThe advent of next-generation sequencing technologies (and notably the Illumina platform) has led to an explosion in the number of samples that can be studied at transcriptomic level, at relatively low cost. Here we describe a robust pipeline for the recovery of mitochondrial genomes from these RNA-seq resources. This pipeline can be used on sequencing of a variety of depths, and reliably recovers the protein coding and ribosomal gene complements of mitochondria from almost any transcriptomic sequencing experiment. The complete sequence of the mitochondrial genome can also be recovered when sequencing is performed in sufficient depth. We evidence the efficacy of our pipeline using data from a number of non-model invertebrates of four disparate phyla, namely Porifera, Nemertea, Mollusca and Annelida. Interestingly, among our poriferan data, where microbiological symbionts are known empirically to make mitochondrial assembly difficult, this pipeline proved especially useful.\n\nOur pipeline will allow the recovery of mitochondrial data from a variety of previously-sequenced samples, and add an additional angle of enquiry to future RNA-seq efforts, simplifying the process of mitochondrial genome assembly for even the most recalcitrant clades and adding this data to the scientific record for a range of future uses.

genomics↗