ParameciumDB 2019: integrating genomic data across the genus for functional and evolutionary biology

Abstract

ParameciumDB (https://paramecium.i2bc.paris-saclay.fr) is a community model organism database for the genome and genetics of the ciliate Paramecium. ParameciumDB development relies on the GMOD (www.gmod.org) toolkit. The ParameciumDB web site has been publicly available since 2006 when the P. tetraurelia somatic genome sequence was released, revealing that a series of whole genome duplications punctuated the evolutionary history of the species. The genome is linked to available genetic data and stocks. ParameciumDB has undergone major changes in its content and website since the last update published in 2011. Genomes from multiple Paramecium species, especially from the P. aurelia complex, are now included in ParameciumDB. A new modern web interface accompanies this transition to a database for the whole Paramecium genus. Gene pages have been enriched with orthology relationships, among the Paramecium species and with a panel of model organisms across the eukaryotic tree. This update also presents expert curation of Paramecium mitochondrial genomes.

Figure 1.

Phylogenetic tree of Paramecium species based on the alignment of all 46 mitochondrial proteins. The tree was built by MAFFT alignment of concatenated protein sequences, where all N- and C-termini are correctly aligned; strict Gblocks curation selects 9135 residues aligned in all species. PhyML aLRT analysis was carried out using the service at https://www.phylogeny.fr with default parameters. This analysis places the caudatum species as closest relatives of the aurelia species. Note the good support for a sexaurelia-sonneborni-jenningsi clade.

Figure 2.

Gene page example. Gene page of ND7, showing the different collapsable sections available for this gene, indicated in the Table of Contents: Overview with general description and cross references, Sequence, Transcription unit structure, Bibliographic references, Protein domain predictions, Homology within Paramecium species and with other organisms, Expression data (RNA-seq, microarray, proteomic), intragenic IES information and information about ND7 alleles, stocks and mutant phenotypes. Selecting proteins adds them to the shopping cart as shown for the Homology section. The shopping cart can be visualized from the User dropdown menu (top right of page) as shown by the inset screenshot at the bottom of the figure. Actions are available for the shopping cart items: multiple alignment (with MUSCLE (34)), expression profiles, submit to a blast at ParameciumDB or NCBI. The items can also be exported, in fasta format by choosing the ‘Sequence(s)’ tab.