Tetrahymena Comparative Genomics Database (TCGD): a community resource for Tetrahymena

Abstract

Ciliates are a large and diverse group of unicellular organisms characterized by having the following two distinct type of nuclei within a single cell: micronucleus (MIC) and macronucleus (MAC). Although the genomes of several ciliates in different groups have been sequenced, comparative genomics data for multiple species within a ciliate genus are not yet available. Here we collected the genome information and comparative genomics analysis results for 10 species in the Tetrahymena genus, including the previously sequenced model organism Tetrahymena thermophila and 9 newly sequenced species, and constructed a genus-level comparative analysis platform, the Tetrahymena Comparative Genomics Database (TCGD). Genome sequences, transcriptomic data, gene models, functional annotation, ortholog groups and synteny maps were built into this database and a user-friendly interface was developed for searching, visualizing and analyzing these data. In summary, the TCGD (http://ciliate.ihb.ac.cn) will be an important and useful resource for the ciliate research community.

Figure 1

Schematic structure of the TCGD. A flow diagram shows the database architecture. Genome sequences, CDS and protein sequences were formatted as a BLAST database. Sequences, annotation information, comparative genomics data and transcriptomic data were stored in the MySQL database. GBrowse and mGSV were used for visualization of genome data and synteny map. Search and visualization allowed user to easily access the data resources in TCGD.

Figure 2

Search functions implemented into TCGD. (A) An integrated search box. (B) Screenshot of search result interface for gene TPYRIF00114600 through the integrated search box. (C) A brief gene description of TPYRIF00114600, including the species the gene belongs to, putative annotation based on NCBI BLAST hits and the gene location.

Figure 3

A gene details page for TPYRIF00114600, showing five types of data. (A) Basic information on the gene, such as the species, putative annotation based on NCBI BLAST hits, and the gene location. (B) A snapshot of the gene structure with a hyperlink to GBrowse. (C) Annotation with InterProScan for protein domains, GO and KEGG function. (D) Homolog information for all 10 species based on OrthoMCL ortholog groups. (E) The predicted CDS and protein sequences.

Figure 4

Visualization of a synteny map in TCGD. (A) The ‘collinear block ID’ or ‘Gene ID’ is inserted into the search box to acquire a synteny map for 10 Tetrahymena species. (B) A summary page shows genome associations and the number of genes for each genome pair for collinear block ID chr4-27. A circular diagram shows a general overview of the associations. To obtain the full synteny display, users can choose to enter either ‘Pairwise view’ or ‘Multiple view’ mode.

Figure 5

Visualization of synteny map in ‘Pairwise view’ mode and ‘Multiple view’ mode. (A) In ‘Pairwise view’ mode, genes are shown as lines between adjacent genomes. Genomes can be rearranged, removed or shown more than once. Genome control panels on the left side of the interface allow the genome viewing range to be adjusted. Master controls at the top apply to all genomes. By using the control panel on the left, users can choose the shape and color of genes. Regions of visible synteny can be filtered based on the numerical criteria specified for genes. (B) In ‘Multiple view’ mode, conserved genes across all selected genomes are shown. The regions associated with one or more specific genome pairs can be hidden using the buttons above the synteny display. Genomes can also be rearranged or removed, and each genome is displayed only once.