MicroAnnot: A Dedicated Workflow for Accurate Microsporidian Genome Annotation

Abstract

With nearly 1700 species, Microsporidia represent a group of obligate intracellular eukaryotes with veterinary, economic and medical impacts. To help understand the biological functions of these microorganisms, complete genome sequencing is routinely used. Nevertheless, the proper prediction of their gene catalogue is challenging due to their taxon-specific evolutionary features. As innovative genome annotation strategies are needed to obtain a representative snapshot of the overall lifestyle of these parasites, the MicroAnnot tool, a dedicated workflow for microsporidian sequence annotation using data from curated databases of accurately annotated microsporidian genes, has been developed. Furthermore, specific modules have been implemented to perform small gene (<300 bp) and transposable element identification. Finally, functional annotation was performed using the signature-based InterProScan software. MicroAnnot's accuracy has been verified by the re-annotation of four microsporidian genomes for which structural annotation had previously been validated. With its comparative approach and transcriptional signal identification method, MicroAnnot provides an accurate prediction of translation initiation sites, an efficient identification of transposable elements, as well as high specificity and sensitivity for microsporidian genes, including those under 300 bp.

Keywords: dedicated workflow; high quality annotation; microsporidia; structural annotation.

Figure 1

Microannot interface. (A) Homepage with the pipeline description. By clicking on help, the user is redirected to MicroAnnot scheme. (B) The analysis section is also available on the homepage. Files containing sequence(s) to be annotated in FASTA format must be loaded onto the application using the select file button. Then, the user can select the minimal size of ORF finding and the parameters used for Glimmer CDS prediction (minimal CDS size and training data set if less than 50 CDS are identified by homology). Here, default parameters are presented for each section. Functional annotation with InterProScan is disabled by default but can be activated by checking the activate box under functional annotation (*).

Figure 2

Web interface seen by the user after job submission. (A) pending, (B) running. (C) When the analysis is finished, different file formats (EMBL, GenBank or GFF) are available for download as well as a warning text file grouping uncertain annotations that must be manually validated. At each step, the sequence name (fasta file) is conserved, along with all the analysis details in the information column.

Figure 3

An overview of the workflow supported by the MicroAnnot pipeline. The different modules, using different bioinformatics programs and databanks, are displayed. A detailed description of each panel and module is provided in the text. Functional analysis by InterProScan, in orange (optional), needs to be selected in the first page of the interface (Figure 1B).