TOA: A software package for automated functional annotation in non‐model plant species

Abstract

The increase of sequencing capacity provided by high‐throughput platforms has made it possible to routinely obtain large sets of genomic and transcriptomic sequences from model and non‐model organisms. Subsequent genomic analysis and gene discovery in next‐generation sequencing experiments are, however, bottlenecked by functional annotation. One common way to perform functional annotation of sets of sequences obtained from next‐generation sequencing experiments, is by searching for homologous sequences and accessing the related functional information deposited in genomic databases. Functional annotation is especially challenging for non‐model organisms, like many plant species. In such cases, existing free and commercial general‐purpose applications may not offer complete and accurate results. We present TOA (Taxonomy‐oriented annotation), a Python‐based user‐friendly open source application designed to establish functional annotation pipelines geared towards non‐model plant species that can run in Linux/Mac computers, HPCs and cloud servers. TOA performs homology searches against proteins stored in the PLAZA databases, NCBI RefSeq Plant, Nucleotide Database and Non‐Redundant Protein Sequence Database, and outputs functional information from several ontology systems: Gene Ontology, InterPro, EC, KEGG, Mapman and MetaCyc. The software performance was validated by comparing the runtimes, total number of annotated sequences and accuracy of the functional information obtained for several plant benchmark data sets with TOA and other functional annotation solutions. TOA outperformed the other software in terms of number of annotated sequences and accuracy of the annotation and constitutes a good alternative to improve functional annotation in plants. TOA is especially recommended for gymnosperms or for low quality sequence data sets of non‐model plants.

Transcriptomic Complexity in Strawberry Fruit Development and Maturation Revealed by Nanopore Sequencing

“…Those transcripts with a log2 -old difference ≥2 or ≤ -2 and the Benjamini–Hochberg (BH) adjusted p < 0.01 were selected. Functional annotation of the isoforms was conducted through Blastp sequentially against plant proteins stored in the PLAZA4.0, NCBI RefSeq plant, and NCBI non-redundant protein sequence database (release 20210620) by using the TOA pipeline (Mora-Márquez et al, 2021 ). Significant isoform switch events were detected by identifying occurrences of the isoform relative abundance change (|dIF| > 0.1 and FDR < 0.05) between replicated stages in the R package IsoformSwitchAnalyzeR (v1.14.0) (Vitting-Seerup et al, 2019 ).…”

A simple guide to de novo transcriptome assembly and annotation

“…(Taxonomy-oriented Annotation) [ 201 ] and [ 202 , 203 ] are transcriptome annotation platforms with a focus on plant species. The former is a platform-agnostic, offline tool while the latter is a web server that requires registration.…”

NGScloud2: optimized bioinformatic analysis using Amazon Web Services

“…For functional annotation with TOA, the main hardware limitations are produced in the BLAST+ or DIAMOND homology search step that requires a minimum of 4 CPUs and 32 GiB instances for small datasets, but larger instance types are required for bigger datasets (e.g., a full transcriptome) or to reduce runtimes. It should be also noted that DIAMOND pipelines can be run in shorter times than BLAST+ pipelines (Buchfink, Xie & Huson, 2015;Mora-Márquez et al, 2021). A sufficient provision of storage volumes is also recommended to run the functional annotation workflow, to take full advantage of TOA capabilities.…”

“…As a last improvement over the original version, NGScloud2 encapsulates our standalone application TOA (Taxonomy-oriented annotation) (Mora-Márquez et al, 2021), so it can run in EC2. This application automates the extraction of functional information from genomic databases, both plant specific (PLAZA) and general-purpose genomic databases (NCBI RefSeq and NR/NT), and the annotation of sequences (Fig.…”