EnTAP: Bringing Faster and Smarter Functional Annotation to Non-Model Eukaryotic Transcriptomes

Abstract

EnTAP (Eukaryotic Non-Model Transcriptome Annotation Pipeline) was designed to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model eukaryotes. This software package addresses the fragmentation and related assembly issues that result in inflated transcript estimates and poor annotation rates, while focusing primarily on protein-coding transcripts. Following filters applied through assessment of true expression and frame selection, open-source tools are leveraged to functionally annotate the translated proteins. Downstream features include fast similarity search across three repositories, protein domain assignment, orthologous gene family assessment, and Gene Ontology term assignment. The final annotation integrates across multiple databases and selects an optimal assignment from a combination of weighted metrics describing similarity search score, taxonomic relationship, and informativeness. Researchers have the option to include additional filters to identify and remove contaminants, identify associated pathways, and prepare the transcripts for enrichment analysis. This fully featured pipeline is easy to install, configure, and runs significantly faster than comparable annotation packages. EnTAP is optimized to generate extensive functional information for the gene space of organisms with limited or poorly characterized genomic resources.

The transcriptome of Pinus pinaster under Fusarium circinatum challenge

“…Annotation Both reference transcriptomes were annotated using the Eukaryotic Non-Model Transcriptome Annotation Pipeline (EnTap) version 0.8.2 [44]. Coding regions of the transcripts were selected by GenemarkS-T v5.1 March 2014 [94].…”

The African Bullfrog (Pyxicephalus adspersus) genome unites the two ancestral ingredients for making vertebrate sex chromosomes

“…To distinguish the genes that are shared or unique on the sex chromosomes of the African Bullfrog, we used RNA-Seq data from the same male and female individuals to predict gene models using BRAKER 45 and identified 49,858 gene models. These gene models were filtered and annotated using EnTAP 46 to provide a high confidence set of 14,716 protein-coding gene models: 13,656 for autosomes, 958 for the Z, and 102 for the W chromosome (Supplemental Table S5). The W chromosome had the lowest gene density and of the 102 genes only 8 were W specific.…”

“…(B) A venn diagram shows the distribution of predicted gene models across the W, pseudoautosomal region, and the single copy Z. Listed of annotated protein-coding genes were extracted from EnTAP 46 and cross referenced with coordinates from BRAKER 45 annotation. When the 81 predicted genes that were identified in both W and single copy Z regions were compared, 38% display potential functional degradation in the copy located on the…”

Strategies of tolerance reflected in two North American maple genomes

“…Transcriptome assemblies were conducted de novo with Trinity v2.20 (Grabherr et al, 2011). EnTAP v0.8.0 (Hart et al, 2018) was used to frame-select, functionally annotate, and identify potential contaminants for filtering, including bacteria, archaea, opisthokonta, rhizaria, and fungi. The resulting translated protein sequences were clustered with USEARCH v9.0.2132 (Edgar, 2010) Watanabe, 2005) and gFACs were compared against the genome annotation using GffCompare v0.11.5 (Pertea, 2018).…”