TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes

Abstract

In support of the international effort to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline. Its modular architecture allows for the annotation and masking of transposable elements, the structural, and functional annotation of protein-coding genes with an evidence-based quality indexing, and the identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in less than 5 days. It is accessible through a web interface for small scale analyses or through a server for large scale annotations. The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, TriAnnot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 genes based on new biological evidences, increasing the percentage of perfect gene prediction to 63%. TriAnnot systematically showed a higher fitness than other annotation pipelines that are not improved for wheat. As it is easily adaptable to the annotation of other plant genomes, TriAnnot should become a useful resource for the annotation of large and complex genomes in the future.

Pseudogenes and Their Genome-Wide Prediction in Plants

“…Ab initio gene prediction programs such as N-SCAN [65], TWINSCAN [66], FGENESH [67], GeneMark.hmm [68], GENSCAN [69], GlimmerR [70] and some popular and comprehensive pipelines such as MIPS [71] and TriAnnot (specifically designed for wheat [72]) can build gene-like structural models from genomic sequences. However, the models may include both “real” genes and pseudogenes [47].…”

Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia

“…The selected BAC and 11 overlapping BACs belonging to two overlapping contigs (SI Appendix, Table S2) were sequenced using a combination of Illumina and 454 sequencing (SI Appendix, Method S2). Annotation was conducted using "Triannot" (72). The assembled sequence was compared with the 5AL arm database of the IWGSC (39), T. urartu (v1.26 plants.…”

The Barley Uniculme4 Gene Encodes a BLADE-ON-PETIOLE-Like Protein That Controls Tillering and Leaf Patterning

“…The BAC clone HVVMRXALLeA0131P08 was sequenced using Roche/454 Genome Sequencer FLX technology and assembled after the removal of short sequences, adapter and vector trimming, and assembly using a previously described procedure (Steuernagel et al, 2009). The Triannot pipeline gene prediction program (Leroy et al, 2012; http://urgi.versailles.inra.fr/Species/Wheat/TriannotPipeline) was used to annotate potential genes. Genomic markers were developed using the same method as above or insertion site-base polymorphism markers (Paux et al, 2010) using the primers listed in Supplemental Table S3.…”