BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database

Abstract

The task of eukaryotic genome annotation remains challenging. Only a few genomes could serve as standards of annotation achieved through a tremendous investment of human curation efforts. Still, the correctness of all alternative isoforms, even in the best-annotated genomes, could be a good subject for further investigation. The new BRAKER2 pipeline generates and integrates external protein support into the iterative process of training and gene prediction by GeneMark-EP+ and AUGUSTUS. BRAKER2 continues the line started by BRAKER1 where self-training GeneMark-ET and AUGUSTUS made gene predictions supported by transcriptomic data. Among the challenges addressed by the new pipeline was a generation of reliable hints to protein-coding exon boundaries from likely homologous but evolutionarily distant proteins. In comparison with other pipelines for eukaryotic genome annotation, BRAKER2 is fully automatic. It is favorably compared under equal conditions with other pipelines, e.g. MAKER2, in terms of accuracy and performance. Development of BRAKER2 should facilitate solving the task of harmonization of annotation of protein-coding genes in genomes of different eukaryotic species. However, we fully understand that several more innovations are needed in transcriptomic and proteomic technologies as well as in algorithmic development to reach the goal of highly accurate annotation of eukaryotic genomes.

Figure 1.

Flowchart of the BRAKER2 pipeline. Input, intermediate and output data are shown by ovals. The tools and processes of the ProtHint pipeline are shown in orange; other components of BRAKER2 are shown in blue.

Figure 2.

Evidence integration in BRAKER2. (A) Target proteins; (B) Introns, gene start and stop sites defined by spliced alignments of target proteins to genome; (C) CDSpart chains; (D) Genome sequence; (E) Genes predicted by GeneMark-EP+ at a given iteration. The high confidence hints are enforced (red arrows); (F) Anchored sites, the splice sites and gene ends predicted ab initio and corroborated by protein hints; (G) Anchored introns and intergenic sequences bounded by anchored gene ends are selected into training of non-coding sequence model for GeneMark-EP+; (H) Anchored multi-exon and single exon genes predicted by GeneMark-EP+ and selected for training AUGUSTUS; (I) Transcripts predicted by AUGUSTUS with support of an external evidence.

Figure 3.

Exon level Sn and Sp determined for each genome in the three runs of BRAKER2 with protein support, the run of BRAKER1 with RNA-seq support and the run of GeneMark-ES. BRAKER2 was run with support of proteins from OrthoDB excluding proteins (i) of the same species, (ii) of all species of the same taxonomic family, (iii) of all species of the same taxonomic order.

Figure 4.

Gene level Sn and Sp determined in the tests described in the legend for Figure 3.