OMIGA: Optimized Maker-Based Insect Genome Annotation

Abstract

Insects are one of the largest classes of animals on Earth and constitute more than half of all living species. The i5k initiative has begun sequencing of more than 5,000 insect genomes, which should greatly help in exploring insect resource and pest control. Insect genome annotation remains challenging because many insects have high levels of heterozygosity. To improve the quality of insect genome annotation, we developed a pipeline, named Optimized Maker-Based Insect Genome Annotation (OMIGA), to predict protein-coding genes from insect genomes. We first mapped RNA-Seq reads to genomic scaffolds to determine transcribed regions using Bowtie, and the putative transcripts were assembled using Cufflink. We then selected highly reliable transcripts with intact coding sequences to train de novo gene prediction software, including Augustus. The re-trained software was used to predict genes from insect genomes. Exonerate was used to refine gene structure and to determine near exact exon/intron boundary in the genome. Finally, we used the software Maker to integrate data from RNA-Seq, de novo gene prediction, and protein alignment to produce an official gene set. The OMIGA pipeline was used to annotate the draft genome of an important insect pest, Chilo suppressalis, yielding 12,548 genes. Different strategies were compared, which demonstrated that OMIGA had the best performance. In summary, we present a comprehensive pipeline for identifying genes in insect genomes that can be widely used to improve the annotation quality in insects. OMIGA is provided at http://ento.njau.edu.cn/omiga.html .

Genome‐wide analysis of chitinase genes and their varied functions in larval moult, pupation and eclosion in the rice striped stem borer, Chilo suppressalis

“…The conserved domain of family 18 chitinases was used to search against the SSB draft genome from the database ChiloDB (Yin et al ., ). This genome was annotated with Optimized Maker based Insect Genome Annotation (OMIGA) (Liu et al ., ). The transcriptome data were used to confirm the sequences and improve the annotation quality.…”

Draft genome of the honey bee ectoparasitic mite, Tropilaelaps mercedesae, is shaped by the parasitic life history

“…Cufflinks (v0.8.2) [69] used the spliced alignments with default setting to reconstruct 44 614 transcripts from which 12 298 transcripts with intact coding sequences were selected by a Perl script developed by Liu et al [70]. Thee ab initio gene prediction programs, including Augustus (v3.0.3) [71], SNAP (v2013-11-29) [72], and Genemarker (v2.3e) [73] were used for de novo gene predictions.…”

Insect genomes: progress and challenges

“…Several different software packages implement this integrated approach, such as augustus (Stanke, 2003), evidencemodeler (Haas et al ., ), glean (Elsik et al ., ), evigan (Liu et al ., ), maker (Cantarel et al ., ), jigsaw (Allen et al ., ) and evigene / evidentialgene (Rago et al ., ). In 2014, an optimized insect genome annotation pipeline, omiga , was developed (Liu et al ., ). In addition to integrating the three streams of evidence, omiga identifies intact coding sequence (CDS) from the assembled transcriptome to retrain the de novo prediction software.…”