Round goby Neogobius melanostomus genome annotation

Annotation file for the round goby genome (sequence deposited as “RGoby_Basel_V2”, BioProject accession PRJNA549924, BioSample SAMN12099445, GenBank genome accession VHKM00000000, release date July 22 2019). 

Supplementary Material S1 for Adrian-Kalchhauser et al, BMC Biology, The round goby genome provides insights into mechanisms that may facilitate biological invasions.

The round goby genome assembly was annotated using Maker v2.31.8. Two iterations were run with assembled transcripts from round goby embryonic tissue and data from eleven other actinopterygian species available in the ENSEMBL database as well as the SwissProt protein set from the uniprot database as evidence (downloaded March 2, 2016). In addition, an initial set of reference sequences obtained from a closely related species, the sand goby (Pomatoschistus minutus), sequenced by the IMAGO marine genomes project of the CeMEB consortium at University of Gothenburg, Sweden was included. The second maker iteration was run after first training the gene modeler SNAP version 2006-07-28 based on the results from the first run. Augustus v3.2.2 was run with initial parameter settings from zebrafish (Danio rerio). Repeat regions in the genome were masked using RepeatMasker known elements and repeat libraries from Repbase as well as de novo identified repeats from the round goby genome assembly obtained from a RepeatModeler analysis.