Gene Annotation for a Genome Assembly of the stalk-eyed fly, Teleopsis dalmanni
Abstract
Stalk-eyed flies in the genus Teleopsis are known to carry selfish genetic elements that induce sex ratio (SR) meiotic drive and impact the fitness of male and female carriers. We have recently produced a chromosome-level genome assembly of the stalk-eyed fly, T. dalmanni, to elucidate the pattern of genomic divergence associated with the presence of drive elements. We find evidence for multiple nested inversions along the sex ratio haplotype and widespread differentiation and divergence between the inversion types along the entire X chromosome. We identify several T. dalmanni orthologs of genes involved in genome defense via the piRNA pathway, including core members maelstrom, piwi and Argonaute3, that are diverging in sequence, expression or copy number between the SR and ST chromosomes, and likely influence TE regulation in flies carrying a SR chromosome. This file contains the locations for the expressed genes used in this study.
Notes
This generic feature format (gff) file contains a set of expressed, protein-coding genes annotated from a Teleopsis dalmanni transcriptome assembly (BioProject PRJNA240197) that were aligned to three chromosome-length scaffolds (BioProject PRJNA391339) using GMAP (Wu and Watanabe 2005) allowing for up to 10 gene alignments (“paths”) per gene (--npaths=10 --format=gff3_gene). Annotations were removed as potential transposable elements (TEs) misannotated as genes if they had >50% alignment overlap with any TE annotation from Repmasker.
Baker, R. H., A. Narechania, R. DeSalle, P. M. Johns, J. A. Reinhardt, and G. S. Wilkinson. 2016. Spermatogenesis Drives Rapid Gene Creation and Masculinization of the X Chromosome in Stalk-Eyed Flies (Diopsidae). Genome Biology and Evolution 8:896–914
Wu, T. D., and C. K. Watanabe. 2005. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21:1859–1875.