Identification of a pseudogene derived from Arr1 in D. ananassae
Authors: Ishtar Olaveja 1; W. Hayden Kee 2; Evan Merkhofer 3; Don Paetkau 4; Wilson Leung 5; Cindy Arrigo 1
Affiliations: 1) New Jersey City University, Jersey City, NJ; 2) California State University Stanislaus, Turlock, CA; 3) Mount Saint Mary College, Newburgh, NY; 4) Saint Mary's College, Notre Dame, IN; 5) Washington University in St. Louis, St. Louis County, MO
Keywords: a. genome evolution; e. heterochromatin
To facilitate investigations into the expansion of the Drosophila ananassae Muller F Element (~19.1 Mb) compared to Drosophila melanogaster (~1.3 Mb), we are manually annotating the protein-coding genes located on the D. ananassae F Element and a ~1.8 Mb region from the D. ananassae Muller D Element. As part of this analysis, we identified a region within scaffold QMES02000178 of the D. ananassae DanaRS2 genome assembly which shows significant sequence similarity to the Arr1 gene in D. melanogaster. Because past studies have shown that more than 90% of the genes remain on the same Muller Element across different Drosophila species, the D. ananassae scaffold QMES02000178 has been tentatively assigned to the D Element based on the protein-coding genes surrounding this Arr1 feature (i.e., CG14109, CG10725, CG10154, CG10713, CG10222, CG33263, flr). In contrast, the Arr1 gene is located on the Muller B Element (chromosome 2L) in D. melanogaster. Analysis based on the evidence provided by computational gene predictors (e.g., genBlastG, GeMoMa, Genscan, Geneid, and Augustus), RNA-seq data, and FlyBase BLASTP search results placed the putative ortholog of Arr1 on scaffold QMES02000007 in the D. ananassae DanaRS2 assembly. The D. ananassae scaffold QMES02000007 has been tentatively assigned to the B Element, suggesting that synteny for Arr1 is preserved between D. melanogaster and D. ananassae. The BLASTX alignments of the genomic regions surrounding the feature on the D. ananassae scaffold QMES02000178 and the protein sequence for D. melanogaster Arr1-PA include multiple frame shifts and in-frame stop codons, thereby supporting the hypothesis that the feature on QMES02000178 is a pseudogene derived from Arr1. The putative Arr1 pseudogene is also flanked by the DNA2-1_DAn and But2 DNA transposons. Future studies will identify and annotate additional pseudogenes located on the D. ananassae F Element and on the euchromatic reference region from the D Element, in order to assess the impact of the expansion of the D. ananassae F Element on the frequency of pseudogenization.