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Genomic Annotation of Drosophila biarmipes Dot Chromosome Contig 19 (LB531)
Author(s) -
McCullough Austin,
Greuel Brian
Publication year - 2014
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.28.1_supplement.lb531
Subject(s) - contig , biology , genetics , genome , gene , drosophila melanogaster , comparative genomics , genome project , gene prediction , chromosome , genomics , pseudogene , computational biology
Comparative analysis of the genome of Drosophila melanogaster with other Drosophila species at various evolutionary distances can reveal information about differences in euchromatic and heterochromatic gene structure, and how evolutionary processes have changed the expression of genes located in these regions. The goal of this project, performed in conjunction with the Genomics Education Partnership at Washington University, was to annotate all the major features of Drosophila biarmipes dot chromosome Contig 19 ‐ including genes, pseudogenes, and repetitive sequences ‐ to generate a high quality section of the genome of this species. Basic Local Alignment Search Tool (BLAST) was used along with Gene Record Finder to compare the protein sequence of D. melanogaster exons to the D. biarmipes contig in order to locate the placement of the homologous exons in the latter species. Gene predicting programs were used to examine regions of the genome not immediately shown to contain genes. This information was entered into Gene Model Checker to compile a comprehensive map of the contig. Contig 19 is on the fourth (dot) chromosome of Drosophila biarmipes and it contains three genes, Syt7, Rad23 and Zip102B. Both the Syt7 and Rad23 genes showed high sequence conservation with their orthologs in D. melanogaster and are present in the same orientation. The Zip102B gene showed evidence of greater sequence divergence. Consistent RNAseq data and agreement between gene prediction programs led to the conclusion that this sequence divergence was due to the accumulation of point mutations relative to a common ancestral species. The contig displayed a repetitive element percentage of 40.32 percent, which is consistent with a heterochromatic DNA classification. No pseudogenes were identified in this contig. Grant Funding Source : Supported by HHMI grant # 52005780 to SCR Elgin at Washington University (St. Louis).