Analysis of 14 BAC sequences from the Aedes aegypti genome: a benchmark for genome annotation and assembly
Autor(es): Lobo, Neil F.; Campbell, Kathy S.; Thaner, Daniel; deBruyn, Becky; Koo, Hean; Gelbart, William M.; Loftus, Brendan J.; Severson, David W.; Collins, Frank H.
Resumo: Aedes aegypti is the principal vector of Yellow fever and Dengue virus throughout the tropical world. To provide a set of manually curated and annotated sequences from the Ae. aegypti genome, 14 mapped BAC clones encompassing 1.57 Mb were sequenced, assembled and manually annotated using a combination of computational gene-finding, EST matches and comparative protein homology. PCR and sequencing were used to experimentally confirm expression and sequence of a subset of these transcripts. Fifty and 43 of the 51 manual annotations demonstrated a high level of similarity to Anopheles gambiae and Drosophila melanogaster genes respectively. Ten of the 12 BAC sequences with more than one annotated gene exhibited synteny with the An. gambiae genome. Putative transcripts from eight BAC clones were found in multiple copies ( two copies in most cases) in the Aedes genome assembly, which point to the probable presence of haplotype polymorphisms and/or misassemblies. This study not only provides a benchmark set of manually annotated transcripts for this genome that can be used to assess the quality of the auto-annotation pipeline and the assembly, but it also looks at the effect of a high repeat content on the genome assembly and annotation pipeline
Palavras-Chave: Yellow fever - Mosquito; Drosophila - Melanogaster; Anopheles - Gambiae; DNA; Organization
Imprenta: Genome Biology, v. 8, n. 5, 2007
Identificador do objeto digital: 10.1186/gb-2007-8-5-r88
Descritores: Aedes aegypti - DNA ; Aedes aegypti - Genome
Data de publicação: 2007
