Affiliation:
1. Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
2. Laboratorio Nacional de la Genómica para la Biodiversidad, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Irapuato, Guanajuato, México
Abstract
Abstract
Three North American cactophilic Drosophila species, D. mojavensis, D. arizonae, and D. navojoa, are of considerable evolutionary interest owing to the shift from breeding in Opuntia cacti to columnar species. The 3 species form the “mojavensis cluster” of Drosophila. The genome of D. mojavensis was sequenced in 2007 and the genomes of D. navojoa and D. arizonae were sequenced together in 2016 using the same technology (Illumina) and assembly software (AllPaths-LG). Yet, unfortunately, the D. navojoa genome was considerably more fragmented and incomplete than its sister species, rendering it less useful for evolutionary genetic studies. The D. navojoa read dataset does not fully meet the strict insert size required by the assembler used (AllPaths-LG) and this incompatibility might explain its assembly problems. Accordingly, when we re-assembled the genome of D. navojoa with the SPAdes assembler, which does not have the strict AllPaths-LG requirements, we obtained a substantial improvement in all quality indicators such as N50 (from 84 kb to 389 kb) and BUSCO coverage (from 77% to 97%). Here we share a new, improved reference assembly for D. navojoa genome, along with a RNAseq transcriptome. Given the basal relationship of the Opuntia breeding D. navojoa to the columnar breeding D. arizonae and D. mojavensis, the improved assembly and annotation will allow researchers to address a range of questions associated with the genomics of host shifts, chromosomal rearrangements and speciation in this group.
Funder
Wellcome Trust
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro
Conselho Nacional de Desenvolvimento Científico e Tecnológico
Consejo Nacional de Ciencia y Tecnología
Publisher
Oxford University Press (OUP)
Subject
Genetics(clinical),Genetics,Molecular Biology,Biotechnology
Cited by
6 articles.
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