title: Heterozygous indels as useful tools in the reconstruction of DNA sequences and in the assessment of ploidy level and genomic constitution of hybrid organisms.
abstract: In this paper we describe a simple approach using double peaks in chromatograms generated as artefacts in the vicinity of heterozygous indels, to identify the specific sequences present in individual strands of a given DNA fragment. This method is useful to assign bases in individuals that are heterozygous at multiple sites. In addition, the relative sizes of the double peaks help to determine the ploidy level and the relative contribution of the parental genomes in hybrids. Our interpretation was confirmed with the analysis of artificial mixtures of DNA of two different species. Results were robust with varying PCR and sequencing conditions. The applicability of this method was demonstrated in hybrids of the Squalius alburnoides complex and in heterozygotes of Chondrostoma oligolepis. Far from being limited to these fish models and the gene where it was tested (beta-actin), this sequence reconstruction methodology is expected to have a broader application.
authors.affiliation: Instituto Superior de Psicologia Aplicada ISPA, Unidade de Investigação em Eco-Etologia, Rua Jardim do Tabaco 34, 1149-041, Lisboa, Portugal. carla.santos@ispa.pt
authors.forename: Carla
authors.initials: C
authors.lastname: Sousa-Santos
authors.forename: Joana I
authors.initials: JI
authors.lastname: Robalo
authors.forename: Maria-João
authors.initials: MJ
authors.lastname: Collares-Pereira
authors.forename: Vitor C
authors.initials: VC
authors.lastname: Almada
mesh_terms: D000818:Animals; D001483:Base Sequence; D002678:Chimera / Q000235:genetics*; D003530:Cyprinidae / Q000235:genetics*; D004274:DNA, Recombinant / Q000235:genetics*; D005260:Female; D016678:Genome; D006579:Heterozygote; D006824:Hybridization, Genetic; D008297:Male; D011003:Ploidies; D013045:Species Specificity
chemical_list: D004274:DNA, Recombinant