title: Ultraconserved Elements Sequencing as a Low-Cost Source of Complete Mitochondrial Genomes and Microsatellite Markers in Non-Model Amniotes.
abstract: Sequence capture of ultraconserved elements (UCEs) associated with massively parallel sequencing has become a common source of nuclear data for studies of animal systematics and phylogeography. However, mitochondrial and microsatellite variation are still commonly used in various kinds of molecular studies, and probably will complement genomic data in years to come. Here we show that besides providing abundant genomic data, UCE sequencing is an excellent source of both sequences for microsatellite loci design and complete mitochondrial genomes with high sequencing depth. Identification of dozens of microsatellite loci and assembly of complete mitogenomes is exemplified here using three species of Poospiza warbling finches from southern and southeastern Brazil. This strategy opens exciting opportunities to simultaneously analyze genome-wide nuclear datasets and traditionally used mtDNA and microsatellite markers in non-model amniotes at no additional cost.
authors.affiliation: Universidade Federal de São Paulo, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Laboratório de Genética Evolutiva, Rua Professor Artur Riedel, 275, Diadema, SP, 09972-270, Brazil.
authors.forename: Fábio
authors.initials: F
authors.lastname: Raposo do Amaral
authors.affiliation: RAPiD Genomics, LLC, 747 SW 2nd Avenue, Gainesville, FL, 32601, United States of America.
authors.forename: Leandro G
authors.initials: LG
authors.lastname: Neves
authors.affiliation: RAPiD Genomics, LLC, 747 SW 2nd Avenue, Gainesville, FL, 32601, United States of America.
authors.forename: Márcio F R
authors.initials: MF
authors.lastname: Resende
authors.affiliation: Universidade Federal de São Paulo, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Laboratório de Genética Evolutiva, Rua Professor Artur Riedel, 275, Diadema, SP, 09972-270, Brazil.
authors.forename: Flávia
authors.initials: F
authors.lastname: Mobili
authors.affiliation: Universidade de São Paulo, Departamento de Genética e Biologia Evolutiva, Rua do Matão, 277, Cidade Universitária, São Paulo, SP, 05508-090, Brazil.
authors.forename: Cristina Y
authors.initials: CY
authors.lastname: Miyaki
authors.affiliation: Universidade Federal de São Paulo, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Laboratório de Genética Evolutiva, Rua Professor Artur Riedel, 275, Diadema, SP, 09972-270, Brazil.
authors.forename: Katia C M
authors.initials: KC
authors.lastname: Pellegrino
authors.affiliation: Universidade Federal do ABC, Centro de Ciências Naturais e Humanas, Rua Arcturus 03, Jardim Antares, São Bernardo do Campo, SP, 09606-070, Brazil.
authors.forename: Cibele
authors.initials: C
authors.lastname: Biondo
mesh_terms: D000818:Animals; D001938:Brazil; D004272:DNA, Mitochondrial / Q000235:genetics; D046369:Finches / Q000235:genetics*; D005819:Genetic Markers / Q000235:genetics*; D054629:Genome, Mitochondrial / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D004272:DNA, Mitochondrial; D005819:Genetic Markers