DOI: 10.5061/dryad.33656
title: Data from: Ultraconserved elements sequencing as a low-cost source of complete mitochondrial genomes and microsatellite markers in non-model amniotes

description: 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.
description: Poospiza cabanisi,
 isolate FRA67, UCE data, raw sequences, end 1Raw sequences resulting
 from sequence capture of 634 UCE loci obtained from Poospiza cabanisi,
 isolate FRA67. End 1 from Illumina paired-end run.Pcabanisi_FRA67_End_1.fastq.gzPoospiza cabanisi, isolate FRA67, UCE data, raw sequences, end 2Raw sequences resulting from sequence capture of 634 UCE loci obtained from Poospiza cabanisi, isolate FRA67. End 2 from Illumina paired-end run.Pcabanisi_FRA67_End_2.fastq.gzPoospiza lateralis, isolate FRA46, UCE data, raw sequences, end 1Raw sequences resulting from sequence capture of 634 UCE loci obtained from Poospiza lateralis, isolate FRA46. End 1 from Illumina paired-end run.Plateralis_FRA46_End_1.fastq.gzPoospiza lateralis, isolate FRA46, UCE data, raw sequences, end 2Raw sequences resulting from sequence capture of 634 UCE loci obtained from Poospiza lateralis, isolate FRA46. End 2 from Illumina paired-end run.Plateralis_FRA46_End_2.fastq.gzPoospiza thoracica, isolate SC04, UCE data, raw sequences, end 1Raw sequences resulting from sequence capture of 634 UCE loci obtained from Poospiza thoracica, isolate SC04. End 1 from Illumina paired-end run.Pthoracica_SC04_End_1.fastq.gzPoospiza thoracica, isolate SC04, UCE data, raw sequences, end 2Raw sequences resulting from sequence capture of 634 UCE loci obtained from Poospiza thoracica, isolate SC04. End 2 from Illumina paired-end run.Pthoracica_SC04_End_2.fastq.gzPoospiza cabanisi, isolate FRA67, assemblyTrinity assembly based on data from sequence capture of 643 UCE loci of Poospiza cabanisi, isolate FRA67.Pcabanisi_FRA67_assembly.fastaPoospiza lateralis, isolate FRA46, assemblyTrinity assembly based on data from sequence capture of 643 UCE loci of Poospiza lateralis, isolate FRA46.Plateralis_FRA46_assembly.fastaPoospiza thoracica, isolate SC04, assemblyTrinity assembly based on data from sequence capture of 643 UCE loci of Poospiza thoracica, isolate SC04.Pthoracica_SC04_assembly.fasta650 probe set used to capture 643 UCE loci650 probesUCE_probeset.xls