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.
Poospiza cabanisi, isolate FRA67, UCE data, raw sequences, end 1
Raw 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.gz
Poospiza cabanisi, isolate FRA67, UCE data, raw sequences, end 2
Raw 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.gz
Poospiza lateralis, isolate FRA46, UCE data, raw sequences, end 1
Raw 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.gz
Poospiza lateralis, isolate FRA46, UCE data, raw sequences, end 2
Raw 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.gz
Poospiza thoracica, isolate SC04, UCE data, raw sequences, end 1
Raw 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.gz
Poospiza thoracica, isolate SC04, UCE data, raw sequences, end 2
Raw 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.gz
Poospiza cabanisi, isolate FRA67, assembly
Trinity assembly based on data from sequence capture of 643 UCE loci of Poospiza cabanisi, isolate FRA67.
Pcabanisi_FRA67_assembly.fasta
Poospiza lateralis, isolate FRA46, assembly
Trinity assembly based on data from sequence capture of 643 UCE loci of Poospiza lateralis, isolate FRA46.
Plateralis_FRA46_assembly.fasta
Poospiza thoracica, isolate SC04, assembly
Trinity assembly based on data from sequence capture of 643 UCE loci of Poospiza thoracica, isolate SC04.
Pthoracica_SC04_assembly.fasta
650 probe set used to capture 643 UCE loci
650 probes
UCE_probeset.xls