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PLoS One
2015 Jan 01;109:e0138446. doi: 10.1371/journal.pone.0138446.
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Ultraconserved Elements Sequencing as a Low-Cost Source of Complete Mitochondrial Genomes and Microsatellite Markers in Non-Model Amniotes.
Raposo do Amaral F
,
Neves LG
,
Resende MF
,
Mobili F
,
Miyaki CY
,
Pellegrino KC
,
Biondo C
.
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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.
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???displayArticle.pmcLink???PMC4574942 ???displayArticle.link???PLoS One
Altschul,
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
1997, Pubmed
Altschul,
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
1997,
Pubmed
Armour,
Isolation of human simple repeat loci by hybridization selection.
1994,
Pubmed
Bejerano,
Ultraconserved elements in the human genome.
2004,
Pubmed
Bernt,
MITOS: improved de novo metazoan mitochondrial genome annotation.
2013,
Pubmed
Bolger,
Trimmomatic: a flexible trimmer for Illumina sequence data.
2014,
Pubmed
Brown,
Mitochondrial DNA sequences of primates: tempo and mode of evolution.
1982,
Pubmed
Burns,
Phylogenetics and diversification of tanagers (Passeriformes: Thraupidae), the largest radiation of Neotropical songbirds.
2014,
Pubmed
Chilamakuri,
Performance comparison of four exome capture systems for deep sequencing.
2014,
Pubmed
Crawford,
More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs.
2012,
Pubmed
Edgar,
MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
2004,
Pubmed
Edwards,
Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies.
2000,
Pubmed
Edwards,
Looking forwards or looking backwards in avian phylogeography? A comment on Zink and Barrowclough 2008.
2009,
Pubmed
Estoup,
(CT)n and (GT)n microsatellites: a new class of genetic markers for Salmo trutta L. (brown trout).
1993,
Pubmed
Etter,
Local de novo assembly of RAD paired-end contigs using short sequencing reads.
2011,
Pubmed
Faircloth,
Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera.
2015,
Pubmed
Faircloth,
A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs).
2013,
Pubmed
Faircloth,
Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales.
2012,
Pubmed
Falk,
Mitochondrial disease genetic diagnostics: optimized whole-exome analysis for all MitoCarta nuclear genes and the mitochondrial genome.
2012,
Pubmed
Gardner,
Rise of the machines--recommendations for ecologists when using next generation sequencing for microsatellite development.
2011,
Pubmed
Grabherr,
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
2011,
Pubmed
Griffin,
Accurate mitochondrial DNA sequencing using off-target reads provides a single test to identify pathogenic point mutations.
2014,
Pubmed
Guo,
MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis.
2013,
Pubmed
Harvey,
Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics.
2016,
Pubmed
Jennings,
Multiplexed microsatellite recovery using massively parallel sequencing.
2011,
Pubmed
Jex,
An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes.
2010,
Pubmed
Kearse,
Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.
2012,
Pubmed
Kmiec,
Heteroplasmy as a common state of mitochondrial genetic information in plants and animals.
2006,
Pubmed
Koskinen,
The benefits of increasing the number of microsatellites utilized in genetic population studies: an empirical perspective.
2004,
Pubmed
Langmead,
Fast gapped-read alignment with Bowtie 2.
2012,
Pubmed
Lerner,
Multilocus resolution of phylogeny and timescale in the extant adaptive radiation of Hawaiian honeycreepers.
2011,
Pubmed
Li,
The Sequence Alignment/Map format and SAMtools.
2009,
Pubmed
McCormack,
Applications of next-generation sequencing to phylogeography and phylogenetics.
2013,
Pubmed
Meglécz,
QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects.
2010,
Pubmed
Meiklejohn,
Incongruence among different mitochondrial regions: a case study using complete mitogenomes.
2014,
Pubmed
Miller,
Complete mitochondrial genomes of the New World jacanas: Jacana spinosa and Jacana jacana.
2016,
Pubmed
Pan,
Mitochondrial genome of the Emberiza pusilla (Emberizidae: Emberiza).
2013,
Pubmed
Payne,
Universal heteroplasmy of human mitochondrial DNA.
2013,
Pubmed
Picardi,
Mitochondrial genomes gleaned from human whole-exome sequencing.
2012,
Pubmed
Quinlan,
BEDTools: a flexible suite of utilities for comparing genomic features.
2010,
Pubmed
Raposo do Amaral,
Multilocus tests of Pleistocene refugia and ancient divergence in a pair of Atlantic Forest antbirds (Myrmeciza).
2013,
Pubmed
Ronquist,
MrBayes 3: Bayesian phylogenetic inference under mixed models.
2003,
Pubmed
Samuels,
Finding the lost treasures in exome sequencing data.
2013,
Pubmed
Smith,
Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales.
2014,
Pubmed
Sorenson,
Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates.
1999,
Pubmed
Untergasser,
Primer3--new capabilities and interfaces.
2012,
Pubmed
Vollmer,
The occurrence of mtDNA heteroplasmy in multiple cetacean species.
2011,
Pubmed
Wyman,
Automatic annotation of organellar genomes with DOGMA.
2004,
Pubmed
Yi,
Sequencing of 50 human exomes reveals adaptation to high altitude.
2010,
Pubmed
