UniPrime: a workflow-based platform for improved universal primer design

Bekaert, Michaël; Teeling, Emma C.

doi:10.1093/nar/gkn191

Cited by 21 publications

(22 citation statements)

References 28 publications

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“…Seventeen cross‐species PCR primers (Table S5) were designed using parameters detailed in Bekaert and Teeling () and primer3 (Rozen and Skaletsky ) to amplify regions of Tecta and Pou3f4 in 38 mammals (Table S3). The taxa chosen for amplification and sequencing of homologous regions were primarily bats (20 echolocating bats from both subordinal clades, five nonecholocating pteropodid bats) and representatives of all other mammalian superordinal groups.…”

Section: Methodsmentioning

confidence: 99%

A phylomedicine approach to understanding the evolution of auditory sensory perception and disease in mammals

Kirwan

Bekaert

Commins

et al. 2013

Evolutionary Applications

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Hereditary deafness affects 0.1% of individuals globally and is considered as one of the most debilitating diseases of man. Despite recent advances, the molecular basis of normal auditory function is not fully understood and little is known about the contribution of single-nucleotide variations to the disease. Using crossspecies comparisons of 11 'deafness' genes (Myo15, Ush1 g, Strc, Tecta, Tectb, Otog, Col11a2, Gjb2, Cldn14, Kcnq4, Pou3f4) across 69 evolutionary and ecologically divergent mammals, we elucidated whether there was evidence for: (i) adaptive evolution acting on these genes across mammals with similar hearing capabilities; and, (ii) regions of long-term evolutionary conservation within which we predict disease-associated mutations should occur. We find evidence of adaptive evolution acting on the eutherian mammals in Myo15, Otog and Tecta. Examination of selection pressures in Tecta and Pou3f4 across a taxonomic sample that included a wide representation of auditory specialists, the bats, did not uncover any evidence for a role in echolocation. We generated 'conservation indices' based on selection estimates at nucleotide sites and found that known disease mutations fall within sites of high evolutionary conservation. We suggest that methods such as this, derived from estimates of evolutionary conservation using phylogenetically divergent taxa, will help to differentiate between deleterious and benign mutations.

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Section: Methodsmentioning

confidence: 99%

A phylomedicine approach to understanding the evolution of auditory sensory perception and disease in mammals

Kirwan

Bekaert

Commins

et al. 2013

Evolutionary Applications

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“…To amplify regions of interest across the study species, degenerate primers were designed using 'Uniprime' (Bekaert and Teeling, 2008) (see Supplementary Materials and Methods for details). For Tmc1, the primers amplified a region (corresponding to human exons 16 to 17) that has been implicated in deafness in mice (Kurima et al, 2002).…”

Section: Dna Isolation Primer Design Amplification and Sequencingmentioning

confidence: 99%

Parallel signatures of sequence evolution among hearing genes in echolocating mammals: an emerging model of genetic convergence

et al. 2011

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Recent findings of sequence convergence in the Prestin gene among some bats and cetaceans suggest that parallel adaptations for high-frequency hearing have taken place during the evolution of echolocation. To determine if this gene is an exception, or instead similar processes have occurred in other hearing genes, we have examined Tmc1 and Pjvk, both of which are associated with non-syndromic hearing loss in mammals. These genes were amplified and sequenced from a number of mammalian species, including echolocating and non-echolocating bats and whales, and were analysed together with published sequences. Sections of both genes showed phylogenetic signals that conflicted with accepted species relationships, with coding regions uniting laryngeal echolocating bats in a monophyletic clade. Bayesian estimates of posterior probabilities of convergent and divergent substitutions provided more direct evidence of sequence convergence between the two groups of laryngeal echolocating bats as well as between echolocating bats and dolphins. We found strong evidence of positive selection acting on some echolocating bat species and echolocating cetaceans, contrasting with purifying selection on non-echolocating bats. Signatures of sequence convergence and molecular adaptation in two additional hearing genes suggest that the acquisition of high-frequency hearing has involved multiple loci.

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“…For the purposes of DNA metabarcoding primer design, this software family is interesting largely for its utility during the final step of the primer design in, in which it can be used to check the thermodynamical properties of primers designed by other programs. UniPrime (Bekaert & Teeling 2008) and Primaclade (Gadberry et al. 2005) work on multiple alignments of short sequences (i.e.…”

Section: Finding and Testing Suitable Dna Metabarcodesmentioning

confidence: 99%

Bioinformatic challenges for DNA metabarcoding of plants and animals

2012

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Almost all empirical studies in ecology have to identify the species involved in the ecological process under examination. DNA metabarcoding, which couples the principles of DNA barcoding with next generation sequencing technology, provides an opportunity to easily produce large amounts of data on biodiversity. Microbiologists have long used metabarcoding approaches, but use of this technique in the assessment of biodiversity in plant and animal communities is under‐explored. Despite its relationship with DNA barcoding, several unique features of DNA metabarcoding justify the development of specific data analysis methodologies. In this review, we describe the bioinformatics tools available for DNA metabarcoding of plants and animals, and we revisit others developed for DNA barcoding or microbial metabarcoding. We also discuss the principles and associated tools for evaluating and comparing DNA barcodes in the context of DNA metabarcoding, for designing new custom‐made barcodes adapted to specific ecological question, for dealing with PCR and sequencing errors, and for inferring taxonomical data from sequences.

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UniPrime: a workflow-based platform for improved universal primer design

Cited by 21 publications

References 28 publications

A phylomedicine approach to understanding the evolution of auditory sensory perception and disease in mammals

A phylomedicine approach to understanding the evolution of auditory sensory perception and disease in mammals

Parallel signatures of sequence evolution among hearing genes in echolocating mammals: an emerging model of genetic convergence

Bioinformatic challenges for DNA metabarcoding of plants and animals

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