Abstract:
:For nonmodel organisms, genome-wide information that describes functionally relevant variation may be obtained by RNA-Seq following de novo transcriptome assembly. While sequencing has become relatively inexpensive, the preparation of a large number of sequencing libraries remains prohibitively expensive for population genetic analyses of nonmodel species. Pooling samples may be then an attractive alternative. To test whether pooled RNA-Seq accurately predicts true allele frequencies, we analysed the liver transcriptomes of 10 bank voles. Each sample was sequenced both as an individually barcoded library and as a part of a pool. Equal amounts of total RNA from each vole were pooled prior to mRNA selection and library construction. Reads were mapped onto the de novo assembled reference transcriptome. High-quality genotypes for individual voles, determined for 23,682 SNPs, provided information on 'true' allele frequencies; allele frequencies estimated from the pool were then compared with these values. 'True' frequencies and those estimated from the pool were highly correlated. Mean relative estimation error was 21% and did not depend on expression level. However, we also observed a minor effect of interindividual variation in gene expression and allele-specific gene expression influencing allele frequency estimation accuracy. Moreover, we observed strong negative relationship between minor allele frequency and relative estimation error. Our results indicate that pooled RNA-Seq exhibits accuracy comparable with pooled genome resequencing, but variation in expression level between individuals should be assessed and accounted for. This should help in taking account the difference in accuracy between conservatively expressed transcripts and these which are variable in expression level.
journal_name
Mol Ecol Resourjournal_title
Molecular ecology resourcesauthors
Konczal M,Koteja P,Stuglik MT,Radwan J,Babik Wdoi
10.1111/1755-0998.12186subject
Has Abstractpub_date
2014-03-01 00:00:00pages
381-92issue
2eissn
1755-098Xissn
1755-0998journal_volume
14pub_type
杂志文章abstract::Pedigree reconstruction using genotypic markers has become an important tool for the study of natural populations. The nonstandard nature of the underlying statistical problems has led to the necessity of developing specialized statistical and computational methods. In this article, a new version of pedigree reconstru...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2011.03061.x
更新日期:2012-01-01 00:00:00
abstract::Our understanding of Glossina fuscipes fuscipes, a major vector of sleeping sickness, has been severely constrained by a lack of genetic markers for mapping and population genetic studies. Here we present 10 newly developed microsatellite loci for this tsetse species. Heterozygosity levels in Moyo, an Ugandan populati...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02328.x
更新日期:2008-11-01 00:00:00
abstract::Noninvasive genetic sampling has increasingly been used in ecological and conservation studies during the last decade. A major part of the noninvasive genetic literature is dedicated to the search for optimal protocols, by comparing different methods of collection, preservation and extraction of DNA from noninvasive m...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2012.03170.x
更新日期:2012-11-01 00:00:00
abstract::Single-nucleotide polymorphisms (SNPs) have potential for broad application in population and conservation genetics, but availability of these markers is limited in many nonmodel species. In this study, genomic and expressed sequence tagged (EST) sequences from closely related salmonids (Chinook salmon and rainbow tro...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2011.02977.x
更新日期:2011-03-01 00:00:00
abstract::Quantitative real-time PCR (qPCR) is slowly becoming established as a tool to quantify abundance of different arbuscular mycorrhizal fungal (AMF) taxa in roots and in soil. Here, we describe the development and field validation of qPCR markers (i.e. primers with associated hydrolysis probes), targeting taxon-specific ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2011.03086.x
更新日期:2012-03-01 00:00:00
abstract::Bactrocera cucurbitae (Coquillett) is an important insect pest of melon fruit causing extensive losses of production in Asia and Pacific areas. Twelve polymorphic microsatellite loci were isolated from an enriched DNA library of this species and their amplification characteristics are described. Genetic parameters wer...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02678.x
更新日期:2009-09-01 00:00:00
abstract::Degraded DNA from suboptimal field sampling is common in molecular ecology. However, its impact on techniques that use restriction site associated next-generation DNA sequencing (RADSeq, GBS) is unknown. We experimentally examined the effects of in situDNA degradation on data generation for a modified double-digest RA...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12404
更新日期:2015-11-01 00:00:00
abstract::The mitochondrial CO1 gene (cytochrome c oxidase I) is a widely accepted metazoan barcode region. In insects, the mitochondrial NADH dehydrogenase subunit 1 (ND1) gene region has proved to be another suitable marker especially for the identification of lower level taxonomic entities such as populations and sister spec...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12125
更新日期:2013-11-01 00:00:00
abstract::Adaptation to different ecological environments can promote speciation. Although numerous examples of such 'ecological speciation' now exist, the genomic basis of the process, and the role of gene flow in it, remains less understood. This is, at least in part, because systems that are well characterized in terms of th...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2012.03121.x
更新日期:2012-05-01 00:00:00
abstract::Genomic data sets are increasingly central to ecological and evolutionary biology, but far fewer resources are available for invertebrates. Powerful new computational tools and the rapidly decreasing cost of Illumina sequencing are beginning to change this, enabling rapid genome assembly and reference marker extractio...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13146
更新日期:2020-05-01 00:00:00
abstract::DNA barcoding has become an important current scientific trend to the understanding of the world biodiversity. In the case of mega-diverse hot spots like Mexico, this technique represents an important tool for taxonomists, allowing them to concentrate in highlighted species by the barcodes instead of analyzing entire ...
journal_title:Molecular ecology resources
pub_type:
doi:10.1111/1755-0998.12149
更新日期:2013-11-01 00:00:00
abstract::Mosquitoes belonging to the Culex pipiens complex are primary vectors for diseases such as West Nile encephalitis, Eastern equine encephalitis, many arboviruses, as well as lymphatic filariases. Despite sharing physiological characteristics, each mosquito species within the Culex complex has unique behavioural and rep...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12083
更新日期:2013-05-01 00:00:00
abstract::We developed nine new nuclear dinucleotide microsatellite loci for Castor canadensis. All loci were polymorphic, except for one. The number of alleles ranged from two to four and from five to 12 in populations from Arizona and Wisconsin, respectively. Average heterozygosity ranged from 0.13 to 0.86 per locus. Since cr...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02364.x
更新日期:2009-03-01 00:00:00
abstract::DNA extraction from minute hymenopterans and their larvae is difficult and challenging because of their small size indicating a low amount of starting material. Hence, 11 DNA extraction methods were compared to determine their efficacy in isolating DNA. Success of each method was scored on a 2% agarose gel after PCR o...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2011.03074.x
更新日期:2012-01-01 00:00:00
abstract::Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough to split data sets as large 104 sequences into putative species in several minutes. Although grounded in evolutionary t...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13281
更新日期:2021-02-01 00:00:00
abstract::Microsatellite markers were developed to assess population structure and patterns of translocation in the introduced European common genet (Genetta genetta). Primer pairs were designed for 60 microsatellite sequences enriched for CA, GA, CATC and TAGA repeat motifs. Eleven loci that proved to be polymorphic were genot...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02277.x
更新日期:2008-11-01 00:00:00
abstract::A genomic library was constructed and 13 polymorphic microsatellite markers were developed for Hakea oldfieldii, a woody shrub endemic to southwest Western Australia. Polymorphism was investigated for these markers in 28 individuals from a single population located in restricted habitat at the base of the Whicher Rang...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02616.x
更新日期:2009-07-01 00:00:00
abstract::Mites (Acari) are one of the most diverse groups of life on Earth; yet, their evolutionary relationships are poorly understood. Also, the resolution of broader arachnid phylogeny has been hindered by an underrepresentation of mite diversity in phylogenomic analyses. To further our understanding of Acari evolution, we ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12962
更新日期:2019-03-01 00:00:00
abstract::The 'One Health' framework emphasizes the ecological relationships between soil, plant, animal and human health. Microbiomes play important roles in these relationships, as they modify the health and performance of the different compartments and influence the transfer of energy, matter and chemicals between them. Stan...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13215
更新日期:2020-11-01 00:00:00
abstract::Anolis lizards are important models in studies of ecology and evolution. Here we describe 13 polymorphic microsatellites for use in population screening in the St Lucia anole, Anolis luciae, that can be used as a natural replicate to Anolis roquet on Martinique to study processes involved in population differentiation...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02206.x
更新日期:2008-11-01 00:00:00
abstract::Type specimens have high scientific importance because they provide the only certain connection between the application of a Linnean name and a physical specimen. Many other individuals may have been identified as a particular species, but their linkage to the taxon concept is inferential. Because type specimens are o...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12474
更新日期:2016-03-01 00:00:00
abstract::Plastid sequencing is an essential tool in the study of plant evolution. This high-copy organelle is one of the most technically accessible regions of the genome, and its sequence conservation makes it a valuable region for comparative genome evolution, phylogenetic analysis and population studies. Here, we discuss re...
journal_title:Molecular ecology resources
pub_type: 杂志文章,评审
doi:10.1111/1755-0998.12626
更新日期:2017-09-01 00:00:00
abstract::We report the development of 10 polymorphic molecular markers containing short tandem repeats in the cosmopolitan reef-building coral, Pocillopora damicornis, an important model species for coral health, physiology, ecology, and genetics. The availability of polymorphic DNA markers in P. damicornis can act as impetus ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1471-8286.2007.02017.x
更新日期:2008-05-01 00:00:00
abstract::We isolated and characterized 52 novel microsatellite markers from Florida largemouth bass, Micropterus salmoides floridanus, for use in conservation, management and population genetic studies. Markers were assessed in M. s. floridanus from peninsular Florida (n = 30) and averaged eight alleles per locus with observed...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1471-8286.2007.01917.x
更新日期:2008-01-01 00:00:00
abstract::Ecological understanding of the role of consumer-resource interactions in natural food webs is limited by the difficulty of accurately and efficiently determining the complex variety of food types animals have eaten in the field. We developed a method based on DNA metabarcoding multiplexing and next-generation sequenc...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12188
更新日期:2014-03-01 00:00:00
abstract::This article documents the public availability of approximately 15 000 polymorphic SNP loci for the bighorn sheep Ovis canadensis. ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12142
更新日期:2013-09-01 00:00:00
abstract::Aleppo pine (Pinus halepensis Mill.) is a relevant conifer species for studying adaptive responses to drought and fire regimes in the Mediterranean region. In this study, we performed Illumina next-generation sequencing of two phenotypically divergent Aleppo pine accessions with the aims of (i) characterizing the tran...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12232
更新日期:2014-07-01 00:00:00
abstract::Interpretation of high-throughput sequence data requires an understanding of how decisions made during bioinformatic data processing can influence results. One source of bias that is often cited is PCR clones (or PCR duplicates). PCR clones are common in restriction site-associated sequencing (RAD-seq) data sets, whic...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13087
更新日期:2020-01-01 00:00:00
abstract::Determining the origin of individuals in mixed population samples is key in many ecological, conservation and management contexts. Genetic data can be analyzed using genetic stock identification (GSI), where the origin of single individuals is determined using Individual Assignment (IA) and population proportions are ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13131
更新日期:2020-03-01 00:00:00
abstract::To characterize microbiomes and other ecological assemblages, ecologists routinely sequence and compare loci that differ among focal taxa. Counts of these sequences convey information regarding the occurrence and relative abundances of taxa, but provide no direct measure of their absolute abundances, due to the techni...
journal_title:Molecular ecology resources
pub_type: 杂志文章,评审
doi:10.1111/1755-0998.13247
更新日期:2021-01-01 00:00:00