当前位置： SCI文献检索 > Molecular Ecology Resources期刊下所有文献 > Modelling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species.

Modelling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species.

Abstract：

:DNA microarrays are a popular technique for the detection of microorganisms. Several approaches using specific oligomers targeting one or a few marker genes for each species have been proposed. Data analysis is usually limited to call a species present when its oligomer exceeds a certain intensity threshold. While this strategy works reasonably well for distantly related species, it does not work well for very closely related species: Cross-hybridization of nontarget DNA prevents a simple identification based on signal intensity. The majority of species of the same genus has a sequence similarity of over 90%. For biodiversity studies down to the species level, it is therefore important to increase the detection power of closely related species. We propose a simple, cost-effective and robust approach for biodiversity studies using DNA microarray technology and demonstrate it on scenedesmacean green algae. The internal transcribed spacer 2 (ITS2) rDNA sequence was chosen as marker because it is suitable to distinguish all eukaryotic species even though parts of it are virtually identical in closely related species. We show that by modelling hybridization behaviour with a matrix algebra approach, we are able to identify closely related species that cannot be distinguished with a threshold on signal intensity. Thus this proof-of-concept study shows that by adding a simple and robust data analysis step to the evaluation of DNA microarrays, species detection can be significantly improved for closely related species with a high sequence similarity.

journal_name

Mol Ecol Resour

journal_title

Molecular ecology resources

authors

Engelmann JC,Rahmann S,Wolf M,Schultz J,Fritzilas E,Kneitz S,Dandekar T,Müller T

doi

10.1111/j.1755-0998.2008.02199.x

subject

Has Abstract

pub_date

2009-01-01 00:00:00

pages

83-93

issue

1

eissn

1755-098X

issn

1755-0998

journal_volume

9

pub_type

杂志文章

相关文献

Molecular Ecology Resources文献大全
  • SNP discovery in nonmodel organisms: strand bias and base-substitution errors reduce conversion rates.

    abstract：:Single nucleotide polymorphisms (SNPs) have become the marker of choice for genetic studies in organisms of conservation, commercial or biological interest. Most SNP discovery projects in nonmodel organisms apply a strategy for identifying putative SNPs based on filtering rules that account for random sequencing error...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/1755-0998.12343

    authors： Gonçalves da Silva A,Barendse W,Kijas JW,Barris WC,McWilliam S,Bunch RJ,McCullough R,Harrison B,Hoelzel AR,England PR

    更新日期：2015-07-01 00:00:00

  • Cross-species amplification of Eucalyptus microsatellite loci.

    abstract：:This study examined the interspecific amplification of nuclear microsatellite loci developed mainly for eucalypts in the subgenus Symphyomyrtus across five species within the second most speciose subgenus, subgenus Eucalyptus. A set of eight to 10 loci, depending on taxon, have been identified that are highly variable...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2008.02362.x

    authors： Nevill PG,Reed A,Bossinger G,Vaillancourt RE,Larcombe M,Ades PK

    更新日期：2008-11-01 00:00:00

  • Characterization of microsatellite markers for Sycoscapter nonpollinating fig wasps.

    abstract：:We isolated 18 microsatellites from Sycoscapter australis, a nonpollinating fig wasp that develops in figs of Ficus macrophylla, and assessed their variability in 20 wasps. We further optimized nine of these loci for use in three other Sycoscapter species that develop in Ficus rubiginosa figs and assessed their variab...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2008.02284.x

    authors： Bouteiller-Reuter C,Hale ML,Cook JM

    更新日期：2009-05-01 00:00:00

  • Identification and validation of single nucleotide polymorphisms as tools to detect hybridization and population structure in freshwater stingrays.

    abstract：:Single nucleotide polymorphism (SNP) markers were identified and validated for two stingrays species, Potamotrygon motoro and Potamotrygon falkneri, using double digest restriction-site associated DNA (ddRAD) reads using 454-Roche technology. A total of 226 774 reads (65.5 Mb) were obtained (mean read length 289 ± 183...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/1755-0998.12564

    authors： Cruz VP,Vera M,Pardo BG,Taggart J,Martinez P,Oliveira C,Foresti F

    更新日期：2017-05-01 00:00:00

  • Isolation, characterization and cross-species testing of microsatellites obtained from a sand smelt (Atherina boyeri) genomic library.

    abstract：:This study reports the isolation and characterization of 11 polymorphic microsatellites from a sand smelt (Atherina boyeri) genomic library. Enrichment was performed with di-, tri- and tetranucleotide motifs following the FIASCO procedure (fast isolation by AFLP of sequences containing repeats). All loci were found to...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2008.02366.x

    authors： Milana V,Sola L,Rossi AR,Barbisan F,Congiu L

    更新日期：2009-05-01 00:00:00

  • Chromosome-level assembly of wild Bactrian camel genome reveals organization of immune gene loci.

    abstract：:Camelids are characterized by their unique adaptive immune system that exhibits the generation of homodimeric heavy-chain immunoglobulins, somatic hypermutation of T-cell receptors, and low genetic diversity of major histocompatibility complex (MHC) genes. However, short-read assemblies are typically highly fragmented...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/1755-0998.13141

    authors： Ming L,Wang Z,Yi L,Batmunkh M,Liu T,Siren D,He J,Juramt N,Jambl T,Li Y,Jirimutu

    更新日期：2020-05-01 00:00:00

  • Isolation and characterization of microsatellite loci in tropical forage Stylosanthes capitata Vogel.

    abstract：:Stylosanthes capitata is an important tropical pasture legume. Knowledge of genetic diversity and structure of S. capitata populations is of great importance for the conservation and germplasm management of this species. Thus, eight microsatellite markers were developed from an S. capitata-enriched library. They were ...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2008.02308.x

    authors： Santos MO,Sassaki RP,Chiari L,Resende RM,DE Souza AP

    更新日期：2009-01-01 00:00:00

  • A new set of primers for COI amplification from freshwater microcrustaceans.

    abstract：:Despite the contribution of DNA barcoding towards understanding the biodiversity and distribution of species, the success of COI amplification has been quite variable when it comes to freshwater zooplankton (Elías-Gutiérrez & Valdez-Moreno 2008; Jeffery et al. 2011). Some genera of microcrustaceans seem to be more dif...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/1755-0998.12132

    authors： Prosser S,Martínez-Arce A,Elías-Gutiérrez M

    更新日期：2013-11-01 00:00:00

  • Genomic Resources Notes Accepted 1 June 2015-31 July 2015.

    abstract：:This article documents the public availability of (i) microbiomes in diet and gut of larvae from the dipteran Dilophus febrilis using massive parallel sequencing, (ii) SNP and SSR discovery and characterization in the transcriptome of the Atlantic mackerel (Scomber scombrus, L) and (iii) assembled transcriptome for an...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/1755-0998.12454

    authors： Genomic Resources Development Consortium.,Álvarez P,Arthofer W,Coelho MM,Conklin D,Estonba A,Grosso AR,Helyar SJ,Langa J,Machado MP,Montes I,Pinho J,Rief A,Schartl M,Schlick-Steiner BC,Seeber J,Steiner FM,Vilas C

    更新日期：2015-11-01 00:00:00

  • DNA barcodes of Philippine accipitrids.

    abstract：:DNA barcoding is a molecular method that rapidly identifies an individual to a known taxon or its closest relative based on a 650-bp fragment of the cytochrome c oxidase subunit I (COI). In this study, DNA barcodes of members of the family Accipitridae, including Haliastur indus (brahminy kite), Haliaeetus leucogaster...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2010.02928.x

    authors： Ong PS,Luczon AU,Quilang JP,Sumaya AM,Ibañez JC,Salvador DJ,Fontanilla IK

    更新日期：2011-03-01 00:00:00

  • A multilocus, temperature stress-related gene expression profile assay in Acropora millepora, a dominant reef-building coral.

    abstract：:We report an accurate multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay, capable of reproducing gene expression profiles from 16 target genes [12 genes of interest (GOIs) and four reference genes (RGs)] in Acropora millepora, a common reef-building model coral species. The 12 GOIs ...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2010.02923.x

    authors： Souter P,Bay LK,Andreakis N,Császár N,Seneca FO,van Oppen MJ

    更新日期：2011-03-01 00:00:00

  • A first step towards inferring levels of long-distance dispersal during past expansions.

    abstract：:Improving the realism of spatially explicit demographic models is important for better inferring the history of past populations and for understanding the genetic bases of adaptation and speciation. One particular type of demographic event to take into account is long-distance dispersal (LDD). The goals of this study ...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2010.02881.x

    authors： Ray N,Excoffier L

    更新日期：2010-09-01 00:00:00

  • TECHNICAL ADVANCES: Effects of genotyping protocols on success and errors in identifying individual river otters (Lontra canadensis) from their faeces.

    abstract：:In noninvasive genetic sampling, when genotyping error rates are high and recapture rates are low, misidentification of individuals can lead to overestimation of population size. Thus, estimating genotyping errors is imperative. Nonetheless, conducting multiple polymerase chain reactions (PCRs) at multiple loci is tim...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1471-8286.2007.01992.x

    authors： Hansen H,Ben-David M,McDonald DB

    更新日期：2008-03-01 00:00:00

  • Sequenced RAPD markers to detect hybridization in the barbary partridge (Alectoris barbara, Phasianidae).

    abstract：:In the Alectoris partridges (Phasianidae), hybridization occurs occasionally as a result of the natural breakdown of isolating mechanisms but more frequently as a result of human activity. No genetic record of hybridization is known for the barbary partridge (A. barbara). This species is distributed mostly in North Af...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2010.02880.x

    authors： Barbanera F,Guerrini M,Bertoncini F,Cappelli F,Muzzeddu M,Dini F

    更新日期：2011-01-01 00:00:00

  • Sunflower genetic, genomic and ecological resources.

    abstract：:Long a major focus of genetic research and breeding, sunflowers (Helianthus) are emerging as an increasingly important experimental system for ecological and evolutionary studies. Here, we review the various attributes of wild and domesticated sunflowers that make them valuable for ecological experimentation and descr...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章,评审

    doi：10.1111/1755-0998.12023

    authors： Kane NC,Burke JM,Marek L,Seiler G,Vear F,Baute G,Knapp SJ,Vincourt P,Rieseberg LH

    更新日期：2013-01-01 00:00:00

  • Population structure of Atlantic mackerel inferred from RAD-seq-derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection.

    abstract：:Restriction-site-associated DNA sequencing (RAD-seq) and related methods are revolutionizing the field of population genomics in nonmodel organisms as they allow generating an unprecedented number of single nucleotide polymorphisms (SNPs) even when no genomic information is available. Yet, RAD-seq data analyses rely o...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/1755-0998.12518

    authors： Rodríguez-Ezpeleta N,Bradbury IR,Mendibil I,Álvarez P,Cotano U,Irigoien X

    更新日期：2016-07-01 00:00:00

  • PERMANENT GENETIC RESOURCES: Characterization of microsatellite markers for the almendro (Dipteryx panamensis), a tetraploid rainforest tree.

    abstract：:The almendro (Dipteryx panamensis, Fabaceae) is a tetraploid tree native to the Atlantic lowland rainforests of Central America. We present nine microsatellite primer pairs amplified in three multiplexed reactions for 549 individuals from four sites in Costa Rica. All loci were polymorphic, ranging from three to 13 al...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1471-8286.2007.01980.x

    authors： Hanson TR,Brunsfeld SJ,Finegan B,Waits LP

    更新日期：2008-03-01 00:00:00

  • The chromosome-level genome sequence and karyotypic evolution of Megadenia pygmaea (Brassicaceae).

    abstract：:Karyotypic changes in chromosome number and structure are drivers in the divergent evolution of diverse plant species and lineages. This study aimed to reveal the origins of the unique karyotype (2n = 12) and phylogenetic relationships of the genus Megadenia (Brassicaceae). A high-quality chromosome-scale genome was a...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/1755-0998.13291

    authors： Yang W,Zhang L,Mandáková T,Huang L,Li T,Jiang J,Yang Y,Lysak MA,Liu J,Hu Q

    更新日期：2020-11-05 00:00:00

  • Development of simple sequence repeat markers for the soybean rust fungus, Phakopsora pachyrhizi.

    abstract：:Twenty-four simple sequence repeat markers were developed for Phakopsora pachyrhizi, a fungal pathogen of soybean (Glycine max) and other legumes. All 24 of the loci were evaluated on 28 isolates of P. pachyrhizi. Twenty-one loci were polymorphic, with allelic diversity ranging from two to eight alleles, and null alle...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2008.02272.x

    authors： Anderson SJ,Stone CL,Posada-Buitrago ML,Boore JL,Neelam BA,Stephens RM,Luster DG,Frederick RD,Pedley KF

    更新日期：2008-11-01 00:00:00

  • New microsatellite markers isolated from mungbean (Vigna radiata (L.) Wilczek).

    abstract：:In this study, we reported the isolation and analysis of new polymorphic microsatellites in mungbean (Vigna radiata (L.) Wilczek). Twelve out of 210 primer pairs screened in 30 mungbean accessions gave polymorphism. The polymorphic markers detected two to three alleles per locus with an average of 2.08. Observed heter...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2008.02219.x

    authors： Somta P,Musch W,Kongsamai B,Chanprame S,Nakasathien S,Toojinda T,Sorajjapinun W,Seehalak W,Tragoonrung S,Srinives P

    更新日期：2008-09-01 00:00:00

  • DNA barcoding in Mexico: an introduction.

    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

    authors： Elías-Gutiérrez M,León-Regagnon V

    更新日期：2013-11-01 00:00:00

  • A chromosome-level genome assembly of rice leaffolder, Cnaphalocrocis medinalis.

    abstract：:The rice leaffolder, Cnaphalocrocis medinalis Guenée (Crambidae, Lepidoptera), is an important agricultural pest that causes serious losses to rice production in rice-growing regions with high humidity and temperature. However, a lack of genomic resources limits in-depth understanding of its biological characteristics...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/1755-0998.13274

    authors： Zhao X,Xu H,He K,Shi Z,Chen X,Ye X,Mei Y,Yang Y,Li M,Gao L,Xu L,Xiao H,Liu Y,Lu Z,Li F

    更新日期：2021-02-01 00:00:00

  • Promising protocols for parasites: Metatranscriptomics improves detection of hyperdiverse but low abundance communities.

    abstract：:Genomic technologies continue to shed light on important ecological and evolutionary questions. Nonetheless, these new tools are applied disproportionately in a small fraction of global biodiversity, partly because of technical challenges to studying highly diverse taxa that occur in low abundances in an environment (...

    journal_title：Molecular ecology resources

    pub_type： 新闻

    doi：10.1111/1755-0998.13122

    authors： Cassin-Sackett L

    更新日期：2020-01-01 00:00:00

  • The quest for absolute abundance: The use of internal standards for DNA-based community ecology.

    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

    authors： Harrison JG,John Calder W,Shuman B,Alex Buerkle C

    更新日期：2021-01-01 00:00:00

  • Identification of molecular markers for DNA barcoding in the Aphidiinae (Hym. Braconidae).

    abstract：:Reliable identification of Aphidiinae species (Braconidae) is a prerequisite for conducting studies on aphid-parasitoid interactions at the community level. However, morphological identification of Aphidiinae species remains problematic even for specialists and is almost impossible with larval stages. Here, we compare...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2011.03083.x

    authors： Derocles SA,LE Ralec A,Plantegenest M,Chaubet B,Cruaud C,Cruaud A,Rasplus JY

    更新日期：2012-03-01 00:00:00

  • DNA barcoding of Canada's skates.

    abstract：:DNA-based identifications have been employed across broad taxonomic ranges and provide an especially useful tool in cases where external identification may be problematic. This study explored the utility of DNA barcoding in resolving skate species found in Atlantic Canadian waters. Most species were clearly resolved, ...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2011.03034.x

    authors： Coulson MW,Denti D,Van Guelpen L,Miri C,Kenchington E,Bentzen P

    更新日期：2011-11-01 00:00:00

  • A primer set to determine sex in the small Indian mongoose, Herpestes auropunctatus.

    abstract：:To enable the accurate sexing of individuals of introduced populations of the small Indian mongoose, Herpestes auropunctatus, we designed a primer set for the amplification of the sex-specific fragments EIF2S3Y and EIF2S3X. Using this primer set, the expected amplification products were obtained for all samples of gen...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2010.02931.x

    authors： Murata C,Ogura G,Kuroiwa A

    更新日期：2011-03-01 00:00:00

  • Close relatives in population samples: Evaluation of the consequences for genetic stock identification.

    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

    authors： Östergren J,Palm S,Gilbey J,Dannewitz J

    更新日期：2020-03-01 00:00:00

  • Advancing ecological understandings through technological transformations in noninvasive genetics.

    abstract：:Noninvasive genetic approaches continue to improve studies in molecular ecology, conservation genetics and related disciplines such as forensics and epidemiology. Noninvasive sampling allows genetic studies without disturbing or even seeing the target individuals. Although noninvasive genetic sampling has been used fo...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2009.02699.x

    authors： Beja-Pereira A,Oliveira R,Alves PC,Schwartz MK,Luikart G

    更新日期：2009-09-01 00:00:00

  • De novo characterization of the Timema cristinae transcriptome facilitates marker discovery and inference of genetic divergence.

    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

    authors： Comeault AA,Sommers M,Schwander T,Buerkle CA,Farkas TE,Nosil P,Parchman TL

    更新日期：2012-05-01 00:00:00