Abstract:
:Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/.
journal_name
Mol Ecol Resourjournal_title
Molecular ecology resourcesauthors
Fan L,Hui JH,Yu ZG,Chu KHdoi
10.1111/1755-0998.12235subject
Has Abstractpub_date
2014-07-01 00:00:00pages
871-81issue
4eissn
1755-098Xissn
1755-0998journal_volume
14pub_type
杂志文章abstract::Thirty-eight microsatellite loci were developed for the bird pollinated, autohexaploid, Eremophila glabra ssp. glabra. A genomic library was screened with dinucleotide and trinucleotide sequence repeats. Polymorphism ranged from one to 21 alleles per locus. Twenty-four loci exhibited null alleles, based on patterns of...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02618.x
更新日期:2009-07-01 00:00:00
abstract::DNA sourced from faeces is notoriously less reliable than that from tissue. Hence, understanding whether faecal pellet quality varies within faecal piles may be important for sample selection. We hypothesized that the order in which faecal pellets are deposited may influence microsatellite polymerase chain reaction (P...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02582.x
更新日期:2009-05-01 00:00:00
abstract::This article documents the addition of 153 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Brassica oleracea, Brycon amazonicus, Dimorphandra wilsonii, Eupallasella percnurus, Helleborus foetidus, Ipomoea purpurea, Phrynops geoffroanus, Prochilodus...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12061
更新日期:2013-03-01 00:00:00
abstract::Incorporating historical tissues into the study of ecological, conservation and management questions can broaden the scope of population genetic research by enhancing our understanding of evolutionary processes and anthropogenic influences on natural populations. Genotyping historical and low-quality samples has been ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2010.02965.x
更新日期:2011-03-01 00:00:00
abstract::We report the characterization of eight microsatellite markers in the big-headed ant Pheidole megacephala, a pest ant registered in the list of '100 of the world's worst invasive alien species'. An enrichment protocol was used to isolate microsatellite loci, and polymorphism was explored with 36 individuals collected ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02116.x
更新日期:2008-07-01 00:00:00
abstract::Sequence-based specimen identification, known as DNA barcoding, is a common method complementing traditional morphology-based taxonomic assignments. The fundamental resource in DNA barcoding is the availability of a taxonomically reliable sequence database to use as a reference for sequence comparisons. Here, we provi...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12440
更新日期:2016-01-01 00:00:00
abstract::Avian malaria and related haemosporidians (Plasmodium, [Para]Haemoproteus and Leucocytoozoon) represent an exciting multihost, multiparasite system in ecology and evolution. Global research in this field accelerated after the publication in 2000 of PCR protocols to sequence a haemosporidian mitochondrial (mtDNA) barco...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12977
更新日期:2019-03-01 00:00:00
abstract::Streamlining the development and genotyping of microsatellites in species for which no genetic information is available represents an important technical challenge to overcome in order to enable mainstream application of state-of-the-art population genetic analysis techniques in nonmodel organisms. Using the example o...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2011.03002.x
更新日期:2011-07-01 00:00:00
abstract::Microsatellite markers have played a major role in ecological, evolutionary and conservation research during the past 20 years. However, technical constrains related to the use of capillary electrophoresis and a recent technological revolution that has impacted other marker types have brought to question the continued...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12594
更新日期:2017-05-01 00:00:00
abstract::Rhizoprionodon lalandii and R. porosus are widely distributed along the Atlantic coast of the Americas, living close to coastal areas and therefore frequently captured by seaboard fisheries. However, morphological identification of species in this genus is very difficult, especially when sharks have their heads and fi...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02524.x
更新日期:2009-05-01 00:00:00
abstract::Global climate change (GCC) may be causing distribution range shifts in many organisms worldwide. Multiple efforts are currently focused on the development of models to better predict distribution range shifts due to GCC. We addressed this issue by including intraspecific genetic structure and spatial autocorrelation ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13024
更新日期:2019-07-01 00:00:00
abstract::The public availability of large quantities of gene sequence data provides a valuable resource of the mining of Simple Sequence Repeat (SSR) molecular genetic markers for genetic analysis. These markers are inexpensive, require minimal labour to produce and can frequently be associated with functionally annotated gene...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12078
更新日期:2013-05-01 00:00:00
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
更新日期:2011-03-01 00:00:00
abstract::The 'Symphyta' is a paraphyletic assemblage at the base of the order Hymenoptera, comprising 14 families and about 8750 species. All have phytophagous larvae, except for the Orussidae, which are parasitoids. This study presents and evaluates the results of DNA barcoding of approximately 5360 specimens of 'Symphyta', m...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12614
更新日期:2017-07-01 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
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::Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morpholo...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12401
更新日期:2015-11-01 00:00:00
abstract::Fifteen polymorphic markers were developed from a microsatellite-enriched library for the lizard Podarcis gaigeae. The loci were checked for variability in 68 individuals from a population on the island of Skyros, Greece. The number of alleles ranged from 3 to 23 per locus and expected heterozygosity from 0.29 and 0.9...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02550.x
更新日期:2009-05-01 00:00:00
abstract::Simple sequence repeats (SSRs) derived from expressed sequence tags (ESTs) are valuable markers because they represent transcribed regions and often transferable to related taxa. Here, we report the development and characterization of EST-SSRs from Shorea leprosula. Fifty-four sequences containing SSRs were identified...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02238.x
更新日期:2009-01-01 00:00:00
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
更新日期:2009-09-01 00:00:00
abstract::Although nematodes are one of the most diverse metazoan phyla, species identification through morphology is difficult. Several genetic markers have been used for their identification, but most do not provide species-level resolution in all groups, and those that do lack primer sets effective across the phylum, preclud...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12082
更新日期:2013-11-01 00:00:00
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 thi...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02199.x
更新日期:2009-01-01 00:00:00
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
更新日期:2015-07-01 00:00:00
abstract::GONe is a user-friendly, Windows-based program for estimating effective size (N(e) ) in populations with overlapping generations. It uses the Jorde-Ryman modification to the temporal method to account for age structure in populations. This method requires estimates of age-specific survival and birth rate and allele fr...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2011.03057.x
更新日期:2012-01-01 00:00:00
abstract::This article documents the whole genome sequence information of the Indian Zaprionus indianus, a member of the fruit fly family Drosophilidae. The sequences were generated on an Illumina platform and reads and whole genome sequence submitted to NCBI to the SRA and BioProject databases, respectively. This is the first ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12582
更新日期:2017-05-01 00:00:00
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
更新日期:2011-01-01 00:00:00
abstract::We identified microsatellite sequences of potential utility in the house sparrow (Passer domesticus) and assigned their predicted genome locations. These sequences included newly isolated house sparrow loci, which we fully characterized. Many of the newly isolated loci were polymorphic in two other species of Passerid...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2012.03115.x
更新日期:2012-05-01 00:00:00
abstract::The vast amount of phenotypic information collected in some wild animal populations makes them extremely valuable for unravelling the genetics of ecologically important traits and understanding how populations adapt to changes in their environment. Next generation sequencing has revolutionized the development of large...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2012.03141.x
更新日期:2012-07-01 00:00:00
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
更新日期:2015-11-01 00:00:00
abstract::Next-generation sequencing is a common method for analysing microbial community diversity and composition. Configuring an appropriate sequence processing strategy within the variety of tools and methods is a nontrivial task and can considerably influence the resulting community characteristics. We analysed the V4 regi...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12726
更新日期:2018-03-01 00:00:00