Streamlining universal single-copy orthologue and ultraconserved element design: A case study in Collembola.

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 extraction. We have developed and tested a practical workflow for developing genomic resources in nonmodel groups with real-world data on Collembola (springtails), one of the most dominant soil animals on Earth. We designed universal molecular marker sets, single-copy orthologues (BUSCOs) and ultraconserved elements (UCEs), using three existing and 11 newly generated genomes. Both marker types were tested in silico via marker capture success and phylogenetic performance. The new genomes were assembled with Illumina short reads and 9,585-14,743 protein-coding genes were predicted with ab initio and protein homology evidence. We identified 1,997 benchmarking universal single-copy orthologues (BUSCOs) across 14 genomes and created and assessed a custom BUSCO data set for extracting single-copy genes. We also developed a new UCE probe set containing 46,087 baits targeting 1,885 loci. We successfully captured 1,437-1,865 BUSCOs and 975-1,186 UCEs across 14 genomes. Phylogenomic reconstructions using these markers proved robust, giving new insight on deep-time collembolan relationships. Our study demonstrates the feasibility of generating thousands of universal markers from highly efficient whole-genome sequencing, providing a valuable resource for genome-scale investigations in evolutionary biology and ecology.

journal_name

Mol Ecol Resour

authors

Sun X,Ding Y,Orr MC,Zhang F

doi

10.1111/1755-0998.13146

subject

Has Abstract

pub_date

2020-05-01 00:00:00

issue

3

eissn

1755-098X

issn

1755-0998

journal_volume

20

pub_type

杂志文章
  • Genomic sequence capture of haemosporidian parasites: Methods and prospects for enhanced study of host-parasite evolution.

    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

    authors: Barrow LN,Allen JM,Huang X,Bensch S,Witt CC

    更新日期:2019-03-01 00:00:00

  • A microarray system for Y chromosomal and mitochondrial single nucleotide polymorphism analysis in chimpanzee populations.

    abstract::Chimpanzee populations are diminishing as a consequence of human activities, and as a result this species is now endangered. In the context of conservation programmes, genetic data can add vital information, for instance on the genetic diversity and structure of threatened populations. Single nucleotide polymorphisms ...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章

    doi:10.1111/j.1471-8286.2007.02000.x

    authors: Andrés O,Rönn AC,Bonhomme M,Kellermann T,Crouau-Roy B,Doxiadis G,Verschoor EJ,Goossens B,Domingo-Roura X,Bruford MW,Bosch M,Syvänen AC

    更新日期:2008-05-01 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

  • Simple identification of mitochondrial lineages in contact zones based on lineage-selective primers.

    abstract::A variety of research projects focus on genetic variation among and within maternal lineages as encompassed by mitochondrial DNA (mtDNA). While mtDNA often differs substantially between species, large differences may also be found within species. The evaluation of such divergent lineages, for example in intraspecific ...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章

    doi:10.1111/j.1471-8286.2007.01894.x

    authors: Lindell J,Murphy RW

    更新日期:2008-01-01 00:00:00

  • Molecular methods for arthropod bloodmeal identification and applications to ecological and vector-borne disease studies.

    abstract::DNA-based methods have greatly enhanced the sensitivity and specificity of hematophagous arthropod bloodmeal identification. A variety of methods have been applied to study the blood-feeding behaviour of mosquitoes, ticks, black flies and other blood-feeding arthropods as it relates to host-parasite interactions and p...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章

    doi:10.1111/j.1755-0998.2008.02469.x

    authors: Kent RJ

    更新日期:2009-01-01 00:00:00

  • New polymorphic microsatellite loci for the Greek smooth newt, Lissotriton vulgaris graecus, and their utility in the nominotypical subspecies.

    abstract::Eight polymorphic microsatellites were isolated from the Greek smooth newt (Lissotriton vulgaris graecus) using a microsatellite enrichment protocol and selective hybridization with a biotinylated (AC)(11) probe. The loci showed different variation patterns in a single breeding population (32 individuals) with mean nu...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章

    doi:10.1111/j.1755-0998.2008.02245.x

    authors: Sotiropoulos K,Eleftherakos K,Tsaparis D,Kasapidis P,Magoulas A,Legakis A

    更新日期:2009-01-01 00:00:00

  • The case of an arctic wild ass highlights the utility of ancient DNA for validating problematic identifications in museum collections.

    abstract::Museum collections are essential for reconstructing and understanding past biodiversity. Many museum specimens are, however, challenging to identify. Museum samples may be incomplete, have an unusual morphology, or represent juvenile individuals, all of which complicate accurate identification. In some cases, inaccura...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章

    doi:10.1111/1755-0998.13130

    authors: Vershinina AO,Kapp JD,Baryshnikov GF,Shapiro B

    更新日期:2020-09-01 00:00:00

  • DNA barcoding of freshwater rotifera in Mexico: evidence of cryptic speciation in common rotifers.

    abstract::DNA barcodes are useful tools to identify and discover new species in a wide range of taxa. Here, we report the first barcode study of monogonont rotifers from fresh and brackish waters in Mexico, and discuss the taxonomic implications of this work. We used DNA barcodes based on the sequence of cytochrome oxidase I to...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章

    doi:10.1111/1755-0998.12080

    authors: García-Morales AE,Elías-Gutiérrez M

    更新日期:2013-11-01 00:00:00

  • Impact of sequence processing and taxonomic classification approaches on eukaryotic community structure from environmental samples with emphasis on diatoms.

    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

    authors: Hardge K,Neuhaus S,Kilias ES,Wolf C,Metfies K,Frickenhaus S

    更新日期:2018-03-01 00:00:00

  • Microsatellite markers for mungbean developed from sequence database.

    abstract::A novel set of microsatellite markers for mungbean [Vigna radiata (L.) Wilczek] was developed from the public sequence database. Seventy-eight primers were designed and evaluated for polymorphism among 22 cultivated accessions. Eight polymorphic loci detected two to three alleles per locus with an average of 2.25. The...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章

    doi:10.1111/j.1755-0998.2009.02655.x

    authors: Seehalak W,Somta P,Sommanas W,Srinives P

    更新日期:2009-05-01 00:00:00

  • GONe: software for estimating effective population size in species with generational overlap.

    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

    authors: Coombs JA,Letcher BH,Nislow KH

    更新日期:2012-01-01 00:00:00

  • Spatial analysis method (sam): a software tool combining molecular and environmental data to identify candidate loci for selection.

    abstract::sam is a Windows program designed to detect candidate loci for selection in whole-genome scans. It also gives valuable clues as regards the ecological factors at stake in the selection process. The method used is based on multiple univariate logistic regression models to test for association between allelic frequencie...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章

    doi:10.1111/j.1755-0998.2008.02162.x

    authors: Joost S,Kalbermatten M,Bonin A

    更新日期:2008-09-01 00:00:00

  • High-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA.

    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

    authors: De Barba M,Miquel C,Lobréaux S,Quenette PY,Swenson JE,Taberlet P

    更新日期:2017-05-01 00:00:00

  • Development and preliminary evaluation of a genomewide single nucleotide polymorphisms resource generated by RAD-seq for the small yellow croaker (Larimichthys polyactis).

    abstract::Recent advances in high-throughput sequencing technologies have offered the possibility to generate genomewide sequence data to delineate previously unidentified genetic structure, obtain more accurate estimates of demographic parameters and to evaluate potential adaptive divergence. Here, we identified 27 556 single ...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章

    doi:10.1111/1755-0998.12476

    authors: Zhang BD,Xue DX,Wang J,Li YL,Liu BJ,Liu JX

    更新日期:2016-05-01 00:00:00

  • New approaches to species delimitation and population structure of anthozoans: Two case studies of octocorals using ultraconserved elements and exons.

    abstract::As coral populations decline worldwide in the face of ongoing environmental change, documenting their distribution, diversity and conservation status is now more imperative than ever. Accurate delimitation and identification of species is a critical first step. This task, however, is not trivial as morphological varia...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章

    doi:10.1111/1755-0998.13241

    authors: Erickson KL,Pentico A,Quattrini AM,McFadden CS

    更新日期:2021-01-01 00:00:00

  • Characterization of the transcriptome and gene expression of four different tissues in the ecologically relevant sea urchin Arbacia lixula using RNA-seq.

    abstract::The sea urchin Arbacia lixula is a keystone species in Mediterranean ecosystems that drive landscape changes in littoral communities. However, genomic information available for the whole order Arbacioida is very limited. Using RNA-seq techniques, we have characterized the transcriptome of four different tissue types i...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章

    doi:10.1111/1755-0998.12500

    authors: Pérez-Portela R,Turon X,Riesgo A

    更新日期:2016-05-01 00:00:00

  • Ten new microsatellite markers for the buttonwood mangrove (Conocarpus erectus L., Combretaceae).

    abstract::We present 10 microsatellite markers for the buttonwood mangrove, Conocarpus erectus, a wide-range mangrove associate species. Polymorphism was assessed among individuals from six different populations along the Pacific Coast of Mexico and Costa Rica, as well as in two individuals from the Yucatan Peninsula in the Atl...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章

    doi:10.1111/j.1755-0998.2008.02088.x

    authors: Nettel A,Dodd RS,Cid-Becerra JA,DE LA Rosa-Velez J

    更新日期:2008-07-01 00:00:00

  • angsd-wrapper: utilities for analysing next-generation sequencing data.

    abstract::High-throughput sequencing has changed many aspects of population genetics, molecular ecology and related fields, affecting both experimental design and data analysis. The software package angsd allows users to perform a number of population genetic analyses on high-throughput sequencing data. angsd uses probabilistic...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章

    doi:10.1111/1755-0998.12578

    authors: Durvasula A,Hoffman PJ,Kent TV,Liu C,Kono TJ,Morrell PL,Ross-Ibarra J

    更新日期:2016-11-01 00:00:00

  • DNA barcoding of freshwater ichthyoplankton in the Neotropics as a tool for ecological monitoring.

    abstract::Quantifying and classifying ichthyoplankton is one of the most effective ways of monitoring the recruitment process in fishes. However, correctly identifying the fish based on morphological characters is extremely difficult, especially in the early stages of development. We examined ichthyoplankton from tributaries an...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章

    doi:10.1111/1755-0998.12385

    authors: Frantine-Silva W,Sofia SH,Orsi ML,Almeida FS

    更新日期:2015-09-01 00:00:00

  • Assessment of loci for DNA barcoding in the genus Thrips (Thysanoptera:Thripidae).

    abstract::Identification of the juveniles of economically important thrips species on imports by morphology alone can be challenging and culturing is usually required. In the case of EU quarantine species such as Thrips palmi, rapid and accurate identification is essential. DNA barcoding using the Cytochrome oxidase I (COI) gen...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章

    doi:10.1111/j.1755-0998.2009.02723.x

    authors: Glover RH,Collins DW,Walsh K,Boonham N

    更新日期:2010-01-01 00:00:00

  • Multiplex preamplification PCR and microsatellite validation enables accurate single nucleotide polymorphism genotyping of historical fish scales.

    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

    authors: Smith MJ,Pascal CE,Grauvogel Z,Habicht C,Seeb JE,Seeb LW

    更新日期:2011-03-01 00:00:00

  • A factorial design experiment as a pilot study for noninvasive genetic sampling.

    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

    authors: Renan S,Speyer E,Shahar N,Gueta T,Templeton AR,Bar-David S

    更新日期:2012-11-01 00:00:00

  • Development of microsatellite markers in the St Lucia anole, Anolis luciae.

    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

    authors: Johansson H,Surget-Groba Y,Gow JL,Thorpe RS

    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

  • Characterization of polymorphic microsatellite DNA markers in Hakea oldfieldii Benth. (Proteaceae).

    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

    authors: Byrne M,Hankinson M

    更新日期:2009-07-01 00:00:00

  • A PCR-RFLP assay for gender assignment in the three-toed sloths (Bradypus, Pilosa, Bradypodidae).

    abstract::The three-toed sloths (Bradypus) are slow-moving arboreal neotropical mammals. Understanding demographic variables (such as sex ratio) of populations is a key for conservation purposes. Nevertheless, gender assignment of Bradypus is particularly challenging because of the lack of sexual dimorphism in infants and in ad...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章

    doi:10.1111/j.1755-0998.2009.02820.x

    authors: Martinelli AB,DE Moraes-Barros N,Alvarenga CS,Chaves PB,Santos LA,Fagundes V

    更新日期:2010-07-01 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

  • 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

  • The effects of read length, quality and quantity on microsatellite discovery and primer development: from Illumina to PacBio.

    abstract::The advent of next-generation sequencing (NGS) technologies has transformed the way microsatellites are isolated for ecological and evolutionary investigations. Recent attempts to employ NGS for microsatellite discovery have used the 454, Illumina, and Ion Torrent platforms, but other methods including single-molecule...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章

    doi:10.1111/1755-0998.12245

    authors: Wei N,Bemmels JB,Dick CW

    更新日期:2014-09-01 00:00:00

  • De novo transcriptomic analyses for non-model organisms: an evaluation of methods across a multi-species data set.

    abstract::High-throughput sequencing (HTS) is revolutionizing biological research by enabling scientists to quickly and cheaply query variation at a genomic scale. Despite the increasing ease of obtaining such data, using these data effectively still poses notable challenges, especially for those working with organisms without ...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章

    doi:10.1111/1755-0998.12077

    authors: Singhal S

    更新日期:2013-05-01 00:00:00