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 Resourjournal_title
Molecular ecology resourcesauthors
Sun X,Ding Y,Orr MC,Zhang Fdoi
10.1111/1755-0998.13146subject
Has Abstractpub_date
2020-05-01 00:00:00issue
3eissn
1755-098Xissn
1755-0998journal_volume
20pub_type
杂志文章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::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
更新日期:2008-05-01 00:00:00
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
更新日期:2013-11-01 00:00:00
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
更新日期:2008-01-01 00:00:00
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
更新日期:2009-01-01 00:00:00
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
更新日期:2009-01-01 00:00:00
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
更新日期:2020-09-01 00:00:00
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
更新日期:2013-11-01 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
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
更新日期:2009-05-01 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::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
更新日期:2008-09-01 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::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
更新日期:2016-05-01 00:00:00
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
更新日期:2021-01-01 00:00:00
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
更新日期:2016-05-01 00:00:00
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
更新日期:2008-07-01 00:00:00
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
更新日期:2016-11-01 00:00:00
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
更新日期:2015-09-01 00:00:00
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
更新日期:2010-01-01 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::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::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::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
更新日期:2008-09-01 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::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
更新日期:2010-07-01 00:00:00
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
更新日期:2008-03-01 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
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
更新日期:2014-09-01 00:00:00
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
更新日期:2013-05-01 00:00:00