Untangling ITS2 genotypes of algal symbionts in zooxanthellate corals.


:Collectively called zooxanthellae, photosynthetic dinoflagellates in the family Symbiodiniaceae are typical endosymbionts that unequivocally mediate coral responses to environmental changes. Symbiodiniaceae are genetically diverse, encompassing at least nine phylogenetically distinct genera (clades A-I). The ribosomal internal transcribed spacer 2 (ITS2) region is commonly utilized for determining Symbiodiniaceae diversity within clades. However, ITS2 is often inadvertently interpreted together with the tailing part of the ribosomal RNA genes (5.8S and 28S or equivalent), leading to unresolved taxonomy and equivocal annotations. To overcome this hurdle, we mined in GenBank and expert reference databases for ITS2 sequences of Symbiodiniaceae having explicit boundaries with adjacent rRNAs. We profiled a Hidden Markov Model of the ITS2-proximal 5.8S-28S rRNA interaction, which was shown to facilitate the delimitation of Symbiodiniaceae ITS2 from GenBank, while considerably reducing sequence ambiguity and redundancy in reference databases. The delineation of ITS2 sequences unveiled intra-clade sequence diversity and inter-clade secondary structure conservation. We compiled the clean data into a non-redundant database that archives the largest number of Symbiodiniaceae ITS2 sequences known to date with definite genotype/subclade representations and well-defined secondary structures. This database provides a fundamental reference catalog for consistent and precise genotyping of Symbiodiniaceae and a tool for automated annotation of user-supplied sequences.


Mol Ecol Resour


Shi T,Niu G,Kvitt H,Zheng X,Qin Q,Sun D,Ji Z,Tchernov D




Has Abstract


2021-01-01 00:00:00












  • A new version of PRT software for sibling groups reconstruction with comments regarding several issues in the sibling reconstruction problem.

    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


    authors: Almudevar A,Anderson EC

    更新日期:2012-01-01 00:00:00

  • Genomic resources notes accepted 1 August 2013-30 September 2013.

    abstract::This article documents the public availability of raw transcriptome sequence data and 63,020 SNPs for the polar bear (Ursus maritimus). ...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章


    authors: Genomic Resources Development Consortium.,Coltman DW,Davis CS,Lunn NJ,Malenfant RM,Richardson ES

    更新日期:2014-01-01 00:00:00

  • A robust, cost-effective method for DNA, RNA and protein co-extraction from soil, other complex microbiomes and pure cultures.

    abstract::The soil microbiome is inherently complex with high biological diversity, and spatial heterogeneity typically occurring on the submillimetre scale. To study the microbial ecology of soils, and other microbiomes, biomolecules, that is, nucleic acids and proteins, must be efficiently and reliably co-recovered from the s...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章


    authors: Thorn CE,Bergesch C,Joyce A,Sambrano G,McDonnell K,Brennan F,Heyer R,Benndorf D,Abram F

    更新日期:2019-03-01 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


    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

  • 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


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

    更新日期:2008-07-01 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


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

    更新日期:2021-01-01 00:00:00

  • Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq).

    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


    authors: Graham CF,Glenn TC,McArthur AG,Boreham DR,Kieran T,Lance S,Manzon RG,Martino JA,Pierson T,Rogers SM,Wilson JY,Somers CM

    更新日期:2015-11-01 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


    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

  • The design and cross-population application of a genome-wide SNP chip for the great tit Parus major.

    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


    authors: Van Bers NE,Santure AW,Van Oers K,De Cauwer I,Dibbits BW,Mateman C,Crooijmans RP,Sheldon BC,Visser ME,Groenen MA,Slate J

    更新日期:2012-07-01 00:00:00

  • Estimating mating rates in wild Drosophila melanogaster females by decay rates of male reproductive proteins in their reproductive tracts.

    abstract::Female Drosophila melanogaster frequently mate with multiple males in nature as shown through parentage analysis. Although polyandry is well documented, we know little about the timing between mating events in wild Drosophila populations due to the challenge of following behaviours of individual females. In this study...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章


    authors: Giardina TJ,Clark AG,Fiumera AC

    更新日期:2017-11-01 00:00:00

  • Let's talk about sex: A rigorous statistical framework to assign the sex of individuals from reduced-representation sequencing data.

    abstract::Molecular markers have been used to identify the sex of sampled individuals for several decades, but the time-consuming development phase prevented their application in many systems. Recently, a growing number of papers have applied reduced-representation sequencing (RRS) protocols to the identification of sex-specifi...

    journal_title:Molecular ecology resources

    pub_type: 评论,新闻


    authors: Moore JS,Benestan L

    更新日期:2018-03-01 00:00:00

  • Polymorphic microsatellite markers in the Melon Fruit Fly, Bactrocera cucurbitae (Coquillett) (Diptera: Tephritidae).

    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


    authors: Wu Y,Li Z,Wu J

    更新日期:2009-09-01 00:00:00

  • Characterization of microsatellite loci in the subsocial spider Stegodyphus lineatus (Araneae: Eresidae).

    abstract::Stegodyphus lineatus spiders live in groups consisting of closely related individuals. There appears to be no discrimination against related individuals as mates but females mate multiply, despite the fact that matings are shown to carry a cost. We have developed eight polymorphic dinucleotide microsatellite markers t...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章


    authors: Bilde T,Tuni C,Cariani A,Santini A,Tabarroni C,Garoia F,Goodacre SL

    更新日期:2009-01-01 00:00:00

  • Real-time PCR to quantify composition of arbuscular mycorrhizal fungal communities--marker design, verification, calibration and field validation.

    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


    authors: Thonar C,Erb A,Jansa J

    更新日期:2012-03-01 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


    authors: Murata C,Ogura G,Kuroiwa A

    更新日期:2011-03-01 00:00:00

  • Applicability of RAD-tag genotyping for interfamilial comparisons: empirical data from two cetaceans.

    abstract::Restriction-site-associated DNA tag (RAD-tag) sequencing has become a popular approach to generate thousands of SNPs used to address diverse questions in population genomics. Comparatively, the suitability of RAD-tag genotyping to address evolutionary questions across divergent species has been the subject of only a f...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章


    authors: Viricel A,Pante E,Dabin W,Simon-Bouhet B

    更新日期:2014-05-01 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


    authors: Kent RJ

    更新日期:2009-01-01 00:00:00

  • The impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters.

    abstract::The ability to detect the identity of a sample obtained from its environment is a cornerstone of molecular ecological research. Thanks to the falling price of shotgun sequencing, genome skimming, the acquisition of short reads spread across the genome at low coverage, is emerging as an alternative to traditional barco...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章


    authors: Rachtman E,Balaban M,Bafna V,Mirarab S

    更新日期:2020-05-01 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


    authors: Wei N,Bemmels JB,Dick CW

    更新日期:2014-09-01 00:00:00

  • Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional and separate models for combined molecular phylogenetic analyses of multilocus sequence data.

    abstract::Proportional and separate models able to apply different combination of substitution rate matrix (SRM) and among-site rate variation model (ASRVM) to each locus are frequently used in phylogenetic studies of multilocus data. A proportional model assumes that branch lengths are proportional among partitions and a separ...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章


    authors: Tanabe AS

    更新日期:2011-09-01 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


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

    更新日期:2008-11-01 00:00:00

  • Permanent genetic resources added to molecular ecology resources database 1 October 2012-30 November 2012.

    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


    authors: Molecular Ecology Resources Primer Development Consortium.,Aksoy S,Almeida-Val VM,Azevedo VC,Baucom R,Bazaga P,Beheregaray LB,Bennetzen JL,Brassaloti RA,Burgess TI,Caccone A,Chang SM,Ciampi AY,Ciancaleoni S,Clímaco GT,Cloue

    更新日期:2013-03-01 00:00:00

  • Attack of the PCR clones: Rates of clonality have little effect on RAD-seq genotype calls.

    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


    authors: Euclide PT,McKinney GJ,Bootsma M,Tarsa C,Meek MH,Larson WA

    更新日期:2020-01-01 00:00:00

  • Development of microsatellite markers in Cordia bifurcata (Boraginaceae) and cross-species amplification in Cordia inermis and Cordia pringlei.

    abstract::We developed 16 microsatellite markers in Cordia bifurcata, a Central and South American shrub. The markers show low polymorphism in C. bifurcata, a species suspected of self-fertilization or apomixis. Of four polymorphic loci, three had only two alleles. However, current research indicates that these markers hold val...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章


    authors: Spoon TR,Kesseli RV

    更新日期:2008-09-01 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


    authors: Cassin-Sackett L

    更新日期:2020-01-01 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


    authors: Ray N,Excoffier L

    更新日期:2010-09-01 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


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

    更新日期:2016-05-01 00:00:00

  • Isolation and characterization of 11 microsatellite primers for a temperate reef fish, the California sheephead (Semicossyphus pulcher).

    abstract::Eleven microsatellites were characterized for Semicossyphus pulcher (California sheephead) using an enrichment protocol. The number of alleles varied from three to 14 for a sample of 40 individuals from two populations. Expected heterozygosities ranged from 0.311 to 0.891. All loci but one were in Hardy-Weinberg equil...

    journal_title:Molecular ecology resources

    pub_type: 杂志文章


    authors: Poortvliet M,Olsen JL,Selkoe KA,Coyer JA,Bernardi G

    更新日期:2009-01-01 00:00:00

  • Microsatellite resources for Passeridae species: a predicted microsatellite map of the house sparrow Passer domesticus.

    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


    authors: Dawson DA,Horsburgh GJ,Krupa AP,Stewart IR,Skjelseth S,Jensen H,Ball AD,Spurgin LG,Mannarelli ME,Nakagawa S,Schroeder J,Vangestel C,Hinten GN,Burke T

    更新日期:2012-05-01 00:00:00

  • DNA barcodes from century-old type specimens using next-generation sequencing.

    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


    authors: Prosser SW,deWaard JR,Miller SE,Hebert PD

    更新日期:2016-03-01 00:00:00