Abstract:
: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.
journal_name
Mol Ecol Resourjournal_title
Molecular ecology resourcesauthors
Shi T,Niu G,Kvitt H,Zheng X,Qin Q,Sun D,Ji Z,Tchernov Ddoi
10.1111/1755-0998.13250subject
Has Abstractpub_date
2021-01-01 00:00:00pages
137-152issue
1eissn
1755-098Xissn
1755-0998journal_volume
21pub_type
杂志文章abstract::Microsatellite loci were identified from the charcoal rot fungus (Macrophomina phaseolina). Primer pairs for 46 loci were developed, and of these, 13 were optimized and screened using genomic DNA from 55 fungal isolates collected predominantly from two soybean fields in Mississippi. Twelve of the optimized loci were p...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02511.x
更新日期:2009-05-01 00:00:00
abstract::We developed four multiplex panels comprising 19 microsatellite loci and tested their amplification in 21 rodent species important for agricultural and conservation management (Microtus, Arvicola, Chionomys). On average, 17.6 loci amplified per species. Number of alleles ranged from 1 to 19 per locus. We report an add...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02521.x
更新日期:2009-05-01 00:00:00
abstract::We isolated and characterized 52 novel microsatellite markers from Florida largemouth bass, Micropterus salmoides floridanus, for use in conservation, management and population genetic studies. Markers were assessed in M. s. floridanus from peninsular Florida (n = 30) and averaged eight alleles per locus with observed...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1471-8286.2007.01917.x
更新日期:2008-01-01 00:00:00
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journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12210
更新日期:2014-05-01 00:00:00
abstract::We describe 10 microsatellite loci for Panulirus argus (Caribbean spiny lobster). The number of alleles at each locus ranged from four to 39 (mean = 21.8) in 89 juvenile specimens collected at two different times at a recruitment site in south Florida. Levels of expected and observed heterozygosities ranged from 0.48 ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1471-8286.2007.02032.x
更新日期:2008-05-01 00:00:00
abstract::Aleppo pine (Pinus halepensis Mill.) is a relevant conifer species for studying adaptive responses to drought and fire regimes in the Mediterranean region. In this study, we performed Illumina next-generation sequencing of two phenotypically divergent Aleppo pine accessions with the aims of (i) characterizing the tran...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12232
更新日期:2014-07-01 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
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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
doi:10.1111/1755-0998.12761
更新日期:2018-03-01 00:00:00
abstract::We report the isolation and characterization of eight microsatellite loci from the scleractinian coral, Acropora nobilis. The microsatellite loci were obtained using compound SSR primers or an enrichment protocol. All the loci were polymorphic with four to eight alleles per locus and observed heterozygosities ranging ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1471-8286.2007.02004.x
更新日期:2008-05-01 00:00:00
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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::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::We implemented multilocus selection in a spatially-explicit, individual-based framework that enables multivariate environmental gradients to drive selection in many loci as a new module for the landscape genetics programs, CDPOP and CDMetaPOP. Our module simulates multilocus selection using a linear additive model, pr...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13121
更新日期:2020-03-01 00:00:00
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
doi:10.1111/1755-0998.12190
更新日期:2014-01-01 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
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journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12474
更新日期:2016-03-01 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
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journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02589.x
更新日期:2009-05-01 00:00:00
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journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02637.x
更新日期:2009-05-01 00:00:00
abstract::Optimal integration of next-generation sequencing into mainstream research requires re-evaluation of how problems can be reasonably overcome and what questions can be asked. One potential application is the rapid acquisition of genomic information to identify microsatellite loci for evolutionary, population genetic an...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02750.x
更新日期:2010-03-01 00:00:00
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
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journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13078
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journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02730.x
更新日期:2010-01-01 00:00:00
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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
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journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13099
更新日期:2020-01-01 00:00:00
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journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02315.x
更新日期:2008-11-01 00:00:00
abstract::Oestrogenic wastewater treatment works (WwTW) effluents discharged into UK rivers have been shown to affect sexual development, including inducing intersex, in wild roach (Rutilus rutilus). This can result in a reduced breeding capability with potential population level impacts. In the absence of a sex probe for roach...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13166
更新日期:2020-07-01 00:00:00
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journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02598.x
更新日期:2009-07-01 00:00:00
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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
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journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1471-8286.2007.01942.x
更新日期:2008-03-01 00:00:00
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journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1471-8286.2007.01885.x
更新日期:2008-01-01 00:00:00