Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2010 – 30 September 2010

Aggarwal, Ramesh K.; Allainguillaume, Joël; Bajay, Miklos Maximiliano; Barthwal, Santan; Bertolino, Paola; Chauhan, Priti; Consuegra, Sofía; Croxford, Adam E.; Dalton, Desiré L.; Belder, E. den; Díaz-Ferguson, Edgardo; Douglas, Margaret R.; Drees, Michael; Elderson, J.; Esselink, G.; Fernández-Manjarrés, Juan F.; Frascaria‐Lacoste, Nathalie; Gäbler‐Schwarz, Steffi; Leániz, Carlos García de; Ginwal, H. S.; Goodisman, Michael A. D.; Guo, Bin; Hamilton, Matthew B.; Hayes, Paul K.; Hong, Yan; Kajita, Tadashi; Kalinowski, Steven T.; Keller, Laurent; Koop, Ben F.; Kotzé, Antoinette; Lalremruata, Albert; Leese, Florian; Li, Chunhong; Liew, W. Y.; Martinelli, Samuel; Matthews, Emily A.; Medlin, Linda K.; Messmer, Amber; Meyer, Elisabeth I.; Monteiro, Magali; Moyer, Gregory R.; Nelson, R. John; Nguyen, Thuy Thi Thu; Omoto, Celso; Ono, Junya; Pavinato, Vitor Antonio Corrêa; Pearcy, Morgan; Pinheiro, José Baldin; Power, Lindsey; Rawat, Anita; Reusch, Thorsten B. H.; Sanderson, Dan; Sannier, Julie; Sathe, Santosh; Sheridan, Carolina; Smulders, M.J.M.; Sukganah, A.; Takayama, Kōji; Tamura, Mariko; Tateishi, Yohei; Vanhaecke, D.; Vu, Ninh V.; Wickneswari, R.; Williams, A. O.; Wimp, Gina M.; Witte, Volker; Zucchi, Maria Imaculada

doi:10.1111/j.1755-0998.2010.02944.x

Cited by 50 publications

(16 citation statements)

References 6 publications

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“…Additional primers were designed to genes of interest based on conserved sequence identified in related species. Primer pair sequences, repeat motifs and other relevant information for the 233 newly identified microsatellites as well as the 13 previously published [8] can be found in Additional file 2: Table S1. For the SNPs, primer and annotation information can be found in Additional file 3: Table S2, with individual SNPs identified in Additional file 4: Table S3.…”

Section: Resultsmentioning

confidence: 99%

“…Sablefish is also in the preliminary stages of commercial aquaculture, with farms in British Columbia already producing 500 tonnes in 2009 [7]. While commercially important, little genetic information is available, with genetic resources limited to a few sequences and 29 microsatellite primer pairs [8-10]. Indeed little is known about the 1,477 species [11] within the economically important order Scorpaeniformes.…”

Section: Introductionmentioning

confidence: 99%

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Genomics of sablefish (Anoplopoma fimbria): expressed genes, mitochondrial phylogeny, linkage map and identification of a putative sex gene

et al. 2013

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BackgroundThe sablefish (order: Scorpaeniformes) is an economically important species in commercial fisheries of the North Pacific and an emerging species in aquaculture. Aside from a handful of sequences in NCBI and a few published microsatellite markers, little is known about the genetics of this species. The development of genetic tools, including polymorphic markers and a linkage map will allow for the successful development of future broodstock and mapping of phenotypes of interest. The significant sexual dimorphism between females and males makes a genetic test for early identification of sex desirable.ResultsA full mitochondrial genome is presented and the resulting phylogenetic analysis verifies the placement of the sablefish within the Scorpaeniformes. Nearly 35,000 assembled transcript sequences are used to identify genes and obtain polymorphic SNP and microsatellite markers. 360 transcribed polymorphic loci from two sablefish families produce a map of 24 linkage groups. The sex phenotype maps to sablefish LG14 of the male map. We show significant conserved synteny and conservation of gene-order between the threespine stickleback Gasterosteus aculeatus and sablefish. An additional 1843 polymorphic SNP markers are identified through next-generation sequencing techniques. Sex-specific markers and sequence insertions are identified immediately upstream of the gene gonadal-soma derived factor (gsdf), the master sex determinant locus in the medaka species Oryzias luzonensis.ConclusionsThe first genomic resources for sablefish provide a foundation for further studies. Over 35,000 transcripts are presented, and the genetic map represents, as far as we can determine, the first linkage map for a member of the Scorpaeniformes. The observed level of conserved synteny and comparative mapping will allow the use of the stickleback genome in future genetic studies on sablefish and other related fish, particularly as a guide to whole-genome assembly. The identification of sex-specific insertions immediately upstream of a known master sex determinant implicates gsdf as an excellent candidate for the master sex determinant for sablefish.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genomics of sablefish (Anoplopoma fimbria): expressed genes, mitochondrial phylogeny, linkage map and identification of a putative sex gene

et al. 2013

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“…Another disadvantage of adopting the refuge-in-a-bag tactic, aimed at managing pest resistance in Brazil, is the scarcity of information on the mobility of target pests on transgenic plants, on the initial frequency of alleles that provide resistance, and on studies of the genetic structure of these populations [33]–[35].…”

Section: Discussionmentioning

confidence: 99%

Feeding and Dispersal Behavior of the Cotton Leafworm, Alabama argillacea (Hübner) (Lepidoptera: Noctuidae), on Bt and Non-Bt Cotton: Implications for Evolution and Resistance Management

et al. 2014

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The host acceptance of neonate Alabama argillacea (Hübner) (Lepidoptera: Noctuidae) larvae to Bt cotton plants exerts a strong influence on the potential risk that this pest will develop resistance to Bt cotton. This will also determine the efficiency of management strategies to prevent its resistance such as the “refuge-in-the-bag” strategy. In this study, we assessed the acceptance of neonate A. argillacea larvae to Bt and non-Bt cotton plants at different temperatures during the first 24 h after hatching. Two cotton cultivars were used in the study, one a Bt DP 404 BG (Bollgard) cultivar, and the other, an untransformed isoline, DP 4049 cultivar. There was a greater acceptance by live neonate A. argillacea larvae for the non-Bt cotton plants compared with the Bt cotton plants, especially in the time interval between 18 and 24 h. The percentages of neonate A. argillacea larvae found on Bt or non-Bt plants were lower when exposed to temperatures of 31 and 34°C. The low acceptance of A. argillacea larvae for Bt cotton plants at high temperatures stimulated the dispersion of A. argillacea larvae. Our results support the hypothesis that the dispersion and/or feeding behavior of neonate A. argillacea larvae is different between Bt and non-Bt cotton. The presence of the Cry1Ac toxin in Bt cotton plants, and its probable detection by the A. argillacea larvae tasting or eating it, increases the probability of dispersion from the plant where the larvae began. These findings may help to understand how the A. argillacea larvae detect the Cry1Ac toxin in Bt cotton and how the toxin affects the dispersion behavior of the larvae over time. Therefore, our results are extremely important for the management of resistance in populations of A. argillacea on Bt cotton.

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“…Amplifications were performed for thirteen microsatellite markers (Aze1-Aze13) originally designed for A. zebra [32], in three separate multiplex PCR reactions (multiplex1: Aze1, Aze2, Aze3, Aze4, Aze5, Aze6; multiplex 2: Aze8, Aze9 and Aze10; multiplex 3: Aze11, Aze12, Aze13 and Aze14) using the QIAGEN Multiplex PCR kit (QIAGEN, Sussex, UK). Touchdown PCR was performed using an initial denaturing step of 15 min at 95°C followed by 8 cycles of 95°C for 45 s, 64°C −56°C annealing for 90 s and extension at 72°C for 1 min.…”

Section: Methodsmentioning

confidence: 99%

“…We sequenced two mitochondrial DNA regions commonly used for fish barcoding ( COI and cyt b ; [30]–[31]) to discriminate between A. zebra and A. taeniatus , and to clarify their distributions in Chilean Patagonia and the Falkland Islands. In addition, we carried for the first time an analysis of genetic diversity and population differentiation of these endangered species, using a set of microsatellite markers that we have recently developed [32].…”

Section: Introductionmentioning

confidence: 99%

DNA Barcoding and Microsatellites Help Species Delimitation and Hybrid Identification in Endangered Galaxiid Fishes

et al. 2012

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The conservation of data deficient species is often hampered by inaccurate species delimitation. The galaxiid fishes Aplochiton zebra and Aplochiton taeniatus are endemic to Patagonia (and for A. zebra the Falkland Islands), where they are threatened by invasive salmonids. Conservation of Aplochiton is complicated because species identification is hampered by the presence of resident as well as migratory ecotypes that may confound morphological discrimination. We used DNA barcoding (COI, cytochrome b) and a new developed set of microsatellite markers to investigate the relationships between A. zebra and A. taeniatus and to assess their distributions and relative abundances in Chilean Patagonia and the Falkland Islands. Results from both DNA markers were 100% congruent and revealed that phenotypic misidentification was widespread, size-dependent, and highly asymmetric. While all the genetically classified A. zebra were correctly identified as such, 74% of A. taeniatus were incorrectly identified as A. zebra, the former species being more widespread than previously thought. Our results reveal, for the first time, the presence in sympatry of both species, not only in Chilean Patagonia, but also in the Falkland Islands, where A. taeniatus had not been previously described. We also found evidence of asymmetric hybridisation between female A. taeniatus and male A. zebra in areas where invasive salmonids have become widespread. Given the potential consequences that species misidentification and hybridisation can have for the conservation of these endangered species, we advocate the use of molecular markers in order to reduce epistemic uncertainty.

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Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2010 – 30 September 2010

Cited by 50 publications

References 6 publications

Genomics of sablefish (Anoplopoma fimbria): expressed genes, mitochondrial phylogeny, linkage map and identification of a putative sex gene

Genomics of sablefish (Anoplopoma fimbria): expressed genes, mitochondrial phylogeny, linkage map and identification of a putative sex gene

Feeding and Dispersal Behavior of the Cotton Leafworm, Alabama argillacea (Hübner) (Lepidoptera: Noctuidae), on Bt and Non-Bt Cotton: Implications for Evolution and Resistance Management

DNA Barcoding and Microsatellites Help Species Delimitation and Hybrid Identification in Endangered Galaxiid Fishes

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