Increasing genomic information in bivalves through new EST collections in four species: Development of new genetic markers for environmental studies and genome evolution

Tanguy, Arnaud; Bierne, Nicolas; Saavedra, Carlos; Piña, Benjamı́n; Bachère, Evelyne; Kube, Michael; Bazin, Éric; Bonhomme, François; Boudry, Pierre; Boulo, Viviane; Boutet, Isabelle; Cancela, M. Leonor; Dossat, Carole; Favrel, Pascal; Huvet, Arnaud; Jarque, Sergio; Jollivet, Didier; Klages, Sven; Lapègue, Sylvie; Leite, Ricardo B.; Moal, Jeanne; Moraga, Dario; Reinhardt, Richard; Samain, Jean-François; Ζούρος, Ε.; Canário, Adelino V.M.

doi:10.1016/j.gene.2007.10.021

Cited by 128 publications

(87 citation statements)

References 62 publications

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“…The most dominant motifs were di-and tri-nucleotides, which totally accounted for 78.0% of EST-SSRs. It was not consistent with the results reported for other clam species (Tanguy et al, 2008). This result also suggested that there was significant heterogeneity in the most dominant type of repeats, i.e.…”

Section: Discussioncontrasting

confidence: 99%

“…They found that the microsatellite density was 2.9 times higher in introns than in exons. Tanguy et al (2008) found that less than 0.5% of EST-SSRs were identified in four bivalve species, Bathymodiolus azoricus, Crassostrea gigas, Mytilus edulis and Ruditapes decussatus. The frequency of EST-SSRs detected in M. meretrix was much higher than that of the bivalve species studied.…”

Section: Discussionmentioning

confidence: 99%

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Mining of EST-SSR markers in clam Meretrix meretrix larvae from 454 shotgun transcriptome

Wang

Huan

et al. 2011

Genes Genet. Syst.

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A total of 2,970 EST-SSRs (2.38%) were identified by transcriptome sequencing of clam Meretrix meretrix (751,970 reads, ~310.82 Mbp), using 454 Genome Sequencer FLX next-generation sequencing platform. Dinucleotide SSR was the dominant repeat type (40.2%), followed by trinucleotide (37.8%), tetranuleotide (12.0%) and pentanucleotide (2.0%) SSR. The dominant repeat motif was AT (71.3%) in the dinucleotide SSR type and AAC (45.6%) in the trinucleotide SSR type. Nearly 79% of all microsatellites had flanking sequences suitable for PCR primer design. Half of PAL were found to be polymorphic in a subset of 40 primer pairs randomly selected. Specifically, the density of dinucleotide, trinucleotide and tetranucleotide repeats showed significant variation among four development stages (trochophore, D-veliger, pediveliger and postlarva). The results suggested that dinucleotide, trinucleotide and tetranucleotide SSRs may play an important role in contributing to the different expression profiles in larval stages.

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Section: Discussioncontrasting

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Mining of EST-SSR markers in clam Meretrix meretrix larvae from 454 shotgun transcriptome

Wang

Huan

et al. 2011

Genes Genet. Syst.

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“…These are the methods of Lewontin and Krakauer (1973), Beaumont and Nichols (1996), Vitalis et al (2003), Beaumont and Balding (2004), Bonhomme et al (2010), and a custom Chromosomal walking along mac-1: We sequenced a region of 3.1 kb around mac-1 taking advantage of published sequences (Daguin et al 2001), an additional upstream sequence (M. Ohresser, personal communication) and looking for homology between coding regions and expressed sequence tags of Mytilus (Tanguy et al 2008). To describe the local variation of the edulis allele frequency around mac-1, we walked along the sequence and looked for evenly spaced genetic polymorphisms (see Figure S2 for a diagram).…”

Section: Multilocus Scanmentioning

confidence: 99%

Gene-Flow in a Mosaic Hybrid Zone: Is Local Introgression Adaptive?

et al. 2014

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Genome-wide scans of genetic differentiation between hybridizing taxa can identify genome regions with unusual rates of introgression. Regions of high differentiation might represent barriers to gene flow, while regions of low differentiation might indicate adaptive introgression-the spread of selectively beneficial alleles between reproductively isolated genetic backgrounds. Here we conduct a scan for unusual patterns of differentiation in a mosaic hybrid zone between two mussel species, Mytilus edulis and M. galloprovincialis. One outlying locus, mac-1, showed a characteristic footprint of local introgression, with abnormally high frequency of edulis-derived alleles in a patch of M. galloprovincialis enclosed within the mosaic zone, but low frequencies outside of the zone. Further analysis of DNA sequences showed that almost all of the edulis allelic diversity had introgressed into the M. galloprovincialis background in this patch. We then used a variety of approaches to test the hypothesis that there had been adaptive introgression at mac-1. Simulations and model fitting with maximum-likelihood and approximate Bayesian computation approaches suggested that adaptive introgression could generate a "soft sweep," which was qualitatively consistent with our data. Although the migration rate required was high, it was compatible with the functioning of an effective barrier to gene flow as revealed by demographic inferences. As such, adaptive introgression could explain both the reduced intraspecific differentiation around mac-1 and the high diversity of introgressed alleles, although a localized change in barrier strength may also be invoked. Together, our results emphasize the need to account for the complex history of secondary contacts in interpreting outlier loci. GENETIC barriers between related lineages are often semipermeable, varying in strength across the genome (Harrison 1986). As such, hybridization can lead to adaptive introgression, the transfer of selectively beneficial alleles between species (Parsons et al. 1993;Arnold 2004;Heliconius Genome Consortium 2012;Hedrick 2013). However, the frequency and importance of such hybridization events remain hotly debated (Mallet 2007;Abbott et al. 2013;Barton 2013). It is now common to address such questions by scanning genome sequences for regions of enhanced or reduced differentiation. Universally advantageous alleles can usually cross barriers to gene flow without much delay (e.g., Piálek and Barton 1997), and neutral loci linked to such alleles are expected to display unusually low levels of differentiation. In contrast, barrier loci will delay the introgression of neutral alleles in proportion to their linkage (Barton 1979;Barton and Bengtsson 1986); that is the basis for the investigation of genomic islands of differentiation (Turner et al. 2005;Hohenlohe et al. 2010;Nadeau et al. 2012).Interpreting regions of unusual differentiation can be difficult, not only because of variation in recombination across the genome (Nachman and Payseur 2012;Roesti ...

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“…Due to their economic importance, oysters have been the subject of several large-scale expressed sequence tags (EST) projects (Fleury et al, 2009;Joubert et al, 2010;Tanguy et al, 2008;Wang and Guo, 2007). Indeed whole genome or transcriptome sequencing has proved a very efficient and cost effective method for expanding the sequence database for bivalves and other non-model species (i.e.…”

Section: Introductionmentioning

confidence: 99%

Key metabolic pathways involved in xenobiotic biotransformation and stress responses revealed by transcriptomics of the mangrove oyster Crassostrea brasiliana

et al. 2015

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Key metabolic pathways involved in xenobiotic biotransformation and stress responses revealed by transcriptomics of the mangrove oyster Crassostrea brasiliana.Aquatic Toxicology http://dx.doi.org/10. 1016/j.aquatox.2015.06.012 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Highlights-Thetranscriptome of the mangrove oyster Crassostrea brasilianawas sequenced.-The sequencing effort dramatically expanded the existing cDNA sequences available for the species.-Global analysis for transcription in the oyster treated with phenanthrene, diesel and domestic sewage was performed.-The pollutants altered mRNAs for genes in biotransformation, antioxidant and stress response pathways. Abstract 2The Brazilian oyster Crassostrea brasiliana was challenged to three common environmental contaminants: phenanthrene, diesel fuel water-accommodated fraction (WAF) and domestic sewage. Total RNA was extracted from the gill and digestive gland, and cDNA libraries were sequenced using the 454 FLX pla orm. The assembled transcriptome resulted in ˜20,000contigs, which were annotated to produce the first de novo transcriptome for C. brasiliana.Sequences were screened to identify genes potentially involved in the biotransformation of xenobiotics and associated antioxidant defence mechanisms. These gene families included those of the cytochrome P450 (CYP450), 70kDa heat shock, antioxidants, such as glutathione Stransferase, superoxide dismutase, catalase and also multi-drug resistance proteins. Analysis showed that the massive expansion of the CYP450 and HSP70 family due to gene duplication identified in the Crassostrea gigas genome also occurred in C. brasiliana, suggesting these processes form the base of the Crassostrea lineage. Preliminary expression analyses revealed several candidates biomarker genes that were up-regulated during each of the three treatments, suggesting the potential for environmental monitoring.

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Increasing genomic information in bivalves through new EST collections in four species: Development of new genetic markers for environmental studies and genome evolution

Cited by 128 publications

References 62 publications

Mining of EST-SSR markers in clam Meretrix meretrix larvae from 454 shotgun transcriptome

Mining of EST-SSR markers in clam Meretrix meretrix larvae from 454 shotgun transcriptome

Gene-Flow in a Mosaic Hybrid Zone: Is Local Introgression Adaptive?

Key metabolic pathways involved in xenobiotic biotransformation and stress responses revealed by transcriptomics of the mangrove oyster Crassostrea brasiliana

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