Analysis of 148 kb of Genomic DNA of Tetraodon nigroviridis Covering an Amylase Gene Family*

Bouneau, Laurence; Lardier, Guillaume; Fischer, Cécile; Ronsin, Muriel; Weissenbach, Jean; Bernot, Alain

doi:10.1080/1042517021000050633

Cited by 12 publications

(5 citation statements)

References 28 publications

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“…Further cloning of alleles indicated that alignment of sequences of each amylase locus were not possible (JL Rolland and B Guinand, unpubl. results), indicating that we probably amplified two different genes of the multigenic α-amylase gene family (Bouneau et al 2003). A new set of primers was defined for the metallothionein (MT) locus.…”

Section: Genetic Analysesmentioning

confidence: 99%

Population structure of the common sole (Solea solea) in the Northeastern Atlantic and the Mediterranean Sea: revisiting the divide with EPIC markers

et al. 2006

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Spatial and temporal population genetic structures of the common sole, Solea solea, were studied in Northeastern Atlantic and Mediterranean Sea populations, using three polymorphic exon-primed intron-crossing (EPIC) markers. Results demonstrated significant multilocus differentiation among Eastern Mediterranean and a group composed by Western Mediterranean and Atlantic populations (θ = 0.150, P < 0.001), but also suggested unrecorded genetic differentiation of the Adriatic Sea population. No pattern of isolation-by-distance was recorded across the range covered by sampling, from the Kattegat to the Aegean Sea. Conversely to genetically structured Mediterranean populations, Atlantic populations ranging from Denmark to Portugal could be considered as representative of the same panmictic unit (θ = 0.009, not significant). Results further demonstrated stability of multilocus genetic structure among temporarily replicated cohort samples [0+, 1+, subadults] from several coastal and estuarine locations from Bay of Biscay, excepted for the amylase locus Am2B3-2 at one location (Pertuis d'Antioche). Despite coherence of such observed patterns of multilocus differentiation with previous allozymic surveys in sole, and with patterns generally obtained for other marine fish species, single-locus results from EPICs indicated divergent coalescence schemes supporting a complex response to ecology and history of sole's populations. Results stress the use of nuclear genes such as EPIC markers to investigate population structure, but also historical, demographic, and possibly selective processes in marine fishes.

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Section: Genetic Analysesmentioning

confidence: 99%

Population structure of the common sole (Solea solea) in the Northeastern Atlantic and the Mediterranean Sea: revisiting the divide with EPIC markers

et al. 2006

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“…This included the intron of the metallothionein gene, and the third intron of pancreatic α-amylase genes. Two amylase loci are co-amplified with the same set of primers, as such loci belong to a multigenic family (Bouneau et al 2003). Further cloning of alleles indicated that sequences of each amylase locus were clearly different and impossible to align (JL Rolland and B Guinand, unpubl.…”

Section: Genetic Analysesmentioning

confidence: 99%

Genetic structure of the common sole (Solea solea) in the Bay of Biscay: Nurseries as units of selection?

Guinand

Rolland

Bonhomme

2008

Estuarine, Coastal and Shelf Science

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Coastal and estuarine areas in the Bay of Biscay are essential nursery habitats for sole (Solea solea). Using three intronic markers, we investigated patterns of genetic differentiation among cohorts of juveniles (0+, 1+, sub-adults) inhabiting four major nurseries in the Vilaine and Loire river estuaries, the Pertuis d'Antioche strait, and the Gironde estuary. Genetic differentiation was not significant for the age 0-and 1-groups, but was among sub-adult samples (θWC = 0.017; P = 0.031). Hierarchical analyses of genotypic frequencies by nested multivariate ANOVA using redundancy analysis indicated that northern nurseries of Loire and Vilaine rivers had different patterns of genotypic variation with age than southern nurseries of the Pertuis d'Antioche and Gironde estuaries (F = 1.36; P = 0.007). Bay of Biscay nurseries appeared to be spatially structured between a southern and a northern group that exhibit different genotypic distributions. Genetic drift and gene flow explains this pattern poorly, but a statistical test (P < 0.035) suggested that the metallothionein (MT) locus may be significantly impacted by selection in southern estuaries. As metallothionein is involved in heavy-metal detoxification, and southern nurseries are known to be affected by cadmium, this indicates a possible correlation between observed genotypic distributions and some nursery habitat features in sole. Some selective patterns might also be proposed to explain patterns of linkage disequilibrium observed at amylase loci in three of the four nurseries.

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“…Both smooth pufferfish species have a very compact genome (8-9 times smaller than the human genome with a similar gene number) characterized by very small intron and intergenic regions, a feature which becomes evident after detailed analysis of completely sequenced regions (see for instance Gellner and Brenner, 1999;Bouneau et al, 2003b). Because of their high percentage of coding sequences (around one third of the genome), short introns (highly biased towards the range of 60-120 bp) and short intergenic regions (generally a few kilobases), these fishes are therefore models of choice for vertebrate genomes sequencing projects.…”

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Diversity and clustered distribution of retrotransposable elements in the compact genome of the pufferfish <i>Tetraodon nigroviridis</i>

Fischer

Bouneau²,

Coutanceau³

et al. 2005

Cytogenet Genome Res

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We report the characterization and chromosomal distribution of retroelements in the compact genome of the pufferfish Tetraodon nigroviridis. We have reconstructed partial/complete retroelement sequences, established their phylogenetic relationship to other known eukaryotic retrotransposons, and performed double-color FISH analyses to gain new insights into their patterns of chromosomal distribution. We could identify 43 different reverse transcriptase retrotransposons belonging to the three major known subclasses (14 non-LTR retrotransposons from seven clades, 25 LTR retrotransposons representing the five major known groups, and four Penelope-like elements), and well as two SINEs (non-autonomous retroelements). Such a diversity of retrotransposable elements, which seems to be relatively common in fish but not in mammals, is astonishing in such a compact genome. The total number of retroelements was approximately 3000, roughly representing only 2.6% of the genome of T. nigroviridis. This is much less than in other vertebrate genomes, reflecting the compact nature of the genome of this pufferfish. Major differences in copy number were observed between different clades, indicating differential success in invading and persisting in the genome. Some retroelements displayed evidence of recent activity. Finally, FISH analysis showed that retrotransposable elements preferentially accumulate in specific heterochromatic regions of the genome of T. nigroviridis, revealing a degree of genomic compartmentalization not observed in the human genome.

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Analysis of 148 kb of Genomic DNA of Tetraodon nigroviridis Covering an Amylase Gene Family*

Cited by 12 publications

References 28 publications

Population structure of the common sole (Solea solea) in the Northeastern Atlantic and the Mediterranean Sea: revisiting the divide with EPIC markers

Population structure of the common sole (Solea solea) in the Northeastern Atlantic and the Mediterranean Sea: revisiting the divide with EPIC markers

Genetic structure of the common sole (Solea solea) in the Bay of Biscay: Nurseries as units of selection?

Diversity and clustered distribution of retrotransposable elements in the compact genome of the pufferfish <i>Tetraodon nigroviridis</i>

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