Identification of endangered Mediterranean cyprinodontiform fish by means of DNA inter-simple sequence repeats (ISSRs)

Maltagliati, Ferruccio; Lai, Tiziana; Casu, Marco; Valdesalici, Stefano; Castelli, Alberto

doi:10.1016/j.bse.2006.02.003

Cited by 40 publications

(33 citation statements)

References 26 publications

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“…Based on the results obtained in the present study, we can conclude that ISSR primers are efficient in detecting species-specific loci in fish, and thus, they may be used as tools to assist in the identification of species, as reported by other authors (Schulz et al, 2004;Maltagliati et al, 2006). The application of these markers is important in identifying species, as well as detecting genetic variability, in order to preserve threatened species and to reestablish stocks with low genetic diversity for conservation purposes.…”

Section: Discussionsupporting

confidence: 78%

“…ISSR (inter-simple sequence repeat) method is based on amplification of DNA fragments by means of a single primer composed of a short microsatellite sequence with one to four degenerate nucleotides anchored at the 5' or 3' end, as described by Gupta et al (1994). ISSR molecular markers (Schulz et al, 2004;Maltagliati et al, 2006;Pazza et al, 2007) and mitochondrial DNA (mtDNA) sequences have been revealed as important tools in studies regarding the genetic structure of populations, phylogeographic relations and phylogenetic reconstruction in fish (Reeves and Bermingham, 2006;Haponski and Stepien, 2008;Almada et al, 2009;Kawamura et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

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Molecular characterization and phylogenetic relationships among species of the genus Brycon (Characiformes: Characidae) from four hydrographic basins in Brazil

Antunes¹,

Gomes²,

Prioli³

et al. 2010

Genet. Mol. Res.

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ABSTRACT. Brycon is one of the main genera of Neotropical freshwater fish. In Brazil, Brycon species have been found in many hydrographic basins, such as the Amazon, Paraná, Paraguay, and AraguaiaTocantins basins. We examined the phylogenetic relationships among the species Brycon orbignyanus, B. hilarii, B. cf. pesu, B. cephalus, B. falcatus, and B. gouldingi, using mitochondrial and nuclear molecular markers. Specimens of B. orbignyanus were collected in the Paraná River. Specimens of B. hilarii were collected in the Manso River. Specimens of B. cephalus were obtained from a fish farm, and 675 ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 9 (2): 674-684 (2010) Phylogenetic relationships among Brycon species specimens of B. cf. pesu, B. falcatus and B. gouldingi were sampled in the Araguaia-Tocantins basin. DNA extraction was carried out using the phenol/chloroform method. Molecular polymorphism studies of Brycon species were carried out with the inter-simple sequence repeat (ISSR) technique, using the total DNA of six specimens of each species. In DNA amplification of B. cf. pesu, eight specimens were used. The partial sequence of mitochondrial cytochrome b was amplified by PCR. The PCR products were used directly in sequencing reactions. Each ISSR primer produced from 7 to 14 scorable and reproducible bands. The (GGAC) 3 A and (GGAC) 3 C primers produced the greatest number of species-specific bands. A 264-bp fragment, corresponding to the partial region of mitochondrial DNA cytochrome b, was sequenced and used for analysis. According to the phylogenetic tree obtained from the data, these Brycon species can be divided into two clades: one comprised only B. cf. pesu, and the second comprised the remaining Brycon species. We conclude that ISSR primers can be used for the identification of species-specific bands in fish, such as Brycon spp.

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Section: Discussionsupporting

confidence: 78%

Section: Introductionmentioning

confidence: 99%

Molecular characterization and phylogenetic relationships among species of the genus Brycon (Characiformes: Characidae) from four hydrographic basins in Brazil

Antunes¹,

Gomes²,

Prioli³

et al. 2010

Genet. Mol. Res.

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“…The segment of DNA amplified by the inter-SSR markers (ISSR) includes the nucleotide sequence located between two blocks of microsatellites, oriented in opposite directions, producing a multilocus maker, which is highly polymorphic, and is useful for the analysis of genetic diversity, making it a good choice for DNA fingerprinting (Bornet & Branchard, 2001;Reddy et al, 2002;Maltagliati et al, 2006). Due to its ease of use, low cost and high sensitivity, ISSR markers have been employed in studies on genetic diversity of several species of plants and animals (Luque et al, 2002;Bornet & Branchard, 2004;Askari et al, 2011;Moresco et al, 2013), as well as studies of sexual differentiation in plants (Ehsanpour et al, 2008) and identification of hybrid fish (Bignotto et al, 2009;AlmeidaFerreira et al, 2011).…”

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confidence: 99%

Genetic diversity of Arapaima gigas (Schinz, 1822) (Osteoglossiformes: Arapaimidae) in the Araguaia-Tocantins basin estimated by ISSR marker

et al. 2015

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The genetic diversity of the specimens of four natural populations of Arapaima from Araguaia-Tocantins basin was assessed within and among these stocks, using five primers for ISSR. COI (cytochrome c oxidase subunit I) partial sequences confirmed that the specimens belongs to Arapaima gigas. The ISSR provided 168 loci, of which 165 were polymorphic. However, the number of loci for each population and expected heterozygosity values were low. AMOVA showed 52.63% intra-population variation and 47.37% inter-population variation. The F ST was high among all populations (F ST ≥ 0.25), however, the cluster analysis (PCoA) and Bayesian inference showed three major groups: Araguaiana-MT + São Félix do Araguaia-MT, Novo Santo Antônio-MT and Itupiranga-PA. The genetic distance was not correlated with geographical distance. The ISSR marker revealed that the populations of the Araguaia-Tocantins are structured and have a low genetic diversity. These are the first data from a population analysis using molecular markers for A. gigas of Araguaia-Tocantins basins and may be used to define the best management strategies and conservation projects for this species.A diversidade genética dos espécimes de quatro populações naturais de Arapaima coletados na bacia do Araguaia-Tocantins foi avaliada com base em cinco primers para marcadores moleculares ISSR. A sequência parcial do COI (cytochrome c oxidase subunit I) confirmou que os espécimes pertencem à espécie Arapaima gigas. Os ISSR forneceram 168 loci, dos quais 165 polimórficos. No entanto, para cada população, os valores de heterozigosidade esperada foram baixos. A AMOVA mostrou 52,63% de variação intrapopulacional e 47,37% interpopulacional. O F ST foi alto entre todas as populações (F ST ≥ 0,25); entretanto, a análise de agrupamento e a inferência Bayesiana mostraram três grandes grupos: Araguaiana-MT + São Félix do Araguaia-MT, Novo Santo Antônio-MT e Itupiranga-PA. A distância genética não teve correlação com a distância geográfica. Os ISSRs se mostraram eficientes para determinar a diversidade genética para a A. gigas, revelando que as populações da bacia Araguaia-Tocantins estão estruturadas e com baixa diversidade genética. Estes são os primeiros dados de análise populacional utilizando ISSR para A. gigas da bacia Araguaia-Tocantins e poderão ser utilizados para definir as melhores estratégias de manejo e projetos de conservação dessa espécie.

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“…Terrestrial plants, invertebrates, birds and mammals have been the focus of several works as well (Tollefsrud et al, 1998;Holder et al, 1999;Ehrich et al, 2000). However, this is the first work, at least to our knowledge, dealing with the population genetic structure of a benthic marine faunal organism in the high Arctic, and using ISSR-PCR markers that just recently have been used in marine species (Casu et al, 2007;Hou et al, 2006;Maltagliati et al, 2006;Lewallen et al, 2007;Varela et al, 2007).…”

Section: Discussionmentioning

confidence: 99%

Population genetic structure of the ascidian Styela rustica at Kongsfjorden, Svalbard, Arctic

Demarchi

Chiappero

Laudien

et al. 2008

Journal of Experimental Marine Biology and Ecology

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The actual Arctic biota shows a strong affinity with that of the Boreal Atlantic and Pacific ones, as a result of an active recolonization process after the Quaternary glaciations. The geographic distribution of sessile species is usually linked to larvae dispersive capabilities which can be directly related with time spent in the plankton. Ascidians larvae are lecitothorphic and short-lived, which suggest that ascidians could be not efficient dispersers. However, the solitary ascidian Styela rustica (Linnaeus, 1767) (Tunicata, Ascidiacea) shows a wide distribution pattern from the North Atlantic to the Arctic that, together with the relatively recent colonization of the Arctic system could indicate that this species efficiently disperses and colonizes new habitats. In this study we used ISSR-PCR markers to study the genetic structure of five populations of the ascidian Styela rustica at Kongsfjorden, west Spitsbergen (Svalbard archipelago). We analyzed whether this species presents a low genetic structure, as can be expected due to the historical process of recent post glaciations colonization, or if there is genetic differentiation at a local scale, caused by short-lived larvae and limited dispersal potential. The genetic diversity in each population assessed using the marker diversity index (M) ranged from 0.288 to 0.324. Population HN, situated close to a fast retreating glacier, showed the lowest diversity. Processes associated with deglatiation (icebergs calving from the glacier that scour the benthos and the increment of inorganic particulate matter on the water column) would drive to reduced population sizes and explain the reduced genetic variability observed in the HN population with respect to the others in the fjord. This suggests a possible linkage with the global warming process. Although the weak genetic structure found among the studied populations could indicate a founder effect, the genetic landscape shape analysis together with a positive relationship between genetic and geographic distances also suggest possible current gene flow among populations in the fjord.

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Identification of endangered Mediterranean cyprinodontiform fish by means of DNA inter-simple sequence repeats (ISSRs)

Cited by 40 publications

References 26 publications

Molecular characterization and phylogenetic relationships among species of the genus Brycon (Characiformes: Characidae) from four hydrographic basins in Brazil

Molecular characterization and phylogenetic relationships among species of the genus Brycon (Characiformes: Characidae) from four hydrographic basins in Brazil

Genetic diversity of Arapaima gigas (Schinz, 1822) (Osteoglossiformes: Arapaimidae) in the Araguaia-Tocantins basin estimated by ISSR marker

Population genetic structure of the ascidian Styela rustica at Kongsfjorden, Svalbard, Arctic

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