Features of DNA fragments obtained by random amplified polymorphic DNA (RAPD) assays

Rabouam, Corinne; Comes, Ana M.; Bretagnolle, Vincent; Humbert, Jean‐François; Périquet, Georges; Bigot, Yves

doi:10.1046/j.1365-294x.1999.00605.x

Cited by 54 publications

(36 citation statements)

References 9 publications

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“…It has been shown that RAPD markers may have low reproducibility (Pérez et al, 1998;Rabouam et al, 1999, but see Ramos et al (2008)), and previous results concerning levels of variability and inferred recombination in S. troendelagicum are therefore difficult to interpret with confidence. The aim of this study is to learn more about the evolutionary history of this species, more specifically to (1) determine which of the parental taxa are maternal and paternal progenitors, respectively; (2) quantify patterns of genetic variability and structuring in natural populations of S. troendelagicum and the parental species using variable markers with high reproducibility; (3) test the hypothesis that the species originated multiple times; (4) quantify historical parameters, most importantly time since speciation event(s), to determine whether the species likely originated in central Norway or whether it immigrated after the last ice age; and finally, (5) make suggestions concerning the continued preservation of S. troendelagicum.…”

Section: Introductionmentioning

confidence: 99%

The narrow endemic Norwegian peat moss Sphagnum troendelagicum originated before the last glacial maximum

et al. 2010

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It is commonly found that individual hybrid, polyploid species originate recurrently and that many polyploid species originated relatively recently. It has been previously hypothesized that the extremely rare allopolyploid peat moss Sphagnum troendelagicum has originated multiple times, possibly after the last glacial maximum in Scandinavia. This conclusion was based on low linkage disequilibrium in anonymous genetic markers within natural populations, in which sexual reproduction has never been observed. Here we employ microsatellite markers and chloroplast DNA (cpDNA)-encoded trnG sequence data to test hypotheses concerning the origin and evolution of this species. We find that S. tenellum is the maternal progenitor and S. balticum is the paternal progenitor of S. troendelagicum. Using various Bayesian approaches, we estimate that S. troendelagicum originated before the Holocene but not before c. 80 000 years ago (median expected time since speciation 40 000 years before present). The observed lack of complete linkage disequilibrium in the genome of this species suggests cryptic sexual reproduction and recombination. Several lines of evidence suggest multiple origins for S. troendelagicum, but a single origin is supported by approximate Bayesian computation analyses. We hypothesize that S. troendelagicum originated in a peat-dominated refugium before last glacial maximum, and subsequently immigrated to central Norway by means of spore flow during the last thousands of years.

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Section: Introductionmentioning

confidence: 99%

The narrow endemic Norwegian peat moss Sphagnum troendelagicum originated before the last glacial maximum

et al. 2010

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“…esterase) on DNA during the extraction stage. Rabouam et al (1999) attributed artefactual RAPD polymorphism to the presence of commensal organisms and fragment rearrangements during PCR amplifi cation. W = water; A = alcohol; the number of bee corresponds to its position on the gel; fragment name is represented by number of band (ex.…”

Section: Discussionmentioning

confidence: 99%

“…Many of these techniques have been widely employed in genetic analysis of a variety of adult insects (Carvalho & Vieira 2001, Watts et al 2004, Keyghobadi et al 2005, Sofi a et al 2005. However, when total genomic DNA is extracted from adult insect body parts, a worrying aspect of the genetic analysis can be the incidence of spurious DNA due, for instance, to the presence of commensal organisms associated with the material under study (Rabouam et al 1999). In researches involving adult bees, or even adult insects in general, the most frequent sources of such DNA are pollen and microorganisms on the insect integument.…”

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confidence: 99%

“…On the other hand, according to several authors, the reproducibility between RAPD reactions can be hard to maintain (Ayliffe et al 1994, Rabouam et al 1999 since small changes in reaction conditions, such as the type of DNA polymerase used, template DNA concentration, magnesium concentration and temperature-profi ling characteristic of the thermalcycler can produce changes in RAPD bands profi les (Pérez et al 1998). Thus, possible solutions proposed to minimize problems in RAPD reproducibility include a careful optimization of the concentrations of components in the reaction mixture and of the amplifi cation conditions of the thermal cycler, which should be consistently maintained throughout the study (Chiappero & Gardenal 2001).…”

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confidence: 99%

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Evaluation of the RAPD profiles from different body parts of Euglossa pleosticta Dressler male bees (Hymenoptera: Apidae, Euglossina)

Pascual¹,

Suzuki²,

Almeida³

et al. 2006

Neotrop. Entomol.

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Neotropical Entomology 35(6):811-817 (2006) Avaliação dos Perfi s de RAPD de Diferentes Partes do Corpo de Machos de Abelhas Euglossa pleostictaDressler (Hymenoptera: Apidae, Euglossina)RESUMO -Na literatura atual, são escassas as informações sobre qual a parte do corpo do inseto adulto é mais adequada para a extração de DNA genômico para estudos de análises genéticas baseadas em marcadores de DNA. Neste estudo, foram analisados os perfi s de RAPD produzidos a partir da amplifi cação do DNA genômico extraído de partes distintas do corpo (cabeça, pernas, tórax + asas e abdome) de 12 machos de Euglossa pleosticta Dressler. Do total de bandas analisadas, 9,0% não mostraram repetibilidade. As porcentagens de variação de bandas em relação às diferentes partes do corpo das abelhas foram: 1,1% (cabeça); 0,4% (pernas); 0,8% (tórax/asas) e 6,7% (abdome). A maior variação observada ( 2 para uma amostra = 10,27; gl = 1; P < 0,01), nos perfi s eletroforéticos de RAPD, produzidos nas amplifi cações do DNA extraído do abdome de machos euglossíneos sugere que essa parte do corpo de insetos adultos deve ser evitada em procedimentos de extração de DNA. De modo diverso, a baixa variação entre os perfi s de RAPD obtidos a partir das amplifi cações de DNA genômico extraído da cabeça, pernas e tórax/asas das abelhas indica que todas essas partes do corpo de machos euglossíneos são igualmente úteis e confi áveis para serem utilizadas para a extração e a amplifi cação do DNA genômico. PALAVRAS-CHAVE: Apoidea, Euglossini, abelha de orquídea, marcador molecular ABSTRACT -In the current literature, information is scarce on which part of the adult insect body is suitable for isolation of genomic DNA for genetic analysis based on DNA-markers. In this study, we evaluated RAPD profi les generated from total genomic DNA isolated from distinct body parts (head, legs, thorax + wings and abdomen) of 12 males of Euglossa pleosticta Dressler. From the total of bands analyzed, 9.0% did not show reproducibility. Percent variations of bands in each body segment were: 1.1% (head); 0.4% (legs); 0.8% (thorax/wings) and 6.7% (abdomen). The much higher variation ( 2 one sample = 10.27; df = 1; P < 0.01) in the RAPD profi les obtained by using DNA isolated from abdomen of the euglossine males suggests that this body part of adult insects should be avoided in DNA extraction procedures. Conversely, the low variation among the RAPD profi les obtained from amplifi cations of genomic DNA extracted from head, legs and thorax/wings indicates that all these body parts of male bees are equally useful and secure for using in isolation and amplifi cation procedures of total genomic DNA.

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“…Plasmids were purified and sequenced as previously described (Rabouam et al 1999). The 25 sequences reported in this paper appear in the DDBJ/EMBL/GenBank sequence database under accession numbers AJ009223-AJ009247.…”

Section: Pcr Amplifications and Fragment Cloningmentioning

confidence: 99%

Features of the mammal mar1 transposons in the human, sheep, cow, and mouse genomes and implications for their evolution

Demattei¹,

Augé-Gouillou²,

Pollet

et al. 2000

Mammalian Genome

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Abstract. Mariner-like elements (MLE) belong to the Tc1/ mariner superfamily of class II transposons. We have analyzed the mariner related to the cecropia subfamily, and called mammal mar1, in four mammalian genomes, Bos taurus (Bovidae), Homo sapiens (Primata), Mus musculus (Rodentia), and Ovis aries (Ovidae). Three kinds of MLE sequences were found in all these species: full-length 1.3-kbp elements, shorter elements 80 bp-1.2 kbp, and single inverted terminal repeats (ITRs). All the 1.3-kbp genomic copies sequenced had an open reading frame encoding a transposase interrupted by stop codons or frame shifts. Phylogenetic analysis of the full-length elements suggested at least two distinct populations of mammal mar1 elements in each species. This was confirmed by using a statistical method that allows defining populations. Finally, the evolutionary origin of the mammal mar1 elements and the paradoxes are discussed.

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Features of DNA fragments obtained by random amplified polymorphic DNA (RAPD) assays

Cited by 54 publications

References 9 publications

The narrow endemic Norwegian peat moss Sphagnum troendelagicum originated before the last glacial maximum

The narrow endemic Norwegian peat moss Sphagnum troendelagicum originated before the last glacial maximum

Evaluation of the RAPD profiles from different body parts of Euglossa pleosticta Dressler male bees (Hymenoptera: Apidae, Euglossina)

Features of the mammal mar1 transposons in the human, sheep, cow, and mouse genomes and implications for their evolution

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