Análises filogenéticas de Cladophora vagabunda (L.) C. Hoek (Cladophorales, Chlorophyta) do Brasil, baseada nas seqüências SSU rDNA

The complete SSU rDNA was sequenced for 10 individuals of Cladophora vagabunda collected along the coast of Brazil. For C. rupestris (L.) Kütz. a partial SSU rDNA sequence (1634 bp) was obtained. Phylogenetic trees indicate that Cladophora is paraphyletic, but the section Glomeratae sensu lato including C. vagabunda from Brazil, Japan and France, C. albida (Nees) Kütz., C. sericea (Hudson) Kütz., and C. glomerata (L.) Kütz. is monophyletic. Within this group C. vagabunda is paraphyletic. The sequence identity for the SSU rDNA varied from 98.9% to 100% for the Brazilian C. vagabunda, and from 98.3% to 99.7% comparing the Brazilian individuals to the ones from France and Japan. Sequence identity of the Brazilian C. vagabunda to C. albida and C. sericea vary from 98.0% to 98.6%. The SSU rDNA phylogeny support partially the morphological characteristics presented by Brazilian populations of C. vagabunda. On the other hand, C. rupestris from Brazil does not group with C. rupestris from France, both sequences presenting only 96.9% of identity. The inclusion of sequences of individuals from Brazil reinforces the need of taxonomical revision for the genus Cladophora and for the complex C. vagabunda.A seqüência completa do SSU rDNA foi obtida para 10 indivíduos de Cladophora vagabunda coletadas ao longo da costa do Brasil. Uma seqüência parcial do SSU rDNA (1634 bp) foi obtida para C. rupestris (L.) Kütz. As árvores filogenéticas indicam que Cladophora é parafilético, mas a seção Glomeratae sensu lato compreendendo C. vagabunda do Brasil, Japão e França, C. albida (Nees) Kütz., C. sericea (Hudson) Kütz. e C. glomerata (L.) Kütz., é monofilética. Dentro deste grupo, C. vagabunda é parafilética. A identidade da seqüência para o SSU rDNA variou de 98,9% à 100% para C. vagabunda brasileira e de 98,3% a 99,7% quando comparados os indivíduos brasileiros aos da França e do Japão. A identidade da seqüência entre C. vagabunda brasileira e as duas outras espécies (C. albida e C. sericea) variou entre 98,0% e 98,6%. A filogenia do SSU rDNA suporta parcialmente as caracteristícas morfológicas apresentadas pelas populações brasileiras de C. vagabunda. Por outro lado, C. rupestris do Brasil não se agrupou a C. rupestris da França, as duas seqüências apresentaram somente 96,9% de identidade. A inclusão de seqüências de indivíduos do Brasil reforçam a necessidade de uma revisão taxonômica para o gênero Cladophora e para o complexo C. vagabunda.Pronex-FacepeCNPqFapes

Molecular diversity of Porphyra species from Brazil

O gene que codifica o rRNA da subunidade pequena do ribossomo (SSU rDNA) de algumas espécies de Porphyra coletadas no Atlântico Sul foi seqüenciado para identificação molecular e inferência filogenética, em uma tentativa de esclarecer a posição dessas espécies dentro da ordem Bangiales. As espécies brasileiras Porphyra acanthophora var. acanthophora, Porphyra acanthophora var. brasiliensis, Porphyra drewiana, Porphyra spiralis var. spiralis, Porphyra spiralis var. amplifolia e Porphyra sp. Piaui formaram um agrupamento monofilético em uma grande politomia que inclui populações de Bangia e espécies de Porphyra de diferentes localidades. A espécie Porphyra sp. Baleia coletada em duas localidades da costa brasileira agrupou com alto suporte com a espécie Porphyra suborbiculata (Japão e Nova Zelândia), indicando que esta espécie cosmopolita também ocorre no Atlântico Sul. Algumas espécies de Porphyra apresentam introns do grupo I inseridos no SSU rDNA, e Bangiopsis sp. (Ordem Stylonematales) apresentou um intron do grupo I em um novo sítio de inserção para o SSU rDNA de Rhodophyta.In an attempt to clarify the position of the South Atlantic Porphyra species within the order Bangiales, phylogenetic trees were inferred on the basis of the nuclear small subunit ribosomal RNA gene (SSU rDNA) sequences. The Brazilian species Porphyra acanthophora var. acanthophora, Porphyra acanthophora var. brasiliensis, Porphyra drewiana, Porphyra spiralis var. spiralis, Porphyra spiralis var. amplifolia and Porphyra sp. Piaui formed a monophyletic group within a large polytomy that includes Bangia collections and Porphyra species from distinct locations. Porphyra sp. Baleia collected from two localities in Brazil grouped strongly with Porphyra suborbiculata from Japan and New Zealand, indicating that this cosmopolitan species also occurs in the South Atlantic. Occurrence of SSU rDNA group I introns is reported for some Porphyra species and a novel position for a group I intron is described for Bangiopsis sp (Order Stylonematales)

Will a DNA barcoding approach be useful to identify Porphyra species (Bangiales, Rhodophyta)?

This paper is part of an extensive study on the biodiversity of the macroalgal flora of So Paulo state, SE Brazil. Previous assessments were based only on morphological descriptions. Here, we tested the effectiveness of DNA barcoding, in comparison with morphological observations for the recognition and cataloging of species. The focus of this study is the genus Porphyra, which is a conspicuous component of the upper intertidal on rocky shores of this region. With five currently accepted species, we have sequenced three short markers: cox1, cox2-3 spacer and UPA to establish the first DNA barcode database for the Porphyra species from the Brazilian coast. The three markers, although with different evolution rates, recovered a cryptic species (Porphyra sp. 77), grouped two different species (Porphyra drewiana and Porphyra spiralis) that are being synonymized, and finally indicated that varieties within P. acanthophora and P. spiralis are merely morphological, with no sequence divergence in the studied molecular markers.Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq), BrazilCAPE

Group I introns and associated homing endonuclease genes reveals a clinal structure for Porphyra spiralis var. amplifolia (Bangiales, Rhodophyta) along the Eastern coast of South America

Abstract Background Group I introns are found in the nuclear small subunit ribosomal RNA gene (SSU rDNA) of some species of the genus Porphyra (Bangiales, Rhodophyta). Size polymorphisms in group I introns has been interpreted as the result of the degeneration of homing endonuclease genes (HEG) inserted in peripheral loops of intron paired elements. In this study, intron size polymorphisms were characterized for different Porphyra spiralis var. amplifolia (PSA) populations on the Southern Brazilian coast, and were used to infer genetic relationships and genetic structure of these PSA populations, in addition to cox 2-3 and rbc L-S regions. Introns of different sizes were tested qualitatively for in vitro self-splicing. Results Five intron size polymorphisms within 17 haplotypes were obtained from 80 individuals representing eight localities along the distribution of PSA in the Eastern coast of South America. In order to infer genetic structure and genetic relationships of PSA, these polymorphisms and haplotypes were used as markers for pairwise Fst analyses, Mantel's test and median joining network. The five cox 2-3 haplotypes and the unique rbc L-S haplotype were used as markers for summary statistics, neutrality tests Tajima's D and Fu's Fs and for median joining network analyses. An event of demographic expansion from a population with low effective number, followed by a pattern of isolation by distance was obtained for PSA populations with the three analyses. In vitro experiments have shown that introns of different lengths were able to self-splice from pre-RNA transcripts. Conclusion The findings indicated that degenerated HEGs are reminiscent of the presence of a full-length and functional HEG, once fixed for PSA populations. The cline of HEG degeneration determined the pattern of isolation by distance. Analyses with the other markers indicated an event of demographic expansion from a population with low effective number. The different degrees of degeneration of the HEG do not refrain intron self-splicing. To our knowledge, this was the first study to address intraspecific evolutionary history of a nuclear group I intron; to use nuclear, mitochondrial and chloroplast DNA for population level analyses of Porphyra; and intron size polymorphism as a marker for population genetics

Group I introns and associated homing endonuclease genes reveals a clinal structure for Porphyra spiralis var. amplifolia (Bangiales, Rhodophyta) along the Eastern coast of South America

Background: Group I introns are found in the nuclear small subunit ribosomal RNA gene (SSU rDNA) of some species of the genus Porphyra (Bangiales, Rhodophyta). Size polymorphisms in group I introns has been interpreted as the result of the degeneration of homing endonuclease genes (HEG) inserted in peripheral loops of intron paired elements. In this study, intron size polymorphisms were characterized for different Porphyra spiralis var. amplifolia (PSA) populations on the Southern Brazilian coast, and were used to infer genetic relationships and genetic structure of these PSA populations, in addition to cox2-3 and rbcL-S regions. Introns of different sizes were tested qualitatively for in vitro self-splicing. Results: Five intron size polymorphisms within 17 haplotypes were obtained from 80 individuals representing eight localities along the distribution of PSA in the Eastern coast of South America. In order to infer genetic structure and genetic relationships of PSA, these polymorphisms and haplotypes were used as markers for pairwise Fst analyses, Mantel's test and median joining network. The five cox2-3 haplotypes and the unique rbcL-S haplotype were used as markers for summary statistics, neutrality tests Tajima's D and Fu's Fs and for median joining network analyses. An event of demographic expansion from a population with low effective number, followed by a pattern of isolation by distance was obtained for PSA populations with the three analyses. In vitro experiments have shown that introns of different lengths were able to self-splice from pre-RNA transcripts. Conclusion: The findings indicated that degenerated HEGs are reminiscent of the presence of a full-length and functional HEG, once fixed for PSA populations. The cline of HEG degeneration determined the pattern of isolation by distance. Analyses with the other markers indicated an event of demographic expansion from a population with low effective number. The different degrees of degeneration of the HEG do not refrain intron self-splicing. To our knowledge, this was the first study to address intraspecific evolutionary history of a nuclear group I intron; to use nuclear, mitochondrial and chloroplast DNA for population level analyses of Porphyra; and intron size polymorphism as a marker for population genetics

Native or introduced? A re-evaluation of <i>Pyropia</i> species (Bangiales, Rhodophyta) from Brazil based on molecular analyses

<div><p>The genus <i>Porphyra sensu lato</i> of the Bangiales has been reported from the Brazilian coast since the 19th century. However, a major worldwide taxonomic revision of the Bangiales indicated that the foliose genus present in Brazil was <i>Pyropia</i> and that <i>Porphyra sensu stricto</i> has not been recorded from this region. A revision of the species of <i>Pyropia</i> in Brazil, based on sequence analysis of molecular markers (<i>rbc</i>L and SSU rDNA) and complemented with morphology, revealed the occurrence of five distinct species in Brazil: <i>P. acanthophora, P. spiralis, P. suborbiculata, P. tanegashimensis</i> and <i>P. vietnamensis.</i> Possible events of <i>Pyropia</i> species introduction in Brazil are discussed in the context of phylogenetic analyses. <i>Pyropia acanthophora</i> and <i>P. spiralis</i>, regarded as southwestern Atlantic species, were not closely related in phylogenetic analyses. <i>Pyropia acanthophora</i> grouped with the possibly introduced Indo-Pacific species <i>P. suborbiculata, P. tanegashimensis</i> and <i>P. vietnamensis</i>. Analysis of available COI-5P and UPA sequences indicated that <i>P. acanthophora</i> occurs in the Hawaiian Islands. These results suggest that <i>P. acanthophora</i>, contrary to previous views, may not be endemic to Brazil. <i>Pyropia spiralis</i>, which is supposedly the only native <i>Pyropia</i> species in Brazil, grouped with species from the Mexican Pacific coast, and its origin along the southwestern Atlantic Ocean and Caribbean Sea is discussed.</p></div