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rbcL Sequences (rbcl + sequence)
Selected AbstractsSYNTHESIS OF MOLECULAR RESEARCH ON BATRACHOSPERMUM HELMINTHOSUM (RHODOPHYTA) FROM STREAM REACHES IN EASTERN NORTH AMERICAJOURNAL OF PHYCOLOGY, Issue 2001Article first published online: 24 SEP 200 Vis, M. L., Hall, M. M., Machesky, N. J. & Miller, E. J. Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701 USA The freshwater red alga Batrachospermum helminthosum was collected from eleven streams throughout the species range in eastern North America as follows: three stream reaches from Ohio, and one each from Michigan, Indiana, Tennessee, Louisiana, North Carolina, Connecticut, Rhode Island and Massachusetts. The molecular marker technique of inter-simple sequence repeats (ISSR) and sequence data from the plastid encoded rubisco large subunit gene (rbcL), the mitochondrial COX2-COX3 gene spacer region, and the nuclear region of ITS1-5.8S rDNA-ITS2 were employed to examine biogeographic trends in this alga. Analysis of the rbcL sequence revealed 5 genotypes with one genotype representing individuals from seven stream reaches. Data from the ISSR molecular markers gave a distinct banding pattern for each of 165 individuals examined. ISSR results showed all individuals within a reach clustered together but did not provide well-defined groupings based on stream reach. The sequence data for the COX2-COX3 gene spacer was invariant among individuals from a stream reach. The individuals from Connecticut, Rhode Island and 2 Ohio stream reaches were identical and similarly the individuals from the North Carolina and another Ohio location did not vary in sequence so that seven genotypes were recorded among the individuals from the eleven stream reaches. Analysis of the ITS1-5.8S rDNA-ITS2 region showed sequence variation not only among individuals from different streams but also among individuals from the same reach. The utility and congruency of these data sets to answer biogeographic questions will be discussed. [source] PHYLOGENETIC RELATIONSHIPS WITHIN THE GENUS HYPNEA (GIGARTINALES, RHODOPHYTA), WITH A DESCRIPTION OF H. CAESPITOSA SP.JOURNAL OF PHYCOLOGY, Issue 2 2010Species discrimination within the gigartinalean red algal genus Hypnea has been controversial. To help resolve the controversy and explore phylogeny within the genus, we determined rbcL sequences from 30 specimens of 23 species within the genus, cox1 from 22 specimens of 10 species, and psaA from 16 species. We describe H. caespitosa as a new species characterized by a relatively slender main axis; a pulvinate growth habit with entangled, anastomosing, and subulate uppermost branches; and unilaterally borne tetrasporangial sori. The new species occurs in the warm waters of Malaysia, the Philippines, and Singapore. The phylogenetic trees of rbcL, psaA, and cox1 sequences showed a distant relationship of H. caespitosa to H. pannosa J. Agardh from Baja California and the marked differentiation from other similar species. The rbcL + psaA tree supported monophyly of the genus with high bootstrap values and posterior probabilities. The analysis revealed three clades within the genus, corresponding to three sections, namely, Virgatae, Spinuligerae, and Pulvinatae first recognized by J. G. Agardh. Exceptions were H. japonica T. Tanaka in Pulvinatae and H. spinella (C. Agardh) Kütz. in Spinuligerae. [source] PHYLOGENY OF THE DASYCLADALES (CHLOROPHYTA, ULVOPHYCEAE) BASED ON ANALYSES OF RUBISCO LARGE SUBUNIT (rbcL) GENE SEQUENCES,JOURNAL OF PHYCOLOGY, Issue 4 2003Frederick W. Zechman The phylogeny of the green algal Order Dasycladales was inferred by maximum parsimony and Bayesian analyses of chloroplast-encoded rbcL sequence data. Bayesian analysis suggested that the tribe Acetabularieae is monophyletic but that some genera within the tribe, such as Acetabularia Lamouroux and Polyphysa Lamouroux, are not. Bayesian analysis placed Halicoryne Harvey as the sister group of the Acetabularieae, a result consistent with limited fossil evidence and monophyly of the family Acetabulariaceae but was not supported by significant posterior probability. Bayesian analysis further suggested that the family Dasycladaceae is a paraphyletic assemblage at the base of the Dasycladales radiation, casting doubt on the current family-level classification. The genus Cymopolia Lamouroux was inferred to be the basal-most dasycladalean genus, which is also consistent with limited fossil evidence. Unweighted parsimony analyses provided similar results but primarily differed by the sister relationship between Halicoryne Lamouroux and Bornetella Munier-Chalmas, thus supporting the monophyly of neither the families Acetabulariaceae nor Dasycladaceae. This result, however, was supported by low bootstrap values. Low transition-to-transversion ratios, potential loss of phylogenetic signal in third codon positions, and the 550 million year old Dasycladalean lineage suggest that dasyclad rbcL sequences may be saturated due to deep time divergences. Such factors may have contributed to inaccurate reconstruction of phylogeny, particularly with respect to potential inconsistency of parsimony analyses. Regardless, strongly negative g1 values were obtained in analyses including all codon positions, indicating the presence of considerable phylogenetic signal in dasyclad rbcL sequence data. Morphological features relevant to the separation of taxa within the Dasycladales and the possible effects of extinction on phylogeny reconstruction are discussed relative to the inferred phylogenies. [source] A SYSTEMATIC STUDY OF GIGAR-TINACEAE FROM PACIFIC NORTH AMERICA BASED ON MOLECULAR AND MORPHOLOGICAL EVIDENCEJOURNAL OF PHYCOLOGY, Issue 2000J.R. Hughey Greater than 50 species of Gigartinaceae have been described from Pacific North America, about half of which are currently recognized. Although the family is treated extensively in the taxonomic literature, many of the species are still confused and a comprehensive revision is required. We sequenced the rbcL (RuBisCO) gene and ITS (Internal Transcribed Spacer) 1, 2, and 5.8S regions from a large number of recent collections and identified a discrete of number data sets. These were analysed in comparison with the morphological evidence for each of the taxa. Uncertain of the possibility that our operational taxonomic units may not correspond to the types, we developed a protocol for isolating PCR-friendly DNA from herbarium specimens, some reaching back as far as 1670. The DNA profiles of types and historically important specimens were compared to those for recently collected silica gel-dried and formalin-fixed material and assigned correct names. Species studied ranged from Alaska to Mexico and the Gulf of California and were compared to outgroup taxa from Pacific South America and the Southern Ocean. Particular attention was paid to variations in morphology as they relate to habitat with emphasis on the presence or absence of different morphological forms among sympatric and allopatric populations. We recognize 10 species in Chondracanthus (including one new combination and one new species) and 16 species in Mazzaella (including two new combinations and two new species). Finally, we tested a phylogenetic hypothesis inferred for the Gigartinaceae from rbcL sequences for congruence with one generated from ITS sequences. [source] Molecular Phylogeny of Caryophyllidae s.l. Based on MatK Sequences with Special Emphasis on Carnivorous TaxaPLANT BIOLOGY, Issue 2 2000H. Meimberg Abstract: Despite intensive morphological, chemical and cladistic studies on Caryophyllidae, the circumscription of this subclass and the interfamilial relationships are still under discussion. Using comparative sequencing of the chloroplast matK gene, hypotheses of relationships between the carnivorous Droseraceae, Nepenthaceae and Dioncophyllaceae and ten other families of the Caryophyllidae s.l. were tested and compared with previously published cladograms based on rbcL, 18S rDNA and ORF2280 sequences. Parsimony analyses indicate two well-differentiated clades. One strongly supported clade comprises the carnivorous families Droseraceae and Nepenthaceae, along with its close relatives Dioncophyllaceae and Ancistrocladaceae. The second clade is restricted to the Polygonaceae, Plumbaginaceae, Tamaricaceae and Frankeniaceae. The Simmondsiaceae are more closely related to Caryophyllales and are at the base of the remaining taxa. Results of this analysis suggest that carnivory within Caryophyllidae s.l. has a monophyletic origin and, with the exception of Triphyophyllum, this syndrome was lost in the taxa of Dioncophyllaceae and Ancistrocladaceae. The exclusion of Drosophyllum from Droseraceae suggests no close relationship with this family. Finally, the data support a sister group relationship between the Plumbaginaceae and Polygonaceae and the Frankeniaceae and Tamaricaceae. An extensive survey of the rpl2 intron via PCR amplification indicates that the intron is absent from chloroplast genomes of Droseraceae and all taxa of Caryophyllales, but is present in Drosophyllum. Consequently, there is evidence for a multiple loss of the intron and strong support that Drosophyllum has affinities outside the Droseraceae. Our sequence data corroborate many aspects of recent cladistic analyses based predominantly on rbcL sequences. This study shows that matK sequences are useful for'phylogenetic inference among closely related members of Caryophyllidae. [source] | ||||||||||