The Internal Transcribed Spacer 2 Exhibits a Common Secondary Structure in Green Algae and Flowering Plants

Jeffrey, Christopher S.; Coleman, Annette W.

doi:10.1007/pl00006143

Cited by 313 publications

(241 citation statements)

References 48 publications

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“…The secondary structure of the ITS was analyzed as described in ref. 45. Blast searches (http://www.ncbi.nlm.nih.gov/BLAST) were performed on all obtained DNA sequences to compare their identity with S. marinoi sequences in the database.…”

Section: Methodsmentioning

confidence: 99%

Hundred years of genetic structure in a sediment revived diatom population

Härnström

Ellegaard²,

Andersen

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

166

171

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This paper presents research on the genetic structure and diversity of populations of a common marine protist and their changes over time. The bloom-forming diatom Skeletonema marinoi was used as a model organism. Strains were revived from anoxic discrete layers of a 210 Pb-dated sediment core accumulated over more than 100 y, corresponding to >40,000 diatom mitotic generations. The sediment core was sampled from the highly eutrophic Mariager Fjord in Denmark. The genetic structure of S. marinoi was examined using microsatellite markers, enabling exploration of changes through time and of the effect of environmental fluctuations. The results showed a stable population structure among and within the examined sediment layers, and a similar genetic structure has been maintained over thousands of generations. However, established populations from inside the fjord were highly differentiated from open-sea populations. Despite constant water exchange and influx of potential colonizers into the fjord, the populations do not mix. One fjord population, accumulated in 1980, was significantly differentiated from the other groups of strains isolated from the fjord. This differentiation could have resulted from the status of Mariager Fjord, which was considered hypereutrophic, around 1980. There was no significant genetic difference between preand posteutrophication groups of strains. Our data show that dispersal potential and generation time do not have a large impact on the genetic structuring of the populations investigated here. Instead, the environmental conditions, such as the extreme eutrophication of the Mariager Fjord, are deemed more important. microevolution | microsatellites

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Section: Methodsmentioning

confidence: 99%

Hundred years of genetic structure in a sediment revived diatom population

Härnström

Ellegaard²,

Andersen

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

166

171

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“…The ribosomal iTS and introns are subjected to evolutionary constraints related to the maintenance of specific secondary structures necessary for the correct processing of mature RNAs (cech 1988, saldanha 1993, Mai & coleMan 1997, coleMan et al 1998. in most cases this structure is relatively conserved and once it has been established, it can serve as a guidance to align divergent sequences (coleMan 2003).…”

Section: Types Of Molecular Datamentioning

confidence: 99%

Phylogeny and classification of Zygnematophyceae (Streptophyta): current state of affairs.

Gontcharov¹

2008

Fottea

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Conjugates (Zygnematophyceae) represent the most species-rich (ca. 4000 spp) algal lineage within the Streptophyta. Studies using various molecular markers have placed the class as one of the crown groups in Streptophyta and even suggested a close relationship between the zygnematophycean algae and land plants. Phenotypic diversity complicates systematics of the class and the relationships between its taxa remain poorly understood. Molecular phylogenetic analyses have established a number of clades in the class and revealed a disagreement between the traditional taxonomic structure of Zygnematophyceae and the pattern of phylogenetic relationships between the class members. in this paper, an overview of recent advances in our understanding of the phylogeny and classification of conjugating green algae is presented, with emphasis on the major clades established in the class, the clades' structure and polyphyly of some genera. We describe the areas of conflict and agreement between molecular phylogeny and traditional morphology-based taxonomy and stress that phenotypic characters provide little evidence for inferring relationships between taxa even at low taxonomic levels.

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“…Comparison of nrDNA sequences across the chlorophyll a+b algal diversity (e.g., Hershkovitz and Lewis, 1996;Mai and Coleman, 1997;Nakayama et al, 1998) reveals how unusual these regions in fact are in Halimeda. Inclusion of SSU nrDNA sequences of Halimeda and Caulerpa in phylogenetic analyses results in trees in which these taxa appear as close sisters on an extremely long branch (Zechman et al, 1999).…”

Section: Sequence Comparisons and Phylogenetic Analysesmentioning

confidence: 99%

“…Several ITS-2 positions, believed to be constant across Chlorophyta Mai and Coleman, 1997) differ or are lacking in Halimeda. Conserved secondary structure and compensatory base changes among the nrDNA sequences included here indicate functionality.…”

Section: Sequence Comparisons and Phylogenetic Analysesmentioning

confidence: 99%

Molecular systematics, historical ecology, and phylogeography of Halimeda (Bryopsidales)

Kooistra

Coppejans

Payri

2002

Molecular Phylogenetics and Evolution

126

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Halimeda (Bryopsidales), a genus of calcified, segmented green seaweeds, abounds in reefs and lagoons throughout the tropics. To investigate phylogenetic, phylogeographic, and historic ecological relationships of the genus, the nuclear rDNA including the SSU and both ITS regions were sequenced. A maximum likelihood tree revealed the following: (1) there were anatomical and morphological synapomorphies for five well-supported lineages; (2) the last common ancestor of one lineage invaded sandy substrata; those of two other lineages established in wave-affected habitats, whereas the cenancestor of the remaining two lineages occupied sheltered rocky slopes. Yet, several species adapted to new habitats subsequently, resulting in several cases of convergence; (3) all lineages separated into Atlantic and Indo-Pacific daughters, likely resulting from the rise of the Panamanian Isthmus. Each daughter pair gave rise to additional convergent species in similar habitats in different oceans; (4) Halimeda opuntia, the only monophyletic pantropical species detected so far, dispersed from the Indo-Pacific into the Atlantic well after the closure event; (5) minor SSU-sequence differences across species and phylogeographic patterns of vicariance indicated a relatively recent diversification of the extant diversity. Cretaceous and Early Tertiary fossil look-alikes of modern species must then have resulted from iterative convergence. Ó

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The Internal Transcribed Spacer 2 Exhibits a Common Secondary Structure in Green Algae and Flowering Plants

Cited by 313 publications

References 48 publications

Hundred years of genetic structure in a sediment revived diatom population

Hundred years of genetic structure in a sediment revived diatom population

Phylogeny and classification of Zygnematophyceae (Streptophyta): current state of affairs.

Molecular systematics, historical ecology, and phylogeography of Halimeda (Bryopsidales)

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