Nuclear SSU rRNA Gene Research Articles

Systematics of Bangia (Bangiales, Rhodophyta) in North America. II. Biogeographical trends in karyology: chromosome numbers and linkage with gene sequence phylogenetic trees

An extensive karyological analysis was carried out on marine and freshwater Bangia from North America (70°N to c. 23°N), including 40 collections from the Pacific, 39 from the Atlantic, 8 from the Laurentian Great Lakes and also 2 freshwater collections from Europe for comparison with the Great Lakes material. Chromosome numbers were determined and linked to gene trees derived from DNA sequence analyses of the chloroplast rbcL and nuclear small-subunit (SSU) rRNA genes. For the first time in one continent, five different chromosomal types were observed among marine populations, viz. monosporic plants with three (n), four (n) or six (2n) chromosomes and sexual plants with three (n)/six (2n) or four (n)/eight (2n) chromosomes. These types were also characterized with respect to seasonality and distribution. Freshwater Bangia filaments were all monosporic, with three chromosomes and a distinctive chromosome morphology: the third chromosome is very much smaller than that in marine three-chromosome collections. Based on these observations and DNA sequence analyses in which freshwater collections of Bangia are positioned on a separate and well-supported branch, we propose resurrecting the name B. atropurpurea to represent this lineage. There also appear to be some distinct entities among the marine Bangia occurring along North American coastlines, judging by chromosome numbers and gene trees. For example, there is a transarctic group of monosporic three-chromosome plants that have identical sequences for rbcL and very similar nuclear SSU rRNA gene sequences. However, populations of Bangia along the mid to southern coasts of North America with the same chromosome number were not always found to cluster together in gene trees, suggesting a mixing of multiple species brought about possibly by vector-assisted transport. At this time, marine populations should continue to be recognized as B. fuscopurpurea until their complex relationships can be resolved.

THE SCUTOCOXIFERA TAX. NOV. AND THE INFORMATION CONTENT OF NUCLEAR SSU RDNA SEQUENCES FOR RECONSTRUCTION OF ISOPOD PHYLOGENY (PERACARIDA: ISOPODA)

The nuclear ssu rRNA gene of several isopods (Crustacea, Peracarida) was sequenced to study its phylogenetic information content. Several areas had to be cut out of the alignment of 31 isopod sequences and selected outgroup arthropod sequences due to the lack of alignable patterns. The final alignment had 2,533 positions and 43 sequences. The length of the isopod nuclear ssu rRNA genes varies between 2,098 and 3,402 bp. In some clades the gene length increases; in others like the cymothoids and bopyrids, long deletions occur. Some insertions are specific for major groups (e.g., amphipods, isopods). Most elongation areas evolve rapidly and are not alignable among higher taxa. Information content is visualized with spectra of supporting positions. Only a few groups are unambiguously supported with a signal distinctly higher than background noise. The results of maximum parsimony analyses are congruent with major aspects of earlier hypotheses on isopod phylogeny. Some contradictions are discussed. The latter are mainly based on a lack of reliable information. A major monophyletic group found in the molecular phylogenies and also supported by distinct morphological characters is named Scutocoxifera tax. nov., composed of the Oniscidea, Valvifera, Sphaeromatidea, Anthuridea, and Cymothoida. SEM photographs are presented to document the apomorphic state of the coxa in the Scutocoxifera.

Molecular Characterization of the Host-Adapted Pathogen Verticillium longisporum on the Basis of a Group-I Intron Found in the Nuclear SSU-rRNA Gene

Verticillium wilt of oilseed rape is caused by the host-adapted pathogen Verticillium longisporum comb. nov. With one set of nuclear SSU-rRNA gene primers, a PCR amplification product of ca. 2.5 kb was generated from all isolates of V. longisporum tested (36 from Europe, Japan, and USA), with the exception of two recombinant isolates. On the contrary, all the other phytopathogenic and nonphytopathogenic species of Verticillium tested (18 species, 46 isolates), with the exception of one isolate of V. lecanii and two of Cordyceps sp., generated a product of ca. 1.65 kb. Sequence analysis of the SSU-rRNA gene of two typical isolates of V. longisporum (wild radish, Japan, and oilseed rape, Germany) revealed that this dimorphism was due to the presence of an identical 839-bp intron located in a highly conserved insertion position (nt 1165 of Saccharomyces cerevisiae). The intron sequence was classified as group-I intron on the basis of conserved sequence and secondary structural elements. Primers designed from the 839-bp intron sequence amplified only the V. longisporum. Phylogenetic analysis based on SSU-rDNA sequences showed that V. longisporum was closely related to the genera of other filamentous Ascomycetes with fruiting bodies.

Phylogeny and Biogeography of Serolid Isopods (Crustacea, Isopoda, Serolidae) and the Use of Ribosomal Expansion Segments in Molecular Systematics

In this study, a molecular phylogenetic hypothesis for 16 species of serolid isopods (Crustacea, Isopoda, Serolidae) from Antarctic waters, the deep sea, South America, and Australia is presented. The genes used are a 500-bp fragment of the mitochondrial LSU rRNA gene and a 700-bp fragment located in the variable region V4 of the nuclear SSU rRNA gene. The species composition and monophyly of morphologically defined genera of which several members were available are confirmed by the molecular data (Ceratoserolis, Spinoserolis, and Cuspidoserolis). The molecular data also support the redefinition of Frontoserolis s.l. and Serolella and the erection of the new genera Septemserolis and Paraserolis, as proposed by Wägele. The relationship among several genera is resolved differently in the molecular hypothesis than in the two existing morphological hypotheses, however. The molecular phylogeny may have important consequences for understanding the biogeography of the Serolidae, indicating that all Antarctic species in this study form a monophyletic group which has probably derived from species with closest extant relatives in South America. All 3 species included in this study living today in deep waters (>2000 m) of the Southern Ocean are most closely related to species living on the Antarctic shelf, so that parallel colonization of the deep sea by way of polar submergence can be reconstructed. In this study, a V4 expansion segment is reported which exceeds the longest crustacean sequences known until now by more than 270 bp. Although the V4 expansion segment has proven useful for phylogenetic purposes in this study, there is circumstantial evidence that its mechanism of evolution may depend not only on inheritance of single-site substitutions, making its routine use in phylogenetic studies potentially dangerous.

The phylogenetic relationship of the Sphaerophoraceae, Austropeltum and Neophyllis (lichenized Ascomycota) inferred by SSU rDNA sequences

Close relationship between the Sphaerophoraceae and Austropeltum and Neophyllis , is established by phylogenetic analysis of nuclear SSU rDNA sequences, including newly produced sequences of Austropeltum glareosum, Neophyllis melacarpa and Sphaerophorus globosus. Anatomical, chemical, and ontogenetical characters, and support for this relationship, are discussed, as is the suitability of the nuclear SSU rRNA gene for phylogenetic analyses at this taxonomic level. The analysis gives no support for regarding Austropeltum (presently classified in the Stereocaulaceae) and Neophyllis (presently in the Cladoniaceae) to be closely related to either Stereocaulon ramulosum and Pilophorus acicularis (Stereocaulaceae), or Cladonia bellidiflora (Cladoniaceae), and it is pointed out that the delimitation of all three families needs further investigation. The homology of podetial and pseudopodetial structures is discussed.

Multiple origins of fungal group I introns located in the same position of nuclear SSU rRNA gene

The archiascomycetous fungus Protomyces pachydermus has two group I introns within the nuclear small subunit (nSSU) rRNA gene. One of these introns has an internal open reading frame (ORF) that encodes a predicted protein of 228 amino acid residues. On the other hand, Protomyces macrosporus has two group I introns that insert at the same positions as P. pachydermus, which have no ORF. Each alignment was constructed with Protomyces group I introns located in the same position and other introns retrieved by the BLAST Search. Each phylogenetic tree based on the alignment shows that Protomyces introns are monophyletic but the relationships among fungal introns do not reflect on the fungal phylogeny. Therefore, it is suggested that two different horizontal transfers of group I introns occurred at the early stage of Protomyces species diversification.

Phylogenetic and structural studies in the Thelebolaceae (Ascomycota)

Several minute dung-inhabiting discomycetes have been classified in the family Thelebolaceae, which has traditionally been included in the order Pezizales. The non-operculate type-genusThelebolus has recently been excluded from the Pezizales. The phylogenetic distribution of other genera associated with Thelebolaceae is still obscure. We have analysed ca. 580 bp from a variable part of the nuclear SSU rRNA gene fromAscozonus, Caccobius, Lasiobolus andThecotheus, and compared these with ca. 1700 bp sequences fromThelebolus, Pleospora, Pezizales, leotiales and Leotiales-related taxa. In the resulting tree,Ascozonus andCaccobius group withThelebolus and the inoperculate discomycetes;Lasiobolus groups withAscodesmis, andThecotheus withAscobolus within Pezizales. SEM pictures of fruit-bodies and ascus apices ofAscozonus, and ascospores fromThecotheus are presented to illustrate characteristic features of these taxa.

Relationships among Eucheuma denticulatum, Eucheuma isiforme and Kappaphycus alvarezii (Gigartinales, Rhodophyta) based on nuclear ssu-rRNA gene sequences

The nuclear genes encoding small-subunit ribosomal RNAs (ssu-rDNAs) of the carrageenophytes Eucheuma denticulatum, E. isiforme and Kappaphycus alvarezii were amplified by the polymerase chain reaction, cloned and sequenced. The sequences range from 1767 (K. alvarezii) to 1781 (E. isiforme) nucleotides in length, and have guanine+cytosine contents between 51.2% (E. isiforme) and 51.5% (E. denticulatum). Pairwise sequence identities among these sequences ranged from 97.6% to 98.5%, levels comparable to some intergeneric identities within Gracilariales. In phylogenetic analyses, the two Eucheuma ssu-rDNAs group stably together vis-a-vis the ssu-rDNA of K. alvarezii, and these three ssu-rDNAs form a monophyletic group within a larger grouping of other carrageenophytes. The results demonstrate quantitatively that analysis of nuclear-encoded ssu-rDNA sequences is likely to be useful in resolving taxonomic, phylogenetic and biogeographic questions among tribe Eucheumatoideae Doty.