Phylogenetic utility of protein (RPB2, β-tubulin) and ribosomal (LSU,SSU) gene sequences in the systematics of Sordariomycetes (Ascomycota,Fungi)

The Sordariomycetes is an important group of fungi whose taxonomic relationships and classification is obscure. There is presently no multi-gene molecular phylogeny that addresses evolutionary relationships among different classes and orders. In this study, phylogenetic analyses with a broad taxon sampling of the Sordariomycetes were conducted to evaluate the utility of four gene regions (LSU rDNA, SSU rDNA, beta-tubulin and RPB2) for inferring evolutionary relationships at different taxonomic ranks. Single and multi-gene genealogies inferred from Bayesian and Maximum Parsimony analyses were compared in individual and combined datasets. At the subclass level, SSU rDNA phylogenies demonstrate their utility as a marker to infer phylogenetic relationships at higher levels. All analyses with SSU rDNA alone, combined LSU rDNA and SSU rDNA, and the combined 28 S rDNA, SSU rDNA and RPB2 datasets resulted in three subclasses: Hypocreomycetidae, Sordariomycetidae and Xylariomycetidae, which correspond well to established morphological classification schemes. At the ordinal level, the best resolved phylogeny was obtained from the combined LSU rDNA and SSU rDNA datasets. Individually, the RPB2 gene dataset resulted in significantly higher number of parsimony informative characters. Our results supported the recent separation of Boliniaceae, Chaetosphaeriaceae and Coniochaetaceae from Sordariales and placement of Coronophorales in Hypocreomycetidae. Microascales was found to be paraphyletic and Ceratocystis is phylogenetically associated to Faurelina, while Microascus and Petriella formed another clade and basal to other members of Halosphaeriales. In addition, the order Lulworthiales does not appear to fit in any of the three subclasses. Congruence between morphological and molecular classification schemes is discussed.     

Savoryellales (Hypocreomycetidae, Sordariomycetes): a novel lineage of aquatic ascomycetes inferred from multiple-gene phylogenies of the genera Ascotaiwania, Ascothailandia, and Savoryella

The taxonomic placement of freshwater and marine Savoryella species has been widely debated, and the genus has been tentatively assigned to various orders in the Sordariomycetes. The genus is characterized as possessing paraphyses that deliquesce early, elongate, clavate to cylindrical asci with a poorly developed apical ring and versicolored, three-septate ascospores. We performed two combined phylogenetic analyses of different genes: (i) partial small subunit rRNA (SSU), large subunit rRNA (LSU), DNA-dependent RNA polymerase II largest subunit (rpb2) dataset and (ii) SSU rDNA, LSU rDNA, DNA-dependent RNA polymerase II largest subunit (rpb1 and rpb2), translation elongation factor 1-alpha (tef1), the 5.8S ribosomal DNA (5.8S rDNA) dataset. Our results indicate that Savoryella species formed a monophyletic group within the Sordariomycetes but showed no affinity to the Hypocreales, Halosphaeriales (now Microascales), Sordariales and Xylariales, despite earlier assignments to these orders. Savoryella, Ascotaiwania and Ascothailandia (and its anamorph, Canalisporium) formed a new lineage that has invaded both marine and freshwater habitats, indicating that these genera share a common ancestor and are closely related. Because they show no clear relationship with any named order we erect a new order Savoryellales in the subclass Hypocreomycetidae, Sordariomycetes. The genera Savoryella and Ascothailandia are monophyletic, while the position of Ascotaiwania is unresolved. All three genera are phylogenetically related and form a distinct clade similar to the unclassified group of marine ascomycetes comprising the genera Swampomyces, Torpedospora and Juncigera (TBM clade: Torpedospora/Bertia/Melanospora) in the Hypocreomycetidae incertae sedis.     

MOLECULAR SYSTEMATICS OF THE FLORIDEOPHYCEAE (RHODOPHYTA) USING NUCLEAR LARGE AND SMALL SUBUNIT rDNA SEQUENCE DATA

Sequence data are presented for approximately 85% of the nuclear large subunit (LSU) rDNA gene for one member of the Bangiophyceae and 47 members of the Florideophyceae, the latter representing all but one of the currently recognized florideophyte orders. Distance, parsimony, and maximum likelihood analyses of these data were used to generate phylogenetic trees, and bootstrap resampling was implemented to infer robustness for distance and parsimony results. LSU phylogenies were congruent with published nuclear small subunit (SSU) rDNA results in that four higher level florideophyte lineages were resolved: lineage 1, containing the order Hildenbrandiales; lineage 2, recovered only under distance analysis, composed of the orders Acrochaetiales, Balliales, Batrachospermales, Corallinales, Nemaliales, Palmariales, and Rhodogorgonales; lineage 3, containing the Ahnfeltiales; and lineage 4, composed of the orders Bonnemaisoniales, Ceramiales, Gelidiales, Gigartinales, Gracilariales, Halymeniales, Plocamiales, and Rhodymeniales. Analyses were also performed on a combined LSU–SSU data set and an SSU-only data set to account for differences in taxon sampling relative to published studies using this latter gene. Combined LSU–SSU analyses resulted in phylogenetic trees of similar topology and support to those obtained from LSU-only analyses. Phylogenetic trees produced from SSU-only analyses differed somewhat in particulars of branching within lineages 2 and 4 but overall were congruent with the LSU-only and combined LSU–SSU results. We close with a discussion of the phylogenetic potential that the LSU has displayed thus far for resolving relationships within the Florideophyceae.     

PHYLOGENY OF THE EUGLENOID LORICATE GENERA TRACHELOMONAS AND STROMBOMONAS (EUGLENOPHYTA) INFERRED FROM NUCLEAR SSU AND LSU rDNA1

Previous studies using the nuclear SSU rDNA and partial LSU rDNA have demonstrated that the euglenoid loricate taxa form a monophyletic clade within the photosynthetic euglenoid lineage. It was unclear, however, whether the loricate genera Trachelomonas and Strombomonas were monophyletic. In order to determine the relationships among the loricate taxa, SSU and LSU nuclear rDNA sequences were obtained for eight Strombomonas and 25 Trachelomonas strains and combined in a multigene phylogenetic analysis. Conserved regions of the aligned data set were used to generate maximum‐likelihood (ML) and Bayesian phylogenies. Both methods recovered a strongly supported monophyletic loricate clade with Strombomonas and Trachelomonas species separated into two sister clades. Taxa in the genus Strombomonas sorted into three subclades. Within the genus Trachelomonas, five strongly supported subclades were recovered in all analyses. Key morphological features could be attributed to each of the subclades, with the major separation being that all of the spine‐bearing taxa were located in two sister subclades, while the more rounded, spineless taxa formed the remaining three subclades. The separation of genera and subclades was supported by 42 distinct molecular signatures (33 in Trachelomonas and nine in Strombomonas). The morphological and molecular data supported the retention of Trachelomonas and Strombomonas as separate loricate genera.     

Interrelationships and evolution of the tapeworms (Platyhelminthes: Cestoda)

Interrelationships of the tapeworms (Platyhelminthes: Cestoda) were examined by use of small (SSU) and large (LSU) subunit ribosomal DNA sequences and morphological characters. Fifty new complete SSU sequences were added to 21 sequences previously determined, and 71 new LSU (D1-D3) sequences were determined for the complementary set of taxa representing each of the major lineages of cestodes as currently understood. New sequences were determined for three amphilinidean taxa, but were removed from both alignments due to their excessively high degree of divergence from other cestode sequences. A morphological character matrix coded for supraspecific taxa was constructed by the modification of matrices from recently published studies. Maximum-parsimony (MP) analyses were performed on the LSU, SSU, LSU+SSU, and morphological data partitions, and minimum-evolution (ME) analyses utilizing a general time reversible model of nucleotide substitution including estimates of among-site rate heterogeneity were performed on the molecular data partitions. Resulting topologies were rooted at the node separating the Gyrocotylidea from the Eucestoda. The LSU data were found to be more informative than the SSU data and were more consistent with inferences from morphology, although nodal support was generally weak for most basal nodes. One class of transitions was found to be saturated for comparisons between the most distantly related taxa (gyrocotylideans vs cyclophyllideans and tetrabothriideans). Differences in the topologies resulting from MP and ME analyses were not statistically significant. Nonstrobilate orders formed the basal lineages of trees resulting from analysis of LSU data and morphology. Difossate orders were basal to tetrafossate orders, the latter of which formed a strongly supported clade. A clade including the orders Cyclophyllidea, Nippotaeniidea, and Tetrabothriidea was supported by all data partitions and methods of analysis. Paraphyly of the orders Pseudophyllidea, Tetraphyllidea, and Trypanorhyncha was consistent among the molecular data partitions. Inferences are made regarding a monozoic (nonsegmented) origin of the Eucestoda as represented by the Caryophyllidea and for the evolution of the strobilate and acetabulate/tetrafossate conditions having evolved in a stepwise pattern.     

SSU rDNA phylogeny of cladoniiform lichens

To examine phylogenetic relationships among the "cladoniiform" lichenized fungi, i.e., the families Cladoniaceae, Baeomycetaceae, Icmadophilaceae, Stereocaulaceae, and Siphulaceae, and to provide evidence for the anticipated independent origins of podetia and pseudopodetia, we conducted phylogenetic analyses of SSU (small subunit) rDNA sequences from 39 lichen-forming fungi. These fungi represent all of the major growth forms of lichen associations, fruticose (including "cladoniiform"), foliose, and crustose. Our analysis suggests that lichen-forming fungi with a "cladoniiform" morphology arose multiple times within the ascomycetes. Additionally, each of the other thallus growth forms, crustose, foliose, and fruticose, have originated multiple times. It also seems to be clear that neither all podetiate nor all pseudopodetiate taxa form a monophyletic group. Therefore the term "podetium" should be restricted to homologous structures that are most probably limited to the genera Cladonia, Cladina, Pycnothelia, and allies. The "pseudopodetia" of Stereocaulon (Stereocaulaceae) and Cladia (Cladiaceae) may represent different states of the same homologous character. Our phylogenetic hypothesis supports the monophyletic origin of the order Lecanorales sensu stricto, including representatives of five suborders Cladoniineae, Lecanorineae, Teloschistineae, Agyriineae and Peltigerineae, but excluding representatives of the suborders Acarosporineae (Acarospora schleicheri and Megaspora verrucosa), Pertusariineae (Pertusaria trachythallina), and Umbilicarineae. The suborder Cladoniineae and the family Cladoniaceae both appear to be polyphyletic assemblages.     

Phylogenetic significance of morphological characters in the tropical Hypotrachyna clade of parmelioid lichens (Parmeliaceae, Ascomycota)

Lichen-forming ascomycetes exhibit often complex morphologies of the vegetative thallus that are usually not found in non-lichenized fungi. This includes the thallus organization and appendical structures associated with the main thallus, such as cilia and rhizines. Such morphological characters are widely employed in the taxonomy of parmelioid lichens, especially at generic level. Within parmelioid lichens, several monophyletic groups can be distinguished, the Hypotrachyna clade being one of them, which includes mostly tropical taxa. In this first molecular study focused specifically on the Hypotrachyna clade, we used maximum parsimony and Bayesian analyses of a combined data set of nuclear ITS and mitochondrial SSU rDNA sequences to (1) test the monophyly of genera presently accepted within the clade and (2) evaluate the phylogenetic value of the morphological characters used to circumscribe genera in parmelioid lichens. Out of the 89 mtSSU and 88 nuITS sequences included in the present study, 121 sequences were newly obtained. Our results show that the taxa within the clade fall into two major groups and that the genus Hypotrachyna is polyphyletic. Everniastrum and Parmelinopsis are nested within Hypotrachyna sensu stricto, the latter being also polyphyletic. Bulbothrix is paraphyletic with Parmelinella nested within and is basal to the second major Hypotrachyna clade. Monophylies of Bulbothrix and Hypotrachyna are significantly rejected. The phylogenetic analysis demonstrates that morphological characters currently used to circumscribe genera in parmelioid lichens, such as cortical anatomy, lobe configuration, cilia, and rhizines have been overestimated and have only minor value in identifying monophyletic groups.     

Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton

Analyses of small subunit ribosomal RNA genes (SSU rDNAs) have significantly influenced our understanding of the composition of aquatic microbial assemblages. Unfortunately, SSU rDNA sequences often do not have sufficient resolving power to differentiate closely related species. To address this general problem for uncultivated bacterioplankton taxa, we analysed and compared sequences of polymerase chain reaction (PCR)-generated and bacterial artificial chromosome (BAC)-derived clones that contained most of the SSU rDNAs, the internal transcribed spacer (ITS) and the large subunit ribosomal RNA gene (LSU rDNA). The phylogenetic representation in the rRNA operon PCR library was similar to that reported previously in coastal bacterioplankton SSU rDNA libraries. We observed good concordance between the phylogenetic relationships among coastal bacterioplankton inferred from SSU or LSU rDNA sequences. ITS sequences confirmed the close intragroup relationships among members of the SAR11, SAR116 and SAR86 clades that were predicted by SSU and LSU rDNA sequence analyses. We also found strong support for homologous recombination between the ITS regions of operons from the SAR11 clade.     

Morphological convergence characterizes the evolution of Xanthophyceae (Heterokontophyta): evidence from nuclear SSU rDNA and plastidial rbcL genes

Xanthophyceae are a group of heterokontophyte algae. Few molecular studies have investigated the evolutionary history and phylogenetic relationships of this class. We sequenced the nuclear-encoded SSU rDNA and chloroplast-encoded rbcL genes of several xanthophycean species from different orders, families, and genera. Neither SSU rDNA nor rbcL genes show intraspecific sequence variation and are good diagnostic markers for characterization of problematic species. New sequences, combined with those previously available, were used to create different multiple alignments. Analyses included sequences from 26 species of Xanthophyceae plus three Phaeothamniophyceae and two Phaeophyceae taxa used as outgroups. Phylogenetic analyses were performed according to Bayesian inference, maximum likelihood, and maximum parsimony methods. We explored effects produced on the phylogenetic outcomes by both taxon sampling as well as selected genes. Congruent results were obtained from analyses performed on single gene multiple alignments as well as on a data set including both SSU rDNA and rbcL sequences. Trees obtained in this study show that several currently recognized xanthophycean taxa do not form monophyletic groups. The order Mischococcales is paraphyletic, while Tribonematales and Botrydiales are polyphyletic even if evidence for the second order is not conclusive. Botrydiales and Vaucheriales, both including siphonous taxa, do not form a clade. The families Botrydiopsidaceae, Botryochloridaceae, and Pleurochloridaceae as well as the genera Botrydiopsis and Chlorellidium are polyphyletic. The Centritractaceae and the genus Bumilleriopsis also appear to be polyphyletic but their monophyly cannot be completely rejected with current evidence. Our results support morphological convergence at any taxonomic rank in the evolution of the Xanthophyceae. Finally, our phylogenetic analyses exclude an origin of the Xanthophyceae from a Vaucheria-like ancestor and favor a single early origin of the coccoid cell form.     

A further phylogenetic study of the heterotrophic dinoflagellate genus, Protoperidinium (Dinophyceae) based on small and large subunit ribosomal RNA gene sequences

The heterotrophic marine dinoflagellate genus Protoperidinium is the largest genus in the Dinophyceae. Previously, we reported on the intrageneric and intergeneric phylogenetic relationships of 10 species of Protoperidinium, from four sections, based on small subunit (SSU) rDNA sequences. The present paper reports on the impact of data from an additional 5 species and, therefore, an additional two sections, using the SSU rDNA data, but now also incorporating sequence data from the large subunit (LSU) rDNA. These sequences, in isolation and in combination, were used to reconstruct the evolutionary history of the genus. The LSU rDNA trees support a monophyletic genus, but the phylogenetic position within the Dinophyceae remains ambiguous. The SSU, LSU and SSU + LSU rDNA phylogenies support monophyly in the sections Avellana, Divergentia, Oceanica and Protoperidinium, but the section Conica is paraphyletic. Therefore, the concept of discrete taxonomic sections based on the shape of 1′ plate and 2a plate is upheld by molecular phylogeny. Furthermore, the section Oceanica is indicated as having an early divergence from other groups within the genus. The sections Avellana and Excentrica and a clade combining the sections Divergentia/Protoperidinium derived from Conica‐type dinoflagellates independently. Analysis of the LSU rDNA data resulted in the same phylogeny as that obtained using SSU rDNA data and, with increased taxon sampling, including members of new sections, a clearer idea of the evolution of morphological features within the genus Protoperidinium was obtained. Intraspecific variation was found in Protoperidinium conicum (Gran) Balech, Protoperidinium excentricum (Paulsen) Balech and Protoperidinium pellucidum Bergh based on SSU rDNA data and also in Protoperidinium claudicans (Paulsen) Balech, P. conicum and Protoperidinium denticulatum (Gran et Braarud) Balech based on LSU rDNA sequences. The common occurrence of base pair substitutions in P. conicum is indicative of the presence of cryptic species.     

Divergent Histories of rDNA Group I Introns in the Lichen Family Physciaceae

The wide but sporadic distribution of group I introns in protists, plants, and fungi, as well as in eubacteria, likely resulted from extensive lateral transfer followed by differential loss. The extent of horizontal transfer of group I introns can potentially be determined by examining closely related species or genera. We used a phylogenetic approach with a large data set (including 62 novel large subunit [LSU] rRNA group I introns) to study intron movement within the monophyletic lichen family Physciaceae. Our results show five cases of horizontal transfer into homologous sites between species but do not support transposition into ectopic sites. This is in contrast to previous work with Physciaceae small subunit (SSU) rDNA group I introns where strong support was found for multiple ectopic transpositions. This difference in the apparent number of ectopic intron movements between SSU and LSU rDNA genes may in part be explained by a larger number of positions in the SSU rRNA, which can support the insertion and/or retention of group I introns. In contrast, we suggest that the LSU rRNA may have fewer acceptable positions and therefore intron spread is limited in this gene. Reviewing Editor: Dr. W. Ford Doolittle     

Ultrastructure and molecular phylogenetic position of a new marine sand-dwelling dinoflagellate from British Columbia,Canada: Pseudadenoides polypyrenoides sp. nov. (Dinophyceae)

Two monospecific genera of marine benthic dinoflagellates, Adenoides and Pseudadenoides, have unusual thecal tabulation patterns (lack of cingular plates in the former; and no precingular plates and a complete posterior intercalary plate series in the latter) and are thus difficult to place within a phylogenetic framework. Although both genera share morphological similarities, they have not formed sister taxa in previous molecular phylogenetic analyses. We discovered and characterized a new species of Pseudadenoides, P. polypyrenoides sp. nov., at both the ultrastructural and molecular phylogenetic levels. Molecular phylogenetic analyses of SSU and LSU rDNA sequences demonstrated a close relationship between P. polypyrenoides sp. nov. and Pseudadenoides kofoidii, and Adenoides and Pseudadenoides formed sister taxa in phylogenetic trees inferred from LSU rDNA sequences. Comparisons of morphological traits, such as the apical pore complex (APC), demonstrated similarities between Adenoides, Pseudadenoides and several planktonic genera (e.g. Heterocapsa, Azadinium and Amphidoma). Molecular phylogenetic analyses of SSU and LSU rDNA sequences also demonstrated an undescribed species within Adenoides.     

Systematics of Halosarpheia based on morphological and molecular data

The genus Halosarpheia (Halosphaeriales) was established for marine ascomycetes with obpyriform to sub-globose, coriaceous, brown to black ostiolate ascomata with long necks; hamathecia of catenophyses; thin-walled, unitunicate, persistent asci with thick-walled apices; and ellipsoid, one septate, hyaline ascospores equipped with coiled, threadlike apical appendages that unfurl in water. Emphasis on ascospore appendage morphology has led to the inclusion in the genus of morphologically disparate fungi from a variety of marine and freshwater habitats. To better understand the evolutionary relationships of Halosarpheia species, phylogenetic analyses were conducted on 16 Halosarpheia species, 13 other species of Halosphaeriales and representatives of the Microascales, Hypocreales, Sordariales and Xylariales using 18S and 28S rDNA sequence data. All of the Halosarpheia species occurred on the Halosphaeriales clade. The type species of the genus, H. fibrosa, occurred on a well-supported clade with two morphologically similar species, H. trullifera and H. unicellularis. This clade, which phylogenetically was distant from the clades of other Halosarpheia species, represents the genus Halosarpheia sensu stricto. The other Halosarpheia species were distributed among eight other well-supported clades clearly separated from one another based on molecular data. New generic names are established for six of these clades, one new species is described, and one species is transferred to Aniptodera. A table (Table I) comparing the morphology, habitat, substrate and distribution of the genera of aquatic ascomycetes with coiled, threadlike apical appendages treated in this study is provided, along with a key for their identification.     

Phylogenetic analysis of Glomeromycota by partial LSU rDNA sequences

We analyzed the large subunit ribosomal RNA (rRNA) gene [LSU ribosomal DNA (rDNA)] as a phylogenetic marker for arbuscular mycorrhizal (AM) fungal taxonomy. Partial LSU rDNA sequences were obtained from ten AM fungal isolates, comprising seven species, with two new primers designed for Glomeromycota LSU rDNA. The sequences, together with 58 sequences available from the databases, represented 31 AM fungal species. Neighbor joining and parsimony analyses were performed with the aim of evaluating the potential of the LSU rDNA for phylogenetic resolution. The resulting trees indicated that Archaeosporaceae are a basal group in Glomeromycota, Acaulosporaceae and Gigasporaceae belong to the same clade, while Glomeraceae are polyphyletic. The results support data obtained with the small subunit (SSU) rRNA gene, demonstrating that the LSU rRNA gene is a useful molecular marker for clarifying taxonomic and phylogenetic relationships in Glomeromycota.     

Concatenated SSU and LSU rDNA data confirm the main evolutionary trends within myxosporeans (Myxozoa: Myxosporea) and provide an effective tool for their molecular phylogenetics

Views on myxosporean phylogeny and systematics have recently undergone substantial changes resulting from analyses of SSU rDNA. Here, we further investigate the evolutionary trends within myxosporean lineages by using 35 new sequences of the LSU rDNA. We show a good agreement between the two rRNA genes and confirm the main phylogenetic split between the freshwater and marine lineages. The informative superiority of the LSU data is shown by an increase of the resolution, nodal supports and tree indexes in the LSU rDNA and combined analyses. We determine the most suitable part of LSU for the myxosporean phylogeny by comparing informative content in various regions of the LSU sequences. Based on this comparison, we propose the D5–3′-end part of the LSU rRNA gene as the most informative region which provides in concatenation with the complete SSU a well resolved and robust tree. To allow for simple amplification of the marker, we design specific primer set for this part of LSU rDNA.     

Molecular phylogeny of the Laboulbeniomycetes (Ascomycota)

A first molecular-based phylogeny is presented for the Laboulbeniomycetes, a group of ascomycete fungi that utilize arthropods for nutrition and/or dispersal. Morphological diversification and life-history evolution has made it difficult to resolve relationships within the group, and to identify close relatives. Here, we infer a preliminary phylogeny based on acquisition of 51 new SSU rDNA sequences, representing a total of 65 taxa. The results of this study demonstrate that Laboulbeniomycetes is monophyletic, and related to Sordariomycetes. The class could be divided into at least 4 or 5 orders, though we refrain from formally giving names to these at this stage. Further evidence for the occurrence of asexuality within the class is provided by the inclusion of the genera Chantransiopsis and Tetrameronycha, both known only as asexual taxa with thalli consisting of linearly superposed cells. The precise placement of the genus Herpomyces (Herpomycetaceae), on cockroaches, remains unresolved in our analysis, but lies outside of the main clade of sexually reproducing Laboulbeniales. There is good support for this latter grouping, comprising taxa that are found on both aquatic and terrestrial hosts. Within this large assemblage, we recognize 5 distinct clades (clades E, F, G, H, I). Relationships among the so-called “aquatic genera” (≡ Ceratomycetaceae + some Euceratomycetaceae and Zodiomyces) are poorly resolved in our analyses, accounting for 3 of these clades (E, F, G), with the remainder of the taxa (largely equivalent to Laboulbeniaceae) split into two major groupings (clades H, I). Across all taxa, antheridial characteristics, features on which the earliest classifications were based, are shown to be homoplastic. On the other hand, features of perithecial development show an overall trend towards reduction, and appear to be phylogenetically informative. Morphological characters are identified that support the dichotomy in the Laboulbeniaceae and subclades within the two major groupings are discussed further in light of information on thallus morphology, development, and host relationships.     

地衣型真菌的I型内含子及其在系统发育中的应用

以蜈蚣衣属、黑蜈蚣衣属地衣样品为材料,结合GenBank中相关数据,对地衣型真菌核糖体小亚基 DNA上的I型内含子分布模式进行归纳,并探讨了其在地衣型真菌系统发育研究中的应用。结果表明在地衣型真菌核糖体小亚基 DNA上存在多个I型内含子插入位点,通过二级结构分析给出了天然状态下I型内含子发生转座的证据。分析显示,I型内含子作为分子标记,只适合用于种下单位的系统发育研究中。     

A REEXAMINATION OF THE SYSTEMATICS OF THE ACROCHAETIALES (RHODOPHYTA) USING LARGE-SUBUNIT RDNA SEQUENCE DATA

The taxonomic history of the red algal order Acrochaetiales is chaotic. There is no consensus in the literature as to how many genera should be recognized or in the assignment of the over 400 species to these genera. Morphological and anatomical studies have provided a suite of possible characters to delineate genera within this order, but there have been major discrepancies in the assessment and use of these features. The phylogenetic placement of the Acrochaetiales has also been the focus of debate. Once thought to be the most ancestral florideophyte lineage, recent molecular systematic studies have illustrated that this order is a derived lineage closely related to the Nemaliales and Palmariales. Phylogenies using sequences of the small-subunit (SSU) rDNA have strongly supported two very divergent lineages within a possibly polyphyletic Acrochaetiales. The relationships between these two groups and among other closely related rhodophyte orders were not resolved. We have generated large-subunit (LSU) rDNA sequence data for representatives of the Acrochaetiales and related taxa. Distance and parsimony phylogenies based on LSU and combined SSU and LSU data will be presented. The increased phylogenetic signal afforded by this approach will shed light on previous conundrums in the systematics of this group.     

Evolution of Filamentous Ascomycetes Inferred from LSU rDNA Sequence Data

Abstract: The nuclear LSU rRNA gene was examined in order to evaluate the current phylogeny of ascomycetes, which is mainly based on nuclear SSU rRNA data. Partial LSU rRNA gene sequences of 19 ascomycetes were determined and aligned with the corresponding sequences of 13 other ascomycetes retrieved from Genbank, including all classes traditionally distinguished and most of the recently accepted classes. The classification based on SSU rDNA data and morphological characters is supported, while the traditional classification and classifications based on the ascus type are rejected. Ascomycetes with perithecia and cleistothecia form monophyletic groups, while the discomycetes are a paraphyletic assemblage. The Pezizales are basal to all other filamentous ascomycetes. The monophyly of Loculoascomycetes is uncertain. The results of the LSU rDNA analysis agree with those of the SSU rDNA and RPB2 gene analyses, suggesting that most classes circumscribed in the filamentous ascomycetes are monophyletic. The branching order and relationships among these classes, however, cannot be elucidated with any of these data sets.