A MOLECULAR APPROACH TO THE CIRCUMSCRIPTION AND EVALUATION OF SOME GENERA SEGREGATED FROMPARMELIAS. LAT.

New sequences have been produced of the ITS rDNA region of twenty-nine species ofParmeliaceae, and analysed by neighbour-joining maximum likelihood distance analysis, and maximum parsimony analysis. Twelve monophyletic groups have been identified, most of which correspond to proposed generic segregated fromParmelias. lat.ParmeliaandParmelina,Melanelia, andPuncteliaappear as independent monophyletic groups; the type species of the two latter genera were, however, not included in the analysis. The parsimony analysis does not supportXanthoparmeliaas a monophyletic group separate fromNeofuscelia, andRimelia reticulatais nested withinParmotrema. Parmelinopsis horrescensis more closely related toHypotrachyna revolutathan toParmelina. Genetic distance values suggest thatFlavoparmelia caperatais closer toParmotremathan to other taxa included, and thatPlatismatia glaucaandHypogymnia tubulosaare closer toParmelias. lat. than to thePhysciaceae. However, there is no conclusive support for any of the latter groupings in the parsimony analysis. We conclude that the ITS region contains valuable information for studying generic delimitations within the familyParmeliaceae, but our study suggests that this region will not conclusively resolve within-family relationships in this group.     

Chemotypes significance of lichenized fungi by structural characterization of heteropolysaccharides from the genera Parmotrema and Rimelia

Galactoglucomannans were isolated from the lichenized fungi of the genus Parmotrema (Parmotrema austrosinense, Parmotrema delicatulum, Parmotrema mantiqueirense, Parmotrema schindlerii, and Parmotrema tinctorum and that of Rimelia (Rimelia cetrata and Rimelia reticulata) via successive hot alkaline extraction and precipitation with Fehling solution. The structure of each polysaccharide was investigated using 13C NMR and HSQC-DEPT spectroscopy, methylation analysis, and HPSEC-MALLS. The galactoglucomannans had a (1-->6)-linked main chain of alpha-Manp units, substituted preferentially at O-2 and O-4 by alpha-Galp and beta-Galp nonreducing end-units, respectively. The C-1 region of the 13C NMR spectra of these heteropolysaccharides is typical of the lichen species, and is an additional tool in lichenized fungi classification.     

Glucans of lichenized fungi: significance for taxonomy of the genera Parmotrema and Rimelia

The glucans of lichenized fungi are an important class of polysaccharides with structural and chemotaxonomic roles. The water-insoluble glucans of the genus Parmotrema (P. austrosinense, P. delicatulum, P. mantiqueirense, P. schindleri, and P. tinctorum) and those of Rimelia (R. cetrata and R. reticulata), were investigated in order to evaluate the significance in chemotyping, with nigeran [(1-->3),(1-->4)-alpha-glucan] and lichenan [(1-->3),(1-->4)-beta-glucan] characterized using (1)H and (13)C NMR, methylation analysis, and controlled Smith degradations. Results from all species were similar, suggesting that glucan chemistry does not support separation of Rimelia from Parmotrema.     

Polyphyletic distribution of bristle formation in Chlorellaceae: Micractinium, Diacanthos, Didymogenes and Hegewaldia gen. nov. (Trebouxiophyceae, Chlorophyta)

In the traditional sense, several families of Chlorococcales sensu lato , such as Golenkiniaceae, Micractiniaceae, and Scenedesmaceae contained taxa with bristle formation, whereas the Chlorellaceae contained only genera without bristles. However, phylogenetic analyses of the small subunit (SSU) and internal transcribed spacer (ITS) rDNA sequences have shown that the genera Micractinium, Diacanthos (formerly Micractiniaceae) and Didymogenes (formerly Scenedesmaceae) are closely related to the genus Chlorella . The bristle formation within the Chlorella -clade is originated independently in four lineages: Micractinium pusillum, Diacanthos belenophorus, Didymogenes anomala , and Micractinium parvulum (also known as Golenkinia minutissima ). The latter species is to exclude from the genus Micractinium . Consequently, we proposed the new genus Hegewaldia and transferred M. parvulum to this genus. In contrast, Diacanthos belenophorus is closely related to Micractinium pusillum . As a result, the new combination ( Micractinium belenophorum comb. nov.) is proposed. Comparisons of the secondary structure of ITS-1 and ITS-2 rDNA sequences among the strains of Didymogenes and Hegewaldia are provided to support the species concept in these genera.     

Genomic organization of the ribosomal DNA of sorghum and its close relatives

Summary The structure and organization of the ribosomal DNA (rDNA) of sorghum (Sorghum bicolor) and several closely related grasses were determined by gel blot hybridization to cloned maize rDNA. Monocots of the genus Sorghum (sorghum, shattercane, Sudangrass, and Johnsongrass) and the genus Saccharum (sugarcane species) were observed to organize their rDNA as direct tandem repeats of several thousand rDNA monomer units. For the eight restriction enzymes and 14 cleavage sites examined, no variations were seen within all of the S. bicolor races and other Sorghum species investigated. Sorghum, maize, and sugarcane were observed to have very similar rDNA monomer sizes and restriction maps, befitting their close common ancestry. The restriction site variability seen between these three genera demonstrated that sorghum and sugarcane are more closely related to each other than either is to maize. Variation in rDNA monomer lengths were observed frequently within the Sorghum genus. These size variations were localized to the intergenic spacer region of the rDNA monomer. Unlike many maize inbreds, all inbred Sorghum diploids were found to contain only one rDNA monomer size in an individual plant. These results are discussed in light of the comparative timing, rates, and modes of evolutionary events in Sorghum and other grasses. Spacer size variation was found to provide a highly sensitive assay for the genetic contribution of different S. bicolor races and other Sorghum species to a Sorghum population.     

中国大陆的梅衣科地衣Ⅶ.缘点梅属

最近世界42位著名地衣学家和分子生物学家基于分子、形态和化学综合证据承认和接受了梅衣类属群中的27个属,影响很大。被承认和接受的27属中包括仅由4个种组成的、由梅衣属中一亚属提升为属级单位的Nipponoparmelia。作者首次将Nipponoparmelia的汉语名称称为缘点梅属。报道中国缘点梅属4种地衣,简述了每个种的表型特征(形态、化学、分布)。订正了作者以前使用的名称Parmotrema pustulatum(Elix&Bawingan)O.Blanco,A.Crespo,Divakar,Elix&Lumbsch,这个种的正确名称应是Parmotrema neopustulatum Kurok.。     

Monophyletic groups within the Parmeliaceae identified by ITS rDNA, β-tubulin and GAPDH sequences

Phylogenetic relationships within the Parmeliaceae are analysed cladistically on the basis of DNA characters from partial β-tubulin, partial glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and ITS sequences. 100 taxa representing 73 of the 88 genera currently recognised are included in the analyses. Eight monophyletic groups including two or more genera were identified in the tree calculated from the combined data matrix. Three of the groups cover almost half of the species of the family. The largest and strongest supported group includes seven genera with their distribution centres in the Southern Hemisphere: Almbornia, Chondropsis, Karoowia, Namakwa, Neofuscelia, Xanthomaculina and Xanthoparmelia. The second group is a clade of four essentially tropical genera: Concamerella, Flavoparmelia, Parmotrema and Rimelia. The third large group with strong support is the core of cetrarioid lichens, distributed primarily in cold areas of the Northern Hemisphere. The genus Parmelia sensu Hale is not closely related with most of its segregates. One new combination, Cetrariella commixta, is proposed. Coelopogon abraxas is reported from South America for the first time.     

The evaluation for generic-level monophyly of Ancyrocephalinae (Monogenea, Dactylogyridae) using ribosomal DNA sequence data

To overcome the limited regional and taxonomic coverage in previous studies of the Ancyrocephalinae (Monogenea, Dactylogyridae), we present further findings on the molecular systematics and phylogeny of a broader selection of specimens, aiming to build a molecular phylogeny of the Ancyrocephalinae, and to assess the monophyly of each available genus, using D1-D2 domain of LSU rDNA and the combined LSU and partial sequence of SSU rDNA data sets. Our studies showed that 18 Haliotrema species were highly dispersive to form several clades with species from ten closely related genera. The host range of Euryhaliotrematoides species was not only restricted in butterfly fishes (Chaetodontidae), but widen to include the Lutjanidae. Euryhaliotrema was phylogenetically more closely related to Aliatrema than to Euryhaliotrematoides. Given that the species Haliotrema kurodai, Haliotrema spirotubiforum and Haliotrema anguiformis had a funnel-shaped base of the coiled male copulatory organ (MCO) lacking an accessory piece, and our molecular evidence, we proposed to transfer the three species to the Aliatrema as new combinations. We proposed to combine Bravohollisia and Caballeria into one genus, mainly based on molecular evidence and their similar MCO characters. Using SSU+ITS1 data set, Scutogyrus was robustly resolved as a polyphyletic group and its status should be questioned. Based on the present molecular evidence and their similar MCO characters, we proposed to combine Cichlidogyrus and Scutogyrus into one genus, Cichlidogyrus, by treating Scutogyrus as the synonym of Cichlidogyrus. Generally, the present study indicated that the vagina can make little contribution for understanding the generic-level monophyly, due to its high variability even among phylogenetically very closely related species, but it was useful for species determination. Given that phylogenetically closely related species from the same or closely related host species may have similar MCO characters but distinct haptoral characters, we consider that it is dangerous to erect a genus mainly based on different haptoral characters, particularly those separated from existing genera. The resultant phylogenetic reconstructions indicated that the radiation of some Haliotrema species has correlated with their hosts, because species from closely related fishes have correspondingly shown close relationships. Though the present study can not provide the comparison of host-parasite associations, phylogenetically closely related Haliotrema species which have similar morphological characters (both MCOs and haptors) but distinct/distantly related host species may indicate a speciation model of host-switching.     

Phylogenetic origins of two cleistothecial fungi, Orbicula parietina and Lasiobolidium orbiculoides, within the operculate discomycetes

Parsimony, maximum-likelihood and Bayesian analyses of SSU rDNA sequences of representative taxa of Pezizomycetes, Eurotiomycetes, Dothideomycetes, Leotiomycetes and Sordariomycetes, all strongly support the cleistothecial fungi Orbicula parietina and Lasiobolidium orbiculoides to be of pezizalean origin. Previous hypotheses of close affinities with cleistothecial or highly reduced fungi now placed in the Thelebolales, Eurotiales or Onygenales are rejected. Orbicula parietina and L. orbiculoides are deeply nested within Pyronemataceae (which subsumes the families Ascodesmidaceae, Glaziellaceae and Otideaceae). LSU rDNA sequences suggest that Orbicula is nested within the apothecia-forming genus Pseudombrophila (including Nannfeldtiella and Fimaria) and that L. orbiculoides is closely related. Ascodesmis and Lasiobolus, which have been suggested as closely related to Orbicula and Lasiobolidium, are identified as a sister lineage to the Pseudombrophila lineage. Cleistothecial forms that have lost the ascus operculum and ability to discharge spores actively have evolved at least once in the Pseudombrophila lineage. Some species of Pseudombrophila produce subglobular ascomata initials that are closed early in development and open only in the mid-mesohymenial phase. We hypothesize that, in the Pseudombrophila lineage, ascomata forms that never open are derived from ascomata that open late in development. The placement of O. parietina and L. orbiculoides within Pseudombrophila is supported by morphological characters, ecology and temperature optima for fruiting.     

Phylogeny of Rozites, Cuphocybe and Rapacea inferred from ITS and LSU rDNA sequences

Phylogenetic relationships of Rozites, Cuphocybe, and Rapacea were assessed using molecular phylogenetic approaches. These three genera are placed in Cortinariaceae and have been regarded as closely related to Cortinarius. Rozites includes more than 20 species, which are characterized by having both a membranaceous partial veil in the form of a persistent annulus and a membranaceous universal veil. Cuphocye (4 species) lacks an annulus or cortina, but has pigmented veil fibrils or scales. The monotypic genus Rapacea accommodates a distinct taxon with pale, nearly smooth and thick-walled basidiospores. We analyzed 56 sequences of the internal transcribed spacer region (ITS1, ITS2, and the intervening 5.8S rRNA gene) for nine species of Rozites, three species of Cuphocybe, 28 species of Cortinarius, Rapacea mariae and Protoglossum luteum. Two species of Hebeloma were used as outgroup. Large subunit (LSU) rDNA sequences from selected taxa were also analyzed. The results clearly demonstrate that Rozites species are nested within the clade/Cortinarius, and that Rozites is polyphyletic, suggesting that membranaceous veils have evolved several times in the genus Cortinarius. Also Rapacea and Cuphocybe are nested within Cortinarius, making the latter genus paraphyletic. Based on phylogenetic studies, Rozites, Cuphocybe and Rapacea are artificial genera and do not reflect natural relationships.     

The Genus Artemisia and its Allies: Phylogeny of the Subtribe Artemisiinae (Asteraceae, Anthemideae) Based on Nucleotide Sequences of Nuclear Ribosomal DNA Internal Transcribed Spacers (ITS)

Abstract: Sequences of the internal transcribed spacers (ITS1 and ITS2) of nuclear ribosomal DNA were analysed for 44 Artemisia species (46 populations) representing all the five classical subgenera and the geographical range of the genus, 11 species from 10 genera closely related to Artemisia, and six outgroup species from five other genera of the Anthemideae. The results definitely support the monophyly of the genus Artemisia in its broadest sense (including some taxa segregated as independent genera, like Oligosporus and Seriphidium ). Eight main clades are established in this molecular phylogeny within Artemisia; they agree in part with the classical subdivision of the genus, but they also suggest that some infrageneric groups must be redefined, especially the subgenus Artemisia. The subgenera Tridentatae and Seriphidium are independent from each other. Some of the satellite genera are clearly placed within Artemisia ( Artemisiastrum, Filifolium, Mausolea, Picrothamnus, Sphaeromeria, Turaniphytum ), whereas some others fall outside the large clade formed by this genus (Brachanthemum, Elachanthemum, Hippolytia, Kaschgaria). Our results, correlated to other data such as pollen morphology, allow us to conclude that the subtribe Artemisiinae as currently defined is a very heterogeneous group. Affinities of the largest genus of the subtribe and tribe, Artemisia, and of other genera of the subtribe to some genera from other subtribes of the Anthemideae strongly suggest that subtribe Artemisiinae needs a deep revision and redefinition. Phylogenetic utility of region trnL-F of the plastid DNA in the genus Artemisia and allies was also evaluated: sequences of the trnL-F region in Artemisia do not provide phylogenetic information.     

16S rDNA sequence analysis of bacterial isolates from biodeteriorated mural paintings in the Servilia tomb (Necropolis of carmona, Seville, Spain)

Bacteria were isolated from damaged mural paintings of the Servilia tomb (necropolis of Carmona, Seville, Spain). Selected strains, representative for different clusters of isolates with similar fatty acid profiles, were analysed by 16S rDNA sequence analysis. Bacillus is the dominant genus among the isolates: members of the rRNA species complexes of B. megaterium, B. pumilus and B. firmus were found as well as several other Bacillus species. One group of halotolerant isolates falls in the Bacillus sensu lato group, with closest relatedness to the genera Salibacillus and Virgibacillus. Other genera found are Artbrobacter, Micrococcus, Streptomyces, Sphingomonas, Paenibacillus, and a genus closely related to Paracraurococcus. Many isolates showed low 16S rDNA sequence similarities with the closest related database entries, a strong indication for the presence of several new species among the isolates.     

丛赤壳科部分属之间的系统学关系

对nrDNA大亚基部分序列进行序列分析,探讨丛赤壳科11个属的属间关系。研究结果表明,Cosmospora不是单起源,它的成员分别与Nectria,Haematonectria以及Neocosmospora3个不同的属聚类在一起;Haematonectria和Neocosmospora的亲缘关系最接近;Lanatonectria为一个独立的属;以Neonectriadiscophoravar.discophora为代表的Neonectria是一个可靠的属。     

CRYPTOMONAD EVOLUTION: NUCLEAR 18S rDNA PHYLOGENY VERSUS CELL MORPHOLOGY AND PIGMENTATION1

A nuclear18S rDNA phylogeny for cryptomonad algae is presented, including 11 species yet to be investigated by molecular means. The phylogenetic positions of the cryptomonad genera Campylomonas and Plagioselmis are assessed for the first time. Campylomonas groups most closely with morphologically similar species with the same accessory pigment from the genus Cryptomonas. Plagioselmis groups with the genera Teleaulax and Geminigera forming a clade whose members are united by unusual thylakoid arrangement. Nuclear 18S rDNA phylogeny divides cryptomonads into seven major lineages, two of which consist of the monospecific genera Proteomonas and Falcomonas. Analysis of nuclear18S rDNA sequence supports suggestions that a Falcomonas‐like cryptomonad gave rise to all other blue‐green cryptomonads. New sequence from the plastid‐lacking cryptomonad genus Goniomonas is also included, and the order of divergence of the major cryptomonad lineages is discussed. The morphology, number, and pigmentation of the cryptomonad plastidial complex are congruent with nuclear 18S rDNA phylogenies. Host cell features, such as periplast type, furrow/gullet system, and cell shape, can be more variable and may be markedly different in species that are closely related by nuclear 18S rDNA phylogeny. Conversely, some species that are not closely related by molecular phylogeny may display a very similar, possibly primitive, periplast and furrow morphology.     

16S rDNA studies on members of Arthrobacter and Micrococcus: An aid for their future taxonomic restructing

Abstract 16S rDNA sequence data was obtained for 11 species of Arthrobacter and 4 species of Micrococcus and compared with that from other members of the arthrobacterial lineage within the order Actinomycetales . The intermixing of members of these two genera and the placement of Renibacterium salmoninarum within the radiation of these two genera, as previously suggested by 16S rRNA cataloguing, is confirmed. The branching pattern reveals several closely related organisms that cluster around the type species of Arthrobacter and Micrococcus ; these species are considered 'core organisms'. A few species, however, branch outside the radiation of core organisms; these include Micrococcus kristinae, Micrococcus halophilus , and, as previously indicated, Micrococcus sedentarius and M. nishinomiyaensis . As phenotypic data that would support the exclusion of these four species from the genus Micrococcus are still lacking taxonomic conclusions should await more thorough comparative studies.     

Molecular Characterization of Gregarines from Sand Flies (Diptera: Psychodidae) and Description of Psychodiella n. g. (Apicomplexa: Gregarinida)

ABSTRACT. Sand fly and mosquito gregarines have been lumped for a long time in the single genus Ascogregarina and on the basis of their morphological characters and the lack of merogony been placed into the eugregarine family Lecudinidae. Phylogenetic analyses performed in this study clearly demonstrated paraphyly of the current genus Ascogregarina and revealed disparate phylogenetic positions of gregarines parasitizing mosquitoes and gregarines retrieved from sand flies. Therefore, we reclassified the genus Ascogregarina and created a new genus Psychodiella to accommodate gregarines from sand flies. The genus Psychodiella is distinguished from all other related gregarine genera by the characteristic localization of oocysts in accessory glands of female hosts, distinctive nucleotide sequences of the small subunit rDNA, and host specificity to flies belonging to the subfamily Phlebotominae. The genus comprises three described species: the type species for the new genus— Psychodiella chagasi ( Adler and Mayrink 1961 ) n. comb., Psychodiella mackiei ( Shortt and Swaminath 1927 ) n. comb., and Psychodiella saraviae ( Ostrovska, Warburg, and Montoya-Lerma 1990 ) n. comb. Its creation is additionally supported by sequencing data from other gregarine species originating from the sand fly Phlebotomus sergenti . In the evolutionary context, both genera of gregarines from mosquitoes ( Ascogregarina ) and sand flies ( Psychodiella ) have a close relationship to neogregarines; the genera represent clades distinct from the other previously sequenced gregarines.     

Methylosulfonomonas methylovora gen. nov., sp. nov., and Marinosulfonomonas methylotropha gen. nov., sp. nov.: novel methylotrophs able to grow on methanesulfonic acid

Two novel genera of restricted facultative methylotrophs are described; both Methylosulfonomonas and Marinosulfonomonas are unique in being able to grow on methanesulfonic acid as their sole source of carbon and energy. Five identical strains of Methylosulfonomonas were isolated from diverse soil samples in England and were shown to differ in their morphology, physiology, DNA base composition, molecular genetics, and 16S rDNA sequences from the two marine strains of Marinosulfonomonas, which were isolated from British coastal waters. The marine strains were almost indistinguishable from each other and are considered to be strains of one species. Type species of each genus have been identified and named Methylosulfonomonas methylovora (strain M2) and Marinosulfonomonas methylotropha (strain PSCH4). Phylogenetic analysis using 16S rDNA sequencing places both genera in the α-Proteobacteria. Methylosulfonomonas is a discrete lineage within the α-2 subgroup and is not related closely to any other known bacterial genus. The Marinosulfonomonas strains form a monophyletic cluster in the α-3 subgroup of the Proteobacteria with Roseobacter spp. and some other partially characterized marine bacteria, but they are distinct from these at the genus level. This work shows that the isolation of bacteria with a unique biochemical character, the ability to grow on methanesulfonic acid as energy and carbon substrate, has resulted in the identification of two novel genera of methylotrophs that are unrelated to any other extant methylotroph genera. Received: 19 July 1996 / Accepted: 7 October 1996     

Phylogeny of the lichen genus Placopsis and its allies based on Bayesian analyses of nuclear and mitochondrial sequences

The phylogenetic relationships of the lichen genus Placopsis and related genera in the Agyriales were analyzed using molecular data. We obtained a total of 66 new sequences from the nuclear ITS, LSU and the mitochondrial SSU rDNA. Phylogenetic analyses were conducted in a Bayesian and a maximum-parsimony framework. Our analyses show that Placopsis is paraphyletic with members of Orceolina nesting within the genus. A morphological character supporting the Placopsis-Orceolina clade is the non-amyloid ascus. The section Aspiciliopsis as defined by sunken fruiting bodies is not supported, but the type species of Aspiciliopsis is more closely related to Orceolina. This clade shares apothecia with reduced amphithecia as apomorphic character. We suggest resurrecting the generic name Aspiciliopsis. Trapelia is the sister genus to Placopsis and Aspiciliopsis/Orceolina.     

火丝菌科(盘菌目)部分属的系统学研究

本文以核糖体小亚基(SSUrDNA)为分子标记,对28个属60个种的71个序列片段进行序列分析,探讨火丝菌科的属间亲缘关系。研究结果支持广义的火丝菌科概念,表明该科是单起源的,显示5个主要分支。腐生或与植物共生形成菌根、囊盘被表面具有毛状物的15个属构成A分支,该分支中仅部分属之间的关系比较明确;与苔藓植物生长在一起的4个属构成B分支;C分支包括Otidea和Otideopsis两属,后者与Otidea的成员混杂在一起;D分支仅包括Acervus的成员;E分支由Geopyxis,Tarzetta,Paurocotylis等5个属组成。分子系统学的研究结果与形态学分类系统之间存在一定差异,依据形态特征和超微结构建立的亚科和族均未获得支持。     

Billburttia, a new genus of Apiaceae (tribe Apieae) endemic to Madagascar

The genus Billburttia is described to include two new species endemic to Madagascar, B. capensoides and B. vaginoides. Both species were tentatively placed within the problematic genus Peucedanum L. (as Peucedanum sp. A and Peucedanum sp. B) based on their dorsally compressed fruits lacking prominent dorsal ribs and with winged marginal ribs. Recently, however, the African members of Peucedanum have been shown to be only distantly related to the type of the genus and have therefore been segregated into six African endemic genera. While the Malagasy species appear superficially similar to members from one of these segregate genera, viz. Notobubon, they differ markedly in their fruit anatomical characters, notably a narrower commissure, six commissural vittae, vascular tissue in the tip of the ribs and sphaerocrystals distributed in and around the epidermis. The latter two characters apparently represent apomorphies for Billburttia. The non-peucedanoid affinity of the genus, as suggested by the fruit anatomical data, was confirmed using ITS and rps16 intron sequences. Both parsimony and Bayesian analyses of these data place Billburttia within the tribe Apieae of subfamily Apioideae and not closely related to either Peucedanum (Selineae) or the African peucedanoid genera (Lefebvrea clade of Tordylieae).