Phylogeny of the European species of the genus Pellia (Hepaticae; Metzgeriales) based on the molecular data from nuclear tRNA(Leu)(CAA) intergenic sequences

Species of the genus Pellia are similar to such an extent that their proper recognition based on morphological and anatomical features is difficult. To solve this problem isozyme methods were developed. As a result of these studies new cryptic species were recognized and new hypotheses concerning phylogenetic relationship in Pellia were formed. To examine hypotheses derived from isozyme data we decided to study species of the genus Pellia at the DNA level. Total DNA from all Polish Pellia species was isolated. The taxonomic and phylogenetic relationships in Pellia were examined using intergenic spacer sequences between nuclear tRNA(Leu) genes organised in tandem arrays. PCR (polymerase chain reaction) amplification of tRNA(Leu) gene spacers produced fragments of different sizes in all species and their restriction analysis showed species-specific patterns. PCR products were cloned and sequenced. Nucleotide sequence data were used for phylogenetic reconstruction. Sequence analysis confirmed previous results based on isozyme studies that P. endiviifolia- species A and species B as well as P. epiphylla- species S and species N (having different isozyme multilocus genotypes) are separate sibling species. Our results also confirmed the allopolyploid character of the only polyploid species in Pellia, P. borealis which was formed by hybridization of P. epiphylla- species N and P. epiphylla- species S cryptic species.     

Organellar Inheritance in Liverworts: An Example of <Emphasis Type="Italic">Pellia borealis</Emphasis>

Liverwort Pellia borealis is an allopolyploid species that originated after the hybridization and chromosome doubling of two cryptic species; Pellia epiphylla species N and Pellia epiphylla species S. A sequence comparison of chloroplast tRNAUCCGly, tRNAUUULys gene introns, the mitochondrial tRNAGCUSer gene intron, and the first intron of the coxIII gene in the case of three liverwort species studied revealed that the chloroplast and mitochondrial sequences are identical in P. borealis and P. epiphylla species N but different from homologous P. epiphylla species S sequences. Both mitochondria and chloroplasts of P. borealis were thus inherited from one parent- P. epiphylla species N. Studies on 14 different populations of P. borealis gave the same result. These are the first data on organellar transmission in liverworts, the earliest land plants. Moreover, we show that the intron sequences of some organellar genes, until now not used in any systematic studies, could be very good markers in studying taxonomic relationships in closely related species and reconstructing historical events.     

Chromosomal distribution of rRNA genes in the karyotypes of two dioicous liverwort species from the genus Pellia Raddi

Over one hundred years have passed since the first cytogenetic studies were made on the liverwort genus Pellia Raddi. The karyotype of Pellia is characterised by large chromosomes, a varying heterochromatin content and the presence of sex chromosomes in the dioicous species. Most of the Pellia species are diploids with n?=?9, but one of them, Pellia borealis Lorb., has been described as an example of allopolyploidy in liverworts. Although the localisation of rRNA genes, which are essential components of the nuclear genome, remains a challenge in bryophytes, data on the number and chromosomal localisation of 35S and 5S rDNA in all of the Pellia species are now available. Previously, fluorescence in situ hybridisation using rDNA probes was performed on the mitotic chromosomes of 2 monoicous species. The aim of this study was to establish the number and chromosomal distribution of rRNA genes in 2 dioicous diploid species—Pellia endiviifolia (Dicks.) Dumort. and Pellia neesiana (Gottsche) Limpr. The relationships between the species within the genus Pellia can now be discussed in the context of the localisation of the rDNA sites and the range in the number of rDNA loci among bryophytes can also be verified.     

Organellar Inheritance in Liverworts: An Example of Pellia borealis

Abstract Liverwort Pellia borealis is an allopolyploid species that originated after the hybridization and chromosome doubling of two cryptic species; Pellia epiphylla species N and Pellia epiphylla species S. A sequence comparison of chloroplast tRNAUCCGly, tRNAUUULys gene introns, the mitochondrial tRNAGCUSer gene intron, and the first intron of the coxIII gene in the case of three liverwort species studied revealed that the chloroplast and mitochondrial sequences are identical in P. borealis and P. epiphylla species N but different from homologous P. epiphylla species S sequences. Both mitochondria and chloroplasts of P. borealis were thus inherited from one parent—P. epiphylla species N. Studies on 14 different populations of P. borealis gave the same result. These are the first data on organellar transmission in liverworts, the earliest land plants. Moreover, we show that the intron sequences of some organellar genes, until now not used in any systematic studies, could be very good markers in studying taxonomic relationships in closely related species and reconstructing historical events.     

Phylogenetic analysis of the mammalian Hoxc8 non-coding region

The non-coding intergenic regions of Hox genes are remarkably conserved among mammals. To determine the usefulness of this sequence for phylogenetic comparisons, we sequenced an 800-bp fragment of the Hoxc9–Hoxc8 intergenic region from several species belonging to different mammalian clades. Results obtained from the phylogenetic analysis are congruent with currently accepted mammalian phylogeny. Additionally, we found a TC mini satellite repeat polymorphism unique to felines. This polymorphism may serve as a useful marker to differentiate between mammalian species or as a genetic marker in feline matings. This study demonstrates usefulness of a comparative approach employing non-coding regions of Hox gene complexes.     

Some PreHminary Observations on the Water Reladons of a Mesophytic Moss,Thamnium alopecurum (Hedw.) B. & S.

Abstract

Measurements of lobe elongation of the thalloid liverworts Pallavicinia lyellii and Pellia epiphylla were made on shaded streambanks at Silwood Park using a photographic technique. The average cumulative growth of Pallavicinia over 12 months from 1 August 1989 was 8.7 mm compared to 24.7 mm for Pellia. Monthly growth increments of Pallavicinia were positively correlated with average air temperature and accumulated temperatures (day-degrees) in each period. Growth of Pellia was unrelated to temperature. Neither species showed a correlation of growth with rainfall amounts or numbers of wet days, probably because thallus hydration is governed predominantly by soil wetness. Pallavicinia appears to coexist with the more vigorous Pellia by tolerating drier niches than can be endured by Pellia. Persistence of Pallavicinia at this site may be due to the presence of both sexes and frequent colonization of fresh surfaces by spores.     

Glomeromycotean associations in liverworts: a molecular, cellular, and taxonomic analysis

Liverworts form endophytic associations with fungi that mirror mycorrhizal associations in tracheophytes. Here we report a worldwide survey of liverwort associations with glomeromycotean fungi (GAs), together with a comparative molecular and cellular analysis in representative species. Liverwort GAs are circumscribed by a basal assemblage embracing the Haplomitriopsida, the Marchantiopsida (except a few mostly derived clades), and part of the Metzgeriidae. Fungal endophytes from Haplomitrium, Conocephalum, Fossombronia, and Pellia were related to Glomus Group A, while the endophyte from Monoclea was related to Acaulospora. An isolate of G. mosseae colonized axenic thalli of Conocephalum, producing an association similar to that in the wild. Fungal colonization in marchantialean liverworts suppressed cell wall autofluorescence and elicited the deposition of a new wall layer that specifically bound the monoclonal antibody CCRC-M1 against fucosylated side groups associated with xyloglucan and rhamnogalacturonan I. The interfacial material covering the intracellular fungus contained the same epitopes present in host cell walls. The taxonomic distribution and cytology of liverwort GAs suggest an ancient origin and multiple more recent losses, but the occurence in widely separated liverwort taxa of fungi related to glomeromycotean lineages that form arbuscular mycorrhizas in tracheophytes, notably the Glomus Group A, is better explained by host shifting from tracheophytes to liverworts.     

Diversity and distribution pattern of epiphyllous liverworts and its ecological determinants

Epiphyllous liverworts form a special group of bryophytes that primarily grow on leaves of understory vascular plants, occurring in constantly moist and warm evergreen forest in tropical and subtropical regions. Epiphyllous liverworts may influence ecosystem processes including carbon, nitrogen and water cycles. Furthermore, they are very sensitive to climate change and forest fragmentation, and can be used as bioindicators for changes in ecological conditions and escalating loss of biodiversity. In this paper, we reviewed studies on morphological traits, species diversity, geographical distribution and environmental conditions (including characteristics of hosts and habitats) of epiphyllous liverworts, discussed the possible reasons for the mechanisms underlying the diversity pattern of epiphyllous liverworts. According to these studies, we proposed that further ecological studies on epiphyllous liverworts should be more focused on their formation, mechanisms of matter exchange and energy flux, ecological functions in forest ecosystem, the response to climate changes and their broader-scale ecology.     

叶附生苔植物物种多样性分布格局及生态成因

叶附生苔植物(以下简称叶附生苔)是一类附生在维管植物叶片表面的、一般只出现在热带雨林和常绿阔叶林中的苔类植物。它们具有重要的生态功能, 如影响碳、氮、水循环, 对气候变化和森林破碎化反应敏感, 可用作环境变化的指示植物。该文对叶附生苔的形态特性、物种多样性的研究历史和进展、地理分布格局, 以及对环境的要求(附主和生境的特性)等进行了综述, 探讨了叶附生苔多样性分布格局形成的可能原因, 即环境(空气湿度高、林冠层发育好、干扰少)和适应特征(无性繁殖、形体微小)的选择。根据全球叶附生苔研究进展状况及所存在的问题提出未来可开展的研究方向, 如叶附生苔的形成原因、与附主间的物质交换和能量流动机制、在森林生态系统中的生态功能、气候变化指示作用研究等, 大尺度上的研究也值得关注。     

RAPD technique for taxonomic studies of Pellia epiphylla‐complex (Hepaticae, Metzgeriales)

The random amplified polymorphic DNA (RAPD) technique was used to study the genomic relationships of three liverworts from the genus Pellia: P. epiphylla, P. borealis and P. neesiana. Altogether 150 characters (150 DNA fragments obtained using PCR) were scored. These characters were used to create a matrix of pairwise distances between all the pairs of taxa. Both distance (UPGMA, Fitch–Margoliash and Neighbor–Joining) and binary character‐state (Wagner and Camin‐Sokal parsimony and compatibility) methods were applied for trees' construction. Our results strongly support distinction of the recently discovered sibling species of P. epiphylla – species N and P. epiphylla – species S, which have an allopatric distribution in Poland (N – North, S – South Poland). Moreover, our data also supports the hypothesis of a hybrid origin (alloploid) of the polyploid P. borealis from P.epiphylla−N×P.epiphylla−S. P. neesiana was excluded as a donor of either of the genomes of P. borealis. This revised version was published online in July 2006 with corrections to the Cover Date.     

A comparison of alpha and beta diversity patterns of ferns,bryophytes and macrolichens in tropical montane forests of southern Ecuador

We present a first comparison of patterns of alpha and beta diversity of ferns, mosses, liverworts and macrolichens in neotropical montane rainforests, and explore the question whether specific taxa may be used as surrogates for others. In three localities in southern Ecuador, we surveyed terrestrial and epiphytic species assemblages in ridge and slope forests in 28 plots of 400 m2 each. The epiphytic habitat was significantly richer in ferns, liverworts, and macrolichens than the terrestrial habitat; mosses, however, were primarily terrestrial. Alpha diversity of ferns and of liverworts was congruent in both habitats. Mosses were similar to ferns and liverworts only in the epiphytic habitat. Macrolichens did not share patterns of alpha diversity with any other group. Beta diversity of ferns, mosses and liverworts (lichens excluded due to low species richness) was similar in the terrestrial habitat, but not in the epiphytic habitat. Our results demonstrate that patterns of alpha diversity of the studied taxa cannot be used to predict patterns of beta diversity. Moreover, diversity patterns observed in epiphytes are different from terrestrial plants. We noted a general coincidence in species patterns of liverworts and ferns. Diversity patterns of macrolichens, in contrast, were completely independent from any other taxonomic group studied.     

A comparison of altitudinal species richness patterns of bryophytes with other plant groups in Nepal, Central Himalaya

Aim To explore species richness patterns in liverworts and mosses along a central Himalayan altitudinal gradient in Nepal (100–5500 m a.s.l.) and to compare these patterns with patterns observed for ferns and flowering plants. We also evaluate the potential importance of Rapoport’s elevational rule in explaining the observed richness patterns for liverworts and mosses. Location Nepal, Central Himalaya. Methods We used published data on the altitudinal ranges of over 840 Nepalese mosses and liverworts to interpolate presence between maximum and minimum recorded elevations, thereby giving estimates of species richness for 100‐m altitudinal bands. These were compared with previously published patterns for ferns and flowering plants, derived in the same way. Rapoport’s elevational rule was assessed by correlation analyses and the statistical significance of the observed correlations was evaluated by Monte Carlo simulations. Results There are strong correlations between richness of the four groups of plants. A humped, unimodal relationship between species richness and altitude was observed for both liverworts and mosses, with maximum richness at 2800 m and 2500 m, respectively. These peaks contrast with the richness peak of ferns at 1900 m and of vascular plants, which have a plateau in species richness between 1500 and 2500 m. Endemic liverworts have their maximum richness at 3300 m, whereas non‐endemic liverworts show their maximum richness at 2700 m. The proportion of endemic species is highest at about 4250 m. There is no support from Nepalese mosses for Rapoport’s elevational rule. Despite a high correlation between altitude and elevational range for Nepalese liverworts, results from null simulation models suggest that no clear conclusions can be made about whether liverworts support Rapoport’s elevational rule. Main conclusions Different demands for climatic variables such as available energy and water may be the main reason for the differences between the observed patterns for the four plant groups. The mid‐domain effect may explain part of the observed pattern in moss and liverwort richness but it probably only works as a modifier of the main underlying relationship between climate and species richness.     

Classification of plant associated bacteria using RIF, a computationally derived DNA marker

A DNA marker that distinguishes plant associated bacteria at the species level and below was derived by comparing six sequenced genomes of Xanthomonas, a genus that contains many important phytopathogens. This DNA marker comprises a portion of the dnaA replication initiation factor (RIF). Unlike the rRNA genes, dnaA is a single copy gene in the vast majority of sequenced bacterial genomes, and amplification of RIF requires genus-specific primers. In silico analysis revealed that RIF has equal or greater ability to differentiate closely related species of Xanthomonas than the widely used ribosomal intergenic spacer region (ITS). Furthermore, in a set of 263 Xanthomonas, Ralstonia and Clavibacter strains, the RIF marker was directly sequenced in both directions with a success rate approximately 16% higher than that for ITS. RIF frameworks for Xanthomonas, Ralstonia and Clavibacter were constructed using 682 reference strains representing different species, subspecies, pathovars, races, hosts and geographic regions, and contain a total of 109 different RIF sequences. RIF sequences showed subspecific groupings but did not place strains of X. campestris or X. axonopodis into currently named pathovars nor R. solanacearum strains into their respective races, confirming previous conclusions that pathovar and race designations do not necessarily reflect genetic relationships. The RIF marker also was sequenced for 24 reference strains from three genera in the Enterobacteriaceae: Pectobacterium, Pantoea and Dickeya. RIF sequences of 70 previously uncharacterized strains of Ralstonia, Clavibacter, Pectobacterium and Dickeya matched, or were similar to, those of known reference strains, illustrating the utility of the frameworks to classify bacteria below the species level and rapidly match unknown isolates to reference strains. The RIF sequence frameworks are available at the online RIF database, RIFdb, and can be queried for diagnostic purposes with RIF sequences obtained from unknown strains in both chromatogram and FASTA format.     

Differentiation of environmental and clinical isolates of Vibrio mimicus from Vibrio cholerae by multilocus enzyme electrophoresis

In this study, we demonstrated that analyzed strains of Vibrio mimicus and Vibrio cholerae could be separated in two groups by using multilocus enzyme electrophoresis (MEE) data from 14 loci. We also showed that the combination of four enzymatic loci enables us to differentiate these two species. Our results showed that the ribosomal intergenic spacer regions PCR-mediated identification system failed, in some cases, to differentiate between V. mimicus and V. cholerae. On the other hand, MEE proved to be a powerful molecular tool for the discrimination of these two species even when atypical strains were analyzed.     

广西中越边境喀斯特地区叶附生苔类植物物种多样性研究

为了解日益恶化的喀斯特环境下叶附生苔类植物的分布状况,对广西中越边境喀斯特地区叶附生苔类植物多样性展开调查。结果表明,广西中越边境喀斯特地区有叶附生苔类植物5科15属43种,其中,九洲疣鳞苔(Cololejeunea yakusimensis)、巴氏薄鳞苔(Leptolejeunea balansae)、斯氏唇鳞苔(Cheilolejeunea streimannii)、麦氏细鳞苔(Lejeunea micholitzii)、巨齿细鳞苔(L.kodamae)和纤细细鳞苔(L.exilis)为广西苔藓植物新记录。该地区叶附生苔类植物区系具有热带性质和东亚分布特点。与邻近地区比较,该地区叶附生苔类植物与贵州茂兰的亲缘关系和区系关系最紧密。该地区叶附生苔类植物分布随海拔增加呈增加趋势。那坡老虎跳保护区、龙州和宁明弄岗保护区以及靖西龙邦镇风水林是叶附生苔类植物分布最丰富的地区,因此,建议应对这些地区的叶附生苔类植物进行优先保护。     

Polymorphic DNA sequences of the fungal honey bee pathogen Ascosphaera apis

The pathogenic fungus Ascosphaera apis is ubiquitous in honey bee populations. We used the draft genome assembly of this pathogen to search for polymorphic intergenic loci that could be used to differentiate haplotypes. Primers were developed for five such loci, and the species specificities were verified using DNA from nine closely related species. The sequence variation was compared among 12 A.?apis isolates at each of these loci, and two additional loci, the internal transcribed spacer of the ribosomal RNA (ITS) and a variable part of the elongation factor 1α (Ef1α). The degree of variation was then compared among the different loci, and three were found to have the greatest detection power for identifying A.?apis haplotypes. The described loci can help to resolve strain differences and population genetic structures, to elucidate host-pathogen interaction and to test evolutionary hypotheses for the world's most important pollinator: the honey bee and one of its most common pathogens.     

Differentiation of Populus species using chloroplast single nucleotide polymorphism (SNP) markers--essential for comprehensible and reliable poplar breeding

Within the genus Populus several species belonging to different sections are cross-compatible. Hence, high numbers of interspecies hybrids occur naturally and, additionally, have been artificially produced in huge breeding programmes during the last 100 years. Therefore, determination of a single poplar species, used for the production of 'multi-species hybrids' is often difficult, and represents a great challenge for the use of molecular markers in species identification. Within this study, over 20 chloroplast regions, both intergenic spacers and coding regions, have been tested for their ability to differentiate different poplar species using 23 already published barcoding primer combinations and 17 newly designed primer combinations. About half of the published barcoding primers yielded amplification products, whereas the new primers designed on the basis of the total sequenced cpDNA genome of Populus trichocarpa Torr. & Gray yielded much higher amplification success. Intergenic spacers were found to be more variable than coding regions within the genus Populus. The highest discrimination power of Populus species was found in the combination of two intergenic spacers (trnG-psbK, psbK-psbl) and the coding region rpoC. In barcoding projects, the coding regions matK and rbcL are often recommended, but within the genus Populus they only show moderate variability and are not efficient in species discrimination.     

Application of PCR ribotyping and tDNA-PCR for Klebsiella pneumoniae identification

PCR analysis of 16S-23S internal transcribed spacer (PCR ribotyping) and tRNA intergenic spacer (tDNA-PCR) were evaluated for their effectiveness in identification of clinical strains of Klebsiella pneumoniae and differentiation with related species. For this purpose both methods were applied to forty-three clinical isolates biochemically identified as K. pneumoniae subsp. pneumoniae isolated from patients clinical specimens attended at five hospitals in three Brazilian cities. References strains of K. pneumoniae subsp. pneumoniae, K. pneumoniae subsp. ozaenae, K. oxytoca, K. planticola and Enterobacter aerogenes were also analyzed. Both PCR methods showed specific patterns for each species. A conserved PCR ribotype pattern was observed for all clinical K. pneumoniae isolates, while differing from other related analyzed species. tDNA-PCR revealed five distinct patterns among the K. pneumoniae clinical isolates studied, demonstrating a predominant group with 90.6% of isolates presenting the same pattern of K. pneumoniae type strain. Both PCR-based methods were not able to differentiate K. pneumoniae subspecies. On the basis of the results obtained, both methods were efficient to differentiate the Klebsiella species analyzed, as well as E. aerogenes. Meanwhile tDNA-PCR revealed different tRNA arrangements in K. pneumoniae, suggesting intra-species heterogeneity of their genome organization, the polymorphism of the intergenic spacers between 16S and 23S rRNA genes appears to be highly conserved whithin K. pneumoniae clinical isolates, showing that PCR ribotyping can be an useful tool for identification of K. pneumoniae isolates.     

Estimates of nuclear DNA content in bryophyte sperm cells: phylogenetic considerations

Nuclear DNA contents of developing sperm were estimated for 17 species of bryophytes by cytophotometry in squash preparations of antheridia after Feulgen staining. Genome sizes are in the lower end of the range for land plants. Two homwort C-values have the lowest recorded for bryophytes at 0.17 and 0.26 pg DNA per nucleus. In liverworts, C-values range from 0.49 pg in Blasia pusilla to 4.05 pg in Pellia epiphylla, while moss genome sizes are less variable, ranging from 0.38 pg in Takakia ceratophylla to 0.92 pg in Atrichum oerstedianum. DNA content is not correlated with chromosome number in these bryophytes, but sperm cell size and cellular complexity are directly related to C-value. Structural variations in the locomotory apparatus are viewed as evolutionary modifications associated with changes in genomic complexity, with a generalized increase in complexity of the motile assemblage accompanying increases in DNA content. Nuclear DNA values are not as variable in bryophytes as they are in pteridophytes and seed plants. We suggest that in plants producing biflagellated gametes, lower DNA contents afford a selective advantage. Comparisons with plants that produce multiflagellated or pollen-dispersed sperm indicate operation of a nucleotypic effect in archegoniates with biflagellated sperm. This effect may be on sperm cell functioning, which in turn influences reproductive success.