Phylogenetic relationships and genetic diversity among members of theFestuca-Lolium complex (Poaceae) based on ITS sequence data

There have been few DNA sequencebased studies of phylogenetic relationships within theFestuca-Lolium complex. Here we infer the phylogeny of 31Festuca-Lolium taxa with a dataset of 116 ITS sequences. The results are consistent with previous studies that resolved two majorFestuca clades: one clade of fine fescues and another clade that containsLolium and associatedFestuca species. This study is unique in suggesting a third, basalFestuca clade, but support for the basal position of this group is low. Extensive sampling permitted investigation of the effects of lineage sorting and reticulate events on the evolution of the complex. Roughly half of the taxa show evidence of lineage sorting or reticulation, and the monophyly ofLolium has likely been obscured by reticulate events. Overall, polyploid species harbor higher levels of ITS sequence diversity than diploids; ITS sequence variants may provide clues to the identity of allopolyploid parents.     

Phylogenetic relationships and genetic polymorphisms in wild Indian mice

Randomly amplified polymorphic DNA (RAPD) analysis was used to examine the extent of variability in 11 Indian wild derived commensal house mice (Mus musculus) populations and compared with inbred strains of musculus and domesticus subspecies as well as commonly used laboratory inbred strains C57BL/6J and DBA/2J. Arbitrary designed 10 mer oligonucleotide primers with 60-70% (G+C) content were used to amplify DNA template. Out of 52 primers screened initially on the laboratory strains, 20 were selected for analysis on the basis of amplification product in the size range of 200-1400 bp. Among 353 total polymorphic bands, 220 bands (64%) were found to be polymorphic in Indian wild mice, 85 bands (25%) in wild derived inbred strains and 37 bands (11%) in laboratory mice strains. The amplification patterns produced by primers were statistically analysed by Jaccard's similarity coefficient the value of which ranged from 0.56 to 0.80. High level of genetic diversity was seen in the Indian wild mice populations as compared to the controls. The UPGMA phenogram grouped mice population into two major clusters except Bikaner [BIK], Bilaspur [BIL] and Ranikhet [RK] populations which were placed outside the close-knit clusters. Inspite of low values of bootstrap estimates obtained by Wagner and Dollo parsimony analysis, the results were comparable with UPGMA phenogram when constitution of the populations in the major cluster was considered. Indian mice populations appeared to be diverse from laboratory inbred mice strains.     

Assessment of cytochrome P450 sequences offers a useful tool for determining genetic diversity in higher plant species

To investigate and develop new genetic tools for assessing genome-wide diversity in higher plant-species, polymorphisms of gene analogues of mammalian cytochrome P450 mono-oxygenases were studied. Data mining on Arabidopsis thaliana indicated that a small number of primer-sets derived from P450 genes could provide universal tools for the assessment of genome-wide genetic diversity in diverse plant species that do not have relevant genetic markers, or for which, there is no prior inheritance knowledge of inheritance traits. Results from PCR amplification of 51 plant species from 28 taxonomic families using P450 gene-primer sets suggested that there were at least several mammalian P450 gene mammalian-analogues in plants. Intra- and inter- specific variations were demonstrated following PCR amplifications of P450 analogue fragments, and this suggested that these would be effective genetic markers for the assessment of genetic diversity in plants. In addition, BLAST search analysis revealed that these amplified fragments possessed homologies to other genes and proteins in different plant varieties. We conclude that the sequence diversity of P450 gene-analogues in different plant species reflects the diversity of functional regions in the plant genome and is therefore an effective tool in functional genomic studies of plants.Communicated by C. Möllers     

Phylogenetic relationships within the fish family Goodeidae based on cytochrome b sequence data

A phylogeny of the species in the family Goodeidae was constructed based on the complete mitochondrial cytochrome b gene (1140 bp). Molecular phylogeny was used to revise current systematic of this group, to characterize the evolution of reproductive characters, and to infer a biogeographical model for the Mesa Central of Mexico during the Cenozoic period. We confirmed the monophyly of the subfamily Goodeinae and defined five different lineages within Goodeinae: Chapalichthyini, Girardinichthyini, Goodiini, Ilyodontini, and Charachontini. The morphology of trophotaeniae widely used to infer phylogenetic relationships within goodeids appears to be homoplasious. In a primitive condition, trophotaeniae seem to be very simple structure as occurs in the Charachontini lineage. There is an evolutionary trend to increase trophotaeniae surface via an increase in the number of branches (ribbon type) or branch widening (rosette type). Goodeidae originated in the middle Miocene and it was in the Pliocene when they radied their highest diversity during a dry period that caused basin splitting in the Mesa Central of Mexico.     

High diversity and complex evolution of fungal cytochrome P450 reductase: cytochrome P450 systems.

Cytochrome P450 reductase (CPR) is the redox partner of P450 monooxygenases, involved in primary and secondary metabolism of eukaryotes. Two novel CPR genes, sharing 34% amino acid identity, were found in the filamentous ascomycete Cochliobolus lunatus. Fungal genomes were searched for putative CPR enzymes. Phylogenetic analysis suggests that multiple independent CPR duplication events occurred in fungi, whereas P450-CPR fusion occurred before the diversification of Dikarya and Zygomycota. Additionally, losses of methionine synthase reductase were found in certain fungal taxa; a truncated form of this enzyme was conserved in Pezizomycotina. In fungi, high numbers of cytochrome P450 enzymes, multiple CPRs, and P450-CPR fusion proteins were associated with filamentous growth. Evolution of multiple CPR-like oxidoreductases in filamentous fungi might have been driven by the complexity of biochemical functions necessitated by their growth form, as opposed to yeast.     

Phylogenetic and functional analyses of the cytochrome P450 family 4

Cytochrome P450 family 4 (CYP4) proteins metabolize fatty acids, eicosanoids, and vitamin D and are important for chemical defense. The purpose of this study was to determine the evolutionary relationships between vertebrate CYP4 subfamilies and raise functional hypotheses regarding CYP4 subfamilies with little empirical data. 132 CYP4 sequences from 28 species were utilized for phylogenetic reconstructions by maximum likelihood and Bayesian inference. Monophyly was not found with the CYP4T and CYP4B subfamilies. CYP4V clustered with invertebrate subfamilies. Evolutionary rates of functional divergence were high in pairwise comparison with CYP4X yet, comparisons with mammalian CYP4F22 genes generally had no statistically significant divergence. Radical biochemical changes were detected in regions associated with substrate binding and the active site in comparisons among the CYP4A, CYP4X, and CYP4B subfamilies. Lastly, gene expression patterns, determined in silico with EST libraries from human, chicken, frog and fish, for CYP4V was markedly different between human and actinopterygian species. Further consideration should be given to the nomenclature of the CYP4T and CYP4B subfamily genes. Strong support was seen for the placement of CYP4A as a basal subfamily to CYP4X and CYP4Z. The B, B', J', K', K″ helices and a region at the end of C-terminus were suggested as conserved regions in CYP4 genes. The function of CYP4X was hypothesized to specialize in metabolism of long chain fatty acids. CYP4F22 genes may share a similar function to other CYP4F genes, although gene expression sites were different.     

Phylogenetic relationships of Cryphonectria and Endothia species, based on DNA sequence data and morphology

The fungal genera Endothia and Cryphonectria include some of the most important pathogens of forest trees. Despite available new technology, no comprehensive comparative study based on DNA sequence data and morphology has been done on the available isolates representing these two genera. The main objectives of this study were to assess the phylogenetic relationships among species of Cryphonectria and Endothia, for which cultures are available, and to establish a taxonomic framework based on DNA sequence and morphological data, which will aid future studies and identification of species in these and related genera. Comparisons were based on sequence variation found in the ITS region of the ribosomal RNA operon and two regions of the β-tu-bulin gene. In addition, the morphology of these species was examined. The phylogenetic data indicated that Endothia and Cryphonectria reside in two distinct phylogenetic clades. Cryphonectria parasitica, C. macrospora, C. nitschkei, C. eucalypti and C. radicalis represented the Cryphonectria clade. Endothia gyrosa and E. singularis were included in the Endothia clade. An isolate representing E. viridistroma grouped outside the Endothia clade and separately from other groups. Other clades outside the one encompassing Cryphonectria were those represented by the C. cubensis isolates and fungi isolated from Elaeocarpus dentatus originating from New Zealand. These clades could be distinguished from Endothia and Cryphonectria, based on anamorph morphology, stromatal structure and ascospore septation. Cryphonectria and Endothia, therefore, appear to be paraphyletic and taxonomic relationships for these fungi need to be revised.     

Phylogeny of Capparaceae and Brassicaceae based on chloroplast sequence data

Capparaceae and Brassicaceae have long been known to be closely related families, with the monophyly of Capparaceae more recently questioned. To elucidate the relationship between Brassicaceae and Capparaceae as well as to address infrafamilial relationships within Capparaceae, we analyzed sequence variation for a large sampling, especially of Capparaceae, of these two families using two chloroplast regions, trnL-trnF and ndhF. Results of parsimony and likelihood analyses strongly support the monophyly of Brassicaceae plus Capparaceae, excluding Forchhammeria, which is clearly placed outside the Brassicaceae and Capparaceae clade and suggest the recognition of three primary clades-Capparaceae subfamily (subf.) Capparoideae, subf. Cleomoideae, and Brassicaceae. Capparaceae monophyly is strongly contradicted with Cleomoideae appearing as sister to Brassicaceae. Two traditionally recognized subfamilies of Capparaceae, Dipterygioideae and Podandrogynoideae, are embedded within Cleomoideae. Whereas habit and some fruit characteristics demarcate the three major clades, floral symmetry, stamen number, leaf type, and fruit type all show homoplasy. Clades within Capparoideae show a biogeographical pattern based on this sampling. These results are consistent with several alternative classification schemes.     

Cholesterol amperometric biosensor based on cytochrome P450scc

A screen-printed enzyme electrode based on flavocytochrome P450scc (RfP450scc) for amperometric determination of cholesterol has been developed. A one-step method for RfP450scc immobilization in the presence of glutaraldehyde or by entrapment of enzyme within a hydrogel of agarose is discussed. The sensitivity of the biosensor based on immobilization procedures of flavocytochrome P450scc by glutaric aldehyde is 13.8 nA microM(-1) and the detection limit is 300 microM with a coefficient of linearity 0.98 for cholesterol in the presence of sodium cholate as detergent. The detection limits and the sensitivity of the agarose-based electrode are 155 microM and 6.9 nA microM(-1) with a linearity coefficient of 0.99. For both types of electrodes, the amperometric response to cholesterol in the presence of detergent was rather quick (1.5-2 min).     

Phylogenetic relationships on 14 morphologically similar species of Pucciniastrum in Japan based on rDNA sequence data

We analyzed the phylogenetic relationships of 49 specimens comprising 14 morphologically similar species of Pucciniastrum distributed in Japan based on the sequence data of the large subunit rDNA (D1/D2), 5.8S rDNA, and internal transcribed spacer (ITS) regions. Neighbor-joining and parsimony analyses generated six major groups for both the D1/D2 and ITS regions. Pucciniastrum circaeae and P. epilobii formed a single group. P. hydrangeae-petiolaris, P. coryli, P. fagi, P. hikosanense, P. tiliae, and P. boehmeriae were each a distinct clade, and P. fagi formed a close relationship with P. hikosanense. However, these analyses did not support the monophyly of the following species: P. kusanoi, P. actinidiae, P. corni, P. styracinum, P. yoshinagai, and P. miyabeanum. Contribution no. 201, Laboratory of Plant Parasitic Mycology, Graduate School of Life and Environmental Sciences, University of Tsukuba, Japan     

基于物种多样性和空间格局的林分稀疏

为了解影响热带天然次生林稀疏的因素,本研究应用地上生物量模型、多样性指数和O-ring统计对固定样地中植物的地上生物量、物种多样性和空间分布格局进行定量研究,并结合Yoda自疏模型计算林分稀疏指数,分析物种多样性与空间格局对林分稀疏的影响。结果表明:林分地上生物量随着林分密度的减小呈现先增大,后减小,再增大的趋势,在径级Ⅲ或径级Ⅳ处,出现变化拐点,在天然林管理时应加以注意。多样性指数与林分稀疏指数总体上无显著的相关性,但中等多样性指数值却对应最大的稀疏指数。说明物种多样性中等情况下,林分稀疏最为强烈。植物个体聚集分布的最大强度与稀疏指数呈显著线性负相关,二者的回归方程为:α=-1.7873O11(r)max+2.3451(R2=0.798,P=0.003)。结果表明,在热带常绿季雨矮林中,过大的聚集强度不但不能促进稀疏过程的进行,反而会对其产生阻碍作用。     

Phylogenetic analysis of Carthamus species based on the nucleotide sequence of the nuclear SACPD gene and chloroplast trnL-trnF IGS region

To clarify the phylogenetic relationships of Carthamus species, we performed sequence analysis of the nuclear stearoyl acyl carrier protein desaturase (SACPD) gene and the chloroplast intergenic spacer region between leucine and phenylalanine tRNA genes (trnL-trnF IGS) in 13 taxa of Carthamus. The previous division of the genus into 4 taxonomic sections and allocation of particular genomes to various taxa on the basis of morphological, cytogenetic, and biosystematic analyses is not supported by the present study. Our results provide evidence of the occurrence of 5 nuclear genomes (A, B, C, X, and Y) and 3 cytoplasm types (A, B, and C) in the genus Carthamus. The cultivated safflower, C. tinctorius (2n = 24), has the B genome and type B cytoplasm. Both of these are not present in the polyploid taxa. This contradicts the earlier view that one of the genomes involved in the origin of the polyploid taxa of Carthamus is the B genome. Comparison with an outgroup species (Cirsium japonicum) indicated that C. arborescens is the most primitive species in the genus. Carthamus palaestinus is genetically closest to the cultivated safflower.     

Inter and intra ethnic variation of vitamin K epoxide reductase complex and cytochrome P450 4F2 genetic polymorphisms and their prevalence in South Indian population

BACKGROUND:

Genetic variation in the vitamin K epoxide reductase complex (VKORC1) and cytochrome P450 4F2 (CYP4F2) genes were found to be strongly associated with the oral anticoagulant (OA) dose requirement. The distribution of genetic variation in these two genes was found to show large inter- and intra-ethnic difference.

MATERIALS AND METHODS:

A total of 470 unrelated, healthy volunteers of South Indians of either sex (age: 18-60 years) were enrolled for the study. A 5 ml of venous blood was collected and the genomic deoxyribonucleic acid (DNA) was extracted by using phenol-chloroform extraction method. Real-time quantitative polymerase chain reaction (RT-PCR) method was used for genotyping.

RESULTS:

The variant allele frequencies of VKORC1 rs2359612 (T), rs8050894 (C), rs9934438 (T) and rs9923231 (A) were found to be 11.0%, 11.8%, 11.7% and 12.0%, respectively. The variant allele VKORC1 rs7294 was (80.1%) more frequent and the variant allele CYP4F2 * 3 was found to be 41.8% in South Indians. The allele, genotype and haplotype frequencies of VKORC1 and CYP4F2 gene were distinct from other compared HapMap populations (P < 0.0001).

CONCLUSION:

The findings of our study provide the basic genetic information for further pharmacogenetic based investigation of OA therapy in the population.     

Phylogenetic relationships among the Ibero-African cobitids (Cobitis, cobitidae) based on cytochrome b sequence data

We estimated the phylogenetic relationships of all Ibero-African spined loaches of the genus Cobitis using the complete mitochondrial cytochrome b gene (1140bp). We analysed 93 individuals of seven cobitid species found in all the principal drainages of the Iberian Peninsula and North Africa. A molecular phylogeny was used to revise current systematics of the Ibero-African Cobitis species and to infer a biogeographical model for Cobitis in the Western Mediterranean area during the Cenozoic period. Phylogenetic analysis provided support for the monophyly of two mtDNA clades: Clade A or Italian Clade with the Italian species (C. bilineata, C. zanandreai), and Clade B or the Ibero-African Clade. The Ibero-African Clade included all species endemic for the Iberian Peninsula (C. vettonica, C. calderoni, and C. paludica) and North Africa (C. maroccana). The species C. paludica does not constitute a natural group, and could be divided into at least four monophyletic mtDNA lineages with moderate to high bootstrap values and posterior probability support. Phylogenetic relationships of the Ibero-African species were not resolved satisfactorily, but in all analyses C. calderoni from Northern Iberian Peninsula was basal. We have re-calibrated a molecular clock for the genus Cobitis (0.68% per million year by pairwise) using populations inhabiting both sides of the Gibraltar Strait. Application of this Cobitis mtDNA clock provides evidence that the Messinian salinity crisis played a primary role in the diversification of some Ibero-African cobitid species. The basal polytomies of the Ibero-African Clade might suggest that all mtDNA lineages diversified rapidly.     

Origins of the diversity of cytochrome P450 CYP74 family based on the results of site-directed mutagenesis

Bioinformatic analysis and site-directed mutagenesis allowed identification of the determinants of catalysis for CYP74, which are located in the central part of the I-helix and ERR triad. Mutations K302S and T366Y in tomato allene oxide syntase LeAOS3 induced possession of hydroperoxide lyase activity. In contrast to the wild-type MtHPL enzyme that produces C₁₂-aldoacid, mutant forms F284I, F287V, G288I, N285A, and N285T of alfalfa hydroperoxide lyase MtHPL synthesized C₁₃- and C₁₁-fragments. Our data provide evidence that the CYP74 family originated from a common ancestor with hydroperoxide lyase activity.     

Phylogenetic relationships among Artemisia species based on nuclear ITS and chloroplast psbA-trnH DNA markers

The taxonomic and phylogenetic relationships within the genus Artemisia s.l. (Asteraceae) are controversial, and it has been considered 1 to 8 different genera. This work re-investigated the phylogenetic relationships in Artemisia using nuclear ribosomal (ITS) and chloroplast psbA-trnH DNA sequences using three sections of Artemisia, Dracunculus, and Serphidium. Three phylogenetic trees were conducted separately on the basis of ITS, psbA-trnH and combined sequences using maximum parsimony. The results showed that the three sections were clearly separated from each other, and that the heterogamous Dracunculus and Artemisia are closely related to each other than either to homogamous Serphidium. This may suggest the taxonomic importance of capitulum morphology in Artemisia s.l. Our data also cast doubt on the use of cytogenetic similarity e.g., basic chromosome number in grouping Serphidium and Artemisia s.s. Furthermore, AMOVA analysis showed a higher level of ITS (55.29%) and combined ITS+cppsbA-trnH (55.63%) variations among sections. This provides further evidence for separation of these three sections and supports the phylogenetic results. The higher ITS nucleotide differences detected in Artemisia (30.4737) compared to very low value in Dracunculus (2.3333) and Serphidium (1.23077) may propose that the Artemisia comprises of several incipient sections. This supports the previous suggestion that Artemisia is a complex group.     

Phylogenetic biogeography of the leafy liverwort Herbertus (Jungermanniales, Herbertaceae) based on nuclear and chloroplast DNA sequence data: correlation between genetic variation and geographical distribution

Aim The cosmopolitan genus Herbertus is notorious for having a difficult taxonomy and for the fact that there is limited knowledge of species ranges and relationships. Topologies generated from variable molecular markers are used to discuss biogeographical patterns in Herbertus and to compare them with the geological history of continents and outcomes reported for other land plants. Location Africa, Asia, Azores, Europe, southern South America, northern South America, North America, New Zealand. Methods Phylogenetic analyses of nuclear ribosomal internal transcribed spacer and chloroplast (cp) trnL–trnF sequences of 66 accessions of Herbertus and the outgroup species Triandrophyllum subtrifidum and Mastigophora diclados were used to investigate biogeographical patterns in Herbertus. Areas of putative endemism were defined based on the distribution of species included in the analyses. Maximum parsimony analyses were undertaken to reconstruct ancestral areas and intraspecies migration routes. Results The analyses reveal species‐level cladograms with a correlation between genetic variation and the geographical distribution of the related accessions. The southern South American Herbertus runcinatus is sister to the remainder of the genus, which is split into two main clades. One contains the Neotropical–African Herbertus juniperoideus and the New Zealand/Tasmanian Herbertus oldfieldianus. An African accession of H. juniperoideus is nested within Neotropical accessions. The second main clade includes species that inhabit Asia, the Holarctic, Africa, and northern South America. Maximum parsimony analyses indicate that this clade arose in Asia. Herbertus sendtneri originated in Asia and subsequently colonized the Holarctic and northern South America. An Asian origin and colonization into Africa is indicated for H. dicranus. Main conclusions The current distribution of Herbertus cannot be explained by Gondwanan vicariance. A more feasible explanation of the range is a combination of short‐distance dispersal, rare long‐distance dispersal events (especially into regions that faced floral displacements as a result of climatic changes) extinction, recolonization, and diversification. The African Herbertus flora is a mixture of Asian and Neotropical elements. Southern South America harbours an isolated species. The molecular data indicate partial decoupling of molecular and morphological variation in Herbertus. Biogeographical patterns in Herbertus are not dissimilar to those of other groups of bryophytes, but elucidation of the geographical ranges requires a molecular approach. Some patterns could be the result of maintenance of Herbertus in the inner Tropics during glacial maxima, and dispersal into temperate regions in warm phases.