Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

A method is presented for the rapid isolation of high molecular weight plant DNA (50,000 base pairs or more in length) which is free of contaminants which interfere with complete digestion by restriction endonucleases. The procedure yields total cellular DNA (i.e. nuclear, chloroplast, and mitochondrial DNA). The technique is ideal for the rapid isolation of small amounts of DNA from many different species and is also useful for large scale isolations.

Rapid isolation of high molecular weight plant DNA

The use of some multiple-sequence alignments in phylogenetic analysis, particularly those that are not very well conserved, requires the elimination of poorly aligned positions and divergent regions, since they may not be homologous or may have been saturated by multiple substitutions. A computerized method that eliminates such positions and at the same time tries to minimize the loss of informative sites is presented here. The method is based on the selection of blocks of positions that fulfill a simple set of requirements with respect to the number of contiguous conserved positions, lack of gaps, and high conservation of flanking positions, making the final alignment more suitable for phylogenetic analysis. To illustrate the efficiency of this method, alignments of 10 mitochondrial proteins from several completely sequenced mitochondrial genomes belonging to diverse eukaryotes were used as examples. The percentages of removed positions were higher in the most divergent alignments. After removing divergent segments, the amino acid composition of the different sequences was more uniform, and pairwise distances became much smaller. Phylogenetic trees show that topologies can be different after removing conserved blocks, particularly when there are several poorly resolved nodes. Strong support was found for the grouping of animals and fungi but not for the position of more basal eukaryotes. The use of a computerized method such as the one presented here reduces to a certain extent the necessity of manually editing multiple alignments, makes the automation of phylogenetic analysis of large data sets feasible, and facilitates the reproduction of the final alignment by other researchers.

/pdf/selection-of-conserved-blocks-from-multiple-alignments-for-i0qfazjwh5.pdf

Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis

The flowering plant Arabidopsis thaliana is an important model system for identifying genes and determining their functions. Here we report the analysis of the genomic sequence of Arabidopsis. The sequenced regions cover 115.4 megabases of the 125-megabase genome and extend into centromeric regions. The evolution of Arabidopsis involved a whole-genome duplication, followed by subsequent gene loss and extensive local gene duplications, giving rise to a dynamic genome enriched by lateral gene transfer from a cyanobacterial-like ancestor of the plastid. The genome contains 25,498 genes encoding proteins from 11,000 families, similar to the functional diversity of Drosophila and Caenorhabditis elegans--the other sequenced multicellular eukaryotes. Arabidopsis has many families of new proteins but also lacks several common protein families, indicating that the sets of common proteins have undergone differential expansion and contraction in the three multicellular eukaryotes. This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.

/pdf/analysis-of-the-genome-sequence-of-the-flowering-plant-3vizsb52m2.pdf

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.

Phylogenetic relationships among 16 species of Lobelia and single representatives of Monopsis and Sclerotheca (Lobeliaceae) were assessed by mapping restriction sites and major structural rearrangements (deletions and inversions) in the large single-copy region of the chloroplast genome. Eleven inversions and five different gene arrangements were found. A deletion involving 0RF5 12 is associated with many of the inversions, and all inversion endpoints are located in intergenic spacer regions. Analysis of 132 phylogenetically informative restriction sites produced three equally parsimonious trees of 2 19 steps, with a consistency index of 0.60. The restriction-site and inversion data yield congruent trees, indicating that the giant lobelias from around the world are derived from diploid herbaceous ancestors. The giant lobelias consist of a Chilean hexaploid group and a pantropical tetraploid group. The woody genus Sclerotheca is clearly derived from a giant Lobelia ancestor, while the herbaceous Monopsis is probably derived from herbaceous lobelias. The giant lobelias from eastern Africa are weakly supported as monophyletic with the inclusion of the Brazilian L. organensis. Relationships among the Pacific and Asian giant lobelias are not fully resolved and await more detailed study.

/pdf/chloroplast-genome-rearrangements-and-the-evolution-of-giant-3wiol9amsv.pdf

Chloroplast genome rearrangements and the evolution of giant lobelias from herbaceous ancestors

We constructed a complete transcriptional map of the 218 kb Brassica campestris (turnip) mitochondrial genome. Twenty-four abundant and positionally distinct transcripts larger than 500 nucleotides were identified by Northern analyses. Approximately 30% (61 kb) of the genome is highly transcribed. In addition, a number of less abundant transcripts, many of which overlap with each other and with the major transcripts, were also detected. If each abundant transcript represents a distinct rRNA or protein species, then plant mitochondria would appear to encode a significantly larger number of proteins than do animal mitochondria. Although B. campestris mitochondrial DNA contains a number of chloroplast DNA-derived sequences, none of these chloroplast sequences appear to be transcribed within the mitochondrion. We determined the positions of 12 genes in the B. campestris mitochondrial genome. The order of these genes in B. campestris is completely different than in maize (1) and spinach (2).

Extensive mitochondrial specific transcription of the Brassica campestris mitochondrial genome

-Phylogenetic relationships of 36 species of Anemone (Ranunculaceae) and seven related genera were explored with three independent data sets: chloroplast DNA restriction sites, nuclear ribosomal DNA restriction fragments, and morphological/cytological variation. In the chloroplast DNA work, 245 phylogenetically informative restriction sites were identified using ten restriction enzymes. The phylogeny based on conventional data was derived from 27 characters for the same taxa used in the molecular work. A subset of species complexes was examined with additional chloroplast and nuclear ribosomal DNA data. Molecular and morphological characters established Clematis as the most suitable outgroup for the phylogenetic analyses. Many of the terminal groups of the cladograms resulting from the molecular and morphological data sets were similar, but basal branching patterns were substantially different. Because the molecular tree was substantially less homoplastic and had higher bootstrap and decay values than the morphological tree, it was accepted as the more reliable in determining basal relationships. Both morphological and chloroplast DNA phylogenies demonstrate that few of the sections of Anemone as established by previous classifications are monophyletic. The phylogenies based on chloroplast DNA restriction sites and the combined data sets indicate that Pulsatilla, Hepatica, and Knowltonia should be subsumed within Anemone. Various morphological characters indicate that Barneoudia and Oreithales should also be included within the genus Anemone. Independent data sets provide phylogenetic hypotheses useful in interpretations of character evolution. A preliminary, revised classification is proposed. Several hypotheses are offered to explain the unusual geographic distributions found in Anemone. Anemone s. str. consist of 70-90 species of perennial, low-growing herbs (Ulbrich 1905-1906; pers. obs.). The genus is characterized by a rosette of basal leaves, an involucrate peduncle bearing a single flower or compound inflorescence, a perianth of petaloid sepals, and an achene fruit. There is considerable morphological variation within the genus. The perennating structures are upright stems, rhizomes, or tubers. The basal leaves vary from trilobed to several times ternate, rarely pinnate. The involucral leaves are various in number and form, sometimes reduced and bract-like. The achenes are glabrous to tomentose, few to many in number, with various morphologies of the style. Base chromosome numbers are either seven or eight. Species are most numerous in the Northern Hemisphere, but also occur in mountainous and cooler regions of the Southern Hemisphere. They inhabit a wide range of habitats including arctic and alpine tundra, prairie, woodlands, Mediterannean regions, and semidesert. Several previous classifications placed Anemone and Clematis in the same tribe, Anemoneae (Langlet 1932; Tamura 1967). A sister genus to Clematis from Africa, Clematopsis, should also be included in this tribe (Hutchinson 1920). Anemoneae are regarded as most closely related to the tribes Ranunculeae and Adonieae. Cladistic analyses based on morphology of the Ranunculaceae (Hoot 1991) place Anemone in a clade with Clematis, Hepatica, Pulsatilla, and Ranunculus, united by two derived character states, presence of achenes and the chemical compound ranunculin. It is not at all clear which of these genera are most closely related to Anemone. The delimitation of Anemone has been debated for years. Early classifications often included the genera Hepatica, Pulsatilla, Knowltonia, Barneoudia, and Oreithales within Anemone (Jan-

Phylogenetic relationships in Anemone (Ranunculaceae) based on morphology and chloroplast DNA

A 78 kb DNA inversion encompassing most of the large single copy region of the chloroplast genome marks a monophyletic group that comprises most genera in the subtribe Phaseo- linae of the legume tribe Phaseoleae. The inversion, whose endpoints map next to and which includes the infA and psbA genes, originally was characterized from the chloroplast genomes of Phaseolus and Vigna (subtribe Phaseolinae), but was known to be absent from that of Glycine (subtribe Glycininae). We report here a survey of 50 genera of Phaseoleae and related tribes screened using small chloroplast DNA probes, whose hybridization patterns are diagnostic for the presence or absence of the inversion. The taxonomic distribution of the inversion is consistent with morpho- logical and other data, and supports recent subtribal classifications. The disputed inclusion of Macrotyloma in the Phaseolinae is supported by the presence of the inversion in the genus. In contrast, other genera whose placement in the Phaseolinae recently has been questioned, lack the inversion (Pachyrhizus, Clitoria, Centrosema, Psophocarpus). Although still possibly related to Phaseolin- ae, the lack of the 78 kb chloroplast DNA inversion in these genera supports taxonomic hypotheses that place them elsewhere.

A Chloroplast DNA Inversion as a Subtribal Character in the Phaseoleae (Leguminosae)

The discovery of plastids in apicomplexan parasites1,3 raised the possibility that these organelles might harbour plastid-specific metabolic activities that could be blocked by therapeutic agents. Ideally, these agents would inhibit the parasites without harming their vertebrate hosts. Roberts et al.4 have made the promising dicovery that Apicomplexa are sensitive to the herbicide glyphosate (better known by its trade names of RoundUp, Zero or Tumbleweed), which is an inhibitor of the enzyme 5-enopyruvyl shikimate 3-phosphate synthase. They suggested that production of aromatic amino acids by the pathway involving this enzyme, the shikimate pathway, might be an essential function of the apicomplexan plastid, but here we present evidence that this pathway actually operates in the cytosol of Apicomplexa.

Jeffrey D. Palmer

Papers

Chloroplast genome rearrangements and the evolution of giant lobelias from herbaceous ancestors

Extensive mitochondrial specific transcription of the Brassica campestris mitochondrial genome

Phylogenetic relationships in Anemone (Ranunculaceae) based on morphology and chloroplast DNA

A Chloroplast DNA Inversion as a Subtribal Character in the Phaseoleae (Leguminosae)

Shikimate pathway in apicomplexan parasites