Nuclear pseudogenes of mitochondrial DNA as a variable part of the human genome

INTRODUCTIONNuclearpseudogenesofmitochondrial(mt)DNAwereinitiallydiscoveredintheearly80's[1--6].However,mechanismsforthegenerationofmtDNApseudogenesarestillnotclearandmayvaryindifferentcases.BothRNA--[7--8]andDNAmediated[9--11]processeshavebeensugges...     

Nuclear ribosomal DNA monophyly versus mitochondrial DNA polyphyly in two closely related mite species: the influence of life history and molecular drive

In two very closely related but reproductively isolated mite species, Tetranychus urticae and T. turkestani, we found nucleotide diversity to be extensive for mitochondrial DNA (mtDNA) cytochrome oxidase 1 (COI) (3-4%) but extremely reduced for nuclear ribosomal DNA (rDNA) internal transcribed spacer (ITS2) (less than 0.5%). By contrast, ITS2 was shown to evolve much faster than COI between species of this genus. Furthermore, we found that these two species are polyphyletic for mtDNA but monophyletic for rDNA. Thus it appears that despite its biparental transmission and multiplicity of copies in the genome, nuclear rDNA has a smaller effective population size than mtDNA in these species. The conjunction of efficient concerted evolution and/or gene conversion in the rDNA cluster, the haplodiploidy of these species and their female-biased sex ratio could account for this apparent contradiction.     

Analysis of the sequences of internal transcribed spacers ITS1, ITS2 and the 5.8S ribosomal gene of species of the Amaranthus genus

Analysis of the sequence ITS1-5.8S-ITS2 in 11 samples of the amaranth species (Amaranthus caudatus, A. cruentus, A. hybridus, A. tricolor, A. paniculatus, A. hypohondriacus) was performed. It has been shown that the variability of the sequences of the intergenic spacers ITS1, ITS2 and 5.8S rRNA gene of the amaranth species analyzed is extremely low. A possible secondary structure of the 5.8S rRNA molecule was determined for the first time; three conservative motifs were identified. A single nucleotide substitution found in A. hybridus did not change the loop topology. In the sample of Celosia cristata taken as an external group, a four-nucleotide insertion in the 5′-end of the gene and a one-nucleotide deletion in the fourth hairpin not affecting the general topology of the 5.8S rRNA molecule were found.     

Tree invasions: a comparative test of the dominant hypotheses and functional traits

Trees act as ecosystem engineers and invasions by exotic tree species profoundly impact recipient communities. Recently, research on invasive trees has dramatically increased, enabling the assessment of general trends in tree invasion. Analysing 90 studies dealing with 45 invasive tree species, we conducted a quantitative review and a meta-analysis to estimate the relevance of eight leading hypotheses for explaining tree invasions. We also tested whether species functional traits (growth rate, density/cover, germination, biomass and survival) equally promote tree invasiveness. Overall, our results suggest that several hypotheses, linked to invasibility or invasiveness, are pertinent to explain tree invasions. Furthermore, more than one hypothesis has been supported for a given species, which indicates that multiple factors lead to the success of invasive tree species. In addition, growth rate appears to be the most efficient predictor of invasiveness for invasive trees and could thus be used as a means to identify potential alien tree invasions. We conclude that further investigations are needed to test the consistency of some hypotheses across a broader pool of invasive tree species, whilst experimental studies with the same tree species across a larger range of sites would help to reveal the full suite of factors that affect tree invasions.     

九子母属的系统位置：来自叶绿体rbcL序列及核核糖体ITS序列的证据

九子母属Dobinea Buch-Ham.ex D.Don是一个东亚特有属,包含贡山九子母D.vulgaris Buch-Ham.ex D.Don和羊角天麻D.delavayi(Baill.)Baill.两种,主要分布于中国两南地区.有关九子母属的系统位置长期存在争议,小同的学者曾将其归入漆树科Anacardiaceae、无忠子科sapindaceae和九子母科Podoaceae.本文基于rbcL和ITs探讨了其系统位置,结果表明,九子母属的两个种自成单系,并且是漆树科的成员.     

Phylogenetic position of the genus Dobinea: Evidence from nucleotide sequences of the chloroplast gene rbcL and the nuclear ribosomal ITS region

Dobinea Buch.-Ham. ex D. Don, a genus with two species endemic to east Asia, has been placed in three different families, the Podoaceae, tribe Acerineae of the Sapindaceae, and tribe Dobineeae of the Anacardiaceae. In this paper, phylogenetic relationships of the genus were examined based on DNA sequences of the chloroplast rbcL gene and the ITS region of nuclear ribosomal DNA. Our data support the monophyly of Dobinea and its placement in the Anacardiaceae.     

Identification of species in the genus Pichia by restriction of the internal transcribed spacers (ITS1 and ITS2) and the 5.8S ribosomal DNA gene

In this study, the variability within the ribosomal DNA region spanning the internal transcribed spacers ITS1 and ITS2 and the 5.8S gene (5.8S-ITS rDNA) was used to differentiate species in the genus Pichia. The 5.8S-ITS rDNA region was PCR-amplified and the PCR product digested with the enzymes CfoI, HinfI, and HaeIII. The variability in the size of the amplified product and in the restriction patterns enabled differentiation between species in the genus Pichia, and between Pichia species and yeast species from other genera in the Yeast-id database (). Moreover, the restriction fragment length polymorphism (RFLP) patterns of the 5.8S-ITS enabled misidentified strains to be detected and revealed genetic heterogeneity between strains within the Pichia membranifaciens and Pichia nakazawae species. Ultimately, the RFLP patterns of the 5.8S-ITS rDNA failed to differentiate between some Pichia and Candida species that could be distinguished on the basis of the sequence of the 5.8S-ITS rRNA region or the sequence of the D1/D2 domain of the 26S rDNA gene.     

Inclusion of the Vietnamese endemic genus Grushvitzkya in Brassaiopsis (Araliaceae): evidence from nuclear ribosomal ITS and chloroplast ndhF sequences

The phylogenetic position of the recently described monotypic Vietnamese genus Grushvitzkya is evaluated using nuclear ribosomal ITS and chloroplast ndh F sequence data . Grushvitzkya stellata has often been considered as intermediate between Brassaiopsis and Trevesia , but differs in having a 5-locular ovary rather than a 2- or 6–16-locular ovary, respectively. The molecular data indicate that Grushvitzkya is deeply nested within Brassaiopsis and has a close relationship with B. phanrangensis from central and southern Indochina, and B. stellata from the regions bordering China and Vietnam. The Kimura 2-parameter distances of the ITS sequences between G. stellata and B. phanrangensis and B. stellata are 0.403 and 0.945%, respectively. Furthermore, G. stellata and B. phanrangensis have an identical ndh F sequence profile. Grushvitzkya stellata differs from B. stellata by a single nucleotide in their ndh F sequences. The available evidence is compatible with the hypothesis that Grushvitzkya diverged recently from B. phanrangensis and B. stellata . Although these three closely related species all possess stellate trichomes, G. stellata and B. phanrangensis have highly similar trichome micromorphology, with almost no difference in size, shape and branching pattern, supporting a very close relationship between the two taxa. The higher number of locules in the ovary of Grushvitzkya appears to be a secondary increase despite earlier interpretations that higher numbers are evolutionarily primitive. Grushvitzkya is herein merged with Brassaiopsis ; because the combination B. stellata is occupied, a new name, Brassaiopsis grushvitzkyi , is proposed.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 142 , 455–463.     

基于染色体计数和ITS序列初步探讨横断山区柴胡属植物(伞形科)的系统发育

横断山区是中国柴胡属Bupleurum植物的分布中心。本文对横断山区6个种2变种进行了染色体记数报道,其中4个种2变种是首次报道。对横断山区的10个种4个变种、中国北方（河北和黑龙江）的3个种的nrDNA ITS进行测序,同时从GenBank里面下载同属的来自非洲和地中海西部的16个nrDNA ITS序列数据,结合染色体数目变化结果,初步探讨了横断山区柴胡属植物的系统发育。结果表明横断山区可能是现代柴胡属植物的频度中心和多样分布中心之一。它们的祖先种可能是非洲北部的木本柴胡属植物B.fruticosum,或者是地中海西部的柴胡属植物,推测是通过中东和高加索扩散而形成的,其中与非洲南部特有种B.mundtii的亲缘关系也较近;染色体基数演化趋势是：8是较原始基数,6和7是次生基数,其染色体异基数变异和多倍化可能是物种形成、进化以及向外扩散的主要方式;在ITS系统发育树中,中国柴胡属植物染色体基数为8的种类聚为一支,染色体基数为6和7的种类聚为了一支,不支持舒璞等（1998）关于中国柴胡属的属下分类系统。结合已有的形态学、细胞学、孢粉学证据和ITS系统发育树,建议窄竹叶柴胡B.marginatum var.stenophyllum独立成种。     

Phylogenetic inference of the genus Bupleurum (Apiaceae) in Hengduan Mountains based on chromosome counts and nuclear ribosomal DNA ITS sequences

pleurum of Apiaceae in China. This paper reports chromosome numbers of six species and two varieties of Bupleurum, and for four species and two varieties their chromosome numbers are reported for the first time. The phylogeny of Bupleurum was investigated based on the ITS region of the nuclear ribosomal DNA (nrDNA) of 14 taxa from the Hengduan Mountains, 3 taxa from the North China (Hebei and Heilongjiang), and 16 taxa from Africa and the Mediterranean region. Varia-tions in chromosome numbers and the ITS sequences were used to infer phylogenetic relationships between Bupleurum species in Hengduan Mountains. The results showed that the Hengduan Mountains might represent one of the frequency and diversity centers for Bupleurum. The ancestors of Bupleurum species in the Hengduan Mountains may be related to the woody B. fruticosum in North Africa, or the species in the western Mediterranean region. It is postulated that the ancestral population migrated into Hengduan Mountains through the Middle East and the Caucasus. Furthermore, the neo-endemic B. mundtii in South Africa appeared to be a close relative of the species in the Hengduan Mountains. In the trend of basic chromosome number evolution, x = 8 should be regarded as the ancestral basic number, while x = 6, 7 as the derived ones. The Bupleurum species in the Hengduan Moun-tains have been undergoing changes in the basic chromosome numbers or the ploidy level. The ITS phylogenetic tree showed that the Chinese species were divided into two clades: one with the basic chromosome number x = 8, and the other with x = 6, 7. The results rejected the previous infrageneric classification of Bupleurum in China. We further suggested to raise B. marginatum var. stenophyllum to species rank based on the combined evidence from morphology, karyology, pollen morphology, and the ITS phylogenetic tree.     

Leishmania: genus identification based on a specific sequence of the 18S ribosomal RNA sequence

The analysis of PvuII restriction patterns of Leishmania spp. and Trypanosoma spp. genomic DNA showed genus distinctive profiles. A specific PvuII site was detected in the 5' domain of 18S ribosomal DNA of Leishmania. A 20-mer oligonucleotide encompassing this PvuII region was synthesized. This sequence, when utilized as probe, on short exposures of dot tests, detected 10(3) whole promastigotes of all Leishmania species analyzed but did not hybridize with T. cruzi or human nucleic acids. Two other oligonucleotides were synthesized to be used as primers for amplification through polymerase chain reaction of the 18S ribosomal DNA region containing the PvuII site. The probes described may be useful for the detection of Leishmania spp. under clinical and epidemiological trials.     

16S ribosomal RNA analysis of Filibacter limicola indicates a close relationship to the genus Bacillus

The phylogenetic relationship of the Gram-negative, filamentous gliding bacterium Filibacter limicola was analysed by 16S rRNA oligonucleotide cataloguing. In contrast to the proposed membership of this asporogenous species in the Flexibacteriaceae, Filibacter limicola clusters phylogenetically with the Gram-positive eubacteria Bacillus pasteurii, Sporosarcina ureae and the asporogenous species Planococcus citreus. The genetic relationship is supported by several common phenotypic properties.     

Infrageneric phylogeny of the genus Gentiana (Gentianaceae) inferred from nucleotide sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA

The internal transcribed spacers (ITSs) of nuclear ribosomal DNA have been sequenced for 20 species of Gentiana. By incorporating previously released sequence data of eight species, phylogenelic analyses using Fitch parsimony and character-state weighted parsimony were carried out. The length of ITS 1 in the taxa surveyed ranged from 223 to 238 bp and ITS2 from 216 to 234 bp. Sequence divergence between pairs of species ranged from 5.0% to 48.9% in ITS1, from 1.1% to 45.3% in ITS2, and from 3.2% to 46.1% in combined data of ITS1 and ITS2. The ITS phylogeny was generally congruent with morphological classifications except that G. asclepiadea was revealed to be closely related to section Gentiana instead of section Pneumonanthe and section Stenogyne was shown to be a paraphyletic group of the genus Gentiana that would be better excluded from the genus. A divergence among the three European endemic sections and the remaining sections of the genus other than section Stenogyne was revealed. Thus the European species of the genus together do not form a monophyletic group. A close relationship between the sections Chondrophyllae s. l. (including section Dolichocarpa), Cruciata and Pneumonanthe was suggested. The section Frigidae s. l. (including sections Monopodiae, Isomeria, Microsperma, and Phyllocalyx) contained two well-supported clades: section Frigidae s. str. and all others together. The monophyly of the typically dysploid group section Chondrophyllae s. l. was confirmed. Optimization of chromosome numbers on the ITS phylogeny suggested that 2/1 = 26 is a plesiomorphic state for the clade comprising sections Frigidae s. l., Cruciata, Pneumonanthe, and Chondrophyllae s. l., and probably 2n = 20 is a plesiomorphic state for the dysploid group, section Chondrophyllae s. l.     

Weintrauboa, a new genus of pimoid spiders from Japan and adjacent islands, with comments on the monophyly and diagnosis of the family Pimoidae and the genus Pimoa (Araneoidea, Araneae)

The spider genus Weintrauboa new genus (Araneae, Pimoidae) is described to place two species of pimoids from Japan and adjacent islands that were formerly classified in the linyphiid genus Labulla . Weintrauboa contortipes (Karsch) new comb., the type species, and W. chikunii (Oi) new comb. are redescribed. Parsimony analysis of morphological characters provides robust support for the monophyly of the genus Weintrauboa and corroborates the monophyly of Pimoa , Pimoidae, and the clade Linyphiidae plus Pimoidae. New diagnoses for Pimoa and Pimoidae are provided.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 139 , 261–281     

Phylogeny of the Neotropical Alibertia group (Rubiaceae), with emphasis on the genus Alibertia, inferred from ITS and 5S ribosomal DNA sequences

Phylogenetic relationships of 38 species of the Alibertia group (Rubiaceae) and two outgroup species were investigated using the nuclear ribosomal 5S nontranscribed spacer (5S-NTS) and the internal transcribed spacers (ITS). Analysis of the data sets separately and in combination resulted in several well-supported and congruent groupings. However, the three analyses yielded different results as to the branching order of the basal clades. With the exception of Alibertia hispida, the species in the genus Alibertia appear in one weakly to moderately supported clade. This clade is in turn composed of two strongly supported subclades. One comprises several Alibertia species, including the type (A. edulis), three Borojoa species, and Randia tessmannii. The other subclade consists of Alibertia species only. This division is also generally supported morphologically by fruit size, corolla size, number of corolla lobes, and pollen aperture (porate vs. colporate). The sister group to the Alibertia clade comprises Duroia with Amaioua species internested. The close relationship of Ibetralia and Kutchubaea is corroborated. In addition, Alibertia hispida is a member of this strongly supported clade. Likewise, the two "Genipa" species are supported as a monophyletic group in 100% of the bootstrap replicates. It is concluded that the 5S spacer is superior to the commonly used ITS region in terms of resolution and robustness among closely related taxa.     

Identification of a protein at the ribosomal donor-site by affinity labeling

p-nitrophenylcarbamyl-methionyl-tRNA_f^Met is shown to act as an analogue of fMet-tRNA_f^Met in initiation complex formation. It binds to E. coli ribosomes in the presence of initiation factors and R 17-RNA as messenger. Covalent bond formation occurs in the complex between the Met-tRNA_f^Met derivative and protein of the 50 S ribosomal subunit. The protein labeled predominantly in the reaction has been identified as L 27 indicating that this protein is located at the donor-site of the ribosome.     

Evolutionary relationships of the salmonid fish genus Salvelinus inferred from DNA sequences of the first internal transcribed spacer (ITS 1) of ribosomal DNA.

DNA sequences of the ribosomal DNA (rDNA) first internal transcribed spacer region (ITS 1) of six species of the salmonid fish genus Salvelinus (alpinus, malma, confluentus, leucomaenis, fontinalis, and namaycush) and the closely related species Hucho perryi were determined. Phylogenetic analysis of the aligned sequences by both phenetic and cladistic methods with H. perryi as an outgroup generated one best topology which pairs S. alpinus with S. malma as the most recently derived species, and pairs S. confluentus with S. leucomaenis. Three other possible topologies favor the pairing of S. namaycush and S. fontinalis, with one tree placing them on separate branches, and vary the branching order of the interior groups. These results agree with previous studies based on comparisons of morphologies, isozymes, karyotypes, and restriction sites showing a close genetic relationship and possible hybridization between the members of this genus.     

Evolution of the plastid ribosomal RNA operon in a nongreen parasitic plant: Accelerated sequence evolution,altered promoter structure,and tRNA pseudogenes

The nucleotide sequence of a 7.4 kb region containing the entire plastid ribosomal RNA operon of the nongreen parasitic plant Epifagus virginiana has been determined. Analysis of the sequence indicates that all four rRNA genes are intact and almost certainly functional. In contrast, the split genes for tRNA^Ile and tRNA^Ala present in the 16S-23S rRNA spacer region have become pseudogenes, and deletion upstream of the 16S rRNA gene has removed a tRNA^Val gene and most of the promoter region for the rRNA operon. The rate of nucleotide substitution in 16S and 23S rRNAs is several times higher in Epifagus than in tobacco, a related photosynthetic plant. Possible reasons for this, including relaxed translational constraints, are discussed.