Isolation and characterization of a rice cDNA which encodes a ubiquitin protein and a 52 amino acid extension protein

We isolated a rice cDNA clone encoding the ubiquitin protein fused to a ribosomal protein. This clone encodes a single ubiquitin polypeptide and extension protein of 53 amino acids. This extension protein shows a high degree of homology with those of the yeast ubil or ubi2 gene, both of which encode the same protein. Northern blot analysis suggested that the expression pattern of this gene is more similar to other ribosomal protein genes not linked to ubiquitin protein than to the polyubiquitin gene.     

cDNA sequence analysis of ribosomal protein S13 gene in Plutella xylostella （Lepidoptera： Plutellidae）

Ribosomal protein S 13 gene has been cloned and analyzed in many organisms,but there are few documents relating to insects. In this communication, the full-length cDNA sequence of ribosomal protein S 13 gene in the diamondback moth, Plutella xylostella(Lepidoptera: Plutellidae), was determined by using PCR amplification technique. The features of the ribosomal protein S 13 gene sequence were analyzed and the deduced amino acids sequence was compared with those from other insects. The results of multi-alignment of the amino acid sequences between the diamondback moth and other insect species revealed that this gene sequence is highly conserved in insects. Based on maximum likelihood method, a phylogenetic tree was constructed from 10 different species using PHYLIP software. It showed that nematode is one separate lineage and the five insect speciesbe long to another lineage, whereas those species higher than insects form the third one. The pattern of this phylogenetic tree evidently represented the evolution of different species.     

Phototactic responses of larvae from the marine sponges Neopetrosia proxima and Xestospongia bocatorensis (Haplosclerida: Petrosiidae)

Abstract. Previous studies suggest that phototaxis in sponge larvae is generated by the bending of a tuft of long posterior cilia (LPC). The photoresponsiveness of these cilia is often assayed by examining their reaction to sudden changes in light intensity. Here, we document and describe the larvae of the tropical marine sponges Neopetrosia proxima and Xestospongia bocatorensis and examine the phototactic behavior of their larvae. Both species brood ovoid, tufted parenchymella larvae, clearly countering an earlier hypothesis that all petrosid sponges are oviparous. Larvae of N. proxima were positively phototactic and settled after 2 d, while larvae of X. bocatorensis were negatively phototactic and settled in as little as 4 h. In both species, LPC quickly responded to changes in the light intensity. When the light intensity is reduced, the larvae of N. proxima fold the cilia inwards immediately without beating, then flare them outwards, beating for a few seconds, and then gradually return to the neutral position while continuing to beat. In contrast, the larvae of X. bocatorensis flare the cilia outwards when the light intensity is reduced and fold them inwards when the light intensity is increased. Comparisons with reported ciliary responses to light for other species demonstrate that these responses do not show the hypothesized one-to-one correspondence with phototactic behaviors and are, therefore, of limited use in explaining the mechanisms that coordinate larval swimming.     

Complete mitochondrial genome sequence of Bonasa sewerzowi(Galliformes: Phasianidae) and phylogenetic analysis

Bonasa sewerzowi, the smallest and most southerly distributed grouse species in the world, is a bird endemic to China. The population of B. sewerzowi had shown a declining trend, which made it to be the endangered species in the China Red Data Book and Category I of nationally protected animals. So far, however, most studies about this species were mainly focused on the morphological and ecological aspects. In order to further study the feature of B. sewerzowi, the complete mitochondrial genome(mitogenome) of B. sewerzowi was sequenced by Illumina Hiseq 2000 high-throughput sequencing. Then, we focused on comparative genomics of two Bonasa species to find their characteristics. Finally, phylogenetic position of Bonasa was made based on the mitogenome dataset. Our results revealed that:(1) the mitogenome of B. sewerzowi, consisting of 16 658 bp, displayed typical genome organization and gene order found in other previously determined Galliformes mitogenomes;(2) the structure and composition of mitogenomes were similar between B. sewerzowi and B. bonasia;(3) the monophyly of Bonasa was well supported, which had a closer phylogenetic relationship with Meleagris gallopavo.     

Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): implications for phylogenetic studies

The internal transcribed spacer regions (ITS1 and ITS2) of the tandemly repeated nuclear ribosomal DNA clusters are frequently used as markers for fine scale analyses in diverse animals. In certain taxa, ITS is nearly exclusively used for population level or inter-specific studies, despite the frequent presence of divergent paralogs within individual genomes that can be phylogenetically misleading. For the first time we survey diverse marine sponges to determine the extent and phylogenetic implications of intragenomic polymorphisms (IGPs) exhibited at their ITS loci. We discover that the extent of IGP varies greatly between taxa (with most taxa exhibiting very few) and cannot be predicted by taxonomy. Furthermore, we demonstrate that ITS can be phylogenetically informative between species when moderate levels of IGPs are detected, but that ITS paralogy can interfere with population level studies. We caution against the routine use of ITS in phylogenetic studies of sponges without (1) screening for IGPs in specimens from every population sampled; (2) including all divergent paralogs in phylogenetic analyses; (3) testing ITS data using other single-copy, unlinked loci (such as nuclear introns).     

Major discrepancy between phylogenetic hypotheses based on molecular and morphological criteria within the Order Haplosclerida (Phylum Porifera: Class Demospongiae)

Taxonomy within the sponge Order Haplosclerida remains somewhat contentious. Both morphology and biochemistry have been employed to help unravel the relationships of the Order with limited results perhaps because of the small number of reliable characters. We employed phylogenetic analysis of 750 base pairs of the 5′ end of the 28S rRNA gene to study relationships between 20 taxa within the Order. While preliminary (low number of taxa, one gene region) results suggested strong discrepancy to former phylogenies, there was no support for the monophyly of the Order and almost all morphologically defined genera appeared to be polyphyletic.     

Cloning of Hsp70 genes from the marine sponges Sycon raphanus (Calcarea) and Rhabdocalyptus dawsoni (Hexactinellida). An approach to solve the phylogeny of sponges

The phylogenetic relationships among the three classes of the Porifera-Demospongiae, Calcarea and Hexactinellida-are still unresolved, despite the use of molecular analyses of rRNA. To determine whether phylogenetic resolution of these classes is possible based on genes coding for specific proteins, in the present study the genes for the 70 kDa heat shock protein [Hsp70] were isolated from Rhabdocalyptus dawsoni [Hexactinellida] and from Sycon raphanus [Calcarea], and compared to that previously isolated from the demosponge Geodia cydonium. The gene from R. dawsoni is 2021 bp long and encodes a predicted Hsp70 of Mr 77, 697; the protein comprises the characteristic sites of eukaryotic, cytoplasmic Hsp70 polypeptides. The Hsp70 isolated from cDNA from S. raphanus is 2326 bp long. It encodes a potential polypeptide of Mr 85, 927 and belongs to the same class of Hsp70s. All three sponge sequences for Hsp70 were found to be highly identical to both human and plant Hsp70s. The degree of identity at the amino acid (aa) level between the sponge sequences and the human sequence for Hsp70 is 77%-84% and at the nucleotide (nt) level, between 69% and 75%. Resolution of the phylogenetic relationship between the three classes of sponges based on the Hsp70 was not possible due to the high degree of identity [similarity] of their respective aa sequences, which ranged from 80% [90%] to 82% [91%]. The evolutionary rates-K_aa-values-calculated for the sponge Hsp70 molecules, are low, reflecting the strong functional contraints placed upon these polypeptides. These values range from 0.125 times 10^-9 for G. cydonium and R. dawsoni to 0.087 times 10^-9 for S. raphanus. Higher values have previously been reported for the G. cydonium galectin molecule [K_aa-value of 1.7 times 10^-9] and the receptor tyrosine kinase [1.24 times 10^-9] from the same animal. The occurrence of at least one double mutation, in the codon for the aa Ser in the conserved regions of the Hsp70 sequences, also suggests that these molecules are subjected to strong functional constraints.     

The Rieske protein: a case study on the pitfalls of multiple sequence alignments and phylogenetic reconstruction

Previously published phylogenetic trees reconstructed on "Rieske protein" sequences frequently are at odds with each other, with those of other subunits of the parent enzymes and with small-subunit rRNA trees. These differences are shown to be at least partially if not completely due to problems in the reconstruction procedures. A major source of erroneous Rieske protein trees lies in the presence of a large, poorly conserved domain prone to accommodate very long insertions in well-defined structural hot spots substantially hampering multiple alignments. The remaining smaller domain, in contrast, is too conserved to allow distant phylogenies to be deduced with sufficient confidence. Three-dimensional structures of representatives from this protein family are now available from phylogenetically distant species and from diverse enzymes. Multiple alignments can thus be refined on the basis of these structures. We show that structurally guided alignments of Rieske proteins from Rieske-cytochrome b complexes and arsenite oxidases strongly reduce conflicts between resulting trees and those obtained on their companion enzyme subunits. Further problems encountered during this work, mainly consisting in database errors such as wrong annotations and frameshifts, are described. The obtained results are discussed against the background of hypotheses stipulating pervasive lateral gene transfer in prokaryotes.     

基于28S rDNA D2基因序列的几种寄生夜蛾科的多胚跳小蜂的分子系统发育（英文）

本文基于28S rDNA D2部分序列, 用MP和ML方法对几种寄生夜蛾科的多胚跳小蜂Copidosoma spp.进行了系统发育研究,并对其形态和生物学关系进行了讨论。结果表明：寄生金翅夜蛾亚科(Plusiinae)的C. floridanum 和寄生实夜蛾亚科(Heliothinae)的C. primulum关系较近,而以夜蛾亚科(Noctuinae)为寄主的C. truncatellum 和 C. agrotis关系更近。结果提示核基因28S D2区可能对研究多胚跳小蜂种间的系统发育关系很有帮助。     

First report on chitinous holdfast in sponges (Porifera)

A holdfast is a root- or basal plate-like structure of principal importance that anchors aquatic sessile organisms, including sponges, to hard substrates. There is to date little information about the nature and origin of sponges’ holdfasts in both marine and freshwater environments. This work, to our knowledge, demonstrates for the first time that chitin is an important structural component within holdfasts of the endemic freshwater demosponge Lubomirskia baicalensis. Using a variety of techniques (near-edge X-ray absorption fine structure, Raman, electrospray ionization mas spectrometry, Morgan–Elson assay and Calcofluor White staining), we show that chitin from the sponge holdfast is much closer to α-chitin than to β-chitin. Most of the three-dimensional fibrous skeleton of this sponge consists of spicule-containing proteinaceous spongin. Intriguingly, the chitinous holdfast is not spongin-based, and is ontogenetically the oldest part of the sponge body. Sequencing revealed the presence of four previously undescribed genes encoding chitin synthases in the L. baicalensis sponge. This discovery of chitin within freshwater sponge holdfasts highlights the novel and specific functions of this biopolymer within these ancient sessile invertebrates.     

SeqMaT: A sequence manipulation tool for phylogenetic analysis

Most bioinformatics tools require specialized input formats for sequence comparison and analysis. This is particularly true for molecular phylogeny programs, which accept only certain formats. In addition, it is often necessary to eliminate highly similar sequences among the input, especially when the dataset is large. Moreover, most programs have restrictions upon the sequence name. Here we introduce SeqMaT, a Sequence Manipulation Tool. It has the following functions: data format conversion,sequence name coding and decoding,redundant and highly similar sequence removal, anddata mining utilities. SeqMaT was developed using Java with two versions, web-based and standalone. A standalone program is convenient to manipulate a large number of sequences, while the web version will guarantee wide availability of the tool for researchers and practitioners throughout the Internet. AVAILABILITY: The database is available for free at http://glee.ist.unomaha.edu/seqmat.     

以礼草属系统发育的分析

基于分支系统学的原理和方法。对禾本科以礼草属进行了系统发育分析,以礼草属是个单系在群,它的３２个外部性状选作极性分析。鹅观草属中的肃草作为外类群,采用ＰＡＵＰ程序对矩阵进行运算,获得了１个最简约的谱系分支图。在分支图上,以民礼草属２６个种可以归为３个组,但不适合于划分系,３个组中各组包含的种数分别与传统分类的３个组基本吻合,从而支持了传统分类的结果。同时,分支图还展示了各个类群间的亲缘演化关系,其     

Molecular phylogenetic analysis of the genus Strongyloides and related nematodes

Strongyloides spp., parasitic nematodes of humans and many other terrestrial vertebrates, display an unusual heterogonic lifecycle involving alternating parasitic and free-living adult reproductive stages. A number of other genera have similar lifecycles, but their relationships to Strongyloides have not been clarified. We have inferred a phylogeny of 12 species of Strongyloides, Parastrongyloides, Rhabdias and Rhabditophanes using small subunit ribosomal RNA gene (SSU rDNA) sequences. The lineage leading to Strongyloides appears to have arisen within parasites of terrestrial invertebrates. Inferred lifecycle evolution was particularly dynamic within these nematodes. Importantly, the free-living Rhabditophanes sp. KR3021 is placed within a clade of parasitic taxa, suggesting that this species may represent a reversion to a non-parasitic lifecycle. Species within the genus Strongyloides are very closely related, despite the disparity of host species parasitised. The highly pathogenic human parasite Strongyloides fuelleborni kelleyi is not supported as a subspecies of the primate parasite S. fuelleborni fuelleborni, but is most likely derived from a local zoonotic source.     

A rice (Oryza sativa L.) cDNA encodes a protein sequence homologous to the eukaryotic ribosomal 5S RNA-binding protein

A rice (Oryza sativa L.) cDNA clone coding for the cytoplasmic ribosomal protein L5, which associates with 5 S rRNA for ribosome assembly, was cloned and its nucleotide sequence was determined. The primary structure of rice L5, deduced from the nucleotide sequence, contains 294 amino acids and has intriguing features some of which are also conserved in other eucaryotic homologues. These include: four clusters of basic amino acids, one of which may serve as a nucleolar localization signal; three repeated amino acid sequences; the conservation of glycine residues. This protein was identified as the nuclear-encoded cytoplasmic ribosomal protein L5 of rice by sequence similarity to other eucaryotic ribosomal 5 S RNA-binding proteins of rat, chicken, Xenopus laevis, and Saccharomyces cerevisiae. Rice L5 shares 51 to 62% amino acid sequence identity with the homologues. A group of ribosomal proteins from archaebacteria including Methanococcus vanniellii L18 and Halobacterium cutirubrum L13, which are known to be associated with 5 S rRNA, also related to rice L5 and the other eucaryotic counterparts, suggesting an evolutionary relationship in these ribosomal 5 S RNA-binding proteins.     

First evidences of surfactant biodegradation by marine sponges (Porifera): an experimental study with a linear alkylbenzenesulfonate

The main objective of this work was to better appreciate the role of benthic macro-organisms in the biodegradation of detergents in the marine environment. Sponges, which could be highly resistant to pollution and which are highly active filter-feeders, appear as interesting organisms in this topic. An experimental study conducted in aquarium with seawater enriched in a pure linear alkylbenzenesulfonate (LAS), namely 1-(p-Sulfophenyl)nonane, has shown that the primary degradation was 10 times more rapid in the presence of the sponge Spongia officinalis than in the presence of only marine bacteria. The main degradation metabolites, 3-(p-sulfophenyl)propionic acid and p-sulfobenzoic acid were produced in greater amounts in the presence of sponge. The very rapid degradation kinetics observed in this study may be due to the symbiotic microbial community present in S. officinalis. The sponge may also have promoted the activity of marine bacteria by transforming the original molecule in a more available secondary product. This study demonstrates for the first time that benthic macro-organisms can play an important role in the transformation of biodegradable contaminants, such as LAS.     

Implications from a 28S rRNA gene fragment for the phylogenetic relationships of halichondrid sponges (Porifera: Demospongiae)

Halichondrida is a pivotal demosponge order of which the classification underwent major changes in the recent history. The monophyly of this order and its intra-ordinal phylogeny cannot be reliably determined on the basis of morphology. Here we present a 28Sr RNA gene tree of selected halichondrids, which supports the hypothesis of halichondrid non-monophyly and elucidates further inter-ordinal relationships. We enlarged the analysis by previously published sequences, discuss how previous analyses suffer from taxon bias and analyse the resulting phylogenetic implications. Most halichondrid families (in particular Axinellidae und Dictyonellidae) cluster polyphyletic and the molecular classification of several genera does not agree with the current (morphological) system.     

Molecular cytogenetic characterisation and phylogenetic analysis of the seven cultivated Vigna species (Fabaceae)

The genomic organisation of the seven cultivated Vigna species, V. unguiculata, V. subterranea, V. angularis, V. umbellata, V. radiata, V. mungo and V. aconitifolia, was determined using sequential combined PI and DAPI (CPD) staining and dual‐colour fluorescence in situ hybridisation (FISH) with 5S and 45S rDNA probes. For phylogenetic analyses, comparative genomic in situ hybridisation (cGISH) onto somatic chromosomes and sequence analysis of the internal transcribed spacer (ITS) of 45S rDNA were used. Quantitative karyotypes were established using chromosome measurements, fluorochrome bands and rDNA FISH signals. All species had symmetrical karyotypes composed of only metacentric or metacentric and submetacentric chromosomes. Distinct heterochromatin differentiation was revealed by CPD staining and DAPI counterstaining after FISH. The rDNA sites among all species differed in their number, location and size. cGISH of V. umbellata genomic DNA to the chromosomes of all species produced strong signals in all centromeric regions of V. umbellata and V. angularis, weak signals in all pericentromeric regions of V. aconitifolia, and CPD‐banded proximal regions of V. mungo var. mungo. Molecular phylogenetic trees showed that V. angularis and V. umbellata were the closest relatives, and V. mungo and V. aconitifolia were relatively closely related; these species formed a group that was separated from another group comprising V. radiata, V. unguiculata ssp. sesquipedalis and V. subterranea. This result was consistent with the phylogenetic relationships inferred from the heterochromatin and cGISH patterns; thus, fluorochrome banding and cGISH are efficient tools for the phylogenetic analysis of Vigna species.     

A revision and phylogenetic analysis of Stapeliopsis (Apocynaceae)

A survey of morphological characters is carried out for Stapeliopsis . The information obtained from this is combined with molecular data from the plastid trn L-F DNA region and ITS1 of the nuclear encoded 18S−26S rRNA cistron, to obtain a hypothesis of the evolutionary relationships among the species. It is shown that Stapeliopsis is monophyletic in a combined molecular and morphological analysis. Stapeliopsis is sister to a clade containing Huernia , Orbea and Tromotriche . The species of Stapeliopsis group into two clades. One contains S. khamiesbergensis , S. neronis and S. urniflora , and this is highly supported. The remaining species fall into an unsupported clade in which S. exasperata is sister to the others. The genera Hermanschwartzia Plowes and Neopectinaria Plowes are rejected. It is shown that a synapomorphy for Stapeliopsis is the laterally flattened inner corona-lobes, which touch the anthers only at their bases. Eight species of Stapeliopsis are recognized, with no subgeneric divisions.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 148 , 125–155.     

Expressed sequence tag (EST) survey of the highly adapted green algal parasite, Helicosporidium

Helicosporidia are obligate invertebrate pathogens with a unique and highly adapted mode of infection. The evolutionary history of Helicosporidia has been uncertain, but several recent molecular phylogenetic studies have shown an unexpectedly close relationship to green algae, and specifically to the opportunistic pathogen Prototheca. To date, molecular sequences from Helicosporidia are restricted to those genes used for phylogenetic reconstruction and genes related to the existence and function of its cryptic plastid. We have therefore conducted a small expressed sequence tag (EST) project on Helicosporidium sp., yielding about 700 unique sequences. We have examined the functional distribution of known genes, the distribution of EST abundance, and the prevalence of previously unknown gene sequences. To demonstrate the potential utility of large amounts of data, we have used ribosomal proteins to test whether the phylogenetic position of Helicosporidium inferred from a small number of genes is broadly supported by a large number of genes. We conducted phylogenetic analyses on 69 ribosomal proteins and found that 98% supported the green algal origin of Helicosporidia and 80% support a specific relationship with Prototheca. Overall, these data multiply the available molecular information from Helicosporidium 100-fold, which should provide the basis for new insights into these unusual but interesting parasites.