Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs.

This corrects the article DOI: 10.1038/hdy.2015.89.

Genetic legacy of tertiary climatic change: a case study of two freshwater loaches, Schistura fasciolata and Pseudogastromyzon myersi, in Hong Kong.

The high biodiversity and strong population structure of freshwater fauna has often been attributed to historical geological and climatic alterations. The impact of these historical changes on obligate freshwater species on a small geographical scale has not been well understood due to the lack of fine-scale comparative phylogeographic studies. Strong population structure has been reported in a goby and a caridean shrimp in Hong Kong, a small but highly developed city in South China, but the common drivers of population differentiation in freshwater fauna in this region remain unclear. This study examined the fine-scale phylogeographic patterns of two freshwater loaches, Schistura fasciolata and Pseudogastromyzon myersi in Hong Kong, using sequence data of mitochondrial control region and two nuclear markers (interphotoreceptor retinoid binding protein gene 2 and ribosomal protein S13 gene). Results show that they exhibit pronounced population structure as supported by high and significant ΦST. Phylogenetic analyses based on the control region reveal six and three distinct lineages in S. fasciolata and P. myersi, respectively. Phylogeographic structure of both species generally follows the paleodrainage pattern, though P. myersi shows a shallower structure on the Mainland, perhaps due to their higher mobility. Most of these lineages diverged during the Pliocene and Late Pleistocene, a period with marked sea-level fluctuations. In a broader context, this suggests that sea-level fluctuation played an important role in shaping even the fine-scale population structure of freshwater fish in South China, implying that the genetic diversity of this fauna may be higher than expected.

Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs.

Whole-genome duplication (WGD) results in new genomic resources that can be exploited by evolution for rewiring genetic regulatory networks in organisms. In metazoans, WGD occurred before the last common ancestor of vertebrates, and has been postulated as a major evolutionary force that contributed to their speciation and diversification of morphological structures. Here, we have sequenced genomes from three of the four extant species of horseshoe crabs-Carcinoscorpius rotundicauda, Limulus polyphemus and Tachypleus tridentatus. Phylogenetic and sequence analyses of their Hox and other homeobox genes, which encode crucial transcription factors and have been used as indicators of WGD in animals, strongly suggests that WGD happened before the last common ancestor of these marine chelicerates >135 million years ago. Signatures of subfunctionalisation of paralogues of Hox genes are revealed in the appendages of two species of horseshoe crabs. Further, residual homeobox pseudogenes are observed in the three lineages. The existence of WGD in the horseshoe crabs, noted for relative morphological stasis over geological time, suggests that genomic diversity need not always be reflected phenotypically, in contrast to the suggested situation in vertebrates. This study provides evidence of ancient WGD in the ecdysozoan lineage, and reveals new opportunities for studying genomic and regulatory evolution after WGD in the Metazoa.

T cell epitope immunotherapy ameliorates allergic responses in a murine model of shrimp allergy.

BACKGROUND: Shellfish allergy is one of the most common food hypersensitivities worldwide but allergen-specific immunotherapy for shellfish allergy is not yet available. We believe that T cell peptide-based immunotherapy holds the potential for modulating allergic responses without IgE cross-linking. OBJECTIVE: We sought to identify the immunodominant T cell epitopes of tropomyosin, the major shrimp allergen of Metapenaeus ensis (Met e 1), and to evaluate their therapeutic effects in a Balb/c mouse model of Met e 1 hypersensitivity. METHODS: T cell epitopes of Met e 1 were first identified based on the proliferation and cytokine responses of splenocytes isolated from Met e 1-sensitized Balb/c mice upon stimulation by 18 synthetic peptides that span the full-length Met e 1. The immunodominant T cell peptides identified were then fed orally to Met e 1-sensitized Balb/c mice twice a week for four weeks. Allergic responses, serological antibody levels, intestinal histology and systemic and local cytokine profiles were compared between the treated and the untreated groups. RESULTS: Six major Met e 1 T cell epitopes were identified. Mice treated with the T cell epitope peptide mixture demonstrated an amelioration of systemic allergic symptoms and a significant reduction in Th2-associated antibody and cytokine responses. These benefits were accompanied by a shift to a balanced Th1/Th2 response, induction of IgG2a antibodies possessing in vitro and in vivo blocking activities and the induction of regulatory T cell responses. CONCLUSIONS AND CLINICAL RELEVANCE: T cell epitope-based oral immunotherapy is effective in reducing allergic responses towards shrimp tropomyosin. This is a novel strategy for clinical management of shellfish allergy and is a model for mechanistic studies of oral immunotherapy.

High-density linkage mapping aided by transcriptomics documents ZW sex determination system in the Chinese mitten crab Eriocheir sinensis.

The sex determination system in crabs is believed to be XY-XX from karyotypy, but centromeres could not be identified in some chromosomes and their morphology is not completely clear. Using quantitative trait locus mapping of the gender phenotype, we revealed a ZW-ZZ sex determination system in Eriocheir sinensis and presented a high-density linkage map covering ~98.5% of the genome, with 73 linkage groups corresponding to the haploid chromosome number. All sex-linked markers in the family we used were located on a single linkage group, LG60, and sex linkage was confirmed by genome-wide association studies (GWAS). Forty-six markers detected by GWAS were heterozygous and segregated only in the female parent. The female LG60 was thus the putative W chromosome, with the homologous male LG60 as the Z chromosome. The putative Z and W sex chromosomes were identical in size and carried many homologous loci. Sex ratio (5:1) skewing towards females in induced triploids using unrelated animals also supported a ZW-ZZ system. Transcriptome data were used to search for candidate sex-determining loci, but only one LG60 gene was identified as an ankyrin-2 gene. Double sex- and mab3-related transcription factor 1 (Dmrt1), a Z-linked gene in birds, was located on a putative autosome. With complete genome sequencing and transcriptomic data, more genes on putative sex chromosomes will be characterised, thus leading towards a comprehensive understanding of the sex determination and differentiation mechanisms of E. sinensis, and decapod crustaceans in general.

Characterization and functional studies of forkhead box protein 3(-) lymphocyte activation gene 3(+) CD4(+) regulatory T cells induced by mucosal B cells.

The induction of mucosal tolerance has been demonstrated to be an effective therapeutic approach for the treatment of allergic diseases. Our previous study demonstrated that Peyer's patch B cells could convert naive T cells into regulatory T cells (so-called Treg -of-B(P) cells); however, it is important to characterize this particular subset of Treg -of-B cells for future applications. This study aimed to investigate the role of lymphocyte activating gene 3 (LAG3) in mediating the regulatory function of Treg -of-B(P) cells induced by mucosal follicular B (FOB) cells. Microarray analysis and real-time polymerase chain reaction (PCR) were used to assess the gene expression pattern of Treg -of-B(P) cells. To evaluate the role of LAG3, the in-vitro suppressive function and the alleviation of airway inflammation in a murine model of asthma was assessed. Our data indicated that FOB cells isolated from Peyer's patches had the ability to generate more suppressive Treg -of-B cells with LAG3 expression, compared with CD23(lo) CD21(lo) B cells. LAG3 is not only a marker for Treg -of-B(P) cells, but also participate in the suppressive ability. Moreover, CCR4 and CCR6 could be detected on the LAG3(+) , not LAG3(-) , Treg -of-B(P) cells and would help cells homing to allergic lung. In the murine model of asthma, the adoptive transfer of LAG3(+) Treg -of-B(P) cells was able to sufficiently suppress T helper type 2 (Th2) cytokine production, eosinophil infiltration and alleviate asthmatic symptoms. LAG3 was expressed in Treg -of-B(P) cells and was also involved in the function of Treg -of-B(P) cells. In the future, this particular subset of Treg -of-B cells might be used to alleviate allergic symptoms.

Malignancies after kidney transplantation: Hong Kong renal registry.

Manystudies have shown that kidney transplant recipients have a higher incidence of cancers when compared with general population. However, most data on the posttransplant malignancies (PTM) are derived from Western literature and large population-based studies are rare. There is also lack of information about the posttransplant cancer-specific mortality rate. We conducted a population-based study of 4895 kidney transplants between 1972 and 2011, with data from the Hong Kong Renal Registry. Patterns of cancer incidence and mortality in our kidney transplant recipients were compared with those of the general population using standardized incidence ratios (SIRs) and standardized mortality ratios (SMRs) respectively. With 40 246 person-years of follow-up, 299 PTM was diagnosed. The SIR of all cancers was 2.94 (female 3.58 and male 2.58). Non-Hodgkin lymphoma (NHL), kidney, and bladder cancers had the highest SIRs. The overall SMR was 2.3 (female 3.4 and male 1.7) and the highest SMR was NHL. The patterns of PTM differ among countries. Increases in cancer incidence can now translate into similar increases in cancer mortality. NHL is important in our kidney transplant recipients. Strategies in cancer screening in selected patient groups are needed to improve transplant outcomes.

Removal of heavy metals in an abandoned mine drainage via ozone oxidation: a pilot-scale operation.

The objective of this study was to evaluate the ozone oxidation of dissolved heavy metals in an abandoned mine drainage (AMD) by conducting a pilot-scale operation at two different ozone doses of 7.5 and 24.0 g O(3)/h into an ozone reactor. A portion of the abandoned mine drainage near the Jungam Mine in Samchuck, Korea was pumped into this pilot-scale plant and used as an influent for the ozone oxidation. Some possible precipitates of metal oxides and hydroxides that resulted from the pilot-scale ozone oxidation of the dissolved Fe and Mn ions in the AMD (with a hydraulic retention time of 106 seconds in the ozone reactor) were effectively removed via sand filtration. A six-hour ozone oxidation with an ozone dose of 24.0 g O(3)/h and subsequent sand filtration, before backwashing the sand filter bed, can meet Korean drinking water quality standards (less than 0.3 mg/L) for Fe and Mn in the sand filter effluent under the operating conditions that were used in this study. The SO(4)(-2) concentrations and alkalinities of the influents were not affected by the ozone oxidation. The pH values of the influents were neutral or slightly alkaline, and after the six-hour oxidation, increased very slightly. These experiment results show that the ozone oxidation of dissolved heavy metals and the subsequent sand filtration of metal precipitates are desirable alternatives to removing heavy metals in an abandoned mine drainage.

Caffeic acid phenethyl ester inhibits nuclear factor-kappaB and protein kinase B signalling pathways and induces caspase-3 expression in primary human CD4+ T cells.

Caffeic acid phenethyl ester (CAPE), an active component in propolis, is known to have anti-tumour, anti-inflammatory and anti-oxidant properties. In this study, the effects of CAPE on the functions of primary human CD4+ T cells were evaluated in vitro. CAPE significantly suppressed interferon (IFN)-gamma and interleukin (IL)-5 production and proliferation of CD4+ T cells stimulated by soluble anti-CD3 and anti-CD28 monoclonal antibodies in both healthy subjects and asthmatic patients. CAPE inhibited nuclear factor (NF)-kappaB activation and protein kinase B (Akt) phosphorylation, but not p38 mitogen-activated protein kinase (MAPK) phosphorylation in T cells. CAPE also induced active caspase-3 expression in CD4+ T cells; CCR4+CD4+ T cells were more sensitive to CAPE induction than CXCR3+CD4+ T cells. Together, these results indicate that CAPE inhibits cytokine production and proliferation of T cells, which might be related to the NF-kappaB and Akt signalling pathways, and that CCR4+CD4+ T cells are more sensitive to CAPE inhibition. This study provides a new insight into the mechanisms of CAPE for immune regulation and a rationale for the use of propolis for the treatment of allergic disorders.

Molecular evidence for the Southern Hemisphere origin and deep-sea diversification of spiny lobsters (Crustacea: Decapoda: Palinuridae).

Spiny lobsters (family Palinuridae) are economically important marine animals that have been the subject of a considerable amount of research. However, the phylogeny of this group remains disputed. Morphological analyses have not been able to resolve the relationships of the various members of the group, and no agreement has yet been reached on its phylogeny as indicated by the different gene trees reported to date. In the present study, we attempt to reconstruct the phylogeny of Palinuridae and its allies using sequences from three nuclear protein-coding genes (phosphoenolpyruvate carboxykinase, sodium-potassium ATPase alpha-subunit and histone 3). The inferred topology receives strong nodal support for most of the branches. The family Palinuridae is found to be paraphyletic with the polyphyletic Synaxidae nested within it. Stridentes forms a monophyletic assemblage, indicating that the stridulating sound producing organ evolved only once in the spiny lobsters. By contrast, Silentes is paraphyletic, as Palinurellus is more closely related to Stridentes than to other Silentes genera. The three genera restricted to the southern high latitudes (Jasus, Projasus and Sagmariasus) constitute the basal lineages in the spiny lobsters, suggesting a Southern Hemisphere origin for the group. Subsequent diversification appears to have been driven by the closure of the Tethys Sea and the formation of the Antarctic circumpolar current, which isolated the northern and southern taxa. Contrary to an earlier hypothesis that postulated evolution from a deep-sea ancestral stock, the shallow-water genus Panulirus is the basal taxon in Stridentes, while the deep-sea genera Puerulus and Linuparus are found to be derived. This indicates that the spiny lobsters invaded deep-sea habitats from the shallower water rocky reefs and then radiated. Our results suggest that Synaxidae is not a valid family, and should be considered to be synonymous with Palinuridae. We also found that the previously proposed subgenera Sagmariasus and Nupalirus are genetically highly diverged, and both warrant a generic status.

Phylogeny of penaeoid shrimps (Decapoda: Penaeoidea) inferred from nuclear protein-coding genes.

Penaeoidea is a diverse group of economically important marine shrimps. Attention to the evolutionary history of the penaeoids has been raised since studies using mitochondrial DNA markers and sperm ultrastructure contradict classification of the penaeoid families based on morphology and hence challenge the long standing taxonomy of this superfamily. In this study, DNA sequences of two nuclear protein-coding genes, phosphoenolpyruvate carboxykinase and sodium-potassium ATPase alpha-subunit, were determined from 37 penaeoid genera to reconstruct the evolutionary relationships and to estimate divergence ages of the penaeoid shrimps. Phylogenetic analyses using maximum likelihood and Bayesian approaches strongly support the monophyly of Solenoceridae, Aristeidae and Benthesicymidae, but find Sicyoniidae nested within Penaeidae, making this family paraphyletic. Penaeoidea comprises two lineages: the former three families in one while the latter two in another. The diversification of these lineages may be related to bathymetry. The penaeid-like lineage diversified in the Triassic, earlier than the aristeid-like lineage with an origin in the Jurassic. Taxonomic revisions within Penaeoidea are also proposed for further investigation. Due to the paraphyly of Penaeidae and the high genetic divergence among the three penaeid tribes of Burkenroad [Burkenroad, M.D., 1983. Natural classification of Dendrobranchiata, with a key to recent genera. In: Schram, F.R. (Ed.), Crustacean Issues I. Crustacean Phylogeny. A.A. Balkema, Rotterdam, pp. 279-290], these tribes should be treated as having the same taxonomic rank as Sicyoniidae, while the family ranking of Benthesicymidae has to be re-considered owing to the low genetic divergence between the benthesicymids and the aristeids.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 May 2009-31 July 2009.

This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.

The first nocturnal home haemodialysis patient in Hong Kong.

We report our experience of the first use of nocturnal home haemodialysis in Hong Kong. The patient, a 40-year-old man with end-stage renal failure, was recruited into the Nocturnal Home Haemodialysis Programme at Princess Margaret Hospital in 2006. He received haemodialysis at home on alternate nights (3.5 sessions per week) for 5.5 to 6 hours per session. After 1 year of nocturnal home haemodialysis, his recombinant human erythropoietin requirement had been reduced by more than 50%. His serum phosphate level decreased by 35% and calcium phosphate product by 34%. After nocturnal home haemodialysis, his blood pressure control has been excellent and he was able to cease taking anti-hypertensive medications soon after commencing nocturnal home haemodialysis. Regression of his left ventricular hypertrophy has also been noted, with a 39% decrease in his left ventricular mass index. The haemodialysis adequacy index, weekly single-pool Kt/V, increased by 59% after switching to nocturnal home haemodialysis and his quality-of-life indices also showed significant improvement. Nocturnal home haemodialysis holds promise as an alternative dialytic therapy for patients on chronic haemodialysis in Hong Kong.

Phylogeny of Decapoda using two nuclear protein-coding genes: origin and evolution of the Reptantia.

The phylogeny of Decapoda is contentious and many hypotheses have been proposed based on morphological cladistic analyses. Recent molecular studies, however, yielded contrasting results despite their use of similar data (nuclear and mitochondrial rDNA). Here we present the first application of two nuclear protein-coding genes, phosphoenolpyruvate carboxykinase and sodium-potassium ATPase alpha-subunit, to reconstruct the phylogeny of major infraorders within Decapoda. A total of 64 species representing all infraorders of Pleocyemata were analyzed with five species from Dendrobranchiata as outgroups. Maximum likelihood and Bayesian inference reveal that the Reptantia and all but one infraorder are monophyletic. Thalassinidea, however, is polyphyletic. The nodal support for most of the infraordinal and inter-familial relationships is high. Stenopodidea and Caridea form a clade sister to Reptantia, which comprises two major clades. The first clade, consisting of Astacidea, Achelata, Polychelida and three thalassinidean families (Axiidae, Calocarididae and Eiconaxiidae), corresponds essentially to the old taxon suborder Macrura Reptantia. Polychelida nests within Macrura Reptantia instead of being the most basal reptant as suggested in previous studies. The high level of morphological and genetic divergence of Polychelida from Achelata and Astacidea justifies its infraorder status. The second major reptant clade consists of Anomura, Brachyura and two thalassindean families (Thalassinidae and Upogebiidae). Anomura and Brachyura form Meiura, with moderate support. Notably thalassinidean families are sister to both major reptant clades, suggesting that the stem lineage reptants were thalassinidean-like. Moreover, some families (e.g. Nephropidae, Diogenidae, Paguridae) are paraphyletic, warranting further studies to evaluate their status. The present study ably demonstrates the utility of nuclear protein-coding genes in phylogenetic inference in decapods. The topologies obtained are robust and the two molecular markers are informative across a wide range of taxonomic levels. We propose that nuclear protein-coding genes should constitute core markers for future phylogenetic studies of decapods, especially for higher systematics.

Enzymatic oxidation of aqueous pentachlorophenol.

The influence of the nonionic surfactant Tween 80 on pentachlorophenol (PCP) oxidation catalyzed by horseradish peroxidase was studied. The surfactant was tested at concentrations below and above its critical micelle concentration (CMC). Enhancement of PCP removal was observed at sub-CMCs. The presence of Tween 80 in the reaction mixture reduced enzyme inactivation which occurred through a combination of free radical attack and sorption by precipitated products. A simple first-order model was able to simulate time profiles for enzyme inactivation in the presence or absence of Tween 80. At supra-CMCs, the surfactant caused noticeable reductions in PCP removal, presumably through micelle partitioning of PCP which precluded the hydrophobic PCP molecule from interacting with the enzyme.

Copper biosorption on immobilized seaweed biomass: column breakthrough characteristics.

The biosorption of copper by the brown seaweed Sargassum baccularia, immobilized onto polyvinyl alcohol (PVA) gel beads, was investigated with fixed-bed experiments. Laboratory-scale column tests were performed to determine breakthrough curves with varying flow rates and feed concentrations. A theoretical fixed-bed model, known as the Bohart-Adams equation, was evaluated in simulating the experimental breakthrough curves. The Bohart-Adams model qualitatively predicted the breakthrough trends. PVA-immobilized seaweed biomass beads were amenable to efficient regeneration with aqueous solution containing the chelating agent ethylenediaminetetraacetic acid (EDTA). The biosorbent retained most of its original uptake capacity over three cycles of use. The excellent reusability of the biosorbent could lead to the development of a viable metal remediation technology.

Development of polymorphic expressed sequence tag-derived microsatellites for the extension of the genetic linkage map of the black tiger shrimp (Penaeus monodon).

In this study, microsatellite markers were developed for the genetic linkage mapping and breeding program of the black tiger shrimp Penaeus monodon. A total of 997 unique microsatellite-containing expressed sequence tags (ESTs) were identified from 10 100 EST sequences in the P. monodon EST database. AT-rich microsatellite types were predominant in the EST sequences. Homology searching by the blastn and blastx programs revealed that these 997 ESTs represented 8.6% known gene products, 27.8% hypothetical proteins and 63.6% unknown gene products. Characterization of 50 markers on a panel of 35-48 unrelated shrimp indicated an average number of alleles of 12.6 and an average polymorphic information content of 0.723. These EST microsatellite markers along with 208 other markers (185 amplified fragment length polymorphisms, one exon-primed intron-crossing, six single strand conformation polymorphisms, one single nucleotide polymorphism, 13 non-EST-associated microsatellites and two EST-associated microsatellites) were analysed across the international P. monodon mapping family. A total of 144 new markers were added to the P. monodon maps, including 36 of the microsatellite-containing ESTs. The current P. monodon male and female linkage maps have 47 and 36 linkage groups respectively with coverage across half the P. monodon genome.

Minimal change disease following exposure to mercury-containing skin lightening cream.

A 34-year-old woman developed nephrotic syndrome after using a skin lightening cream that contained an extremely high level of mercury. Blood and urine mercury levels were elevated and a renal biopsy revealed minimal change disease. Membranous nephropathy was excluded using immunofluorescence and electron microscopy. Her proteinuria remitted 9 months after she stopped using the cosmetic cream. This is the first reported case in the English literature of proven minimal change disease secondary to mercury exposure. It is important that mercury poisoning due to cosmetic cream is considered in the differential diagnoses for any woman who presents with nephrotic syndrome.

Removal of arsenate from aqueous solution by adsorption onto titanium dioxide nanoparticles.

Titanium dioxide (TiO2) was investigated for the removal of pentavalent arsenate from aqueous solution. Kinetic results revealed that arsenate adsorption was almost instantaneous. The extent of arsenate adsorption decreased with increasing pH owing to the decrease of positively charged binding sites on the TiO2 surface. Adsorption isotherms measured at pH 3 and 7 generally followed the Langmuir model. The maximum uptake capacity ranged from 8 mg g-1 at pH 3 to 2.7 mg g-1 at pH 7. Addition of phosphate resulted in a significant reduction in arsenate adsorption, indicating that phosphate-a molecular analogue of arsenate-competes with arsenate for the same surface binding sites. By contrast, bicarbonate had little effect on arsenate adsorption, whereas sulfate exhibited a moderate suppression effect. A considerable reduction in arsenate adsorption was also observed in the presence of relatively high concentrations of background electrolytes (>50 mmol L-1).

Ribosomal RNA as molecular barcodes: a simple correlation analysis without sequence alignment.

MOTIVATION: We explored the feasibility of using unaligned rRNA gene sequences as DNA barcodes, based on correlation analysis of composition vectors (CVs) derived from nucleotide strings. We tested this method with seven rRNA (including 12, 16, 18, 26 and 28S) datasets from a wide variety of organisms (from archaea to tetrapods) at taxonomic levels ranging from class to species. RESULT: Our results indicate that grouping of taxa based on CV analysis is always in good agreement with the phylogenetic trees generated by traditional approaches, although in some cases the relationships among the higher systemic groups may differ. The effectiveness of our analysis might be related to the length and divergence among sequences in a dataset. Nevertheless, the correct grouping of sequences and accurate assignment of unknown taxa make our analysis a reliable and convenient approach in analyzing unaligned sequence datasets of various rRNAs for barcoding purposes. AVAILABILITY: The newly designed software (CVTree 1.0) is publicly available at the Composition Vector Tree (CVTree) web server http://cvtree.cbi.pku.edu.cn.