Morphological and molecular phylogenetic analysis of two Saprolegnia sp (Oomycetes) isolated from silver crucian carp and zebra fish

Two Saprolegnia isolates, JY isolated from silver crucian carp (Carassius auratus gibelio Bloch) and BMY isolated from zebra fish (Brachydanio rerio Hamilton) came from infections occurring concurrently in different locations in China. To confirm whether the two isolates were from the same Saprolegnia clone, comparative studies have been carried out based on their morphological, physiological and molecular characteristics. Observations showed that morphologically (both asexual and sexual organs) the two isolates were broadly similar and both isolates under-went repeated zoospore emergence. Comparing 704 base pairs of internal transcribed spacer (ITS) region and the 5.8S rDNA, we found isolates JY and BMY shared an identical ITS sequence with a minor variation (99.6 % similarity). Forty available sequences for representatives Saprolegnia spp. belonged to four phylogenetically separate clades. The two studied isolates fell within clade I that comprised a group of isolates which showed almost an identical ITS sequence but had been identified as a number of different morphological species. our findings suggest that isolates JY and BMY appear to belong to the S. ferax clade and this clade (1) contains a number of closely related phylogenetic species. This is distinct from the more common fish pathogenic isolates, which belong to the S. parasitica clade (III) and are characterized by having cysts decorated by bundles of long hooked hairs and two further clades (II and IV) containing largely saprotrophic or soil born species. (C) 2009 Published by Elsevier Ltd on behalf of The British Mycological Society.

Isolation and characterization of microsatellite loci from mangrove red snapper Lutjanus argentimaculatus

Lutjanus argentimaculatus, also called mangrove red snapper, is a commercially important fish in East Asia. A proper understanding of population structure is primarily linked with the management of genetic resources in exploiting marine fisheries. Herein, seven microsatellite loci, which showed high polymorphism (observed heterozygosity per locus ranging from 0.3571 to 0.7857 and expected heterozygosity per locus ranging from 0.6236 to 0.8821), were isolated and characterized from L. argentimaculatus. Cross-species amplifications also indicate that primers designed for these loci may be useful for further studies about other closely phylogenetic species of the family Lutjanidae.

Phylogenetic implications of the 38 putative ancestral chromosome segments for four canid species

Chromosome homologies between the Japanese raccoon dog (Nectereutes procyonoides viverrinus, 2n = 39 + 2-4 B chromosomes) and domestic dog (Canis familiaris, 2n = 78) have been established by hybridizing a complete set of canine paint probes onto high-res

Phylogenetic relationships among two species of golden monkey and three species of leaf monkey inferred from rDNA variation

Restriction maps of rDNA repeats of five species of Colobinae and three outgroup taxa, Hylobates leucogenys, Macaca mulatta, and Macaca irus, were constructed using 15 restriction endonucleases and cloned 18S and 28S rRNA gene probes. The site variation between Rhinopithecus roxellana and Rhinopithecus bieti is comparable to that between Presbytis francoisi and Presbytis phayrei, implying that R. bieti is a valid species rather than a subspecies of R. roxellana. Phylogenetic analysis on the 47 informative sites supports the case for Rhinopithecus being an independent genus and closely related to Presbytis. Furthermore, branch lengths of the tree seem to support the hypothesis that the leaf monkeys share some ancestral traits as well as some automorphic characters.

Phylogenetic relationships of five pika species (genus Ochotona) based on mitochondrial DNA restriction maps

Restriction site mapping of mitochondrial DNA (mtDNA) with 16 restriction endonucleases was used to examine the phylogenetic relationships of Ochotona cansus, O. huangensis, O. thibetana, O. curzoniae and O. erythrotis. A 1-kb length variation between O. erythrotis of subgenus Pika and other four species of subgenus Ochotona was observed, which may be a useful genetic marker for identifying the two subgenera. The phylogenetic tree constructed using PAUP based on 61 phylogenetically informative sites suggests that O. erythrotis diverged first, followed by O. cansus, while O. curzoniae and O. huangensis are sister taxa related to O. thibetana, The results indicate that both O. cansus and O. huangensis should be treated as independent species. If the base substitution rate of pikas mtDNA was 2% per million years, then the divergence time of the two subgenera, Pika and Ochotana, is about 8.8 Ma ago of late Miocence, middle Bao-dian of Chinese mammalian age, and the divergence of the four species in subgenus Ochotona would have occurred about 2.5 - 4.2 Ma ago, Yushean of Chinese mammalian age. This calculation appears to be substantiated by the fossil record.

Molecular phylogenetic systematics of twelve species of acipenseriformes based on mtDNA ND4L-ND4 gene sequence analysis

Acipenseriformes is an endangered primitive fish group, which occupies a special place in the history of ideas concerning fish evolution, even in vertebrate evolution. However, the classification and evolution of the fishes have been debated. The mitochondrial DNA (mtDNA) ND4L and partial ND4 genes were first sequenced in twelve species of the order Acipenseriformes, including endemic Chinese species. The following points were drawn from DNA sequences analysis: (i) the two species of Huso can be ascribed to Acipenser; (ii) A. dabryanus is the mostly closely related to A. sinensis, and most likely the landlocked form of A. sinensis; (iii) genus Acipenser in trans-Pacific region might have a common origin; (iv) mtDNA ND4L and ND4 genes are the ideal genetic markers for phylogenetic analysis of the order Acipenseriformes.

Phylogenetic relationships of 12 Penaeoidea shrimp species deduced from mitochondrial DNA sequences

DNA sequences of an 847 bp fragment of mitochondrial cytochrome oxidase subunit I (COI) gene and a 514 bp fragment of 16s rRNA gene were determined to examine the phylogenetic relationships of 12 Penaeoidea shrimp species (Penaeus chinensis, Penaeus japon

Phylogenetic relationships of Drosophila melanogaster species group deduced from spacer regions of histone gene H2A-H2B

Nucleotide sequences of the spacer region of the histone gene H2A-H2B from 36 species of Drosophila melanogaster species group were determined. The phylogenetic trees were reconstructed with maximum parsimony, maximum likelihood, and Bayesian methods by u

The complete mitochondrial genomes of two species from Sinocyclocheilus (Cypriniformes: Cyprinidae) and a phylogenetic analysis within Cyprininae

We determined the complete mitochondrial DNA sequences for two species of surface- and cave-dwelling-cyprinid fishes, Sinocyclocheilus grahami and S. altishoulderus. Sequence comparison of 13 protein-coding genes shows that the mutation pattern of each single gene is quite similar to those of other vertebrate animal species. Analysis of the ratios of Ka/Ks at these loci between Sinocyclocheilus and two other cyprinid species (Cyprinus carpio and Procypris rabaudi) show that Ka/Ks ratios are differed, consistent with purifying selection and variation in functional constraint among genes. Bayesian analysis and maximum likelihood analysis of the concatenated mitochondrial protein sequences for 14 cyprinid taxa support the monophyly of the family Cyprininae, and further confirm the monophyly of the genus Sinocyclocheilus. The two Sinocyclocheilus species fall within the Cyprinion-Onychostoma lineage, including Cyprinus, Carassius, and Procypris, rather than among the Barbinae, as previously suggested on morphological grounds.

Phylogenetic relationships among Rhacophorinae (Rhacophoridae, Anura, Amphibia), with an emphasis on the Chinese species

The partial nucleotide sequence of mitochondrial 12S and 16S rRNA genes was determined for 23 Chinese species of Rhaeophoridae (Amphibia: Anura), representing four of the eight recognized genera. Using Buergeriinae as the outgroup, phylogenetic analyses (

Phylogenetic analysis of the family Thermaceae with an emphasis on signature position and secondary structure of 16S rRNA

The sequences of the 16S rRNA genes from 38 strains of the family Thermaceae were compared by alignment analysis. The genus-specific and species-specific base substitutions or base deletions (signature positions) were found in three hypervariable regions (in the helices 6, 10 and 17). The differentiation of secondary structures of the high variable regions in the 5' end (38-497) containing several signature positions further supported the concept. Based on the comparisons of the secondary structures in the segments of 16S rRNAs, a key to the species of the family Thermaceae was proposed. (C) 2003 Published by Elsevier Science B.V. on behalf of the Federation of European Microbiological Societies.

Morphological characteristics and phylogenetic relationship of Anabaena species from Lakes Dianchi and Erhai, China

Although Anabaena is one of the most prevalent planktonic freshwater genus in China, there are few taxonomic reports of Anabaena strains by morphology and genetics. In this study, morphological characteristics and phylogenetic relationships of seven Anabaena strains isolated from two plateau lakes, Lakes Dianchi and Erhai, were investigated. Morphological characteristics such as morphology of filament, cellular shapes and sizes, relative position of heterocytes and akinetes, and presence or absence of aerotopes, were described for these seven strains. Phylogenetic relationships were determined by constructing 16S rRNA gene tree using the neighbor-joining algorithm. The seven strains were morphologically identified as three groups, and phylogenetic analysis based on 16S rRNA gene sequences also showed that these seven strains were in three groups. Strains EH-2, EH-3, and EH-4 were in group A belonging to the Anabaena circinalis and A. crassa group, and strains DC-1, DC-2, and EH-1 were in group B and identified as A. flos-aquae. Strain DC-3 without aerotopes was significantly different from the other isolated strains and was determined as A. cylindrica.