Chloroplast genome evolution in the genus Avena

The genus Avena contains five different chloroplast genomes, I-V. A physical map of chloroplast (ct) DNA of Avena sativa (type I chloroplast genome) was constructed using three restriction endonucleases, PstI, SalI and SmaI. This genome is ca. 135.5 kbp in size, and contains two inverted repeats of ca. 22.5 kbp each, separated by a large (ca. 79.0 kbp) and small (ca. 12.5 kbp) single copy region. The rbcL gene which codes for the large subunit of ribulose 1,5-bisphosphate carboxylase, was located in the map. Restriction fragment patterns of all five chloroplast genomes were compared, and among them five fragment size and five restriction site mutations were disclosed. Four site mutations were found in two or more chloroplast genomes, the other site and five fragment size mutations were specific to one or another of the chloroplast genomes. A dendrogram showing phylogenetic relationships among the five chloroplast genomes, based on the distribution of the common and specific mutations among them, indicates that chloroplast genome divergence characterized by three restriction site mutations occurred first between two diploid groups, each carrying A and C genome (nuclear), respectively, followed by further speciation in each group.     

Organization and variation of the mitochondrial DNA control region in five Caprinae species

The complete mitochondrial DNA (mtDNA) control region was analyzed from five species of the subfamily Caprinae; Naemorhedus caudatus, N. goral, Capra hircus, Capricornis swinhoei, and Capricornis crispus. Among these species, the control region ranged from 1,096 to 1,212 bp in length. Our results were compatible with the scheme of three domains (ETAS, Central, and CSB) within the control region. A + T < G + C was observed in all the domains. In the Korean gorals, of the 31 variable sites in the whole control region resulting in 15 haplotypes, 27 variable sites were in the ETAS domain. We found two to three tandem repeat in all five species examined in this study, three in N. caudatus and N. goral, two in Capra hircus and C. crispus, and one in C. swinhoei, respectively. All of these repeat units include two short sections of mirror symmetry (TACAT and ATGTA). Short mirror symmetries were well-resolved among five different species, although left domain has high substitution rates. By Kimura’s two parameter method, the genetic distances between the genera Naemorhedus and Capricornis were calculated and divergence time between Naemorhedus and Capricornis may be nearly 2Myr.     

Bipolar disjunctions in Carex: Long-distance dispersal,vicariance, or parallel evolution?

The long-standing fascination of naturalists and scientists in the evolutionary and biogeographical causes behind the pattern of distribution of bipolar plants has lead to an intense debate around the three well-known biogeographical hypotheses of vicariance, long-distance dispersal, and parallel evolution. Genus Carex, despite lacking any general long-distance dispersal devices, represents six of the 30 plant species with bipolar distribution. We aimed to evaluate the role of the three alternative mechanisms mentioned above in the origin and evolution of five bipolar Carex species. Phylogenetic and phylogeographical reconstructions using Bayesian Inference, maximum parsimony, and statistical parsimony were performed with plastid (rps16 intron) and nuclear (ITS) DNA sequences. As a result, five cases of long-distance dispersal are proposed (C. canescens, C. macloviana, C. magellanica, C. maritima, C. microglochin s.str.) with an inferred southward migration from Northern to Southern Hemisphere for three of them. On the other hand, parallel evolution seems to be the most plausible explanation to understand the particular case of the bipolar species C. microglochin s.l.     

Diterpenoids from halimium viscosum

In addition to three known acids, five new diterpenoid acids with a rearranged ent-labdane skeleton (ent-halimane) have been isolated from the acid fraction of Halimium viscosum as their methyl ester derivatives.     

Comparative genomics and reverse genetics analysis reveal indispensable functions of the serine acetyltransferase gene family in Arabidopsis

Ser acetyltransferase (SERAT), which catalyzes O-acetyl-Ser (OAS) formation, plays a key role in sulfur assimilation and Cys synthesis. Despite several studies on SERATs from various plant species, the in vivo function of multiple SERAT genes in plant cells remains unaddressed. Comparative genomics studies with the five genes of the SERAT gene family in Arabidopsis thaliana indicated that all three Arabidopsis SERAT subfamilies are conserved across five plant species with available genome sequences. Single and multiple knockout mutants of all Arabidopsis SERAT gene family members were analyzed. All five quadruple mutants with a single gene survived, with three mutants showing dwarfism. However, the quintuple mutant lacking all SERAT genes was embryo-lethal. Thus, all five isoforms show functional redundancy in vivo. The developmental and compartment-specific roles of each SERAT isoform were also demonstrated. Mitochondrial SERAT2;2 plays a predominant role in cellular OAS formation, while plastidic SERAT2;1 contributes less to OAS formation and subsequent Cys synthesis. Three cytosolic isoforms, SERAT1;1, SERAT3;1, and SERAT3;2, may play a major role during seed development. Thus, the evolutionally conserved SERAT gene family is essential in cellular processes, and the substrates and products of SERAT must be exchangeable between the cytosol and organelles.     

Five new Simplicillium species (Cordycipitaceae) from soils in Tokyo,Japan

Eighteen Simplicillium isolates were discovered from soil samples collected on the Honshu, Bonin, and Izu islands in areas under the jurisdiction of Tokyo, Japan. Using a combination of micro-morphological characteristics and sequences of the ribosomal RNA gene ITS region, the isolates were classified as six Simplicillium species, and five of them were previously undescribed. The five species (Simplicillium aogashimaense, Simplicillium cylindrosporum, Simplicillium obclavatum, Simplicillium subtropicum and Simplicillium sympodiophorum) were discovered from the Chichi-jima, Hachijo, and Aogashima islands, and Simplicillium minatense was discovered from Honshu. The five new species and three known species are distinguished by conidial morphology.     

Comparison of Culture Methods for Isolation of Salmonella in Yak Fecal Samples

To compare the effectiveness of culture methods for identifying yak Salmonella, three selective enrichment broths (SC, TTB, MSRV) and three media (SS, XLD, CAS) for detecting Salmonella were evaluated in this study. The results showed that TTB broth was better than SC broths and MSRV broths, and SS medium has the highest isolation rate, significantly higher than those of CAS and XLD media (P < 0.05). It is worth noticing that there was no overlapping of the positive results given by TTB, SC and MSRV broths. In addition, all of the yak Salmonella isolates were detected positive by the five reported PCR assays, targeting the invA, srfC, invE, stn and 16S–23S rRNA genes. The combination of TTB and MSRV broths and SS and CAS media (or XLD) recommended in this study was relatively efficient in recovering Salmonella from yak feces, and the five PCR assays can be successfully used to identify yak Salmonella.     

Chemical constituents from Cynanchum paniculatum (Bunge) Kitag

Twenty-nine compounds, including five acetophenone derivatives (1–5), three phenanthroindolizidine alkaloids (12–14), seven pentacyclic triterpenoids (15–21) and five C₂₁ steroidal sapogenins (22–26), were isolated from the root of Cynanchum paniculatum (Bunge) Kitag. Their structures were determined by spectroscopic methods and comparison with reported data. Moreover, the chemotaxonomic relationships were also discussed. As a result, acetophenone derivatives, pentacyclic triterpenoids and C₂₁ pregnane sapogenins can be recognized as chemotaxonomic markers for Cynanchum genus, and C. paniculatum has close relationships with some species of genus Cynanchum.     

Patterns of chemical defense among Caribbean gorgonian corals: a preliminary survey

Ship-board assays employing the common Caribbean wrasse Thalassoma bifasdatum (Bloch) were undertaken to determine the palatability of food pellets coated with freshly-extracted, lipid-soluble metabolites of 37 types of Caribbean gorgonian corals representing at least 19 species from 11 genera. Extracts of 19 types (51%) were highly unpalatable (zero or one of five pellets eaten), four types (11%) were moderately unpalatable (two or three of five pellets eaten) and 14 (38%) were palatable (four or five of five pellets eaten) to fish in feeding assays. Gorgonians of the genera Pterogorgia (three types) and Eunicea (nine types) were consistently highly unpalatable, those of the genus Plexaurella (four types) were palatable and those of the genus Plexaura were most frequently palatable (six of eight types). Further assays of serial dilutions of extracts from seven representative, unpalatable types revealed that extracts inhibited fish feeding at pellet concentrations near or below the concentrations that metabolites occur in the gorgonian soft tissue. Extracts of Erythropodium caribaeorum (Duchassaing and Michelotti) and Pseudopterogorgia rigida (Bielschowsky) deterred fish feeding at pellet concentrations less than an order of magnitude lower than those found in the soft tissues of the corresponding gorgonians. Thin layer chromatographic analyses of extracts revealed the presence of lipid-soluble, secondary metabolites in a majority of the highly unpalatable extracts, although secondary metabolites were also present in a smaller percentage of palatable extracts. These data support the hypothesis that the soft tissues of many gorgonian corals contain lipid-soluble feeding deterrents which act as a defense against predation.     

Population genetic diversity and geographical differentiation of MHC class II DAB genes in the vulnerable Chinese egret (<Emphasis Type="Italic">Egretta eulophotes</Emphasis>)

Major histocompatibility complex (MHC) genes are excellent markers for the study of adaptive genetic variation occurring over different geographical scales. The Chinese egret (Egretta eulophotes) is a vulnerable ardeid species with an estimated global population of 2600–3400 individuals. In this study, we sampled 172 individuals of this egret (approximately 6 % of the global population) from five natural populations that span the entire distribution range of this species in China. We examined their population genetic diversity and geographical differentiation at three MHC class II DAB genes by identifying eight exon 2 alleles at Egeu-DAB1, eight at Egeu-DAB2 and four at Egeu-DAB3. Allelic distributions at each of these three Egeu-DAB loci varied substantially within the five populations, while levels of genetic diversity varied slightly among the populations. Analysis of molecular variance showed low but significant genetic differentiation among five populations at all three Egeu-DAB loci (haplotype-based ?_ST: 0.029, 0.020 and 0.042; and distance-based ?_ST: 0.036, 0.027 and 0.043, respectively; all P < 0.01). The Mantel test suggested that this significant population genetic differentiation was likely due to an isolation-by-distance pattern of MHC evolution. However, the phylogenetic analyses and the Bayesian clustering analysis based on the three Egeu-DAB loci indicated that there was little geographical structuring of the genetic differentiation among five populations. These results provide fundamental population information for the conservation genetics of the vulnerable Chinese egret.     

Characterization of a family of ice-active proteins from the Ryegrass,Lolium perenne

Five genes coding for ice-active proteins were identified from an expressed sequence tag database of Lolium perenne cDNA libraries. Each of the five genes were characterized by the presence of an N-terminal signal peptide, a region enriched in hydrophilic amino acids and a leucine-rich region in four of the five genes that is homologous with the receptor domain of receptor-like protein kinases of plants. The C-terminal region of all five genes contains sequence homologous with Lolium and Triticum ice-active proteins. Of the four ice-active proteins (IAP1, IAP2, IAP3 and IAP5) cloned, three could be expressed in Escherichia coli and recovered in a functional form in order to study their ice activity. All three ice-active proteins had recrystallization inhibition activity but showed no detectable antifreeze or ice nucleation activity at the concentration tested. IAP2 and IAP5 formed distinct hexagonal-shaped crystals in the nanolitre osmometer as compared to the weakly hexagonal crystals produced by IAP3.     

Isolation and characterization of homologues of plant blue-light photoreceptor (cryptochrome) genes from the fern Adiantum capillus-veneris

Many blue-light mediated physiological responses have been studied in the fern Adiantum capillus-veneris. We have isolated genomic clones encoding sequences similar to those encoding blue-light photoreceptors (cryptochromes) in higher plants using the Arabidopsis CRY1 cDNA as a probe, and these positive clones fall into five independent groups. Using RACE procedures, we obtained full-length cDNA sequences for three of these five groups. The deduced amino acid sequences include the photolyase-homologous domain in the N-terminal half, and they also contain a C-terminal extension of about 200 amino acids in length. These structural features indicate that the genes indeed encode Adiantum cryptochromes and represent a small gene family having at least three members.     

Substratum selection and egg-capsule deposition in Nassarius reticulatus (L.)

When offered a range of 14 pairs of different substrata consisting of five brown algae, five red algae, three bivalve shells, and sandstone pebbles, spawning Nassarius reticulatus (L.) selected only four species of red algae on which to deposit egg capsules. There was some evidence of a greater preference for the red alga Gigartina stellata (Stackhouse). When offered a choice between only Gigartina and another red weed, Polyides rotundus (Hudson), there was a highly significant preference for the former. Some reasons for the selectivity are suggested and discussed.     

Molecular phylogeny and genetic variation in the genus Lilium native to China based on the internal transcribed spacer sequences of nuclear ribosomal DNA

We present a comprehensive phylogeny derived from nuclear ribosomal DNA (nrDNA) for 214 samples representing 98 species and five varieties, including 44 species and five varieties native to China. Our collection of 25 species and five varieties (44 samples) covering all five sections of the genus (Comber) distributed in China also were included in the internal transcribed spacer (ITS) database. This study incorporates previous research with an emphasis on Chinese species, including the controversial subsection, Sinomartagon 5c Comber. In the phylogenetic tree obtained by maximum parsimony (PAUP) and maximum likelihood (RAxML) analyses, the samples were divided into four major groups. Our results suggest that the subsection (subsect.) 5c Comber should be classified into the true subsect. 5c and the section (sect.) Lophophorum. And the latter was divided into three subsections (subsect. Lophophorum I, subsect. Lophophorum II, and subsect. Lophophorum III). Based on molecular phylogenetic analysis and fluorescence in situ hybridization, we report that L. henryi and L. rosthornii are closely related, and we propose their classification into subsect. Leucolirion 6a. Our results support Comber’s subdivision of sect. Leucolirion, which was primarily based on bulb color. Chinese species were divided into five sections: sect. Martagon, sect. Archelirion, sect. Leucolirion, sect. Sinomartagon, and sect. Lophophorum. These findings contribute to our understanding of the phylogeny, origin, and classification of Lilium.     

Cytotoxic and anti-oxidant biphenyl derivatives from the leaves and twigs of Garcinia multiflora

Three new biphenyl derivatives (1–3), together with five known compounds, were isolated from the leaves and twigs of Garcinia multiflora. Their structures were determined by extensive spectroscopic techniques including NMR spectroscopy and mass spectrometry. All eight isolates showed weak cytotoxicity on five human tumor cell lines. In addition, the three biphenyl derivatives showed moderate anti-oxidant activity with IC₅₀ values ranging from 7.78 to 8.78 μM.     

Host-Adapted Cryptosporidium spp. in Canada Geese (Branta canadensis)

The prevalence and distribution of Cryptosporidium spp. in the fecal droppings of the free-living waterfowl Canada geese were examined at 13 sites in Ohio and Illinois. On the basis of the analysis of the small-subunit rRNA gene by PCR, followed by restriction fragment length polymorphism analysis and DNA sequencing, 49 (23.4%) of 209 fecal specimens collected from 10 sites (76.9%) were positive for Cryptosporidium spp. The following five Cryptosporidium species and genotypes were identified: Cryptosporidium goose genotype I (in 36 specimens), Cryptosporidium goose genotype II (in 9 specimens), Cryptosporidium duck genotype (in 1 specimen), Cryptosporidium parvum (in 4 specimens), and C. hominis (in 2 specimens). Cryptosporidium goose genotype I was the most prevalent parasite and was found at all five Cryptosporidium-positive sites in Ohio and at four of five positive sites in Illinois, followed by Cryptosporidium goose genotype II, which was found at two of five positive sites in Ohio and at four of five positive sites in Illinois. Cryptosporidium goose genotype II was detected for the first time, and it is phylogenetically related to goose genotype I and the duck genotype. All three genotypes have not so far been reported in humans, and their pathogenicity in geese has not been determined. Only 10.2% of the Cryptosporidium-positive specimens had C. parvum and C. hominis. The results of this study indicate that Canada geese might only serve as accidental carriers of cryptosporidia infectious to humans and probably play a minor role in the animal-to-human transmission cycle of the pathogen.     

Low genetic differentiation among widely separated populations of the pearl oyster Pinctada fucata as revealed by AFLP

Genetic variation within and among five populations of the pearl oyster Pinctada fucata, from China (Daya Bay, Sanya Bay and Beibu Bay), Japan (Mie Prefecture) and Australia (Port Stephens) was studied using AFLP. Three primer pairs generated 184 loci among which 91.8-97.3% is polymorphic. An overall genetic diversity of 0.38 among populations and an average of 0.37 within populations (ranging from 0.35 in Japanese population to 0.39 in Beibu Bay population) were observed. Genetic differentiation among the five populations is low but significant as indicated by pairwise G_ST (0.0079-0.0404). AMOVA further shows that differentiation is significant among the five populations but is not significant at a broader geographical scale, among the three groups of Chinese, Japanese and Australian populations or among the two groups of Australian and north Pacific populations. The low level of genetic differentiation indicated that P. fucata populations in the west Pacific are genetically linked. Among the five populations, the Australian one is more differentiated from the others, based on both pairwise AMOVA and G_ST analyses, and is genetically isolated by distance as indicated by Mantel test. However, genetic differences among the three Chinese populations are not correlated with the geographic distances, suggesting that Hainan Island and Leizhou Peninsula may act as barriers blocking gene flow.