Genetic differentiation between two color morphs of <Emphasis Type="Italic">Apogon taeniophorus</Emphasis> from southern Japan

The anterior half of the mitochondrial 16S rRNA gene (ca. 610bp) was compared for two color morphs (spotted and lined types) of a dark-striped cardinalfish, previously identified as Apogon taeniophorus. Phylogenetic analyses using maximum-parsimony (MP) and neighbor-joining (NJ) methods, with haplotypes of A. cookii as an outgroup, showed that the haplotypes of each color-morph were reciprocally monophyletic with 100% bootstrap values. In addition, the degree of sequence difference between the two morphs was comparable to that existing between the other clearly distinct congeneric species. These results, together with the differences in coloration and overlapped geographical ranges, indicated that the two color morphs of A. taeniophorus represent two distinct species.     

Genetic comparison of two color-morphs of <Emphasis Type="Italic">Apogon properuptus</Emphasis> from southern Japan

The anterior half of the mitochondrial 16S rRNA gene (ca. 650bp) was compared for two color-morphs (dotted and lined types) of the orange-lined cardinalfish, previously identified as Apogon properuptus. Twelve and nine specimens, respectively, of dotted and lined types were collected from four and three localities along the coasts of southern Japan and the Ryukyu Islands, specimens of both color-morphs being collected from one of these localities on the southern coast of the Shikoku Island. Phylogenetic analyses using maximum parsimony (MP) and neighbor-joining (NJ) methods, with haplotypes of A. semilineatus and A. cyanosoma as an outgroup and comparative OTU, respectively, showed that the haplotypes of each color-morph were reciprocally monophyletic with 100% bootstrap values. These results, together with their distinct coloration and partly overlapping geographical ranges, indicated that the two color-morphs of A. properuptus from Japanese waters represent two distinct species.     

Comparison of genetic population structure between two cyprinids, <Emphasis Type="Italic">Hemigrammocypris rasborella</Emphasis> and <Emphasis Type="Italic">Pseudorasbora pumila</Emphasis> subsp., in the Ise Bay basin,central Honshu,Japan

Two small cyprinid fishes, Hemigrammocypris rasborella and Pseudorasbora pumila subsp. (sensu Nakamura 1963), inhabit similar habitats and often occur sympatrically in the Ise Bay basin, central Honshu Island, Japan. Their genetic population structures were revealed, using sequence data from the mitochondrial cytochrome b gene, and then compared. Hemigrammocypris rasborella populations in the Ise Bay area formed a monophyletic group that has been isolated from eastern (Tenryu River) and western (Lake Biwa–Yodo River) populations at least for several hundred thousand years. Pseudorasbora pumila subsp., endemic to the Ise Bay area, was estimated to have become isolated from its sister subspecies, P. p. pumila, about 5 million years ago. Both H. rasborella and P. pumila subsp. had centers of genetic diversity around the Okazaki Plain in the eastern part of the basin and showed trans-bay distribution of haplotypes or haplotype groups. Their common population structure was explained by geological features in the Ise Bay area, in which a large paleo-river system developed in regression periods, suggesting gene flow among populations of each species in the mid to lower reaches of the paleo-river. Based on the estimated expansion or divergence time, however, not all populations experienced gene flow during the Last Glacial. In contrast to the maintenance of high genetic diversity in H. rasborella, almost all populations of P. pumila subsp. have lost mitochondrial DNA genetic diversity. This implies that effective population size of P. pumila subsp. tended to be smaller, probably because of differences in reproductive ecology, even though the two species have been exposed to similar environmental changes. For conservation of the two species, genetic and adaptive differentiation among local populations should be considered, and attention should be paid to inbreeding depression, especially in P. pumila subsp. An erratum to this article can be found at     

Genetic divergence between two forms of a tongue sole <Emphasis Type="Italic">Cynoglossus interruptus</Emphasis>

Genetic differences between trilinear and dilinear forms of a tongue sole, Cynoglossus interruptus, were examined by use of isozymes. Unequivocal differences were detected between the two forms, including complete replacement of alleles at the FBALD-2*, MDH-3*, PROT-1*, and SOD-1* loci, almost complete replacement at the AAT-3*, AH-1*, AH-2*, EST-3*, G3PDH-3*, GPI-2*, IDHP-1*, and MDH-1* loci, and extreme differences in allelic frequencies at the GPI-1* and PGDH* loci. The genetic distances (D values) between the two forms were 0.4207–0.4353, figures predicatively significant at the specific level. The considerable genetic differences strongly suggested that the two forms represent distinct species. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The <Emphasis Type="Italic">Caenorhabditis</Emphasis><Emphasis Type="Italic">briggsae</Emphasis> genome contains active <Emphasis Type="Italic">CbmaT1</Emphasis> and <Emphasis Type="Italic">Tcb1</Emphasis> transposons

The maT clade of transposons is a group of transposable elements intermediate in sequence and predicted protein structure to mariner and Tc transposons, with a distribution thus far limited to a few invertebrate species. We present evidence, based on searches of publicly available databases, that the nematode Caenorhabditis briggsae has several maT-like transposons, which we have designated as CbmaT elements, dispersed throughout its genome. We also describe two additional transposon sequences that probably share their evolutionary history with the CbmaT transposons. One resembles a fold back variant of a CbmaT element, with long (380-bp) inverted terminal repeats (ITRs) that show a high degree (71%) of identity to CbmaT1. The other, which shares only the 26-bp ITR sequences with one of the CbmaT variants, is present in eight nearly identical copies, but does not have a transposase gene and may therefore be cross mobilised by a CbmaT transposase. Using PCR-based mobility assays, we show that CbmaT1 transposons are capable of excising from the C. briggsae genome. CbmaT1 excised approximately 500 times less frequently than Tcb1 in the reference strain AF16, but both CbmaT1 and Tcb1 excised at extremely high frequencies in the HK105 strain. The HK105 strain also exhibited a high frequency of spontaneous induction of unc-22 mutants, suggesting that it may be a mutator strain of C. briggsae.     

Phylogenetic analyses of <Emphasis Type="Italic">Uromyces viciae-fabae</Emphasis> and its varieties on <Emphasis Type="Italic">Vicia</Emphasis>, <Emphasis Type="Italic">Lathyrus</Emphasis>, and <Emphasis Type="Italic">Pisum</Emphasis> in Japan

A pea rust fungus, Uromyces viciae-fabae, has been classified into two varieties, var. viciae-fabae and var. orobi, based on differences in urediniospore wall thickness and putative host specificity in Japan. In principal component analyses, morphological features of urediniospores and teliospores of 94 rust specimens from Vicia, Lathyrus, and Pisum did not show definite host-specific morphological groups. In molecular analyses, 23 Uromyces specimens from Vicia, Lathyrus, and Pisum formed a single genetic clade based on D1/D2 and ITS regions. Four isolates of U. viciae-fabae from V. cracca and V. unijuga could infect and sporulate on P. sativum. These results suggest that U. viciae-fabae populations on different host plants are not biologically differentiated into groups that can be recognized as varieties.Contribution no. 184, Laboratory of Plant Parasitic Mycology, Institute of Agriculture and Forestry, University of Tsukuba, Japan     

Genetic variability among <Emphasis Type="Italic">Pholiota aurivella</Emphasis> isolates from a small natural population

Genetic differences between 36 Pholiota aurivella wild isolates collected from 13 decayed logs of Salicaceae trees distributed along about 1200 m of a streambed in a forest were characterized by somatic incompatibility and mating tests, and by restriction fragment length polymorphism (RFLP) analysis of mitochondrial DNA (mtDNA). There was a perfect correlation between somatic incompatibility and mating type groups, and isolates could be divided into 15 genets (genetically identical clones). Because the mtDNAs of the 36 wild isolates have 14 different EcoRI RFLP patterns, they likely originated from at least 14 distinct wild strains, indicating that multiple wild strains with distinct genetic compositions coexist in the forest investigated in this study. mtDNA variation of P. aurivella is apparently very high despite the close proximity of sample collection sites within the forest. The territories of single P. aurivella genets within a host log are apparently larger than other nonpathogenic wood-decaying basidiomycetes reported previously, such as Flammulina velutipes and Lentinula edodes.     

Floral development and systematic position of <Emphasis Type="Italic">Arillastrum</Emphasis>, <Emphasis Type="Italic">Allosyncarpia</Emphasis>, <Emphasis Type="Italic">Stockwellia</Emphasis> and <Emphasis Type="Italic">Eucalyptopsis</Emphasis> (Myrtaceae)

We have investigated the floral ontogeny of Arillastrum, Allosyncarpia, Stockwellia and Eucalyptopsis (of the eucalypt group, Myrtaceae) using scanning electron microscopy and light microscopy. Several critical characters for establishing relationships between these genera and to the eucalypts have been determined. The absence of compound petaline primordia in Arillastrum, Allosyncarpia, Stockwellia and Eucalyptopsis excludes these taxa from the eucalypt clade. Post-anthesis circumscissile abscission of the hypanthium above the ovary in Stockwellia, Eucalyptopsis and Allosyncarpia is evidence that these three taxa form a monophyletic group; undifferentiated perianth parts and elongated fusiform buds are characters that unite Stockwellia and Eucalyptopsis as sister taxa. No floral characters clearly associate Arillastrum with either the eucalypt clade or the clade of Stockwellia, Eucalyptopsis and Allosyncarpia.We gratefully acknowledge Clyde Dunlop and Bob Harwood (Northern Territory Herbarium) for collecting specimens of Allosyncarpia, and Bruce Gray (Atherton) for collecting specimens of Stockwellia. The Australian National Herbarium (CANB) kindly lent herbarium specimens of Eucalyptopsis for examination. This research was supported by a University of Melbourne Research Development Grant to Andrew Drinnan.     

Quantitative study of interactions between <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> and <Emphasis Type="Italic">Oenococcus </Emphasis><Emphasis Type="Italic">oeni</Emphasis> strains

This study examines the interactions that occur between Saccharomyces cerevisiae and Oenococcus oeni strains during the process of winemaking. Various yeast/bacteria pairs were studied by applying a sequential fermentation strategy which simulated the natural winemaking process. First, four yeast strains were tested in the presence of one bacterial strain leading to the inhibition of the bacterial component. The extent of inhibition varied widely from one pair to another and closely depended on the specific yeast strain chosen. Inhibition was correlated to weak bacterial growth rather than a reduction in the bacterial malolactic activity. Three of the four yeast strains were then grown with another bacteria strain. Contrary to the first results, this led to the bacterial stimulation, thus highlighting the importance of the bacteria strain. The biochemical profile of the four yeast fermented media exhibited slight variations in ethanol, SO(2) and fatty acids produced as well as assimilable consumed nitrogen. These parameters were not the only factors responsible for the malolactic fermentation inhibition observed with the first bacteria strain. The stimulation of the second has not been reported before in such conditions and remains unexplained.     

<Emphasis Type="Italic">Drosophila</Emphasis><Emphasis Type="Italic">P</Emphasis> transposons of the urochordata <Emphasis Type="Italic">Ciona intestinalis</Emphasis>

P transposons belong to the eukaryotic DNA transposons, which are transposed by a cut and paste mechanism using a P-element-coded transposase. They have been detected in Drosophila, and reside as single copies and stable homologous sequences in many vertebrate species. We present the P elements Pcin1, Pcin2 and Pcin3 from Ciona intestinalis, a species of the most primitive chordates, and compare them with those from Ciona savignyi. They showed typical DNA transposon structures, namely terminal inverted repeats and target site duplications. The coding region of Pcin1 consisted of 13 small exons that could be translated into a P-transposon-homologous protein. C. intestinalis and C. savignyi displayed nearly the same phenotype. However, their P elements were highly divergent and the assumed P transposase from C. intestinalis was more closely related to the transposase from Drosophila melanogaster than to the transposase of C. savignyi. The present study showed that P elements with typical features of transposable DNA elements may be found already at the base of the chordate lineage. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

In planta transformation of <Emphasis Type="Italic">Notocactus scopa</Emphasis> cv. <Emphasis Type="Italic">Soonjung</Emphasis> by <Emphasis Type="Italic">Agrobacterium </Emphasis><Emphasis Type="Italic">tumefaciens</Emphasis>

Notocactus scopa cv. Soonjung was subjected to in planta Agrobacterium tumefaciens-mediated transformation with vacuum infiltration, pin-pricking, and a combination of the two methods. The pin-pricking combined with vacuum infiltration (20-30 cmHg for 15 min) resulted in a transformation efficiency of 67-100%, and the expression of the uidA and nptII genes was detected in transformed cactus. The established in planta transformation technique generated a transgenic cactus with higher transformation efficiency, shortened selection process, and stable gene expression via asexual reproduction. All of the results showed that the in planta transformation method utilized in the current study provided an efficient and time-saving procedure for the delivery of genes into the cactus genome, and that this technique can be applied to other asexually reproducing succulent plant species.     

Genetic mapping of the novel <Emphasis Type="Italic">Turnip mosaic virus</Emphasis> resistance gene <Emphasis Type="Italic">TuRB03</Emphasis> in <Emphasis Type="Italic">Brassica napus</Emphasis>

A new source of resistance to the pathotype 4 isolate of Turnip mosaic virus (TuMV) CDN 1 has been identified in Brassica napus (oilseed rape). Analysis of segregation of resistance to TuMV isolate CDN 1 in a backcross generation following a cross between a resistant and a susceptible B. napus line showed that the resistance was dominant and monogenic. Molecular markers linked to this dominant resistance were identified using amplified fragment length polymorphism (AFLP) and microsatellite bulk segregant analysis. Bulks consisted of individuals from a BC₁ population with the resistant or the susceptible phenotype following challenge with CDN 1. One AFLP and six microsatellite markers were associated with the resistance locus, named TuRB03, and these mapped to the same region on chromosome N6 as a previously mapped TuMV resistance gene TuRB01. Further testing of TuRB03 with other TuMV isolates showed that it was not effective against all pathotype 4 isolates. It was effective against some, but not all pathotype 3 isolates tested. It provided further resolution of TuMV pathotypes by sub-dividing pathotypes 3 and 4. TuRB03 also provides a new source of resistance for combining with other resistances in our attempts to generate durable resistance to this virus.     

Effect of <Emphasis Type="Italic">cra</Emphasis> gene knockout together with <Emphasis Type="Italic">edd</Emphasis> and <Emphasis Type="Italic">iclR</Emphasis> genes knockout on the metabolism in <Emphasis Type="Italic">Escherichia coli</Emphasis>

To elucidate the physiological adaptation of Escherichia coli due to cra gene knockout, a total of 3,911 gene expressions were investigated by DNA microarray for continuous culture. About 50 genes were differentially regulated for the cra mutant. TCA cycle and glyoxylate shunt were down-regulated, while pentose phosphate (PP) pathway and Entner Doudoroff (ED) pathway were up-regulated in the cra mutant. The glucose uptake rate and the acetate production rate were increased with less acetate consumption for the cra mutant. To identify the genes controlled by Cra protein, the Cra recognition weight matrix from foot-printing data was developed and used to scan the whole genome. Several new Cra-binding sites were found, and some of the result was consistent with the DNA microarray data. The ED pathway was active in the cra mutant; we constructed cra.edd double genes knockout mutant to block this pathway, where the acetate overflowed due to the down-regulation of aceA,B and icd gene expressions. Then we further constructed cra.edd.iclR triple genes knockout mutant to direct the carbon flow through the glyoxylate pathway. The cra.edd.iclR mutant showed the least acetate production, resulting in the highest cell yield together with the activation of the glycolysis pathway, but the glucose consumption rate could not be improved. Dayanidhi Sarkar and Khandaker Al Zaid Siddiquee have contributed equally.     

<Emphasis Type="Italic">Funastrum rupicola</Emphasis> (<Emphasis Type="Italic">Apocynaceae:</Emphasis><Emphasis Type="Italic">Asclepiadoideae</Emphasis>), a new species from Bolivia

Summary   Funastrum rupicola Goyder, a new species of Apocynaceae: Asclepiadoideae from Bolivia, is described and illustrated. The conservation status of this species is assessed.     

Two new species of <Emphasis Type="Italic">Lirula</Emphasis> on <Emphasis Type="Italic">Abies</Emphasis> from Japan

Two new species of Lirula (L. japonica and L. exigua) on Abies mariesii collected in subalpine areas of northern Japan are described as members of Rhytismatales, Discomycetes. Lirula japonica causes needle cast in fir, but L. exigua seems to occur on the needles of physically damaged twigs. Morphological characteristics of both species are discussed.     

<Emphasis Type="Italic">HLA-A</Emphasis> allele associations with viral <Emphasis Type="Italic">MER9-LTR</Emphasis> nucleotide sequences at two distinct loci within the <Emphasis Type="Italic">MHC alpha</Emphasis> block

The study of the association of the Human Leukocyte Antigen (HLA) alleles and polymorphic retrotransposons such as Alu, HERV, and LTR at various loci within the Major Histocompatibility Complex allows for a better identification and stratification of disease associations and the origins of HLA haplotypes in different populations. This paper provides sequence and association data on two structurally polymorphic MER9-LTR retrotransposons that are located 54 kb apart and in close proximity to the multiallelic HLA-A gene involved in the regulation of the human immune system. Direct DNA sequencing and analysis of the PCR products identified DNA nucleotide variations between the MER9-LTR sequences at the two loci and their associations with HLA-A alleles as potential haplotype and evolutionary markers. All MER9-LTR sequences were haplotypic when associated with common HLA-A alleles. The number of SNP loci was 2.5 times greater for the solo LTR at the AK locus, which is located closer to the HLA-A gene than the solo or 3′ LTR at the HG locus. Our study shows that the nucleotide variations of the MER9-LTR DNA sequences are additional informative markers in fine mapping HLA-A genomic haplotypes for future population, evolutionary, and disease studies.     

A new species of <Emphasis Type="Italic">Gymnopilus</Emphasis> Sect. <Emphasis Type="Italic">Microspori</Emphasis> from Japan

Gymnopilus ombrophilus sp. nov., growing on rotten wood of conifers and hardwoods from Niigata, Japan is described and illustrated. It is characterized by its medium-sized, brownish-orange basidiocarps with a finely squamulose pileus, stipe lacking an annulus, and mild taste, and microscopically by dextrinoid, small, broadly ellipsoid basidiospores. The new species belongs to the section Microspori. The differences between the taxon and similar species are briefly discussed.