Description of <Emphasis Type="Italic">Gosztonyia antarctica</Emphasis>, a new genus and species of Zoarcidae (Teleostei: Perciformes) from the Antarctic Ocean

A new genus and species of zoarcid fish, Gosztonyia antarctica, is described on the basis of four specimens collected from the Bellingshausen Sea, Antarctic Ocean, at a depth of 615 m. Gosztonyia is placed in the subfamily Lycodinae and can be distinguished from all other zoarcid genera by the following combination of characters: seven branchiostegal rays, interdigitating ceratohyal–epihyal articulation, palatal arch reduced, posterior hyomandibular ramus longer than anterior, cranium narrowed, supratemporal commisure and occipital pores absent. A new species, Gosztonyia antarctica, is described and the relationships of the new genus are discussed.     

Frequencies of the <Emphasis Type="Italic">DRB1</Emphasis>, <Emphasis Type="Italic">DQA1</Emphasis>, <Emphasis Type="Italic">DQB1</Emphasis> and <Emphasis Type="Italic">TNFA</Emphasis> alleles in immigrant population of west Siberia

Based on population analysis of the DRB1, DQA1, DQB1 and TNFA allele frequency distribution patterns, regional features of immunogenetic structure of the population of West Siberia were investigated. Statistically significant linkage disequilibrium within the HLA class II region, as well as between the TNFA and DRB1, DQA1, and DQB1 was demonstrated. Population frequency distribution patterns of two- and multilocus haplotypes were examined.     

Morphological analysis and taxonomical status of four fish species of the genera <Emphasis Type="Italic">Opisthocentrus</Emphasis> and <Emphasis Type="Italic">Pholidapus</Emphasis> (Perciformes: Stichaeidae)

No common opinion on the systematics position of species of the fishes of the subfamily Opisthocentrinae, Stichaeidae family has been formed up to the present. Therefore, a morphological analysis of fishes belonging to taxa Opisthocentrus ocellatus, O. tenuis, O. zonope, and Pholidapus dybowskii was undertaken. The obtained data treated by various methods of statistics implied the species independence of these taxa, which sympatrically occurred in the coastal areas of the northwest of the Sea of Japan. All the four studied species were similar in some attributes and distinct by other. Minor differences in the structure of the seismosensory system of Ph. dybowskii and Opisthocentrus species gave no basis on which to distinguish the independent genus Pholidapus. It would be correct to consider this as a subgenus of the Opisthocentrus genus, which includes three other species.     

Systematic Rearrangement of Korean <Emphasis Type="Italic">Scirpus</Emphasis> L. s.l. (Cyperaceae) as Inferred from Nuclear ITS and Chloroplast <Emphasis Type="Italic">rbcL</Emphasis> Sequences

The genus Scirpus L. s.l. (Cyperaceae) has been accepted as a polyphyletic taxon by most plant taxonomists. This genus was separated into different genera by several different authors: Scirpus s. str., Trichophorum Pers., Bolboschoenus (Asch.) Palla, Schoenoplectus (Rchb.) Palla, and Schoenoplectiella Lye. The heterogeneity of Korean Scirpus s.l. has not yet been studied. We examined 17 taxa of Korean Scirpus s.l. by morphological characters and phylogenetic analyses based on nuclear ITS and chloroplast rbcL sequences. Phylogenetic analyses using maximum parsimony, maximum likelihood, and Bayesian method provided sufficient resolution. The phylogeny revealed the polyphyly of Korean Scirpus s.l. with five distinct clades. These clades correspond to Bolboschoenus, Schoenoplectus s.str., and Schoenoplectiella, Scirpus s.str., and Trichophorum, respectively. These five genera were delimited in terms of the morphology of tuber, bract, and inflorescence. By virtue of our findings, we suggest that the 17 taxa of Korean Scirpus s.l. should be placed into five genera as follows: Bolboschoenus (two species), Schoenoplectus (three species), Schoenoplectiella (six species), Scirpus s.str. (five species), and Trichophorum (one species).     

Mining metadata from unidentified ITS sequences in GenBank: A case study in <Emphasis Type="Italic">Inocybe</Emphasis> (<Emphasis Type="Italic">Basidiomycota</Emphasis>)

Background  

The lack of reference sequences from well-identified mycorrhizal fungi often poses a challenge to the inference of taxonomic affiliation of sequences from environmental samples, and many environmental sequences are thus left unidentified. Such unidentified sequences belonging to the widely distributed ectomycorrhizal fungal genus Inocybe (Basidiomycota) were retrieved from GenBank and divided into species that were identified in a phylogenetic context using a reference dataset from an ongoing study of the genus. The sequence metadata of the unidentified Inocybe sequences stored in GenBank, as well as data from the corresponding original papers, were compiled and used to explore the ecology and distribution of the genus. In addition, the relative occurrence of Inocybe was contrasted to that of other mycorrhizal genera.     

<Emphasis Type="Italic">Maireina afibulata</Emphasis> and <Emphasis Type="Italic">M. attenuatipilis</Emphasis>, new members of the cyphelloid genus <Emphasis Type="Italic">Maireina</Emphasis> (Basidiomycota,Agaricomycetes)

Maireina afibulata and M. attenuatipilis are proposed as new members of the recently revised genus Maireina, one of the few anatomically well-studied cyphelloid groups in the Basidiomycota. Maireina species have brownish basidiomes, smooth, parietally unpigmented spores, and are characterized by non-ramified external hyphae with more or less thick, yellow to brown cell walls and distinct crystalline incrustations that always include their distal ends. A key to the species of the genus Maireina is presented, and M. afibulata as well as M. attenuatipilis are described and discussed in detail. Taxonomic novelties: Maireina afibulata Bodensteiner, M. attenuatipilis Bodensteiner     

Revision of “<Emphasis Type="Italic">Septonema ochraceum</Emphasis>” revealed three new species of <Emphasis Type="Italic">Venturiaceae</Emphasis> and <Emphasis Type="Italic">Herpotrichiellaceae</Emphasis>

Survey of seven strains determined as Septonema ochraceum (Dothideomycetes, inc. sed.) isolated from pine litter or obtained from public collections revealed three new species, Fusicladium cordae, F. sicilianum (Venturiaceae), Cladophialophora matsushimae (Herpotrichiellaceae) and a cryptic species morphologically identical to Devriesia americana (Teratosphaeriaceae), but phylogenetically distinct. Morphological survey and phylogenetic analysis using nucleotide sequence data from the nuclear ribosomal subunit genes indicate a close relationship within three species colonising pine litter needles, F. cordae, F. pini and F. ramoconidii. F. sicilianum is most related to F. rhodense. C. matsushimae represents a species belonging to one of the lineages of the polyphyletic genus Cladophialophora. None of the strains observed can be classified morphologically as S. ochraceum, of which the type material does not exist.     

Comparative seed morphology of <Emphasis Type="Italic">Leandra</Emphasis> (Miconieae,Melastomataceae)

The seed morphology of 79 species of neotropical Miconieae (Melastomataceae) is presented. These species have been chosen, in majority, from the polyphyletic genus Leandra. A few other species from the polyphyletic genera Miconia, Ossaea, and Clidemia were also sampled, because of potential similarities. Sixteen morphological seed types are defined after analysis through light microscopy and scanning electron microscopy. The seed morphology appears to possess a great deal of variability on the level of the overall shape as well as the structure and the surface of the testa. The different types defined here do not match with genera or sections, but rather are composed of species coming from different genera. In comparison with a preliminary molecular phylogeny study done on Leandra, some types of seeds are related to well supported clades. In some cases seed morphology corresponds with natural groups of species, thus being of high phylogenetic importance.     

Overexpression of the Chitosanase Gene in <Emphasis Type="Italic">Fusarium solani</Emphasis> via <Emphasis Type="Italic">Agrobacterium</Emphasis><Emphasis Type="Italic">tumefaciens</Emphasis>-Mediated Transformation

To overexpress the chitosanase gene (csn) in F. solani, a vector based on pCAMBIA 1300 was constructed. The csn gene, which is under control of the Aspergillus nidulans gpdA promoter and A. nidulans trpC terminator, was introduced back into the F. solani genome by Agrobacterium tumefaciens-mediated transformation, and the herbicide-resistance gene bar from Streptomyces hygroscopicus was used as the selection marker. Transformants which showed a significant increase in chitosanase production (~2.1-fold than control) were obtained. Southern blot analysis indicated that most transformants had a single-copy T-DNA integration.     

Origin of the Genus <Emphasis Type="Italic">Homo</Emphasis>

The origin of the genus Homo in Africa signals the beginning of the shift from increasingly bipedal apes to primitive, large-brained, stone tool-making, meat-eaters that traveled far and wide. This early part of the human genus is represented by three species: Homo habilis, Homo rudolfensis, and Homo erectus. H. habilis is known for retaining primitive features that link it to australopiths and for being the first stone tool makers. Little is known about H. rudolfensis except that it had a relatively large brain and large teeth compared to H. habilis and that it overlapped in time and space with other early Homo. Our understanding of the paleobiology and evolution of the larger-brained H. erectus is enhanced due to its rich fossil record. H. erectus was the first obligate, fully committed biped, and with a body adapted for modern striding locomotion, it was also the first in the human lineage to disperse outside of Africa. The early members of the genus Homo are the first to tip the scale from the more apish side of our evolutionary history toward the more human one.     

Numerical Taxonomy of <Emphasis Type="Italic">Vibrionaceae</Emphasis> Isolated from Cultured Amberjack (<Emphasis Type="Italic">Seriola dumerili</Emphasis>) and Surrounding Water

A numerical taxonomic study was performed on 148 isolates of Gram-negative, heterotrophic, facultative anaerobic bacteria isolated from amberjack (Seriola dumerili) and its surrounding culture water. The study included 30 type and reference strains belonging to genera Vibrio, Listonella, and Photobacterium. The strains were characterized by 109 morphological, biochemical, physiological, and nutritional tests. Cluster analysis of similarity matrices obtained with S_SM and S_J coefficients was carried out. UPGMA (unweighted pair group mathematical average) analysis defined 11 phena at S_SM values ≥ 86%. Nine phena were identified as Vibrio alginolyticus, V. fischeri, V. harveyi, V. carchariae, V. mediterranei, V. splendidus, V. furnissii, V. parahaemolyticus, and Photobacterium damselae subsp. damselae. The two latter comprised strains isolated from diseased fish. Received: 27 March 2002 / Accepted: 24 May 2002     

<Emphasis Type="Italic">Cantharellus pseudoformosus</Emphasis>, a new species associated with <Emphasis Type="Italic">Cedrus deodara</Emphasis> from India

The genus Cantharellus is known to have a global distribution and to form ectomycorrhizal associations with a diverse set of host plants. Here we describe Cantharellus pseudoformosus as a species new to science with a possible association with Cedrus deodara. ITS and LSU data demonstrated that the material from India is distinct from Cantharellus formosus and other closely related species.     

Phylogeny of <Emphasis Type="Italic">Gunnera</Emphasis>

 The phylogeny of the genus Gunnera is investigated for the first time. Twelve species representing the six currently recognised subgenera are analysed. Two chloroplast DNA regions, the rbcL gene and the rps16 intron, together provide 46 informative characters out of 2335. A combined analysis of both genes gives four most parsimonious trees, firmly establishing the east South American G. herteri as sister group to the rest of the genus. The African G. perpensa is sister group to two well-supported clades, one including the South American subgenera Misandra and Panke, the other the Australian/New Zealand/Malayan species of subgenera Milligania and Pseudogunnera. Thus, South America is a composite area for Gunnera, showing up at two different levels in the cladogram. Our analysis supports a close biogeographic relationship between Australia and New Zealand. The evolution of some morphological characters is discussed. Lastly, the unusual structure of some of the rbcL sequences is reported. Received July 6, 2000 Accepted October 24, 2000     

Identification of phenotypically and genotypically related <Emphasis Type="Italic">Lactobacillus</Emphasis> strains based on nucleotide sequence analysis of the <Emphasis Type="Italic">groEL,rpoB, rplB</Emphasis>, and <Emphasis Type="Italic">16S rRNA</Emphasis> genes

Sixty-eight cultures of lactic acid bacteria were isolated and identified from national fermented milk drinks (airan, koumiss, kurunga, shubat) home-made in different regions of the Republic of Kazakhstan and the Buryat Republic of Russia. The cultures of lactic acid bacteria of the genus Lactobacillus were identified as L. paracasei and L. rhamnosus related to the L. casei group and as L. brevis, L. buchneri, L. diolivorans, and L. parabuchneri (the L. buchneri group) using the classical microbiological methods and on the basis of the 16S rRNA gene sequence analysis. The polymorphism of the nucleotide sequences of the genes groEL, rpoB, and rplB encoding specific proteins was studied for intraspecific differentiation of the lactobacilli. The analysis of these genes allowed a more accurate identification of the lactobacilli that are genetically and phenotypically related to the L. casei group as L. paracasei subsp. paracasei and L. paracasei subsp. tolerans. The gene nucleotide sequences of all the genotyped strains were deposited in the GenBank database.     

Retrotransposon <Emphasis Type="Italic">gtwin</Emphasis>: Structural analysis and distribution in <Emphasis Type="Italic">Drosophila</Emphasis> strains

A search for noncanonical variants of the gypsy retrotransposon ( MDG4 ) in the genome of the Drosophila melanogaster strain G32 led to the cloning of four copies of the poorly studied 7411-bp gtwin element. Sequence analysis showed that gtwin belongs to a family of endogeneous retroviruses, which are widespread in the Drosophila genome and have recently been termed insect erantiviruses. The gtwin retrotransposon is evolutionarily closest to MDG4, as evident from a good alignment of their nucleotide sequences including ORF2 (the pol gene) and ORF3 (the env gene), as well as the amino acid sequences of their protein products. These regions showed more than 75% homology. The distribution of gtwin was studied in several strains of the genus Drosophila. While strain G32 contained more than 20 copies of the element, ten other D. melanogaster strains carried gtwin in two to six copies per genome. The gtwin element was not detected in D. Hydei or D. Virilis. Comparison of the cloned gtwin sequences with the gtwin sequence available from the D. melanogaster genome database showed that the two variants of the mobile element differ by the presence or absence of a stop codon in the central region of ORF3. Its absence from the gtwin copies cloned from the strain G32 may indicate an association between the functional state of ORF3 and amplification of the element.Translated from Genetika, Vol. 41, No. 1, 2005, pp. 23–29.Original Russian Text Copyright © 2005 by Kotnova, Karpova, Feoktistova, Lyubomirskaya, Kim, Ilyin.     

Taxonomic genetics of <Emphasis Type="Italic">Zygowilliopsis</Emphasis> yeasts

Genetic hybridization analysis was conducted with 16 natural Zygowilliopsis strains isolated in different geographical regions and maintained in collections under species names Z. californica, Hansenula dimennae, and Pichia populi. Genetic relatedness was determined on the basis of mating, viability of hybrid progeny, and meiotic recombination of markers. Four new biological species are recognized in the former monotypic genus Zygowilliopsis. Species Z. californica and Zygowiliopsis sp. 3 probably include divergent geographical populations. It is necessary to reconsider the species composition of the genus Zygowiliopsis and generic assignment of P. populi yeasts. Genetic and molecular identifications of the Zygowiliopsis species are in perfect agreement.     

Photosynthetic characteristics in <Emphasis Type="Italic">Oryza</Emphasis> species

Photosynthetic rate (P _N), SPAD value, specific leaf area (SLA), flag leaf area (FLA), and nitrogen content (LN) of genus Oryza were investigated and their correlation was analyzed to assess some of the main photosynthetic traits among different species in the genus Oryza. The results revealed wide variation in these traits. The species O. rufipogon and O. australiensis exhibited maximum photosynthetic rate. Comparison of different types of genomes (diploid: 2n=2x=24; tetraploid: 2n=4x=48) and growth habit (shade- or sun-grown) showed the species of diploid (with genome symbol EE; 2n=2x=24) genomes, with perennial and sun-grown species, had high apparent photosynthesis compared to others. The species with BB/BBCC, shade-grown and the tetraploids showed high SPAD value, and the flag leaf in sun-grown species and diploids were thicker (low SLA) compared with others. However, no significant difference could be noticed among the different types of genomes. Higher leaf area was noticed among the species of CC/CCDD genome, perennial shade-grown species and tetraploids than in others. The variety IR 36 exhibited highest leaf nitrogen concentration. Correlation analysis showed a strong relationship between P _N and leaf nitrogen concentration while no marked relationships were observed among other characteristics. It implies that the species with thick and small leaves with high nitrogen concentration and high photosynthesis evolved better than others. O. rufipogon, with the same genome as O. sativa, could be one of the wild rice resources for elite crop improvement.     

Phylogenetic analysis of Altai osmans of the genus <Emphasis Type="Italic">Oreoleuciscus</Emphasis> (Pisces,Cyprinidae, Leuciscinae), based on the analysis of the cytochrome oxidase 1 gene (<Emphasis Type="Italic">Co-1</Emphasis>) sequence

Molecular genetic analysis of Altai osmans of the genus Oreoleuciscus from two different parts of the range was carried out. In this study, based on the mitochondrial Co-1 gene sequence, a total of 25 fish specimens belonging to four genera were examined: (1) O. humilis, 2 specimens; O. potanini, 13 specimens; (2) Pseudaspius leptocephalus, 1 specimen; (3) Tribolodon brandtii, T. hakonensis, and T. sachalinensis from the GanBank database, 9 speciens; and (4) Leuciscus waleckii, 1 specimen (used as an outgroup). The p-distances were very low both within and between the species: (1) 0.20 ± 0.03%; (2) 0.40 ± 0.12%; and (1–2) 0.80 ± 0.04%. To visualize the relationships among all of the species examined, the neighbor joining (NJ), maximum parsimony (MP), Bayesian (BA), and maximum likelihood (ML) trees were constructed. The results obtained using these methods were very similar. It was demonstrated that species assignment of the individuals (barcoding) with the help Co-1 gene was effective, despite of very low divergence of the two osman taxa, which was comparable with typical intraspecific values in other animal groups. Taxonomic status of O. potanini and O. humilis requires further investigation with paying attention to low genetic distances between these species along with the lack of material from sympatric parts of the ranges.     

Transfer of <Emphasis Type="Italic">Asterosporium orientale</Emphasis> to the genus <Emphasis Type="Italic">Prosthemium</Emphasis> (Pleosporales,Ascomycota): a common coelomycetous fungus with stellate conidia occurring on twigs of <Emphasis Type="Italic">Betula</Emphasis> spp.

Asterosporium orientale, described on Betula ermanii, is transferred to the genus Prosthemium, and a new combination, P. orientale, is proposed. Because of the morphological similarities, P. asterosporum originally described from twigs of B. pendula is considered as a synonym of P. orientale.