<Emphasis Type="Italic">Ty</Emphasis>1<Emphasis Type="Italic">/copia</Emphasis>- and <Emphasis Type="Italic">Ty</Emphasis>3<Emphasis Type="Italic">/gypsy</Emphasis>-like DNA sequences in <Emphasis Type="Italic">Helianthus </Emphasis>species

Two repeated DNA sequences isolated from a partial genomic DNA library of Helianthus annuus, p HaS13 and p HaS211, were shown to represent portions of the int gene of a Ty3 /gypsy retroelement and of the RNase-Hgene of a Ty1 /copia retroelement, respectively. Southern blotting patterns obtained by hybridizing the two probes to BglII- or DraI-digested genomic DNA from different Helianthus species showed p HaS13 and p HaS211 were parts of dispersed repeats at least 8 and 7 kb in length, respectively, that were conserved in all species studied. Comparable hybridization patterns were obtained in all species with p HaS13. By contrast, the patterns obtained by hybridizing p HaS211 clearly differentiated annual species from perennials. The frequencies of p HaS13- and p HaS211-related sequences in different species were 4.3x10(4)-1.3x10(5) copies and 9.9x10(2)-8.1x10(3) copies per picogram of DNA, respectively. The frequency of p HaS13-related sequences varied widely within annual species, while no significant difference was observed among perennial species. Conversely, the frequency variation of p HaS211-related sequences was as large within annual species as within perennials. Sequences of both families were found to be dispersed along the length of all chromosomes in all species studied. However, Ty3 /gypsy-like sequences were localized preferentially at the centromeric regions, whereas Ty1/ copia-like sequences were less represented or absent around the centromeres and plentiful at the chromosome ends. These findings suggest that the two sequence families played a role in Helianthusgenome evolution and species divergence, evolved independently in the same genomic backgrounds and in annual or perennial species, and acquired different possible functions in the host genomes.     

Muscle fat composition of pheasants (<Emphasis Type="Italic">Phasianus colchicus)</Emphasis>, wild ducks (<Emphasis Type="Italic">Anas platyrhynchos</Emphasis>) and black coots (<Emphasis Type="Italic">Fulica atra</Emphasis>)

The aim of this investigation was to characterise the fatty acid composition within intramuscular fat (IMF) of two muscles (breast and thigh) from 28 pheasants, ten wild ducks and 27 black coots from Slovakia. A high variability for all single fatty acids (FA) and the total fat concentration in muscles of wild birds was identified. Black coots deposited the highest fat in breast muscle whereas wild ducks and pheasants accumulated more lipids in thigh muscle. In general, the content of polyunsaturated fatty acids (PUFA) of the IMF in wild bird muscles was high, and the saturated FA concentration was lower compared with muscles of domestic farm animals. The ratio between PUFA and saturated fatty acids (PSQ) ranked between 0.6 and 1.2, and the ratio of n-6/n-3 fatty acid was favourably low in black coot and wild pheasants (3.2 and 2.9, respectively). Farmed pheasants had increased IMF and more saturated and n-6 fatty acids deposited in thigh muscle but not in breast muscle.     

Genetic population structure of <Emphasis Type="Italic">Lefua echigonia</Emphasis> inferred from allozymic and mitochondrial cytochrome <Emphasis Type="Italic">b</Emphasis> variations

We examined the genetic population structure of Lefua echigonia (Japanese name, hotoke-dojo) using polymerase chain reaction restriction-fragment length polymorphisms (PCR-RFLPs) of the mitochondrial cytochrome b gene and two allozymic loci. The phylogenetic relationships of L. echigonia and those among L. echigonia, Lefua sp. (nagare hotoke-dojo), and L. nikkonis (ezo hotoke-dojo) were also investigated based on the nucleotide sequences of the cytochrome b gene. PCR-RFLP analysis revealed 18 mitotypes in L. echigonia, 2 in Lefua sp., and 1 in L. nikkonis. Phylogenetic trees based on the cytochrome b sequences indicated that the 18 mitotypes in L. echigonia were divided into five distinct groups (South-Kanto, North-Kanto, Tohoku, Echigo, and Tokai-Kinki clades) that differed by 8.5–15.3%, reflecting region-specific geographic distributions. The distributions of alleles in two allozymic loci roughly corresponded to those of the mitotype groups. The divergence times of the five groups were estimated to be about 3.4–7.7 million years ago by applying a general rate for mitochondrial DNA, suggesting that the divergence among them might have occurred in the late Tertiary. It can be inferred that the regional differentiation of each group was mainly due to geographic isolation and that this has been maintained, because the boundaries among the groups corresponded to geological features. The trees also supported the existence of three taxa, L. echigonia, Lefua sp., and L. nikkonis. We concluded that Lefua sp. was distinguished from other species in Lefua by morphological and ecological characters and also by genetic divergences of the cytochrome b gene. Our study also demonstrated the superior efficacy and simplicity of PCR-RFLP analysis as a method for detecting genetic variation in L. echigonia.     

Genetic structure of Schrenck newt <Emphasis Type="Italic">Salamandrella schrenckii</Emphasis> populations by mitochondrial cytochrome <Emphasis Type="Italic">b</Emphasis> variation

The nucleotide sequence variation of the mitochondrial cytochrome b gene was studied in Schrenck newt Salamandrella schrenckii (Strauch, 1870) from populations of Primorye and the Khabarovsk region. Phylogenetic analysis revealed two haplotype clusters, southern cluster 1 and northern cluster 2, with a divergence of 3%. Analysis of the mtDNA and cytochrome b amino acid sequence variations made it possible to assume that the modern range of Schrenck newt was colonized from south Primorye northwards. In contrast to the southern cluster, the northern one demonstrated all the signs of demographic expansion (a unimodal distribution of pairwise nucleotide differences, specific results of tests for selective neutrality of mtDNA variation, and a good correspondence of genetic parameters to those expected from demographic expansion models).     

Genetic variation of <Emphasis Type="Italic">Colletotrichum magnum</Emphasis> isolated from <Emphasis Type="Italic">Carica papaya</Emphasis> as revealed by DNA fingerprinting

Mexico is one of the five largest producers of papaya worldwide, but losses caused by pathogens, mainly fungus, at the pre- and post-harvest stages are often more than 50% of the crop. Papaya anthracnose, caused by three different species of the Colletotrichum genus in Mexico, occupies a preponderant place in this problem. Although two of these species, C. gloeosporiodes and C. truncatum, have been characterized morphologically and genotypically, this has not occurred with C. magnum, the third species involved, about which there is very little information. Because of this, it is vital to know its genetic characterization, much more so considering that the studies carried out on the other two species reveal a wide genetic diversity, differences in pathogenicity and in the response to fungicides of the different strains characterized. In this work, Colletotrichum spp. isolates were collected at different papaya orchards in the south-southeast of Mexico. C. magnum isolates identified by species-specific primers were characterized by morphological and molecular approaches. Differences in colony characteristics resulted in five morphological groups. AP-PCR, DAMD and ISSR markers were found to be very efficient for revealing the interspecific variability of this species. The high genetic variability found in the accessions of C. magnum was linked to the geographical area where they were collected. Isolates from Chiapas State were the most variable, showing point mutations in the ITS1-ITS2 region. These results will enable a better phytosanitary management of anthracnose in papaya in this region of Mexico.     

Genetic characterization of ticks from southwestern Romania by sequences of mitochondrial <Emphasis Type="Italic">cox</Emphasis>1 and <Emphasis Type="Italic">nad</Emphasis>5 genes

In the present study, samples representing three hard tick species and one soft tick species, namely Dermacentor marginatus, Haemaphysalis punctata, Ixodes ricinus and Argas persicus from southwestern Romania, and one hard tick, Haemaphysalis longicornis, from China were characterized genetically by a portion of mitochondrial cytochrome c oxidase subunit 1 gene (pcox1) and a portion of nicotinamide adenine dinucleotide dehydrogenase subunit 5 gene (pnad5). The pcox1 and pnad5 were amplified separately from individual ticks by PCR, sequenced and analyzed. The length of pcox1 and pnad5 sequences of all samples was 732 and 519 bp, respectively. The intra-specific sequence variation in De. marginatus was 0.1–1.0% for pcox1 and 0.2–1.2% for pnad5, whereas in Ha. punctata it was 0.4–1.9% for pcox1 and 0.4–1.0% for pnad5. For the tick species examined in the present study, sequence comparison revealed that the inter-specific sequence differences were higher: 15.9–27.6% for pcox1 and 20.3–42.4% for pnad5. This suggests that the cox1 and nad5 sequences could provide useful genetic markers for the specific identification and genetic characterization of ticks in Romania and elsewhere.     

Molecular phylogenetic analysis of key <Emphasis Type="Italic">Jatropha</Emphasis> species inferred from nrDNA ITS and chloroplast (<Emphasis Type="Italic">trn</Emphasis>L-F and <Emphasis Type="Italic">rbc</Emphasis>L) sequences

The genus Jatropha (Euphorbiaceae) contains species that are of significant economic and ornamental value. However, Jatropha breeding material is rather limited due to incomplete information regarding phylogenetic relationships among germplasm resources. Phylogenetic analyses were performed based on the internal transcribed spacer of nuclear ribosomal DNA (nrDNA ITS), two chloroplast regions (trnL-F and rbcL), and the combined (ITS+trnL-F+rbcL) dataset among twenty-five specimens representing six key Jatropha species. Phylogenetic relationships of Jatropha were well resolved between subgenus Curcas and subgenus Jatropha, and demonstrated the intermediate position of section Polymorphae among sections of both subgenera. Jatropha curcas and J. integerrima demonstrated a close phylogenetic relationship. The molecular data agreed with the morphological classification that recognized J. multifida and J. podagrica in sec. Peltatae. The distinct intraspecific divergence that occurred in J. curcas could be attributed to restricted gene flow caused by geographical isolation and different ecological conditions. Phylograms produced with trnL-F and rbcL sequence data suggested slow rates of sequence divergence among Jatropha spp., while the ITS gene tree had good resolution suggesting high genetic variation of ITS among Jatropha species.     

Genetic variation in populations of <Emphasis Type="Italic">Allothrombium pulvinum</Emphasis> (Acari: Trombidiidae) from Northern Iran revealed by mitochondrial <Emphasis Type="Italic">cox</Emphasis>I and nuclear rDNA <Emphasis Type="Italic">ITS</Emphasis>2 sequences

Allothrombium pulvinum Ewing is a common natural enemy of aphids and some other arthropods. So far, there are no studies that have addressed genetic variation of this predatory mite. We investigated genetic variation of A. pulvinum across its whole known range in Iran. A 410 bp portion of the mitochondrial cytochrome c oxidase subunit I gene (coxI) and 797–802 bp portion of the internal transcribed spacer 2 of rDNA (ITS2) were sequenced for 55 individuals from 11 populations, resulting in 12 and 26 haplotypes, respectively. In the coxI region, haplotype and nucleotide diversities varied among populations from 0.00 to 0.90 and from 0.0000 to 0.0110, respectively. In the ITS2 region they varied from 0.20 to 0.91 and from 0.0006 to 0.0023, respectively. For both gene regions the highest haplotype and nucleotide diversities were detected in population Mahmoud Abad from northern Iran. Statistically significant population differentiation (F _ST) was detected in most pair-wise population comparisons. The results of population differentiation for both gene regions were generally congruent indicating that A. pulvinum from Iran consists of genetically different populations. This suggests that A. pulvinum comprises at least two geographically distinct populations or even more than one species. This study is an initial step towards understanding genetic variation of A. pulvinum, a taxon for which little molecular information is available. More intensive sampling and analysis of additional DNA regions are necessary for more detailed classification of this taxon.     

<Emphasis Type="Italic">Agrobacterium</Emphasis><Emphasis Type="Italic">tumefaciens</Emphasis>-mediated transformation of callus cells of <Emphasis Type="Italic">Crataegus</Emphasis><Emphasis Type="Italic">aronia</Emphasis>

A genetic transformation system has been developed for callus cells of Crataegus aronia using Agrobacterium tumefaciens. Callus culture was established from internodal stem segments incubated on Murashige and Skoog (MS) medium supplemented with 5 mg l⁻¹ Indole-3-butyric acid (IBA) and 0.5 mg l⁻¹ 6-benzyladenine (BA). In order to optimize the callus culture system with respect to callus growth and coloration, different types and concentrations of plant growth regulators were tested. Results indicated that the best average fresh weight of red colored callus was obtained on MS medium supplemented with 2 mg l⁻¹ 2,4-dichlorophenoxyacetic acid (2,4-D) and 1.5 mg l⁻¹ kinetin (Kin) (callus maintenance medium). Callus cells were co-cultivated with Agrobacterium harboring the binary plasmid pCAMBIA1302 carrying the mgfp5 and hygromycin phosphotransferase (hptII) genes conferring green fluorescent protein (GFP) activity and hygromycin resistance, respectively. Putative transgenic calli were obtained 4 weeks after incubation of the co-cultivated explants onto maintenance medium supplemented with 50 mg l⁻¹ hygromycin. Molecular analysis confirmed the integration of the transgenes in transformed callus. To our knowledge, this is the first time to report an Agrobacterium-mediated transformation system in Crataegus aronia.     

Genetic structure of the sable <Emphasis Type="Italic">Martes zibellina</Emphasis> L. populations from Magadan oblast as inferred from mitochondrial DNA variation

Restriction polymorphism of the mtDNA cytochrome b gene was studied in nine sable Martes zibellina L. populations from three introduction foci of Khabarovsk and Kamchatka sables in Magadan oblast: Olya, Kolyma, and Omolon. For comparison, similar studies were performed with the populations of central Kamchatka and Khabarovsk krai. In total, 444 DNA specimens were examined. Three mtDNA haplotypes (A, B, and C) proved to occur at various frequencies in the populations under study. The sable population system displayed high differentiation (F _ST = 22.3%). The populations of the Olya focus were most similar genetically to the populations of Kamchatka; those of the Omolon focus were similar to the Khabarovsk populations, and those of the Kolyma focus occupied an intermediate place. The observed spatial heterogeneity of the sable populations of Magadan oblast was explained in terms of the formation of the introduction foci of Kamchatka and Khabarovsk sables, starting from the 1950s.     

<Emphasis Type="Italic">Galleria</Emphasis><Emphasis Type="Italic">mellonella</Emphasis> are Resistant to <Emphasis Type="Italic">Pneumocystis</Emphasis><Emphasis Type="Italic">murina</Emphasis> Infection

Studying Pneumocystis has proven to be a challenge from the perspective of propagating a significant amount of the pathogen in a facile manner. The study of several fungal pathogens has been aided by the use of invertebrate model hosts. Our efforts to infect the invertebrate larvae Galleria mellonella with Pneumocystis proved futile since P. murina neither caused disease nor was able to proliferate within G. mellonella. It did, however, show that the pathogen could be rapidly cleared from the host.     

Revision of the <Emphasis Type="Italic">Serrulati</Emphasis> species of <Emphasis Type="Italic">Penstemon</Emphasis> section <Emphasis Type="Italic">Saccanthera</Emphasis> subsection <Emphasis Type="Italic">Serrulati</Emphasis>

A revision of Penstemon sect. Saccanthera subsect. Serrulati includes a new species (P. salmonensis), a new variety (P. triphyllus var. infernalis), and the elevation of a subspecies to species (P. curtiflorus), bringing the total number of species to eight, which are keyed and described, complete with nomenclature and type citations.     

Genetic diversity of flat-headed vole (<Emphasis Type="Italic">Alticola strelzowi</Emphasis> (Kastschenko, 1899)) inferred from cytochrome <Emphasis Type="Italic">b</Emphasis> variation

Variation of the cytochrome b gene fragment was examined in 27 flat-headed voles Alticola strelzowi from different parts of the species range. A total of 15 haplotypes were described, while the species is characterized by low levels of genetic differentiation and polymorphism. The haplotypes form three haplogroups, one of which corresponded to the subspecies A. s. strelzowi, and the other two, to A. s. desertorum. Based on different indices, the level of genetic polymorphism in the later subspecies was considered to be higher than in the first one. Phylogeographic analysis suggested post-glacial dispersal of flat-headed voles from a single refugium located in Western Altai. Using different techniques, relatively recent colonization of the Central Altai territory was demonstrated (subspecies A. s. strelzowi), which determined low level of genetic variation in this territory.     

Genetic divergence of mykizha (<Emphasis Type="Italic">Parasalmo</Emphasis> (<Emphasis Type="Italic">Oncorhynchus</Emphasis>) <Emphasis Type="Italic">mykiss</Emphasis>) from Kamchatka inferred from restriction analysis and sequencing of mtDNA cytochrome b gene

The populations of mykizha Parasalmo (O.) mykiss from western and eastern coasts of Kamchatka were studied by restriction analysis of a fragment of fish mitochondrial genome that included the control region and the region of the cytochrome b gene ( cytb). The restriction patterns obtained with five enzymes ( MspI; Tru1I; RsaI; BsuRI; DdeI) were identical in all studied individuals. Sequencing of the cytb gene showed high similarity between all samples (99.6–100%). In general, the geographical group of mykiss from Kamchatka is monophyletic with low genetic divergence at the population level. Shantarian mykiss originates most likely from that native to Kamchatka.Translated from Genetika, Vol. 40, No. 12, 2004, pp. 1695–1701.Original Russian Text Copyright © 2004 by Pavlov, Kolesnikov, Melnikova, Ushakova.     

New combinations and typifications in <Emphasis Type="Italic">Bistorta</Emphasis>, <Emphasis Type="Italic">Persicaria</Emphasis>, <Emphasis Type="Italic">Polygonum,</Emphasis> and <Emphasis Type="Italic">Rumex</Emphasis> (Polygonaceae)

New combinations are proposed in anticipation of the Polygonaceae treatment in the forthcoming volume of Intermountain Flora: Polygonum kelloggii var. esotericum, P. kelloggii var. watsonii , Rumex densiflorus var. pycnanthus , R. salicifolius var. utahensis, and R. occidentalis var. tomentellus. Typifications are proposed to facilitate ongoing studies in Polygonaceae and to maintain current usage.     

The genetic structure of chum salmon (<Emphasis Type="Italic">Oncorhynchus keta</Emphasis> Walbaum) populations inferred from the nucleotide variation of the mitochondrial DNA cytochrome <Emphasis Type="Italic">b</Emphasis> gene

The nucleotide sequences of a fragment of the mitochondrial DNA cytochrome b gene were determined in 12 chum salmon populations from the Russian Far East. The level of genetic diversity in the chum salmon populations from the Iturup Island, northern coast of the Sea of Okhotsk, and Anadyr’ River was found to be higher than in the populations from Kamchatka and Sakhalin, which may be related to the history of their origin and dispersal. The proportions of intrapopulation genetic variability (F _CT) and interpopulation genetic variability within the groups (F _SC) account for 90.87 and 0.9%, respectively, and the intergroup component (F _ST) comprises 8.23%. The predominance of one haplotype, B1, which is common for all populations studied, and a low share of intergroup variability suggest the beginning of colonization by the species of the given region from a common source (group of founders) and a relatively recent time of divergence of the chum salmon populations from the region examined.     

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.     

<Emphasis Type="Italic">Sex combs reduced</Emphasis> (<Emphasis Type="Italic">Scr</Emphasis>) regulatory region of <Emphasis Type="Italic">Drosophila</Emphasis> revisited

The Hox gene Sex combs reduced (Scr) is responsible for the differentiation of the labial and prothoracic segments in Drosophila. Scr is expressed in several specific tissues throughout embryonic development, following a complex path that must be coordinated by an equally complex regulatory region. Although some cis-regulatory modules (CRMs) have been identified in the Scr regulatory region (~75 kb), there has been no detailed and systematic study of the distinct regulatory elements present within this region. In this study, the Scr regulatory region was revisited with the aim of filling this gap. We focused on the identification of Initiator elements (IEs) that bind segmentation factors, Polycomb response elements (PREs) that are recognized by the Polycomb and Trithorax complexes, as well as insulators and tethering elements. To this end, we summarized all currently available information, mainly obtained from high throughput ChIP data projects. In addition, a bioinformatic analysis based on the evolutionary conservation of regulatory sequences using the software MOTEVO was performed to identify IE and PRE candidates in the Scr region. The results obtained by this combined strategy are largely consistent with the CRMs previously identified in the Scr region and help to: (i) delimit them more accurately, (ii) subdivide two of them into different independent elements, (iii) identify a new CRM, (iv) identify the composition of their binding sites and (v) better define some of their characteristics. These positive results indicate that an approach that integrates functional and bioinformatic data might be useful to characterize other regulatory regions.     

Genetic variability of the banded murex (<Emphasis Type="Italic">Hexaplex trunculus</Emphasis>) revealed by <Emphasis Type="Italic">ND2</Emphasis> and <Emphasis Type="Italic">ITS2</Emphasis> sequences

The gastropod Hexaplex trunculus is widely distributed in a relatively large range of habitats, but has no dispersal stage. We investigated its genetic structure across its distribution range, from Mediterranean Sea to adjacent Atlantic coasts, by sequencing mitochondrial DNA portions of the NADH dehydrogenase gene ND2 (420 pb) and the internal transcribed spacer ITS2 (450 pb). Our results suggested a significant genetic variability of ND2 (π = 0.009 and Hd = 0.629) and low variability of the ITS2 sequences. A strong phylogeographic break, separated the Aegean populations from those of Western/Eastern Mediterranean and the Atlantic ones, was founded. The tow lineages may have been separated by vicariance events due to the Peloponnese break that separates the Aegean populations from other populations and was maintained until now by the quasi-circular anticyclonic front associated to the straits of Cretan Arc of the Peloponnesian Peninsula. Tunisian coasts appear particularly diverse since the two divergent lineages co-occured. These results may have management consequences since H. trunculus is a high commercial value harvested species.