Genetic variability of Siberian fir (Abies sibirica Ledeb.) inferred from AFLP markers

Genetic variability of AFLP markers was studied in 20 populations of Siberian fir (Abies sibirica (Pinaceae) and in two populations of Far-Eastern Manchurian fir A. nephrolepis and Sakhalin fir A. sachalinensis each. Four pairs of selective primers were used. In total, 168 samples from three fir species were genotyped for 117 polymorphic loci. According to the AMOVA results, the variability proportion characterizing the differences between three Abies species was several times higher (F(CT) = 0.53) than that accounting for among-population differences within the species (F(SC) = 0.125). Differentiation of the A. sibirica populations based on AFLP markers exceeded 14% (F(ST) = 0.141). Significant correlation between the genetic distances calculated from the AFLP data and the geographic distances between populations was found. The results of AFLP variability analysis supported and supplemented the conclusions inferred previously from allozyme and cpSSR data: several genetically similar geographic groups of Siberian fir were identified. These groups differ both in allele frequencies and in the levels of genetic variation.     

Specific features of meiosis in the Siberian fir (<Emphasis Type="Italic">Abies sibirica</Emphasis> Ledeb.) artificial populations

Meiosis was studied in the Siberian fir (Abies sibirica Ledeb.) at the arboretum of the Sukachev Institute of Forest. Specific features of meiosis in planted trees have been described. Both general and specific types of irregularities have been identified. The range of irregularities under the arboretum conditions was much wider than in natural ecosystems.     

A karyological study of swamp and dry valley populations of Siberian fir (<Emphasis Type="Italic">Abies sibirica</Emphasis> Ledeb.)

The karyological data on populations of Siberian fir (Abies sibirica Ledeb.) growing in lowland swamp and dry valleys are given. The diploid set of both populations included 24 chromosomes (2n = 24). Polykaryogram analysis revealed seven pairs of metacentric and five pairs of submetacentric chromosomes. The revealed differences between the populations included the absolute length of chromosomes, number of nucleolar organizer regions, and number of nucleoli. Changed chromosome numbers (mixoploidy and aneuploidy) as well as chromosomal aberrations were recorded. For the first time, mitosis was studied in this species and anaphase/telophase aberrations were revealed. The population of Siberian fir growing under extreme conditions of lowland swamp featured the widest range of mutations.Translated from Izvestiya Akademii Nauk, Seriya Biologicheskaya, No. 1, 2005, pp. 23–29.Original Russian Text Copyright © 2005 by Sedelnikova, Pimenov.     

Development of microsatellite genetic markers in Siberian larch (<Emphasis Type="Italic">Larix sibirica</Emphasis> Ledeb.) based on the <Emphasis Type="Italic">de novo</Emphasis> whole genome sequencing

This special issue of the journal is devoted to the outstanding population geneticist Yuri Petrovich Altukhov, who paid much attention in his research to the development of molecular genetic markers for population studies. Over the past time markers and methods of their development have undergone significant change. Thanks to modern methods of whole genome sequencing, it has become possible to develop markers of very different types—selectively neutral, as well as functional. Among them, microsatellite markers remain the most informative, convenient, reproducible, relatively inexpensive, and polymorphic. Whole genome sequencing greatly facilitates their discovery and development. This paper is devoted to the development of new microsatellite markers for a very important species of boreal forest—Siberian larch (Larix sibirica Ledeb.). Using a draft assembly of the larch genome, several thousand contigs containing microsatellite loci with di-, tri, tetra-, and pentanucleotide motifs were selected. A total of 59 pairs of PCR primers were tested for loci with dinucleotide motifs as the most variable. From them, 11 pairs were finally selected for 11 loci with dinucleotide repeats, which showed a high level of polymorphism and can be used in various population genetic studies and to identify the origin of wood and plant material. This study was done at the Laboratory of Forest Genomics of the Genome Research and Education Center of the Siberian Federal University with the support of the Department of Forest Genetics and Forest Tree Breeding of the Georg-August University of Göttingen, the Department for Monitoring of Forest Genetic Resources of the Forest Protection Center of the Krasnoyarsk Territory, and the Laboratory of Forest Genetics and Selection of the Sukachev Institute of Forest of the Siberian Branch of the Russian Academy of Sciences within the framework of the project “Genomics of the Key Boreal Forest Conifer Species and Their Major Phytopathogens in the Russian Federation” funded by the Government of the Russian Federation (grant no. 14.Y26.31.0004).     

Karyological characteristics of Siberian fir (<Emphasis Type=Italic>Abies sibirica</Emphasis> Ledeb.) in Central Siberia

Data are presented on the karyotype structure of the Siberian fir (Abies sibirica Ledeb.) from five populations of the Central Siberia. The chromosome set (2n = 24) contains seven pairs of metacentric (I–VII), four pairs of submetacentric (VIII and X–XII), and one pair of intercentric (IX) chromosomes. The morphometric parameters of the identified chromosome groups had close values in the studied populations. The variation coefficients of chromosomal parameters of the Siberian fir correspond to very low and low variability. The intraspecific chromosome polymorphism of the Siberian fir is connected mainly to variations in the number and peculiarities of the nucleolar organizing regions of chromosomes. In the territory with technogenic loading, a wide spectrum of genomic mutations of the mixoploidy type was observed in the seed off-spring of the Siberian fir; triploid seedlings, as well as rare cases of somatic reduction of chromosomes, were revealed.     

Chromosomal mutations in Siberian larch (<Emphasis Type="Italic">Larix sibirica</Emphasis> Ledeb.) on Taimyr Peninsula

Chromosomal mutations were studied in the Norilsk population of Siberian larch (Larix sibirica Ledeb.) growing at the northeastern boundary of the species range affected by airborne smelter emissions. Different types of frequent chromosomal mutations have been revealed in the Norilsk population of L. sibirica and B-chromosomes have been found in this species for the first time.     

Carbon autonomy of reproductive shoots of Siberian alder (<Emphasis Type="Italic">Alnus hirsuta</Emphasis> var.<Emphasis Type="Italic"> sibirica</Emphasis>)

Carbon autonomy of current-year shoots in flowering, and of current-year shoots plus 1-year-old shoots (1-year-old shoot system) in fruiting of Siberian alder (Alnus hirsuta var. sibirica) was investigated using a stable isotope of carbon, ¹³C. The current-year shoot and 1-year-old shoot systems were fed ¹³CO₂ and the atom% excess of ¹³C in flowers and fruits was determined. The majority of photosynthate allocated to flower buds was originally assimilated in the leaves of the flowering current-year shoots. Of all the current-year shoots on fruiting 1-year-old shoots, only those nearest to the fruits allocated the assimilated photosynthate to fruit maturation. These results indicate that the current-year shoots and 1-year-old shoot systems are carbon-autonomous units for producing flowers and maturing fruits, respectively.     

Seasonal dynamics of chlorophyll and microelement content in developing conifer needles of <Emphasis Type="Italic">Abies sibirica</Emphasis> and <Emphasis Type="Italic">Picea abies</Emphasis>

Composition of microelements and photosynthetic pigment content (chlorophylls (Chl) a and b) were monitored in growing needles of spruce (Picea abies (L.) Karst.) and Siberian fir (Abies sibirica Ledeb.) during spring-autumn vegetation period. The dynamics of fresh weight and needle length for the first-year needles of spruce and fir revealed a number of shared and species-specific features in growth patterns of photosynthetic organs. In the beginning of growth period (in May), the needles elongated rapidly, while June–July were marked by the increase in needle weight. In P. abies the needle weight accumulated rapidly (specific growth rates μ_max up to 0.20 day⁻¹) over a short period (14 days), while in A. sibirica the needle weight increased slower (μ_max ≤ 0.11 day⁻¹) but over a longer period (≥30 days). The dynamics of Chl a and Chl b content and their ratio were identical in needles of both species over the growth period, although changes in Chl a were pronounced stronger than those in Chl b. In spring (May), a relatively high total Chl content per needle dry weight was noted. In summer (June–August), the total Chl content declined appreciably. In autumn (September–November), the total chlorophyll content in first-year needles increased slightly. Microelements were classified into two groups according to seasonal dynamics of their relative content in first-year needles. The first group includes Ba, Mn, Zn, B, Cu, Co, Cr, Pb, and Mo, whose relative content had a distinctive maximum in July, coincident with the peak in Chl content. The second group comprises Ni, V, Ag, Be, Cd, and As, whose relative content was minimal at this period. Seasonal changes in microelement composition were similar for the two conifer species examined, which is likely due to different physiological values of various microelements for photosynthetic organs.     

<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.     

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.     

<Emphasis Type="Italic">Diplazium</Emphasis> hybrids involving <Emphasis Type="Italic">D. plantaginifolium</Emphasis> and <Emphasis Type="Italic">D</Emphasis>. <Emphasis Type="Italic">ternatum</Emphasis> from Mexico and Central America

Here we evaluate the origins and relationships of Mexican and Central American Diplazium hybrids derived from crosses involving either D. plantaginifolium or D. ternatum. Based on study of live plants and herbarium specimens, we distinguish D. ×verapax from the similar D. riedelianum and present evidence that the former is a sterile hybrid derived from a cross between D. plantaginifolium and D. werckleanum. We also describe new hybrids, D. ×torresianum and D. ×subternatum from Mexico and northern Central America. Both involve D. ternatum as one parent. Diplazium. cristatum is the other putative parent of D. ×torresianum, and D. plantaginifolium is the second parent of D. ×subternatum. We also designate lectotypes for D. cordovense and D. dissimile.     

<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 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.     

<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.     

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.     

Common genomic features of <Emphasis Type="Italic">Campylobacter jejuni</Emphasis> subsp. <Emphasis Type="Italic">doylei</Emphasis> strains distinguish them from <Emphasis Type="Italic">C. jejuni</Emphasis> subsp. <Emphasis Type="Italic">jejuni</Emphasis>

Background  

Campylobacter jejuni has been divided into two subspecies: C. jejuni subsp. jejuni (Cjj) and C. jejuni subsp. doylei (Cjd). Nearly all of the C. jejuni strains isolated are Cjj; nevertheless, although Cjd strains are isolated infrequently, they differ from Cjj in two key aspects: they are obtained primarily from human clinical samples and are associated often with bacteremia, in addition to gastroenteritis. In this study, we utilized multilocus sequence typing (MLST) and a DNA microarray-based comparative genomic indexing (CGI) approach to examine the genomic diversity and gene content of Cjd strains.     

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.     

Development of microsatellite genetic markers in Siberian stone pine (<Emphasis Type="Italic">Pinus sibirica</Emphasis> Du Tour) based on the <Emphasis Type="Italic">de novo</Emphasis> whole genome sequencing

Siberian stone pine, Pinus sibirica Du Tour is one of the most economically and environmentally important forest-forming species of conifers in Russia. To study these forests a large number of highly polymorphic molecular genetic markers, such as microsatellite loci, are required. Prior to the new high-throughput next generation sequencing (NGS) methods, discovery of microsatellite loci and development of micro-satellite markers were very time consuming and laborious. The recently developed draft assembly of the Siberian stone pine genome, sequenced using the NGS methods, allowed us to identify a large number of microsatellite loci in the Siberian stone pine genome and to develop species-specific PCR primers for amplification and genotyping of 70 microsatellite loci. The primers were designed using contigs containing short simple sequence tandem repeats from the Siberian stone pine whole genome draft assembly. Based on the testing of primers for 70 microsatellite loci with tri-, tetra- or pentanucleotide repeats, 18 most promising, reliable and polymorphic loci were selected that can be used further as molecular genetic markers in population genetic studies of Siberian stone pine.     

<Emphasis Type="Italic">Quinua</Emphasis> and Relatives (<Emphasis Type="Italic">Chenopodium</Emphasis> sect.<Emphasis Type="Italic">Chenopodium</Emphasis> subsect.<Emphasis Type="Italic">Celluloid</Emphasis>)

Traditionally viewed as an Andean grain crop,Chenopodium quinoa Willd. includes domesticated populations that are not Andean, and Andean populations that are not domesticated. Comparative analysis of leaf morphology and allozyme frequencies have demonstrated that Andean populations, both domesticated(quinua) and free-living(ajara), represent an exceptionally homogeneous unit that is well differentiated from allied domesticates of coastal Chile(quingua) and freeliving populations of the Argentine lowlands(C. hircinum). This pattern of relationships indicates that Andean populations represent a monophyletic crop/weed system that has possibly developed through cyclic differentiation (natural vs. human selection) and introgressive hybridization. Relative levels of variation suggest that this complex originated in the southern Andes, possibly from wild types allied withC. hircinum, with subsequent dispersal north to Colombia and south to the Chilean coast. Coastal populations were apparently isolated from post-dispersal differentiation and homogenization that occurred in the Andes. Other data point toward a center of origin in the northern Andes with secondary centers of genetic diversity subsequently developing in the southern Andes and the plains of Argentina. Comparative linkage of South American taxa, all tetraploid, with North American tetraploids of the subsection will eventually clarify this problem. While the possibility of a direct phyletic connection betweenC. quinoa and the Mexican domesticate(C. berlandieri subsp. nuttalliae,) cannot be excluded, available evidence indicates that the latter represents an autonomous lineage that is associated with the basal tetraploid, C. b. subsp.berlandieri, through var.sinuatum, whereas South American taxa show possible affinities to either var. zschackei or var.berlandieri. An extinct domesticate of eastern North America,C. b. subsp.jonesianum, represents either another instance of independent domestication, possibly from subsp. b. var.zschackei, or a northeastern outlier of subsp.nuttalliae.     

Current-year shoot based approach for annual variation in the reproductive output in Siberian alder (<Emphasis Type="Italic">Alnus hirsuta</Emphasis> var. <Emphasis Type="Italic">sibirica</Emphasis>)

Siberian alder (Alnus hirsuta var. sibirica) shows annual variation in reproductive output. However, this phenomenon has not been explained by hypotheses proposed in previous studies. In this study, we constructed a matrix model of current-year shoot dynamics to estimate and compare the reproductive output of current-year shoot population with or without annual variation, and explained the annual variation of reproductive output in terms of a reproductive strategy of the current-year shoot population of Siberian alder. The current-year shoot population of Siberian alder was divided into three functional groups: reproductive, maintenance, and explorative shoot sub-populations. A transition matrix was calculated from the relationships between 1-year-old shoots and the current-year shoots on them. The dynamics of the current-year shoot population was simulated using the estimated matrix on the patterns with or without annual variation in reproductive output. The pattern with annual variation in reproductive output yielded more reproductive current-year shoots than the pattern with high reproductive output every year. The annual variation of reproductive output may well be regarded as a reproductive strategy of current-year shoots to increase lifetime fecundity.