Retrotransposon-based molecular markers for linkage and genetic diversity analysis in wheat

Retrotransposon-based molecular markers have been developed to study bread wheat ( Triticum aestivum) and its wild relatives. SSAP (Sequence-Specific Amplification Polymorphism) markers based on the BARE-1/ Wis-2-1A retrotransposons were assigned to T. aestivum chromosomes by scoring nullisomic-tetrasomic chromosome substitution lines. The markers are distributed among all wheat chromosomes, with the lowest proportion being assigned the D wheat genome. SSAP markers for BARE-1/ Wis-2-1A and three other wheat retrotransposons, Thv19 , Tagermina and Tar1, are broadly distributed on a wheat linkage map. Polymorphism levels associated with these four retrotransposons vary, with BARE-1/ Wis-2-1A and Thv19 both showing approximately 13% of bands polymorphic in a mapping population, Tagermina showing approximately 17% SSAP band polymorphism and Tar1 roughly 18%. This suggests that Tagermina and Tar1 have been more transpositionally active in the recent evolutionary past, and are potentially the more useful source of molecular markers in wheat. Lastly, BARE-1 / Wis-2-1A markers have also been used to characterise the genetic diversity among a set of 35 diploid and tetraploid wheat species including 26 Aegilops and 9 Triticum accessions. The SSAP-based diversity tree for Aegilops species agrees well with current classifications, though the Triticum tree shows several significant differences, which may be associated with polyploidy in this genus.Communicated by M.-A. Grandbastien     

Karyotypic evolution,morphological variability and phylogeny inMedicago sect.Intertextae

Karyotype and external morphological analyses were conducted onMedicago ciliaris, M. intertexta, M. muricoleptis andM. granadensis which comprise theIntertextae section of the genusMedicago. All species were found to have 2n = 16 chromosomes (= 2 ×), including one pair of satellite chromosomes in each respective complement. Karyotypic evolution in theIntertextae involves changes in absolute chromosome size and in centromeric and relative size symmetry. Numerical taxonomic analyses were conducted independently on 17 karyotypic features and on 16 features of external morphology. The results of the two sets of analyses proved comparable, withM. ciliaris andM. intertexta forming a fairly close pair, and the remaining two species appearing to have more distant relationships to each other and to the first pair. These observations are consistent with the infertility relationships and chorologies of the species. It is suggested thatM. muricoleptis andM. granadensis are derived from theM. ciliaris/intertexta species complex withM. granadensis arising fromM. muricoleptis, or these two species independently evolving from a common species complex. Chromosomal and numerical analyses suggest thatM. ciliaris is the most primitive andM. granadensis the most derived species of theIntertextae.     

Allozymic variation in four Indian species of genusMus: A comparative analysis

The present study focusses on allozyme variation in the commensal house mouseMus musculus, the pygmy field miceM. booduga andM. terricolor, and the spiny mouseM. platythrix. Genetic heterozygosity was estimated using a set of 24 polymorphic biochemical genetic markers. The extent of variability present inM. booduga, M. terricolor andM. platythrix has been compared with that in theM. musculus complex. Levels of allozyme variation at species level indicate thatM. musculus has the maximum heterogeneity, followed byM. booduga andM. terricolor, whileM. platythrix shows comparatively homogeneous genetic make-up. Gene frequency data have been used to trace phylogenetic relationships among these four species.     

A phylogenetic analysis of the Euterpeinae (Palmae; Arecoideae; Areceae) based on morphology and anatomy

The Euterpeinae contains six neotropical genera. There has been continual disagreement on generic and subgeneric boundaries in the subtribe.Euterpe andPrestoea, andJessenia andOenocarpus, have been repeatedly united and separated. A phylogenetic analysis based on 54 morphological and anatomical characters gave one tree of 127 steps.Euterpe is separate fromPrestoea, butJessenia andOenocarpus are best treated as one genus. Subgeneric relationships ofEuterpe andOenocarpus are also analyzed and discussed.     

Allozyme variation in relation to morphology and taxonomy inMedicago sect.Spirocarpos subsect.Intertextae (Fabaceae)

Medicago intertexta andM. ciliaris have been controversially recognized as separate species. The only reliable diagnostic character, gland-tipped trichomes on the fruits inM. ciliaris, is controlled by presence of a single dominant allele, and such one-character taxonomies are debatable. Contributing to the difficulty,M. muricoleptis andM. granadensis, the other two species ofMedicago sectionSpirocarpos subsectionIntertextae, are sometimes confusingly similar toM. intertexta or to each other. Allozyme differences provided 95% verification of the suitability of the gland-tipped trichome character for separatingM. intertexta andM. ciliaris, thus corroborating their recognition as separate taxa. Several measures of allozyme variation indicated thatM. intertexta is more polymorphic than its sister species. Heterozygosity was also highest inM. intertexta, suggestive of a higher outcrossing rate, which is also consistent with larger floral size. Heterozygosity ofM. intertexta was concentrated in Sicily and nearby countries. Taxonomic difficulties in identifying SicilianM. intertexta are well known, and may be the result of interspecific hybridization and introgression.Medicago muricoleptis differed from the above two species in the frequency of several alleles, whileM. granadensis possessed numerous unique alleles consistent with its complete absence of genetic exchange with the other three substantially interfertile species.     

三种厚朴叶绿体基因组的比较研究

为了深入发掘日本厚朴、厚朴、凹叶厚朴叶绿体基因组差异,筛选厚朴优良性状候选基因,开展三种厚朴的分子遗传研究,该文利用Illumina HiSeq高通量测序平台首次对日本厚朴叶绿体进行测序、组装,并与已有的厚朴、凹叶厚朴叶绿体基因组共同注释,获得三个物种叶绿体基因图谱,筛选出三个基因组中的差异基因,又与同科中11个亲缘物种进行叶绿体基因组比对,构建NJ遗传树。结果表明:(1)日本厚朴叶绿体基因组的Clean Reads为19 791 019,Q30为91.33%,组装后基因组全长160 051 bp,GC含量为39.2%,含tRNA 37个,rRNA 8个。(2)比对分析发现三种厚朴具有相似的IR、LSC和SSC结构,以及GC含量和tRNA数量,但编码基因种类和数量、内含子和外显子的数量和结构等存在差异。(3)日本厚朴的功能基因数目较厚朴、凹叶厚朴分别多6个和4个,主要分布于LSC区和IR区,涉及核糖体大亚基、核糖体小亚基和未知功能基因类群。(4)系统发育分析结果进一步显示日本厚朴与凹叶厚朴亲缘关系较近,其次是厚朴。该研究表明日本厚朴具有更丰富的叶绿体基因组结构、组成和变异特征,是其适应高纬度地区弱光、低温环境的分子机制,这为厚朴类优良品种的分子选育提供有力的指导。     

Phylogenetic relationships in the genera<Emphasis Type="Italic"> Zostera</Emphasis> and<Emphasis Type="Italic"> Heterozostera</Emphasis> (Zosteraceae) based on<Emphasis Type="Italic"> matK</Emphasis> sequence data

Phylogenetic analysis of the plastid (chloroplast) DNA matK gene of Zosteraceae species was undertaken. A molecular phylogenetic tree based on matK sequence data showed the monophyly of Heterozostera tasmanica and subgenus Zosterella and did not support the separation of Heterozostera from the genus Zostera. The tree based on matK supported the monophyly of the subgenus Zostera, and showed that Zosteraceae consist of three main groups: Phyllospadix, which is clearly defined by being dioecious; the subgenus Zosterella and Heterozostera; and the subgenus Zostera. Character-state reconstruction of chromosome number and geographic distribution for our molecular phylogenetic tree showed that 2n=12 is a plesiomorphic character for Zostera and Heterozostera, that the chromosome number was doubled or tripled in two lineages, and that the initial speciation of Zostera and Heterozostera occurred in the Northern Hemisphere. The matK tree showed the close affinity of Z. noltii and Z. japonica, which have disjunct distributions. Zostera marina, which is the only widely distributed species in the subgenus Zostera, also occurring in the northern Atlantic, was shown to be embedded within other subgenus Zostera species.     

Allozyme diversity and the evolution ofSymplocos (Symplocaceae) on the Bonin (Ogasawara) Islands

To study the origin and speciation of plants in oceanic islands, electrophoretic analyses have been done on three endemic species ofSymplocos in the Bonin Islands as well as on three other species;S. kuroki, S. nakaharae andS. tanakae which are considered to be closely related to the Bonin endemics. There occur three species:S. kawakamii, S. pergracilis andS. boninensis in Bonin. The genusSymplocos is one which is considered to be diversified in the Bonin Islands. Seven enzyme systems presumed to be encoded by 18 loci were examined. The genetic diversity was low in the island species, as reported in some oceanic island plants of Hawaii and the Bonin Islands. The three endemics share high genetic identities and they clustered together in the tree drawn by the UPGMA method, suggesting that they are a monophyletic group, that is, they result from a single introduction.     

Additions to the genusXenidiocercus (coelomycetes) from Ghana

Two new species of the coelomycete genusXenidiocercus are described and illustrated,X. macrospora on leaves ofMacaranga rowlandii andX. pyriformis on leaves ofM. huraefolia. They differ from the type species in having wider and ellipsoidal or pyriform conidia. A key to species ofXenidiocercus andIdiocercus is provided.     

Comparative genomics of yeast species: new insights into their biology

The genomes of two hemiascomycetous yeasts (Saccharomyces cerevisiae and Candida albicans) and one archiascomycete (Schizosaccharomyces pombe) have been completely sequenced and the genes have been annotated. In addition, the genomes of 13 more Hemiascomycetes have been partially sequenced. The amount of data thus obtained provides information on the evolutionary relationships between yeast species. In addition, the differential genetic characteristics of the microorganisms explain a number of distinctive biological traits. Gene order conservation is observed between phylogenetically close species and is lost in distantly related species, probably due to rearrangements of short regions of DNA. However, gene function is much more conserved along evolution. Compared to S. cerevisiae and S. pombe, C. albicans has a larger number of specific genes, i.e., genes not found in other organisms, a fact that can account for the biological characteristics of this pathogenic dimorphic yeast which is able to colonize a large variety of environments.     

Phylogenetics of the slipper orchids (Cypripedioideae, Orchidaceae): Nuclear rDNA ITS sequences

Cypripedioideae (Orchidaceae) have been the subject of numerous taxonomic treatments with conflicting interpretations of relationships among the five genera and the 150–170 species. We have produced nuclear ribosomal ITS nucleotide sequences for nearly 100 slipper orchid species and used parsimony analysis to investigate their relationships. Our results demonstrate that each genus, as currently circumscribed, is monophyletic (Mexipedium andSelenipedium being represented by a single taxon). LikerbcL data, ITS sequences placeMexipedium sister toPhragmipedium. Relationships at the sectional level inPaphiopedilum are largely as described byCribb. However, the division ofPaphiopedilum into subgg.Brachypetalum andPaphiopedilum is not supported; subg.Brachypetalum is paraphyletic to subg.Paphiopedilum. Phragmipedium species are divided into the same three major clades as in the taxonomic scheme ofMcCook. The plicate-leaved genera,Cypripedium andSelenipedium, are successive sister groups to the rest of the subfamily, confirming generally held opinions that they display plesiomorphic characters compared to the conduplicate-leaved genera. A survey of karyotypes in the context of the ITS tree reveals a general trend toward increased chromosome number, probably brought about by centric fission. These data also accord with a previously suggested biogeographic hypothesis of a widespread Northern Hemisphere distribution, followed by range fragmentation due to Miocene cooling.     

Investigations into the evolutionary history of theAntennaria rosea (Asteraceae: Inuleae) polyploid complex

TheAntennaria rosea polyploid agamic complex is one of the most morphologically diverse and widespread complexes of N. AmericanAntennaria. The group is taxonomically confusing because of numerous agamospermous microspecies, having been recognized as distinct species. Morphometric analyses have demonstrated that the primary source of morphological variability in the complex derives from six sexually reproducing progenitors,A. aromatica, A. corymbosa, A. media, A. microphylla, A. racemona, andA. umbrinella. Additionally, two other sexually reproducing species,A. marginata andA. rosulata, may have contributed to the genetic complexity of theA. rosea complex. Cluster analysis indicates that four discrete morphological groups exist within theA. rosea complex. Each group could be the result of predominance of genes from different groups of sexual progenitors. AsA. rosea is of multiple hybrid origin, from among several sexual progenitors, it is advisable to recognizeA. rosea as a distinct species from its sexual progenitors.Investigations into the evolutionary history of the polyploid complexes inAntennaria (Asteraceae: Inuleae). 3. TheA. rosea complex.     

Numerical morphological analysis of Lettuce cultivars and species (Lactuca sect.Lactuca,Asteraceae)

L. sativa L. cultivars were compared morphologically with accessions ofL. saligna L.,L. serriola L., andL. virosa L. in order to define the infra- and interspecific variation. Multivariate analysis (principal component analysis) distinguished four groups corresponding with the four species. Infraspecific variation (e.g., colour, leaf shape) withinL. sativa is the largest, because breeding has caused a large variation in vegetative features; infraspecific variation withinL. serriola is also large. Three plants of one accession were placed betweenL. sativa andL. serriola because they showed morphological characteristics of both species. They are still classified asL. sativa. The morphological differences betweenL. sativa andL. serriola are too large to consider these two as one species. The descent of the cultivar groups and the four species is described.     

Phylogeny ofTyphonium (Araceae) inferred from restriction fragment analysis of chloroplast DNA

The interrelationship of the ten species of the genusTyphonium and related genera in subtribe Arinae of the Araceae was inferred by chloroplast DNA restriction fragment analysis. A total of 42 site mutations were observed and 26 site mutations were shared by two or more species. A majority rule consensus tree was made by performing 100 bootstrap replicates using Wagner Parsimony. Two groups ofTyphonium were recognized significantly as monophyletic groups, i.e. 1)Typhonium larsenii andT. kunmingense, and 2)T. trilobatum, T. blumei andT. flagelliforme.     

A monograph ofAgathis

This first study of the whole genusAgathis makes use of recent local revisions of the New Caledonian and Australian species which are all maintained. The male cone is shown to have most of the taxonomically useful variation, and this confirms the findings of two partial revisions centred on Indonesian species. Thirteen species are recognized, two of which have two subspecies. New Caledonia has five, and Australia three, sympatric species. Otherwise the species are allopatric except for a few populations of central MalesianA. dammara within the range of west MalesianA. borneensis. One of these montane populations is the distinctiveA. dammara subsp.flavescens of Malaya, formerly a full species.Two groups and three individually distinctive species can be recognized on microsporophyll characters. The larger, group B, comprizes eight species,A. australis (New Zealand),A. corbassonii, A. lanceolata andA. montana (New Caledonia),A. macrophylla (Melanesian islands and includingA. obtusa andA. vitiensis),A. atropurpurea (Australia),A. dammara (mainly central Malesia) andA. borneensis (west Malesia); both the last have long synonymies. The smaller species, group (A), comprizesA. microstachya (Australia) andA. labillardieri (west New Guinea and the Sepik basin). The individually distinctive species areA. moorei andA. ovata of New Caledonia andA. robusta of Australia with its new subspeciesnesophila, described here, of eastern New Guinea and New Britain.     

Population structure,gene diversity,and differentiation in natural populations of Cedar pines (Pinus subsect.Cembrae,Pinaceae) in the USSR

Twelve natural populations of four cedar pine species,Pinus sibirica, P. cembra, P. pumila, andP. koraiensis, occurring in the Soviet Union were investigated by starch-gel electrophoresis. Frequencies of 55 alleles at 19 loci were determined. Interpopulation genetic diversity inP. sibirica andP. pumila was only 2–4 per cent of the total genetic diversity. Nei's distance coefficient (Dn) was used to estimate the level of genetic differentiation among conspecific populations and among species. Dn values among populations ranged from 0.006 to 0.038. A dendrogram constructed using Dn values divided cedar pines species into 2 clusters:sibirica-cembra (Dn = 0.030) andpumila-koraiensis (Dn = 0.143). Nei's distance between these clusters was 0.232. On the basis of the data obtained it was possible to draw the following conclusion:P. sibirica, P. pumila, andP. koraiensis are distinct species, whileP. cembra should apparently be regarded as geographicalP. sibirica race.     

AreAltica carduorumandAltica cirsicola(Coleoptera: Chrysomelidae) Different Species? Implications for the Release ofA. cirsicolafor the Biocontrol of Canada Thistle in Canada

Altica carduorumandAltica cirsicolaare two species of leaf-feeding beetle (Coleoptera: Chrysomelidae) which appear to be morphologically indistinguishable and reportedly hybridize in the laboratory. A European population ofA. carduorumwas previously screened for host-plant specificity and released in North America for the control of Canada thistle,Cirsium arvense.A population ofA. cirsicolafrom China is currently being considered as a biocontrol agent forC. arvenseand, as a different beetle species, must be screened using host-specificity tests similar to those used forA. carduorum.IfA. carduorumandA. cirsicolaare, in fact, one species, the screening requirements forA. cirsicolacould be significantly reduced. Hence, we investigated the taxonomic relationship betweenA. carduorumandA. cirsicolausing morphometric analyses, hybridization experiments, and DNA fingerprinting using random amplified polymorphic DNA (RAPD) analysis. Discriminant function analyses indicate thatA. carduorumandA. cirsicolacannot be reliably distinguished by their morphologies, and interspecific matings produce fertile F₁offspring. However, because interspecific matings produce significantly fewer offspring than intraspecific matings, and because of clear differences in their DNA profiles, we conclude thatA. carduorumandA. cirsicolaare separate species. This study serves to highlight the value of genetic analyses in taxonomic studies and their role in biological control programs.     

Host specificity ofAcanthoscelides quadridentatus andA. Puniceus [Col.: Bruchidae] for biological control ofMimosa pigra (with preliminary data on their biology)

The biology and host specificity of the seed-feeding bruchids,Acanthoscelides quadridentatus (Schaeffer) andA. puniceus Johnson, from Mexico were studied in quarantine facilities in Australia. Distinguishing characters in the genitalia of each species are illustrated. Oviposition was recorded on 16 of 73 species of plants tested but larvae died without entering pods or seeds, except onMimosa invisa K. F. P. von Martius andM. pigra L. Larvae entering seeds ofM. invisa died in the first instar. The bruchids were clearly specific toM. pigra and were subsequently released as part of a program for biological control of this weed in the Northern Territory, Australia in April 1983 and thailand in July 1984.      

Allozyme variation and phylogeny in annual species ofCicer (Leguminosae)

Allozymic variation at 30 isozyme loci was examined electrophoretically in nine annual and one perennial species ofCicer. While most of the accessions examined were monomorphic, species can be differentiated on the basis of their enzyme phenotypes. Several groups of species were identified based upon genetic distance values. For example,C. arietinum, C. reticulatum, andC. echinospermum shared the same alleles for most of the loci exmained. PerennialC. anatolicum is also closely related to this group. Similarly,C. judaicum, C. bijugum, andC. pinnatifidum formed another group. Two annual species,C. chorassanicum andC. yamashitae clustered together, whereasC. cuneatum was the most distantly related species. Correlations were found between genetic distances and geographic distribution. Results from enzyme electrophoresis tend to support the previously reported taxonomic treatments based upon crossability and morphological similarity. However,C. yamashitae, which has been classified in the second crossability group, is quite distinct genetically and morphologically from the remaining species of the group. An isozyme gene duplication observed in the genus suggested the monophyletic origin of the species examined in the present study.