Microarray-based survey of repetitive genomic sequences in Vicia spp.

A modified DNA microarray-based technique was devised for preliminary screening of short fragment genomic DNA libraries from three Vicia species (V. melanops, V. narbonensis, and V. sativa) to isolate representative highly abundant DNA sequences that show different distribution patterns among related legume species. The microarrays were sequentially hybridized with labeled genomic DNAs of thirteen Vicia and seven other Fabaceae species and scored for hybridization signals of individual clones. The clones were then assigned to one of the following groups characterized by hybridization to: (1) all tested species, (2) most of the Vicia and Pisum species, (3) only a few Vicia species, and (4) preferentially a single Vicia species. Several clones from each group, 65 in total, were sequenced. All Group I clones were identified as rDNA genes or fragments of chloroplast genome, whereas the majority of Group II clones showed significant homologies to retroelement sequences. Clones in Groups III and IV contained novel dispersed repeats with copy numbers 10²–10⁶/1C and two genus-specific tandem repeats. One of these belongs to the VicTR-B repeat family, and the other clone (S12) contains an amplified portion of the rDNA intergenic spacer. In situ hybridization using V. sativa metaphase chromosomes revealed the presence of the S12 sequences not only within rDNA genes, but also at several additional loci. The newly identified repeats, as well as the retroelement-like sequences, were characterized with respect to their abundance within individual genomes. Correlations between the repeat distributions and the current taxonomic classification of these species are discussed.     

Phylogenetic relationships betweenVicia faba (Fabaceae) and related species inferred from chloroplasttrnL sequences

The chloroplasttrnL intron from 46 differentVicia accessions, representing five of the nine sections of the genusVicia subg.Vicia sensuMaxted (1991a) were amplified by the Polymerase Chain Reaction (PCR) using oligonucleotide primers homologous to conserved regions intrnL. The products fell into two distinct groups; those of approximately 250 nt and those of around 450 nt in length. Of these, products from 17 differentVicia species were cloned and their nucleotide sequences determined. Multiple alignments were assembled and phylogenetic trees constructed by the weighted least-squares distance method. ALathyrus latifolius trnL intron sequence was used as an outgroup. The resulting trees clearly group and separate the sectt.Narbonensis, Bithynica andFaba species but were less able to distinguish species from sectt.Hypechusa andPeregrinae. Based on these sequence data,V. faba appears to be more distant from sect.Narbonensis than sectt.Hypechusa andPeregrinae. The results are in general agreement with a recent treatment ofVicia subg.Vicia (Maxted 1993) and lend further support to placingV. faba in the monospecific sect.Faba.     

Changes in DNA composition in the evolution of Vicia species

Summary The composition of nuclear DNA in 3 Vicia species are compared. The species V. eriocarpa, V. johannis and V. melanops are from three separate subgeneric sections of Vicia and show a fourfold variation in their amounts of nuclear DNA. DNA melting experiments, buoyant density gradient analysis and Cot reassociation experiments show that the quantitiative change in nuclear DNA between the three species is achieved by changes in the amounts of both repetitive and nonrepetitive DNA sequences. It is suggested that while the increase in the repetitive fraction is achieved by the proliferation of repetitive base sequences the increase in the nonrepetitive fraction is due to the steady accretion of highly diverged base sequences resulting from mutations, deletions, insertions and base sequence rearrangements among families of repetitive sequences.     

Comparison of purified acid phosphatase allozymes inDrosophila virilis: Differences in carbohydrate content and composition of the allozymes

Three acid phosphatase (EC 3.1.3.2) allozymes (ACPH¹, ACPH², and ACPH⁴) ofDrosophila virilis show different activities as measured by electrophoretic techniques. Recently, it was suggested that these differences are attributable to the variable ability of the allozymes to be incorporated into lysosomes (Narise, S.,Genet. Res. Cambr., 45:143, 1985). Immunoelectrophoresis demonstrated that the activity differences between these electrophoretic variants coincided with differences in the amount of the enzyme protein in soluble fractions but not in whole cell-free extracts. These results support the idea that acid phosphatase allozymes inD. virilis are cell-localization variants. We examined the problem by structural analysis of both the protein and the carbohydrate moieties of these allozyme glycoproteins, since lysosomal enzymes are known to become localized in lysosomes through their carbohydrate moieties. The three ACPH allozymes were purified to homogeneity from their respective homozygotes and compared with respect to amino acid composition and carbohydrate content and composition. Amino acid compositions were similar, while content and compositions of neutral sugars were significantly different. The neutral sugar content of ACPH¹ was 9.2%; that of ACPH², 21.0%; and that of ACPH⁴, 7.3%. A trace of hexosamines, but noN-acetylneuraminic acid, was found in the ACPH allozymes. Isoelectric points varied corresponding to their electrophoretic mobilities, which were not changed by treatment with alkaline phosphatase and neuraminidase.     

Nuclear DNA contents, rDNAs, and karyotype evolution in subgenus Vicia: III. The heterogeneous section Hypechusa

Summary. Nuclear DNA contents, automated karyotype analyses, and sequences of internal transcribed spacers from ribosomal genes have been determined in the species belonging to section Hypechusa of the subgenus Vicia. Karyomorphological results and phylogenetic data generated from the comparison of rDNA (genes coding for rRNA) sequences showed that sect. Hypechusa is not monophyletic; however, some monophyletic units are apparent (one including Vicia galeata, V. hyrcanica, V. noeana, and V. tigridis, another including V. assyriaca, V. hybrida, V. melanops, V. mollis, and V. sericocarpa), which partly correspond to morphology-based infrasectional groups. The relationships among these species and the species in sections Faba, Narbonensis, Bithynicae, and Peregrinae have been also investigated. Correspondence and reprints: Dipartimento di Agrobiologia ed Agrochimica, Università della Tuscia, via San Camillo de Lellis, 01100 Viterbo, Italy.     

Distribution of low molecular weight carbohydrates in the subgenusCeratotropis of the genusVigna (Leguminosae)

The seeds of 9 members of the subgenusCeratotropis (Piper) Verdc., namelyVigna aconitifolia (Jacq.) Maréchal,V. angularis (Willd.) Ohwi et Ohashi,V. minima (Roxb.) Ohwi et Ohashi,V. nakashimae (Ohwi) Ohwi et Ohashi,V. reflexo-pilosa Hayata,V. umbellata (Thumb.) Ohwi et Ohashi,V. mungo (L.) Hepper,V. radiata (L.) Wilczek andV. sp., have been examined. On their low molecular weight carbohydrate compositions, this subgenus has been divided into 2 subgroups, mungo-radiata group and angularis group. Four other species referred to the subgeneraPlectotropis (Schumach.) Bak.,Lasiospron (Benth. emend Piper) Maréchal, Mascherpa et Stainier andVigna, V. vexillata (L.) A. Rich.,V. lasiocarpa (Benth.) Verdc.,V. marina (Burm.) Merr. andV. unguiculata (L.) Walp., were also analyzed and they had distinctive carbohydrate compositions. 1d-4-O-methyl-myo-inositol and 1d-5-O-(α-d-galactopyranosyl)-4-O-methyl-myo-inositol were detected in all species examined exceptV. vexillata, V. mungo andV. radiata.     

TheTy1-copia group retrotransposons inVicia species: copy number, sequence heterogeneity and chromosomal localisation

We present an in-depth study of theTy1-copia group of retrotransposons within the plant genusVicia, which contains species with widely differing genome sizes. We have compared the numbers and sequence heterogeneities of these genetic elements in three diploidVicia species chosen to represent large (V. faba, 1C=13.3 pg), medium (V. melanops, 1C=11.5 pg) and small (V. sativa, 1C=2.3 pg) genomes within the genus. The copy numbers of the retrotransposons are all high but vary greatly, withV. faba containing approximately 10⁶ copies,V. melanops about 1000 copies andV. sativa 5000 copies. The degree of sequence heterogeneity ofTy1-copia group elements correlates with their copy number within each genome, but neither heterogeneity nor copy number are related to the genome size of the host. In situ hybridization to metaphase chromosomes shows that the retrotransposons inV. faba are distributed throughout all chromosomes but are much less abundant in certain heterochromatic regions. These results are discussed in the context of plant retrotransposon evolution.     

Sphingoid long-chain base composition of glucosylceramides in Fabaceae: a phylogenetic interpretation of Fabeae

The sphingoid long-chain base (LCB) composition of glucosylceramides was characterized in 31 species of Fabaceae including the model legumes Lotus japonicus and Medicago truncatula. With the exception of Lupinus texensis L, the 8-trans/cis-unsaturated isomers of 4-hydroxy-8-sphingenines [i.e., t18:1 (8t) plus t18:1 (8c)] were the major components in each species. In tribe Fabeae, each species from four genera—Pisum, Lathyrus, Lens, and Vicia—showed that more than 50% of dihydroxy sphingoid LCBs are 8-sphingenines [i.e., d18:1 (8t) plus d18:1 (8c)]. These results suggest that the sphingoid LCB composition of glucosylceramides reflects the phylogenetic relationships within the Fabeae.     

Isoenzyme variation in the wild relatives ofVicia faba (Fabaceae)

Electrophoretic analysis of five enzyme systems, LAP, PGI, SKDH, SOD and 6-PGDH, among 102Vicia accessions representingV. bithynica and seven species of theV. narbonensis complex, namelyV. eristalioides, V. kalakhensis, V. johannis, V. galilaea, V. serratifolia, V. narbonensis andV. hyaeniscyamus, has been performed. The recorded variation was tentatively assigned to 41 allelic genes at eight loci; intraspecific variation was observed in all species except forV. eristalioides. The results obtained were compared with the corresponding data reported earlier forV. faba. Hierarchical grouping of the investigated taxa, includingV. faba, was based onNei's genetic identities calculated from the allozyme frequency data.Vicia faba andV. bithynica were shown to be most distantly related to one another and to the remaining species investigated.Vicia serratifolia appeared to be a peripheral member of theV. narbonensis complex. The results are discussed with reference to genetic diversity and taxonomic relationships of the species under study.     

Retrotransposon populations of <Emphasis Type="Italic">Vicia</Emphasis> species with varying genome size

The (non-LTR) LINE and Ty3-gypsy-type LTR retrotransposon populations of three Vicia species that differ in genome size (Vicia faba, Vicia melanops and Vicia sativa) have been characterised. In each species the LINE retrotransposons comprise a complex, very heterogeneous set of sequences, while the Ty3-gypsy elements are much more homogeneous. Copy numbers of all three retrotransposon groups (Ty1-copia, Ty3-gypsy and LINE) in these species have been estimated by random genomic sequencing and Southern hybridisation analysis. The Ty3-gypsy elements are extremely numerous in all species, accounting for 18–35% of their genomes. The Ty1-copia group elements are somewhat less abundant and LINE elements are present in still lower amounts. Collectively, 20–45% of the genomes of these three Vicia species are comprised of retrotransposons. These data show that the three retrotransposon groups have proliferated to different extents in members of the Vicia genus and high proliferation has been associated with homogenisation of the retrotransposon population.Electronic Supplementary Material Supplementary material is available for this article at .     

Electrophoretic seed albumin patterns and species relationships inVicia sect.Faba (Fabaceae)

Electrophoretic analysis of seed albumins (PAGE) covered 173 accessions representing nine species ofVicia sect.Faba. The number of albumin bands recorded in particular species varied from three inV. eristaloides to 23 inV. faba; in total, 38 bands were distinguished in the investigated material. The examined species, exceptV. eristalioides, showed intraspecific variation with respect to the number and relative staining intensity of albumin bands; individual variation was especially marked inV. faba and inV. narbonensis. Hierarchical clustering of the investigated taxa was based onBhattacharyya distances calculated from the electrophoretic data. The taxa grouped in three main clusters.Vicia faba and the rather remotely relatedV. kalakhensis formed one cluster. The second cluster was composed ofV. narbonensis distantly related toV. hyaeniscyamus. The third cluster comprised three subgroups: 1.V. johannis, V. galilaea andV. serratifolia, 2.V. eristalioides, and 3.V. bithynica. The obtained results are discussed with reference to taxonomic relationships inVicia sect.Faba.     

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

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

The analysis of core and symbiotic genes of rhizobia nodulating Vicia from different continents reveals their common phylogenetic origin and suggests the distribution of Rhizobium leguminosarum strains together with Vicia seeds

In this work, we analysed the core and symbiotic genes of rhizobial strains isolated from Vicia sativa in three soils from the Northwest of Spain, and compared them with other Vicia endosymbionts isolated in other geographical locations. The analysis of rrs, recA and atpD genes and 16S–23S rRNA intergenic spacer showed that the Spanish strains nodulating V. sativa are phylogenetically close to those isolated from V. sativa and V. faba in different European, American and Asian countries forming a group related to Rhizobium leguminosarum. The analysis of the nodC gene of strains nodulating V. sativa and V. faba in different continents showed they belong to a phylogenetically compact group indicating that these legumes are restrictive hosts. The results of the nodC gene analysis allow the delineation of the biovar viciae showing a common phylogenetic origin of V. sativa and V. faba endosymbionts in several continents. Since these two legume species are indigenous from Europe, our results suggest a world distribution of strains from R. leguminosarum together with the V. sativa and V. faba seeds and a close coevolution among chromosome, symbiotic genes and legume host in this Rhizobium–Vicia symbiosis.     

Taxonomic relationships between V. faba and its relatives based on nuclear and mitochondrial RFLPs and PCR analysis

Summary The taxonomic relationships between 52 accessions of 12 Vicia species and three accessions of Lathyrus were examined using nuclear RFLP- and PCR-generated data. Two hundred and sixty informative restriction fragments or amplification products were analysed by single linkage analysis, average cluster analysis, and the Wagner parsimony method. Dendrograms constructed from each type of analysis showed similar overall topologies and could be divided into three parts corresponding respectively to the Lathyrus outgroup, the species grouped in the section Faba/narbonemis complex, and the species belonging to the sections Hypechusa and Peregrinae. With few exceptions, the majority of accessions belonging to one species grouped together before branching to other species. An analysis of mitochondrial DNA phenotypes was both consistent with and complemented the results from the nuclear data. Overall, the species relationships show a good correlation with the classification of Maxted et al. but suggest that V. faba is more closely aligned to species from the sections Hypechusa and Peregrinae than to those in the narbonensis complex. In addition, the position of two new species, V. kalakhensis and V. eristaloides, as members of the narbonensis complex was supported by the molecular data, which also allowed a preliminary classification for recently collected Vicia accessions.     

Diverse bacteria isolated from root nodules of wild Vicia species grown in temperate region of China

In the present study, a total of 154 bacterial strains isolated from nodules of eighteen Vicia species mainly grown in the temperate Chinese provinces were characterized by ARDRA, ITS PCR–RFLP, BOX-PCR, sequencing of 16S rDNA, nodC, nifH, atpD and glnII, and nodulation tests. The results demonstrated that most of the R. leguminosarum strains were effective microsymbionts of the wild Vicia species, while genomic species related to Rhizobium gallicum, Mesorhizobium huakuii, Ensifer meliloti and Bradyrhizobium spp. were symbiotic bacteria occasionally nodulating with Vicia species. In addition, fourteen strains related to Agrobacterium, Phyllobacterium, Ensifer, Shinella and R. tropici, as well as 22 strains of R. leguminosarum might be nodule endophytes without symbiotic genes. Diverse symbiotic gene lineages were found among the test strains and a strong association was found among the symbiotic gene types and genomic species, indicating the absence of lateral gene transfer. These results greatly enlarged the rhizobial spectrum of Vicia species. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Taxonomy, evolution and domestication of Vicia in relation to aphid resistance

Thirty Vicia species and 28 V. faba cultivars were evaluated for Aphis fabae resistance by measuring rates of aphid population increase (r_m) on the host plants. A subset of these species (22) and cultivars (five) were evaluated for resistance to Acyrthosiphon pisum and Megoura viciae. For the same subset of 22 Vicia species and all three aphid species, positive correlations were observed between the concentration and numbers of leaf and stem non-protein amino acids and the level of aphid resistance. Correlations were also observed between trichome density, on some organs of the host, and both nymphal survival and development time. Aphid resistance, together with these possible physical and chemical resistance mechanisms, showed a pattern which was described in relation to the taxonomy of the genus Vicia and the degree of domestication of the host. The least advanced Vicia species were most resistant whilst the more specialised species and those most closely related to V. faba and V. faba itself were most susceptible. Within each taxonomic group (subgenus or section), the most domesticated species were least resistant. The merits of utilising the resistance found in some V. faba cultivars and in other wild Vicia species were considered.     

The identification of gibberellins in immature seeds of Vicia faba,and some chemotaxonomic considerations

GA₁₇, GA₁₉, GA₂₀, GA₂₉, GA₄₄ and 13-hydroxy-GA₁₂, now named GA₅₃, were identified by GC-MS in immature seeds of Vicia faba (broad bean). Also identified were a GA catabolite, two polyhydroxykauranoic acids, and abscisic, phaseic and dihydrophaseic acids. The GAs of Vicia are hydroxylated at C-13, in common with those of other legumes. However the GAs of Vicia are not hydroxylated at C-3, nor do they appear to be readily conjugated. In these respects Vicia resembles Pisum, another member of the tribe Viciae. Vicia differs from Phaseolus and Vigna, of the tribe Phaseoleae, in both these respects.Abbreviations ABA abscisic acid - DPA dihydrophaseic acid - GA_n gibberellin A_n - GC gas chromatography - GC-MS gas chromatography mass spectrometry - KA kauranoic acid - PA phaseic acid - TLC thin layer chromatography     

Neue Beobachtungen zur Bestäubung vonOphrys (Orchidaceae) in Südspanien,mit besonderer Berücksichtigung des FormenkreisesOphrys fusca agg.

An investigation of pseudocopulation behaviour in species ofOphrys from southern Spain confirms the close relationship betweenCampsoscolia ciliata (Scoliidae) andOphrys speculum, and betweenEucera nigrilabris (Apoidea) andOphrys tenthredinifera. It could be demonstrated thatEucera barbiventris is the pollinator ofOphrys scolopax subsp.scolopax, whereas other species ofEucera andTetralonia which are active at the same time show no interest at all for the flowers of this species. Special attention was paid to the forms of the taxonomically confusedOphrys fusca group:O. fusca s. str.,O. iricolor, O. omegaifera andO. atlantica. WhileO. fusca s. str. is widespread, small-flowered and has late anthesis,O. iricolor has very large flowers and early anthesis. Each of the four members ofO. fusca agg. in S. Spain is pollinated by a different bee, and selective experiments show that each of these four species of bees is specifically attracted only to one of theOphrys species:Andrena flavipes is the pollinator ofO. fusca s. str.,Colletes cunicularius infuscatus ofO. iricolor, Anthophora atroalba ofO. omegaifera, andChalicodoma parietina ofO. atlantica. These four pollinators belong to 4 different bee families (Andrenidae, Colletidae, Anthophoridae, Megachilidae). As this type of pollination represents a very effective pregamic isolation mechanism, these four taxa ofOphrys fusca agg., at least in southern Spain, behave and should be regarded as genuine species.

     

The in vivo anthelmintic efficacy of some Verbascum species growing in Turkey

Verbascum L. (Scrophulariaceae) species are used for desiccating wounds and as a fish poison in Anatolia as well as for diarrhea and dysentery of animals in several countries. To further evaluate their activity, methanolic extracts obtained from 13 Verbascum species growing in Turkey, including V. chionophyllum Hub.-Mor., V. cilicicum Boiss., V. dudleyanum (Hub.-Mor.) Hub.-Mor., V. lasianthum Boiss., V. latisepalum Hub.-Mor., V. mucronatum Lam., V. olympicum Boiss., V. pterocalycinum var. mutense Hub.-Mor., V. pycnostachyum Boiss. & Heldr., V. salviifolium Boiss., V. splendidum Boiss., V. stachydifolium Boiss. & Heldr. and V. uschackense (Murb.) Hub.-Mor. were evaluated for their in vivo anthelmintic activity. The extracts from V. lasianthum, V. latisepalum, V. mucronatum and V. salviifolum showed the highest inhibitory rates against Aspiculuris tetraptera at 100 mg/kg in mice. Additionally, extracts from V. dudleyanum and V. pterocalycinum var. mutense were found generally highly effective. The remaining species did not show any activity. Results of the present study support the utilization of these plant species employed in Turkish folk medicine.     

Phylogenetic significance of stylar features in genus Vicia (Leguminosae): an analysis with molecular phylogeny

Tribe Fabeae consists of five genera, Lathyrus (160 spp.), Lens (4–6 spp.), Pisum (2–3 spp.), Vavilovia (monotypic), and Vicia (160 spp.), and shows a diversity in stylar features. At least six different stylar types are known in the tribe. In order to reclassify the tribe at the rank of genus, we tried to discover apomorphies in stylar features using a molecular phylogenetic study. We surveyed internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA of representative species, selected from each group having different types of styles in the tribe. We paid particular attention in sampling to members of Vicia section Vicilla, as stylar features are heterogeneous within this section. Consequently, our sample set included 15 species of section Vicilla, 23 species of other Fabeae, and two species of Trifolieae, which were used as a sister group of Fabeae. Based on our analysis, we found that a laterally compressed style and an abaxially tufted hairy style would be advanced against a dorsiventrally compressed style and an evenly hairy style, respectively, in genus Vicia. The species group, which shares the latter apomorphy, is composed of 56 species and was dispersed into 11 sections of two subgenera in the recent system of genus Vicia. We consider future revision of Fabeae should treat this species group as a single higher taxon.