Phylogenetic relationships of Iranian Allium sect. Allium (Amaryllidaceae,Allioideae) as inferred from nrDNA ITS,cpDNA rps16 and trnL–F sequences

Allium is a particularly species rich (more than 800 species) and economically important genus, with numerous taxonomic problems at all levels of classification. In this study, we try to uncover the phylogenetic relationships of the common leek Allium ampeloprasum based on selected samples of this species and its putative relatives in A. sect. Allium from Iran. The silica‐dried leaf samples of 56 accessions representing 23 species of Allium were sequenced; 53 sequences of nrDNA ITS, 35 sequences of plastid rps16 and 52 sequences of trnL–F were generated and additional accessions were extracted from GenBank in order to cover all recognized main lineages in the genus. Maximum Parsimony and Bayesian Inference generated similar trees, but the placement of A. ampeloprasum and its relatives differed slightly between the nuclear and the plastid phylogenies. In the nrITS tree, A. ampeloprasum is retrieved as a highly supported clade with A. iranicum, while in the combined plastid tree A. ampeloprasum formed a highly supported clade with A. vineale. This supports the hypothesis of a possible hybrid origin of A. ampeloprasum. Allium iranicum formed a clade in the plastid tree, but was resolved as paraphyletic in the nrITS tree, probably due to presence of multiple non‐concerted copies of nrITS. Close relationships are suggested between the following species: A. aznavense and A. wendelboi with A. talyschense, A. erubescens and A. rotundum with A. scorodoprasum and A. abbasii with A. phanerantherum.     

Bulb tunic anatomy and its taxonomic implication in Allium L. (Amaryllidaceae: Allioideae)

Abstract

Allium is taxonomically a difficult genus with blurred taxonomic borders at all taxonomic ranks. In this research, anatomy and morphology of bulb tunics in 42 species of the genus representing its 16 currently recognized sections and 6 subgenera (Allium, Cepa, Reticulatobulbosa, Amerallium, Polyprason and Melanocrommyum) were investigated. Our results indicated the following characters to be most informative at sectional and subgeneric levels: features of calcium oxalate crystals and subepidermal cell layer of the outermost bulb tunic, type of tracheids, and bulbils presence. Three main types of crystals, i.e. prismatic, sand and druses, were fairly common among the investigated species except for the members of A. sect. Acanthoprason (A. subg. Melanocrommyum) that often lack crystals. The subepidermal layers of outer tunics were mostly composed of hexagonal, rectangular, or elongated cells but A. paradoxum (A. subg. Amerallium, sect. Briseis) showed the pentagonal type and A. longisepalum (A. subg. Amerallium, sect. Molium) the elliptic type of subepidermal cells. The members of A. sub. Melanocrommyum showed various types of tunic cells and crystals.     

Relationships among Old and New World Alliums according to ITS DNA sequence analysis

 Phylogenetic analysis of ITS DNA sequences of various Old and New World Alliums suggests the reinclusion of Nectaroscordum and affirms the reestablishment of Caloscordum as subgenera of genus Allium. The results sanction the elimination of the Old World Allium species from subg. Amerallium Traub and endorse Wendelbo’s definition of subg. Molium (excluding sect. Porphyrason). Received: 29 July 1998 / Accepted: 13 August 1998     

A new species and a new combination of <Emphasis Type="Italic">Allium</Emphasis> sect. <Emphasis Type="Italic">Rhizirideum</Emphasis> (Alliaceae) from northeastern China and Korea

A new species, Allium pseudosenescens, belonging to sect. Rhizirideum (Alliaceae), is described from northeastern China. It is easily distinguished from A. senescens by the slender pedicels, pale pink perianths, narrower tepals and ovaries, yellowish anthers, and sometimes toothed subulate filaments. Also, A. senescens var. minus in sect. Rhizirideum is raised to the rank of species, as A. minus. This Korean endemic taxon is shown to be a biologically distinct species based on morphological and cytological characters. Taxonomic keys for the species of Allium sect. Rhizirideum in northeastern China and Korea are provided.     

Distribution of a 375 bp repeat sequence inAllium (Alliaceae) as revealed by FISH

Information about evolutionary relationships between species of the genusAllium is desirable in order to facilitate breeding programmes. One approach is to study the distribution of repetitive DNA sequences among species thought on taxonomic grounds, to be closely related. We have used fluorescent in-situ hybridisation (FISH) to examine seven species within sect.Cepa of the genus (A. altaicum, A. cepa, A. fistulosum, A. galanthum, A. pskemense, A. oschaninii andA. vavilovii), one species from sect.Rhizirideum (A. roylei), two species from sect.Allium (A. sativum andA. porrum) and one species from sect.Schoenoprasum (A. schoenoprasum). Each species was probed using a 375 bp repeat sequence isolated fromA. cepa (Barnes & al. 1985), which was generated and labelled by polymerase chain reaction (PCR). No signals were detected in anyAllium species not belonging to sect.Cepa with the exception ofA. roylei, whose designation in sect.Rhizirideum is now questioned. Within sect.Cepa the probe was found to hybridize to the terminal regions of the chromosome arms of all the species examined. In addition a number of interstitial bands were detected. Use of FISH reveals a more detailed map of the location of the repeat sequences than has previously been obtained by C-banding and other staining procedures. The distribution of the terminal and interstitial sites when compared, allow us to identify three species groups namely,A. altaicum andA. fistulosum; A. cepa, A. roylei, A. oschaninii andA. vavilovii; andA. galanthum andA. pskemense.     

Restriction enzyme analysis of the chloroplast and nuclear 45s ribosomal DNA ofAllium sectionsCepa andPhyllodolon (Alliaceae)

Estimates of the phylogenetic relationships among cultivated and wildAllium species would benefit from identification of molecular characters. Restriction enzyme analysis of the chloroplast DNA (cpDNA) of the bulb onion (Allium cepa), Japanese bunching onion (A. fistulosum), wildAllium species in sect.Cepa andPhyllodolon, and the outgroupsA. ampeloprasum andA. tuberosum detected 39 polymorphisms.Allium cepa andA. vavilovii were identical for all characters. Cladistic analysis generated three most-parsimoniousWagner trees of 44 steps differing only in a zero-length branch.Allium fistulosum andA. altaicum (sect.Phyllodolon) comprised a monophyletic lineage separated from theA. cepa andA. vavilovii of sect.Cepa. The unresolved node was composed ofA. galanthum, A. roylei, and the lineage containingA. cepa, A. vavilovii, A. fistulosum, andA. altaicum. The clade containingA. altaicum, A. cepa, A. fistulosum, A. galanthum, A. roylei, andA. vavilovii remained resolved for strict consensus ofWagner trees of 48 steps or less.Allium pskemense andA. oschaninii were increasingly distant.Allium oschaninii has been proposed as the progenitor of the bulb onion, but was more closely related to the common progenitor of all species in sect.Cepa andPhyllodolon. Phylogenies estimated from cpDNA characters usingDollo parsimony resulted in a single most-parsimonious tree of 46 steps and agreed with phylogenies based onWagner parsimony. Polymorphic restriction enzyme sites in the 45s ribosomal DNA were not used to estimate phylogenies because of uncertain homologies, but are useful for identifying interspecific hybrids. The maternal phylogenies estimated in this study help to distinguish wildAllium species closely related to the bulb onion. Although not in agreement with classifications based on morphology, the phylogenies closely reflected crossability among species in sect.Cepa andPhyllodolon.     

Three new species of Allium sect. Codonoprasum from Greece

Abstract

Three new species of Allium from Greece are described. They are A. dirphianum, A. phitosianum and A. rausii, all included in A. sect. Codonoprasum. Morphology, karyology, distribution and relationships are examined for each of them.     

Contributions of Chemical Content and Biological Activity to Plant Taxonomy Based on the Four Allium L. Taxa (Sect. Cupanioscordum - Amaryllidaceae)

Garlic and onions are used as food and for medicinal purposes worldwide. Allium L. species are rich in bioactive organosulphur compounds that exhibit many biological activities like anticancer, antimicrobial, antihypertensive, antidiabetic activities. In this study, macro- and micromorphological characteristics of four Allium taxa were examined and the results suggested that A. callimischon subsp. haemostictum was the outgroup to sect. Cupanioscordum. Also, for the genus Allium, which is a taxonomically difficult genus, the hypothesis that chemical content and bioactivity can also be used taxonomically in addition to micro and macromorphological characters has been questioned. The bulb extract was analyzed to determine their volatile compositions and anticancer activities against human breast cancer, human cervical cancer, and rat glioma cells for the first time in the literature. To detect the volatiles, the Head Space-Solid Phase Micro Extraction method was used followed by Gas Chromatography-Mass Spectrometry. The main compounds were found as dimethyl disulfide that (36.9 %, 63.8 %, 81.9 %, 12.2 %) and methyl (methylthio)-methyl disulfide (10.8 %, 6.9 %, 14.9 %, 60.0 %) for A. peroninianum, A. hirtovaginatum and A. callidyction, respectively. Additionally, methyl-trans-propenyl disulfide is detected for A. peroniniaum (36 %). As a result, all extracts have shown significant efficacy against MCF-7 cells depending on applied concentrations. The treatment of MCF-7 cells for 24 h with 10, 50, 200, or 400 μg/mL ethanolic bulb extract of four Allium species resulted in DNA synthesis inhibition. Survival rates for A. peroninianum was 51.3 %, 49.7 %, 42.2 %, 42.0 %, for A. callimischon subsp. haemostictum 62.5 %, 63.0 %, 23.2 %, 22 %, for A. hirtovaginatum 52.9 %, 42.2 %, 42.4 %, 39.9 %, for A. callidyction 51.8 %, 43.2 %, 39.1 %, 31.3 %, for cisplatin 59.6 %, 59.9 %, 50,9 %, 48.2 %, respectively. Moreover, taxonomic evaluation according to biochemical compounds and bioactivities is almost in agreement with that made according to micro and macromorphological characters.     

Amounts of ribosomal DNA inAllium (Liliaceae)

Eight species ofAllium subgen.Allium sect.Allium have been studied at the cytological level by means of karyological analyses and at the biochemical level with regard to the proportions of ribosomal DNA. All the species have a basic genome of x = 8.A. sativum, A. commutatum, A. ampeloprasum, andA. vineale possess approximately 0.050% rDNA and two nucleolus organizer regions per basic chromosome set.A. sphaerocephalon andA. arvense have two nucleolus organizers, andA. amethystinum three nucleolus organizers per haploid (n = x) genome: the three species possess approximately 0.075% rDNA.A. acutiflorum has five nucleolus organizer regions per haploid genome and 0.121% rDNA. An attempt to relate these differences with functional and ecological characteristics indicates that evolutionary variation of rDNA proportions is not casual. Such data also can help to define systematic affinities and circumscribe infrageneric taxa.     

Karyological studies of Iranian <Emphasis Type="Italic">Allium</Emphasis> L. (Amaryllidaceae) species with focus on sect. <Emphasis Type="Italic">Acanthoprason</Emphasis>. 1. Mitotic chromosomes

Eighteen species and subspecies (34 accessions) of Allium sect. Acanthoprason and 11 species (17 accessions) belonging to other subgenera and sections of Allium were karyologically investigated and include first reports for 12 species. The examined plants of 47 accessions were diploid, three accessions of two species were tetraploid, and in the A. bisotunense accession, we found a mix of di- and triploid individuals. B chromosomes were found in 10 accessions. A basic chromosome number of x = 8 was confirmed for all investigated members of subg. Melanocrommyum and subg. Allium, and x = 9 for Allium tripedale of subg. Nectaroscordum. Idiograms were drawn for each accession, and metaphase images are presented illustrating observed chromosomal variations. Also, karyotype features and asymmetry parameters were calculated for all accessions. Chromosomal aberrations, e.g. aneuploid cells or loss of whole or parts of chromosome arms, were rarely observed. In general, the karyotypes showed low variation in inter- and intrachromosomal asymmetry especially inside of the taxonomic groups, though satellited chromosomes were good markers for subgenera and even specific for two studied sections of subg. Allium. Six different types of satellites were recognized, two of them were newly described: Type P was prevalent in subg. Melanocrommyum, and type O in sect. Codonoprasum. Statistical analyses were performed on five karyological parameters to test correct relationships and also to test previous grouping hypotheses. Although our data confirm distinct karyological characters for the subgenera investigated, the remarkable morphological diversity inside of subg. Melanocrommyum is not mirrored by striking karyological differences.     

Echidnopsis thulinii sp. nov. (Apocynaceae–Asclepiadoideae) with a review of the infrageneric classification of the genus

Echidnopsis thulinii M. G. Gilbert is described from northern Somalia. The infrageneric classification of Echidnopsis Hook. f. is reviewed in the light of recently published molecular phylogenies. The new species belongs to E. sect. Echidnopsis and a key to the species of this section is provided. A lectotype, supported by an epitype, is designated for E. virchowii K. Schum. Echidnopsis sect. Profundicoronata Bruyns is included within sect. Vadosicoronata Bruyns and two new sections recognised: E. sect. Pseudopectinaria (Lavranos) M. G. Gilbert, based on the genus Pseudopectinaria Lavranos, and E. sect. Sobolifera M. G. Gilbert. A key is given to the sections of Echidnopsis.     

Phylogenetic relationships among cultivated Allium species from restriction enzyme analysis of the chloroplast genome

Summary The genus Allium contains many economically important species, including the bulb onion, chive, garlic, Japanese bunching onion, and leek. Phylogenetic relationships among the cultivated alliums are not well understood, and taxonomic classifications are based on relatively few morphological characters. Chloroplast DNA is highly conserved and useful in determining phylogenetic relationships. The size of the chloroplast genome of Allium cepa was estimated at 140 kb and restriction enzyme sites were mapped for KpnI, PstI, PvuII, SalI, XbaI, and XhoI. Variability at restriction enzyme sites in the chloroplast DNA was studied for at least three accessions of each of six cultivated, old-world Allium species. Of 189 restriction enzyme sites detected with 12 enzymes, 15 mutations were identified and used to estimate phylogenetic relationships. Cladistic analysis based on Wagner and Dollo parsimony resulted in a single, most-parsimonious tree of 16 steps and supported division of the species into sections. Allium species in section Porrum were distinguished from species in sections Cepa and Phyllodolon. Two species in section Rhiziridium, A. schoenoprasum and A. tuberosum, differed by five mutations and were placed in separate lineages. Allium cepa and A. fistulosum shared the loss of a restriction enzyme site and were phylogenetically closer to each other than to A. schoenoprasum. This study demonstrates the usefulness of restriction enzyme site analysis of the chloroplast genome in the elucidation of phylogenetic relationships in Allium.     

A New Autumn-Flowering Species of Allium (Alliaceae) from Croatia

Here we describe Allium telmatum Bogdanovi?, Brullo, Giusso & Salmeri, a new species of Allium sect. Codonoprasum from North Dalmatia (Croatia). Its chromosome number (2n?=?32), karyotype, leaf anatomy, ecology and taxonomical relationships are examined. Several features, such as phenology (flowering in autumn), occurrence in coastal salt marshes, tetraploid chromosome number, and morphology, indicate that it is most closely related to the Tyrrhenian species Allium savii. On the basis of our herbarium survey, we present here a distribution map of the autumn-flowering species of Allium sect. Codonoprasum in the Mediterranean area.     

Phylogeny of Allium L. subg. Melanocrommyum (Webb et Berth.) Rouy based on DNA sequence analysis of the internal transcribed spacer region of nrDNA

 Sequence analysis of the ITS region of nuclear ribosomal DNA from subgeneric representatives of Allium L. produced phylogenetic trees which concurred with previous conclusions based on classical taxonomy. Phylogenetic analysis revealed a closer relationship between Nectaroscordum siculum and Allium cernuum (representing Amerallium) than between A. cernuum and the rest of the Allium species employed in this study. The phylogeny of subg. Melanocrommyum based on ITS sequences largely agreed with inferences made by previous researchers based on morphology or a restriction analysis of chloroplast DNA. However, the phylogenetic positions of Allium protensum and Allium macleanii based on ITS sequences did not correspond to their morphological similarity with Allium schubertii and Allium giganteum, respectively. Received: 15 February 1998 / Accepted: 12 March 1998     

Nuclear DNA contents, rDNAs, and karyotype evolution in Vicia subgenus Vicia: II. Section Peregrinae

Summary. Nuclear DNA contents, automated karyotype analyses, and sequences of rDNA spacers have been determined for the species of Vicia belonging to sect. Peregrinae, as well as for V. mollis. The phylogenetic data generated from the comparison of rDNA sequences and karyomorphological results would both indicate that Vicia mollis is a sister group to sect. Peregrinae. The relationships among the species belonging to the Peregrinae section and species enclosed in sections Faba, Narbonensis, and Bithynicae have been also investigated: a clade including V. mollis and sect. Peregrinae is a sister group to a clade including V. bithynica and sect. Narbonensis. With our choice of outgroup, Vicia faba (including subsp. paucijuga) is external to the above mentioned inclusive group. Correspondence and reprints: Dipartimento di Agrobiologia ed Agrochimica, Università della Tuscia, via San Camillo de Lellis, 01100 Viterbo, Italy.     

Pyrus cordifolia sp. nov. and two new records of Pyrus (Rosaceae) from Iran

A new species, namely Pyrus cordifolia (P. sect. Pashia) is described as new to science, and two new records including P. tamamschianiae (P. sect. Pyrus) and P. theodorovii var. latifolia (P. sect. Argyromalon) are reported for the flora of Iran. These taxa are compared with their closest relatives. Photographs and a distribution map of these taxa as well as an illustration of the new species are presented. An identification key to members of P. sect. Pashia in Iran is provided.     

Restriction enzyme analysis of the nuclear 45s ribosomal DNA of six cultivated Alliums (Alliaceae)

Estimates of the phylogenetic relationships among cultivated and wildAllium species would benefit from identification of objective molecular characters. Restriction fragment length polymorphisms in the nuclear 45s ribosomal DNA (rDNA) were identified among two of five accessions of each of six cultivated Alliums. Restriction enzyme sites forBamHI,DraI,EcoRI,EcoRV,SacI, andXbaI were mapped. Different lengths of the rDNA repeat unit among the cultivated Alliums were due to sizes of the intergenic spacer. Nineteen polymorphic restriction enzyme sites were discovered and used to estimate phylogenetic relationships. Cladistic analyses based on Wagner parsimony were completed without an outgroup and resulted in two equally most parsimonious trees of 22 steps. A combined analysis of differences at RE sites in the ribosomal (19 characters) and chloroplast (15 characters) DNA generated a single most parsimonious tree of 39 steps. Single trichotomies were observed at 40 and 41 steps. Strict consensus of the three trees of 41 or fewer steps consisted of a lineage forA. tuberosum, a second forA. ampeloprasum andA. sativum, and a third forA. cepa, A. fistulosum, andA. schoenoprasum. Estimates of phylogenetic relationships based on variability at restriction enzyme sites in the rDNA and chloroplast DNA agree with the classification scheme ofTraub. Because of the predominance of autapomorphies, restriction enzyme analysis of the nuclear 45s rDNA is of limited use in estimating phylogenies amongAllium sections. However it is useful in the establishment of interspecific hybridity.     

Stable transformation and regeneration of transgenic plants of Pinus radiata D. Don

A biolistic particle delivery system was used to genetically transform embryogenic tissue of Pinus radiata. The introduced DNA contained a uidA reporter gene under the control of either the tandem CaMV 35S or the artificial Emu promoter, and the npt II selectable marker controlled by the CaMV 35S promoter. The average number of stable, geneticin-resistant lines recovered was 0.5 per 200 mg fresh weight bombarded tissue. Expression of the uidA reporter gene was detected histochemically and fluorimetrically in transformed embryogenic tissue and in derived mature somatic embryos and regenerated plants. The integration of uidA and npt II genes into the Pinus radiata genome was demonstrated using PCR amplification of the inserts and Southern hybridisation analysis. The expression of both genes in transformed tissue was confirmed by Northern hybridisation analysis. More than 150 transgenic Pinus radiata plants were produced from 20 independent transformation experiments with four different embryogenic clones. Received: 9 May 1997 / Revision received: 18 September 1997 / Accepted: 18 October 1997