RAPD and FAME analyses of Astragalus species growing in eastern Anatolia region of Turkey

Fatty acid (FAs) and RAPD profiles were used to examine phenotypic and genetic relationships between eight Astragalus species including Astragalus maximus Willd. var. maximus, Astragalus coadunatus Hub. Mor. & Chamb., Astragalus kurdicus Boiss. var. kurdicus, Astragalus lagurus Willd, Astragalus christianus L., Astragalus cicer L., Astragalus atrocarpus Champ & Matthews and Astragalus onobrychioides Bieb., which were wildly growing in eastern Anatolia region of Turkey. All of the eight Astragalus species tested in this study were separated based on the presence and composition of 45 different FAs. Four of the Astragalus species including A. coadunatus, A. lagurus, A. christianus, and A. atrocarpus were rich in terms of FA contents containing at least 22–31 different FAs. The relative proportions of two fatty acids, 16:0, and 18:1:ω8c were higher in these four Astragalus species. The remaining species have limited number of FAs with unique FAMEs profiles. Six of the 10 decamer primers examined were selected to find out genetic polymorphism in Astragalus species. A total of 98 polymorphic bands were observed, ranging in size from 250 bp to 3000 bp. The RAPD results suggested that A. atrocarpus, A. onobrychioides and A. kurdicus are closely related and completely different from the other species. Six genetically distinct groups were found among the species of Astragalus. High genetic variations among Astragalus species growing wildly in eastern Anatolia region of Turkey may imply the differences in their origins. The results in the present study suggested that both RAPD and FA analyses are useful for differentiation of Astragalus species.     

Karyological studies in IberianSonchus (Asteraceae: Lactuceae): S. oleraceus, S. microcephalus andS. asper and a general discussion

Chromosome numbers and karyotypes ofSonchus oleraceus (n=16, 2n=32),S. asper (n=9, 2n=18 for subsp.asper and subsp.glaucescens, andS. microcephalus (n=15, 2n=30) are studied; for the first time their idiograms are given. Karyotypes mainly comprise small chromosomes with a degree of asymmetry 2B inS. oleraceus andS. microcephalus and 2A or 2A-2B inS. asper. No karyological differences can be pointed out betweenS. asper subspecies. Data presented support the amphiploid character ofS. oleraceus, and the origin ofS. microcephalus through a dysploid process involving the former taxon. In Iberian representatives of the genus, diagrams of karyotype asymmetry indices show a cluster grouping for species, with the detached exceptions ofS. maritimus andS. crassifolius, which spontaneously hybridize in central Spain. A review of available karyological data shows that in the evolution of the genusSonchus s.l. and relatives, the basic chromosome number x=9 has generally been maintained. Dysploidy is restricted to the seriesS. bourgeaui (n=8) —S. tenerrimus (n=7) andS. oleraceus (n=16) —S. microcephalus (n=15), evolutionarily related and included in the present subgenusSonchus. Polyploidy has been detected in a total of nine taxa ofSonchus and in the generaEmbergeria, Kirkianella, andDendroseris, being more common in peripheral regions of the distribution area of the group. Five diversification centers are proposed for the whole group, of which the Western Mediterranean area, including the Iberian Peninsula, is related to diversification of the present subgenusSonchus.     

Taxonomic notes on astragalus section leptocarpi subsection californici (Fabaceae)

A recently completed study of Astragalus sect. Leptocarpi subsect. Californici shows that the following taxonomic adjustments are required: 1) Astragalus tener var. ferrisiae, a new variety, is described. It is compared to A. tener var. tener, as well as to A. rattanii var. jepsonianus in which it was previously included, and to the superficially similar A. clarianus with which it was confused. An illustration of the new variety, and of the fruits of these related taxa, is included. 2) Astragalus nyensis was placed in subsect. Californici by Barneby in his 1964 monograph. Morphological, anatomical, and allozyme data suggest that A. nyensis should be placed in the subsect. Leptocarpi closely allied to A. nuttallianus.     

Two new Talaromyces species from soil in Thailand

Two new Talaromyces species, T. thailandensis and T. tratensis, isolated from forest soil in Trat in Thailand are described. ITS barcodes were used to show the relationships between the newly described species and other Talaromyces taxa. β-tubulin and RPB1 sequences were used for the detailed analysis and the phylogenetic data showed that Talaromyces tratensis resolved in a clade closely related to T. rotundus, T. phialosporus and T. tardifaciens, which contain species that typically display restricted growth. Talaromyces thailandensis was resolved in different clades for each gene in a position closely related to T. macrosporus and T. flavus where they can be distinguished by length of stipe and shape of conidia.     

Reproductive success and genetic divergence among varieties of the rare and endangered <Emphasis Type="Italic">Astragalus cremnophylax</Emphasis> (Fabaceae) from Arizona,USA

Populations of Astragalus cremnophylax from Arizona and related A. humillimus from New Mexico were assessed for morphological, reproductive, genetic, and ecological differences. Results suggest that some of the taxa (i.e., A. cremnophylax var. cremnophylax and A. humillimus) are poor reproducers and environmental fluctuation is not likely a factor contributing to low fecundity in these species. Astragalus cremnophylax var. cremnophylax appears to have low fecundity due to inbreeding depression. Allozyme data from 18 loci show little within-population and taxon genetic variability. Most genetic variability is distributed among populations and taxa. The population of A. cremnophylax var. cremnophylax from the Grand Canyon (South Rim) was genetically depauperate, indicative of the bottleneck caused by historic trampling at this viewpoint. Cape Final, a population of A. cremnophylax var. cremnophylax on the Grand Canyon (North Rim) is genetically different from typical materials of this taxon (South Rim) and is more closely related to other taxa within this species complex. However, the other varieties of A. cremnophylax are more closely related to A. humillimus than the population at Cape Final, suggesting potential species status for Cape Final materials based on allozyme divergence.     

The complete mitochondrial genome sequence of the little egret (Egretta garzetta)

Many phylogenetic questions in the Ciconiiformes remain unresolved and complete mitogenome data are urgently needed for further molecular investigation. In this work, we determined the complete mitogenome sequence of the little egret (Egretta garzetta). The genome was 17,361 bp in length and the gene organization was typical of other avian mtDNA. In protein-coding genes (PCGs), a C insertion was found in ND3, and COIII and ND4 terminated with incomplete stop codons (T). tRNA-Val and tRNA-Ser (AGY) were unable to fold into canonical cloverleaf secondary structures because they had lost the DHU arms. Long repetitive sequences consisting of five types of tandem repeats were found at the 3′ end of Domain III in the control region. A phylogenetic analysis of 11 species of Ciconiiformes was done using complete mitogenome data and 12 PCGs. The tree topologies obtained with these two strategies were identical, which strongly confirmed the monophyly of Ardeidae, Threskiorothidae and Ciconiidae. The phylogenetic analysis also revealed that Egretta was more closely related to Ardea than to Nycticorax in the Ardeidae, and Platalea was more closely related to Threskiornis than to Nipponia in the Threskiornithidae. These findings contribute to our understanding of the phylogenetic relationships of Ciconiiformes based on complete mitogenome data.     

Isoenzyme variation patterns and species concept in Astragalus gossypinus and Astragalus persicus complexes (Fabaceae) in Iran

Isoenzyme electrophoresis was employed to examine the relationships of 21 individuals representing four populations of Astragalus gossypinus complex as well as 20 individuals representing five populations of Astragalus persicus complex. A total of 27 bands from three enzyme systems (superoxide dismutase, esterase, and peroxidase) were obtained. UPGMA clustering method resulted in two distinct clusters for different populations corresponding to the two species complexes analysed. In both species, populations distributed on Alborz mountain range in northern Iran form separated clusters from those distributed on Zagros mountain range in the West. The results also show that both species complexes exhibit a high diversity based on Shannon–Weaver diversity index (H′) compared with other species of Astragalus reported previously. The mean number of bands per each presumed isoenzyme ranges from 2.14 to 3.57. The value of Euclidean distance ranges from 1.251 to 3.152. Our data suggest that both species should be circumscribed wider than that treated by most taxonomists, and several taxonomic names should be reduced under synonymy of the corresponding species.     

Identification of the rhizobial symbiont of Astragalus glombiformis in Eastern Morocco as Mesorhizobium camelthorni

Astragalus gombiformis is a desert symbiotic nitrogen-fixing legume of great nutritional value as fodder for camels and goats. However, there are no data published on the rhizobial bacteria that nodulate this wild legume in northern Africa. Thirty-four rhizobial bacteria were isolated from root nodules of A. gombifomis grown in sandy soils of the South-Eastern of Morocco. Twenty-five isolates were able to renodulate their original host and possessed a nodC gene copy. The phenotypic and genotypic characterizations carried out illustrated the diversity of the isolates. Phenotypic analysis showed that isolates used a great number of carbohydrates as sole carbon source. However, although they were isolated from arid sandy soils, the isolates do not tolerate drought stress applied in vitro. The phenotypic diversity corresponded mainly to the diversity in the use of some carbohydrates. The genetic analysis as assessed by repetitive extragenic palindromic (REP)-polymerase chain reaction (PCR) showed that the isolates clustered into 3 groups at a similarity coefficient of 81 %. The nearly-complete 16S rRNA gene sequence from a representative strain of each PCR-group showed they were closely related to members of the genus Mesorhizobium of the family Phyllobactericeae within the Alphaproteobacteria. Sequencing of the housekeeping genes atpD, glnII and recA, and their concatenated phylogenetic analysis, showed they are closely related to Mesorhizobium camelthorni. Sequencing of the symbiotic nodC gene from each strain revealed they had 83.53 % identity with the nodC sequence of the type strain M. camelthorni CCNWXJ 40-4^T.     

The composition of the proteinaceous polysaccharides exuded by astragalus microcephalus,A. Gummifer and A. Kurdicus—The sources of turkish gum tragacanth

Gum tragacanth is a variable commodity because commercial samples may legitimately be admixtures, in any relative proportions, of the exudates from Asiatic Astragalus spp. Analytical data show that the exudates collected from the three major contributing Turkish spp., A. microcephalus, A. gummifer and A. kurdicus, differ extensively, particularly in terms of their fucose, xylose, galacturonic acid and methoxyl contents and in the relative proportions of their soluble (tragacanthin) and insoluble (bassorin) components. In addition, these three Astragalus exudates are shown to be proteinaceous polysaccharides; their amino acid compositions differ, particularly in terms of their hydroxyproline, histidine, aspartic acid and arginine content. In contrast, the amino acid compositions of the soluble and insoluble components of A. kurdicus do not differ extensively.     

Cladistic and phylogenetic analyses of the genus Cicer in Turkey

Fifteen taxa of the genus Cicer L. growing naturally in Turkey and out-groups were classified by phylogenetic and cladistic analysis. Taxa of the genus Cicer and the out-group taxa belonging to the closest genera Phaseolus L., Vicia L., Lathyrus L. and Ononis L., which are placed in Phaseoleae, Vicieae and Ononideae tribes, respectively, were used in molecular studies in order to derive their phylogenetic relationships. Morphological, palynological and seed characters were used on the basis of 143 traits. The micromorphological characters of seed and pollen grains were revealed by SEM. Lathyrus L. and Vicia L. species were used as out-groups for numerical analysis. Ten specimens were used for the measurements of metric characters related to the morphological structures of the taxa used for statistical analysis via PAUP and NTSYS-pc packages. Phylogenetic relationships between species and populations of the same species growing in different locations and their variations were determined using molecular methods performed on regions of the Inter Simple Sequence Repeat (ISSR). DNA was isolated from the collected samples, using modified CTAB protocols. ISSR was used for phylogenetic fingerprinting. The data were analyzed with NTSYS-pc package. Standardized data were used to generate a dendrogram that revealed the phylogenetic relationships of the taxa. Geographic distribution of the Cicer taxa appears to be closely related to the Anatolian Diagonal. As a result of this study, four new endemic taxa were added and evaluated for the first time.     

Phenotypic characterization of Astragalus glycyphyllos symbionts and their phylogeny based on the 16S rDNA sequences and RFLP of 16S rRNA gene

In this study, the nitrogen fixing Astragalus glycyphyllos symbionts were characterized by phenotypic properties, restriction fragment length polymorphism (RFLP), and sequences of 16S rDNA. The generation time of A. glycyphyllos rhizobia in yeast extract mannitol medium was in the range 4–6 h. The studied isolates exhibited a low resistance to antibiotics, a moderate tolerance to NaCl, assimilated di- and trisaccharides, and produced acid in medium containing mannitol as a sole carbon source. In the cluster analysis, based on 86 phenotypic properties of A. glycyphyllos symbionts and the reference rhizobia, examined isolates and the genus Mesorhizobium strains were placed on a single branch, clearly distinct from other lineages of rhizobial genera. By the comparative analysis of 16S rRNA gene sequences and 16S rDNA–RFLP, A. glycyphyllos nodulators were also identified as the members of the genus Mesorhizobium. On the 16S rDNA sequence phylogram, the representatives of A. glycyphyllos nodule isolates formed a robust, monophyletic cluster together with the Mesorhizobium species at 16S rDNA sequence similarity of these bacteria between 95 and 99 %. Similarly, the cluster analysis of the combined RFLP–16S rDNA patterns, obtained with seven restriction endonucleases, showed that A. glycyphyllos rhizobia are closely related to the genus Mesorhizobium bacteria. The taxonomic approaches used in this paper allowed us to classify the studied bacteria into the genus Mesorhizobium.     

A phenetic analysis on the genus Lolium (Poaceae) in Iran

In this study, 68 specimens of the genus Lolium were scored for 27 characters, comprising 12 vegetative, 12 inflorescence and 3 seed characters. The aim of the study was to investigate the species relationships within the genus in Iran. The data were analysed using principal components analysis (PCA) and cluster analysis. Both analyses separated L. perenne, L. persicum, L. temulentum, L. multiflorum from each other. According to previous authors, L. rigidum and L. loliaceum show little difference from each other and are not separable to a species level. In this study these two species separated clearly from the other species, but were most closely related to L. perenne following cluster analysis and to L. multiflorum following PCA. L. persicum was found to be the most distinct species within the genus Lolium in Iran.     

Identification of parental genomes and genomic organization in <Emphasis Type="Italic">Aster microcephalus</Emphasis> var. <Emphasis Type="Italic">ovatus</Emphasis>

The karyotype of diploid Aster iinumae is morphologically similar to that of diploid Aster ageratoides var. ageratoides, however, its chromosome size is apparently smaller (S-type chromosomes versus L-type chromosomes, respectively). The hybrid origin of tetraploid Aster microcephalus var. ovatus (LS-type chromosomes) has previously been suggested by cytogenetics and chloroplast DNA (cp DNA) data. The cp DNA phylogeny also implies that the S-type chromosome is apomorphic, which means that genome size reduction occurred on the evolutionary way to A. iinumae. In this study, we have demonstrated that the chromosome size difference does not depend on the intensity of chromosome condensation but on the DNA content. The simultaneous genomic in situ hybridization (GISH) results show the similarity between S-type chromosomes of A. iinumae and A. microcephalus var. ovatus, and between L-type chromosomes of A. ageratoides and A. microcephalus var. ovatus, which provide additional evidence for A. microcephalus var. ovatus being a tetraploid amphidiploid produced by hybridization between S-type chromosomes and L-type chromosomes. The distribution patterns of Ty1-copia-like retrotransposons were similar in L- and S-type chromosomes. The copies of this retrotransposon dispersed uniformly on all chromosomes, and it is not yet apparent how the Ty1-copia-like retrotransposon affects the size difference between them.     

The relationships among the species of the <Emphasis Type="Italic">Drosophila virilis</Emphasis> group inferred from the gene <Emphasis Type="Italic">Ras1</Emphasis> sequences

Comparative analysis of a group of closely related Drosophila species (D. virilis, D. lummei, D. novamexicana, D. americana texana, D. flavomontana, D. montana, D. borealis, D. lacicola, D. littoralis, D. kanekoi, and D. ezoana) was conducted based on an incomplete sequence of gene Ras1. The pattern of the relationships among the species corresponded to that expected from analysis of morphological and cytogenetic characters. Statistical data favoring neutrality of the substitutions examined in the Ras1 gene are presented. This character of the gene Ras1 evolution confers more reliability to reconstruction of phylogenetic relationships among closely related species. The resultant tree for main phylads of the group is as follows: D. virilis (D. lummei, D. montana, D. ezoana).     

Inoculation of Astragalus racemosus and Astragalus convallarius with selenium-hyperaccumulator rhizosphere fungi affects growth and selenium accumulation

Little is known about how fungi affect plant selenium (Se) accumulation. Here we investigate the effects of two fungi on Se accumulation, translocation, and chemical speciation in the hyperaccumulator Astragalus racemosus and the non-accumulator Astragalus convallarius. The fungi, Alternaria astragali (A3) and Fusarium acuminatum (F30), were previously isolated from Astragalus hyperaccumulator rhizosphere. A3-inoculation enhanced growth of A. racemosus yet inhibited growth of A. convallarius. Selenium treatment negated these effects. F30 reduced shoot-to-root Se translocation in A. racemosus. X-ray microprobe analysis showed no differences in Se speciation between inoculation groups. The Astragalus species differed in Se localization and speciation. A. racemosus root-Se was distributed throughout the taproot and lateral root and was 90 % organic in the lateral root. The related element sulfur (S) was present as a mixture of organic and inorganic forms in the hyperaccumulator. Astragalus convallarius root-Se was concentrated in the extreme periphery of the taproot. In the lateral root, Se was exclusively in the vascular core and was only 49 % organic. These findings indicate differences in Se assimilation between the two species and differences between Se and S speciation in the hyperaccumulator. The finding that fungi can affect translocation may have applications in phytoremediation and biofortification.     

Genetic relationships among Eurasian Puccinellia distans genotypes

Puccinellia distans (Jacq.) Parl. is a common grass species found throughout the world. It can grow in arid and saline environments as well as under toxic boron concentrations. In this work we performed sequence related amplified polymorphism (SRAP) marker analysis on 20 wild P. distans genotypes to understand the genetic relationships among different genotypes and subspecies. We tested 119 SRAP primer pairs and found that 43 were polymorphic. The molecular data were then analyzed to determine the genetic relationships and population structure of the genotypes. We were able to trace the origin of genotypes that were carried to distant locations or gathered for research purposes. We also found that geographical distance between genotypes was not an important determinant of genetic relationships as even distantly located Puccinellia genotypes were closely related. As P. distans is known to be tolerant to salinity stress and toxic mineral concentrations, the findings of this work can be used as a starting point for selection of genotypes that should be tested under such conditions.     

Dealing with Discordant Genetic Signal Caused by Hybridisation,Incomplete Lineage Sorting and Paucity of Primary Nucleotide Homologies: A Case Study of Closely Related Members of the Genus Picris Subsection Hieracioides (Compositae)

We investigated genetic variation and evolutionary history of closely related taxa of Picris subsect. Hieracioides with major focus on the widely distributed P. hieracioides and its closely related congeners, P. hispidissima, P. japonica, P. olympica, and P. nuristanica. Accessions from 140 sample sites of the investigated Picris taxa were analyzed on the infra- and the inter-specific level using nuclear (ITS1-5.8S-ITS2 region) and chloroplast (rpl32-trnL ^(UAG) region) DNA sequences. Genetic patterns of P. hieracioides, P. hispidissima, and P. olympica were shown to be incongruent and, in several cases, both plastid and nuclear alleles transcended borders of the taxa and genetic lineages. The widespread P. hieracioides was genetically highly variable and non-monophyletic across both markers, with allele groups having particular geographic distributions. Generally, all gene trees and networks displayed only a limited and statistically rather unsupported resolution among ingroup taxa causing their phylogenetic relationships to remain rather unresolved. More light on these intricate evolutionary relationships was cast by the Bayesian coalescent-based analysis, although some relationships were still left unresolved. A combination of suite of phylogenetic analyses revealed the ingroup taxa to represent a complex of genetically closely related and morphologically similar entities that have undergone a highly dynamic and recent evolution. This has been especially affected by the extensive and recurrent gene flow among and within the studied taxa and/or by the maintenance of ancestral variation. Paucity of phylogenetically informative signal further hampers the reconstruction of relationships on the infra- as well as on the inter-specific level. In the present study, we have demonstrated that a combination of various phylogenetic analyses of datasets with extremely complex and incongruent phylogenetic signal may shed more light on the interrelationships and evolutionary history of analysed species groups.     

IS6110 Transposition and Evolutionary Scenario of the Direct Repeat Locus in a Group of Closely Related Mycobacterium tuberculosis Strains

In recent years, various polymorphic loci and multicopy insertion elements have been discovered in the Mycobacterium tuberculosis genome, such as the direct repeat (DR) locus, the major polymorphic tandem repeats, the polymorphic GC-rich repetitive sequence, IS6110, and IS1081. These, especially IS6110 and the DR locus, have been widely used as genetic markers to differentiate M. tuberculosis isolates and will continue to be so used, due to the conserved nature of the genome of M. tuberculosis. However, little is known about the processes involved in generating these or of their relative rates of change. Without an understanding of the biological characteristics of these genetic markers, it is difficult to use them to their full extent for understanding the population genetics and epidemiology of M. tuberculosis. To address these points, we identified a cluster of 7 isolates in a collection of 101 clinical isolates and investigated them with various polymorphic genetic markers, which indicated that they were highly related to each other. This cluster provided a model system for the study of IS6110 transposition, evolution at the DR locus, and the effects of these on the determination of evolutionary relationships among M. tuberculosis strains. Our results suggest that IS6110 restriction fragment length polymorphism patterns are useful in grouping closely related isolates together; however, they can be misleading if used for making inferences about the evolutionary relationships between closely related isolates. DNA sequence analysis of the DR loci of these isolates revealed an evolutionary scenario, which, complemented with the information from IS6110, allowed a reconstruction of the evolutionary steps and relationships among these closely related isolates. Loss of the IS6110 copy in the DR locus was noted, and the mechanisms of this loss are discussed.     

The genus Juniperus in Mexico and Guatemala: Numerical and chemosystematic analysis

The variation leaf constituents (mostly terpenoids) was analyzed from each of the taxa of Juniperus in Mexico and Guatemala by numerical taxonomic methods. These results were compared with those of a previous study utilizing morphological characters. In general, the two agree on the major groups. Differences between more closely related species were more apparent with the chemical data, whereas more distantly related taxa sometimes appeared to be more closely related chemically due to the presence of a single component such as α-pinene in high concentration in each of the oils. Four large groups are apparent; the deppeanan; flaccidan; monticolan; and the oneseeded (pinchotii) complex. Some taxa (J. durangensis, J. standleyi, J.jaliscana) are still of uncertain affinities. This study confirms the morphological data indicating that J. patoniana Martínez should be reduced to a variety of J. deppeana (J. deppeana var. patoniana (Martínez) Zanoni, comb. et stat. nov). No samplestypical of J. monosperma were found in Mexico and J. monosperma var. gracilis (sensu Martinez) was found to not be closely allied with J. monosperma from the USA but has some uncertain affinities with species of the one-seeded complex. These relationships need to be examined in more detail. J. blancoi appears to be closely related to J. scopulorum. This information on the junipers of Mexico and Guatemala should prove invaluable to future studies on the evolution of the Juniperus in North America.     

Taxonomic notes on Astragalus sect. Malacothrix (Fabaceae) from Iran

Astragalus porphyrogrammus , occurring in the Zarin-Abad of Zanjan (Iran), is described and illustrated. This species belongs to A. sect. Malacothrix and seems to be distinct and interesting among the Iranian species. In this research, A. sect. Grammocalyx which was very artificial placed in A. subgen. Calycophysa transferred to A. subgen. Hypoglottis. Moreover, relationships between A. subgen. Hypoglottis and the closely related subgenera in genus Astragalus are discussed. Also A. lineatus is recorded for Iran.