Genetic relationship among Paspalum species of the subgenus Anachyris: Taxonomic and evolutionary implications

Paspalum is one of the most important genera of the Poaceae family due to its large number of species and diversity. The subgenus Anachyris comprises six species mainly from South America grouped together by sharing rare spikelet characteristics. A genetic analysis using ISSR markers, compared with the morphological and phenotypic variation observed in each one species, was used to establish genetic relationships among 40 accessions with several ploidy levels, belonging to 5 species of the subgenus Anachyris. Fourteen accessions of Paspalum malacophyllum (2x and 4x), 12 of P. simplex (2x, 3x, 4x and 6x), 4 of P. procurrens (2x and 4x), 4 of P. usterii (4x) and 6 of P. volcanensis (4x) were analysed. A total of 227 ISSR loci (98.7% polymorphic) were detected among all accessions, with variable loci number and percentages of polymorphism according to species delimitations. Six main groups were identified by cluster analysis based on Jaccard's genetic distance and UPGMA, four of which matched all the respective accessions of P. simplex, P. procurrens, P. usterii and P. volcanensis, while the other two were consistent with two different groups of accessions of P. malacophyllum, one involving most tetraploid accessions, and the other one grouping together a tetraploid and two diploid accessions. The distinctive morphological characteristics and the separate clustering of these tetraploid and diploid cytotypes suggest to consider a new multiploid species complex inside the subgenus Anachyris. Both cytotypes of P. procurrens, and the four co-specific cytotypes of P. simplex consistently clustered together forming two specific groups for the two multiploid taxons. This is in agreement with the existence of high phenotypic similarities between diploid and tetraploid cytotypes of P. procurrens, and among diploid, triploid, tetraploid and hexaploid cytotypes of P. simplex. Since the polyploid cytotypes of these species are reproduced by apomixis, the specific genetic clustering by ISSR markers and morphological and cytological results support the hypothesis that the two multiploid species were originated by autopolyploidy. Our results confirm previous studies suggesting a monophyletic origin for the subgenus Anachyris and are concordant with previous data regarding genomic homologies and phylogenetic analyses in the genus.     

Are the microcyclic rust species Puccinia melampodii and Puccinia xanthii conspecific?

The taxonomic relationship between two microcyclic rust species, Puccinia melampodii and Puccinia xanthii, recorded from a number of Asteraceae hosts, was explored by comparing teliospore morphology, host specificity and sequence data. Teliospore morphology varied between and within individual rust accessions but, in general, teliospores of P. xanthii were larger than those of P. melampodii. Field observations and cross-inoculation greenhouse studies showed that P. melampodii accessions were highly specific to their original host species and unable to establish compatible interactions with related Asteraceae species. Though small amounts of genetic variation were detected between P. melampodii and P. xanthii accessions, the ITS and TEF phylogenetic analyses comprising several other rust species grouped these accessions within a well supported clade. Our data indicate that despite differences between P. xanthii and P. melampodii accessions these rusts cannot readily be separated at the species level, supporting earlier taxonomic conclusions and the recent proposal to group them into a morphospecies. Based on host-specificity data, the name Puccinia xanthii var. parthenii-hysterophorae is proposed to accommodate all Mesoamerican records of P. melampodii associated with the host Parthenium hysterophorus.     

Amplification, contraction and genomic spread of a satellite DNA family (E180) in Medicago (Fabaceae) and allied genera

Background and Aims

Satellite DNA is a genomic component present in virtually all eukaryotic organisms. The turnover of highly repetitive satellite DNA is an important element in genome organization and evolution in plants. Here we assess the presence and physical distribution of the repetitive DNA E180 family in Medicago and allied genera. Our goals were to gain insight into the karyotype evolution of Medicago using satellite DNA markers, and to evaluate the taxonomic and phylogenetic signal of a satellite DNA family in a genus hypothesized to have a complex evolutionary history.

Methods

Seventy accessions from Medicago, Trigonella, Melilotus and Trifolium were analysed by PCR to assess the presence of the repetitive E180 family, and fluorescence in situ hybridization (FISH) was used for physical mapping in somatic chromosomes.

Key Results

The E180 repeat unit was PCR-amplified in 37 of 40 taxa in Medicago, eight of 12 species of Trigonella, six of seven species of Melilotus and in two of 11 Trifolium species. Examination of the mitotic chromosomes revealed that only 13 Medicago and two Trigonella species showed FISH signals using the E180 probe. Stronger hybridization signals were observed in subtelomeric and interstitial loci than in the pericentromeric loci, suggesting this satellite family has a preferential genomic location. Not all 13 Medicago species that showed FISH localization of the E180 repeat were phylogenetically related. However, nine of these species belong to the phylogenetically derived clade including the M. sativa and M. arborea complexes.

Conclusions

The use of the E180 family as a phylogenetic marker in Medicago should be viewed with caution. Its amplification appears to have been produced through recurrent and independent evolutionary episodes in both annual and perennial Medicago species as well as in basal and derived clades.     

Seed and gland morphology in Euphorbia (Euphorbiaceae) with focus on their systematic and phylogenetic importance, a case study in Iranian highlands

A comprehensive study based on gland and seed micromorphology in Euphorbia (Euphorbiaceae) for species distributed in Iranian highlands is presented. A total of 86 species were studied. The gland structure was examined by direct field observations. Taxonomically important characters of glands were observed and measured: size, texture, shape, color, and horns. For species out of Iran herbarium materials were studied. Seed characteristics were examined using scanning electron microscopy (SEM) as well as dissecting light microscopy. Significant features are: seed size, seed shape, presence of caruncle, shape of caruncle, and seed surface ornamentation. A phylogenetic study using Maximum Parsimony (MP) and Bayesian Inference (BI) was performed based on sequences of nuclear DNA internal transcribed spacers (ITS) for selected species representing the main clades known in Euphorbia and with special focus on the species distributed in Iranian highlands. ITS sequences for 20 accessions representing 19 species are provided for the first time, and 48 accessions of 47 species were used from GenBank. The topologies of both analyses were congruent. The results indicate: (1) four main clades with high supports in subgen. Esula which are appropriate to be recognized at sectional rank. (2) E. larica is nested within clade A including few members of subgen. Rhizanthium and is closely related to sect. Balsamis, which is suggested here to be transferred from subgen. Esula into subgen. Rhizanthium. (3) E. osyridea of the monotypic subsect. Osyrideae is closely related to E. buhsei and to the members of sect. Esula. Tracing morphological characters on the phylogenetic tree shows that several morphological characters, such as seed ornamentation applied in previous subgeneric classification of the subgen. Esula, are homoplasious, but the gland structure and capsule surface characters are more reliable for classification purposes.     

Patterns of plastid and nuclear variation among apomictic polyploids of Hieracium: evolutionary processes and taxonomic implications

Background and Aims

Apomictic species (with asexual seed production) make up for 20–50 % of all taxonomically recognized species in northern Europe, but the phylogenetic relationships of apomictic species and the mode of evolution and speciation remain largely unknown and their taxonomy is consequently disputed.

Methods

In the present study, plastid psbD-trnT sequences (349 accessions) and 12 nuclear microsatellite loci (478 accessions) were used to create an overview of the molecular variation in (mainly) northern European members of the most species-rich of all plant genera, Hieracium s.s. The results are discussed and interpreted in the context of morphological and cytological data on the same species.

Key Results and Conclusions

The complete psbD-trnT alignment was 1243 bp and 50 polymorphisms defined 40 haplotypes. All haplotypes found in the sections of the genus distributed in the northern European lowlands fell into one of two main groups, group H and group V, mutually separated by seven or eight polymorphisms. All accessions belonging to H. sects. Foliosa, Hieracioides (viz. H. umbellatum) and Tridentata and all but one accession of triploid species of H. sects. Oradea and Vulgata showed haplotypes of group V. Haplotypes of group H were found in all accessions of H. sects. Bifida and Hieracium and in all tetraploid representatives of H. sects. Oreadea and Vulgata. Additional haplotypes were found in accessions of the genus Pilosella and in southern European and Alpine sections of Hieracium. In contrast, the distribution of individual haplotypes in the two major groups appeared uncorrelated with morphology and current taxonomy, but polymorphisms within species were only rarely encountered. In total, 160 microsatellite alleles were identified. Levels of variation were generally high with only nine pairs of accessions being identical at all loci (in all cases representing accessions of the same species). In the neighbor-joining analysis based on the microsatellite data, accessions of the same species generally clustered together and some smaller groups of species congruent with morphology and/or current taxonomy were recovered but, except for H. sect. Oreadea, most larger groups were not correlated with morphology. Although the plastid DNA sequences show too little variation and the nuclear microsatellites are too variable to resolve relationships successfully among species or to fully understand processes of evolution, it is concluded that both species and sections as defined by morphology are largely congruent with the molecular data, that gene flow between the sections is rare or non-existent and that the tetraploid species may constitute the key to understanding evolution and speciation in this genus.     

Pepper Rootstock Graft Compatibility and Response to Meloidogyne javanica and M. incognita

Resistance of pepper species (Capsicum annuum, C. baccatum, C. chinense, C. chacoense, and C. frutescens), cultivars and accessions to the root-knot nematodes Meloidogyne incognita race 2 and M. javanica, and their graft compatibility with commercial pepper varieties as rootstocks were evaluated in growth chamber and greenhouse experiments. Most of the plants tested were highly resistant to M. javanica but susceptible to M. incognita. Capsicum annuum AR-96023 and C. frutescens accessions as rootstocks showed moderate and relatively high resistance to M. incognita, respectively. In M. incognita-infested soil in a greenhouse, AR-96023 supported approximately 6-fold less nematode eggs per gram root and produced about 2-fold greater yield compared to a nongrafted commercial variety. The commercial variety grafted on AR-96023 produced a yield as great as the non-grafted variety in the root-knot nematode-free greenhouse. Some resistant varieties and accessions used as rootstocks produced lower yields (P < 0.01) than that of the non-grafted variety in the noninfested greenhouse. Use of rootstocks with nematode-resistance and graft compatibility may be effective for control of root-knot nematodes on susceptible pepper.     

Natural variation in the genes responsible for maturity loci E1, E2, E3 and E4 in soybean

Background and Aims

The timing of flowering has a direct impact on successful seed production in plants. Flowering of soybean (Glycine max) is controlled by several E loci, and previous studies identified the genes responsible for the flowering loci E1, E2, E3 and E4. However, natural variation in these genes has not been fully elucidated. The aims of this study were the identification of new alleles, establishment of allele diagnoses, examination of allelic combinations for adaptability, and analysis of the integrated effect of these loci on flowering.

Methods

The sequences of these genes and their flanking regions were determined for 39 accessions by primer walking. Systematic discrimination among alleles was performed using DNA markers. Genotypes at the E1–E4 loci were determined for 63 accessions covering several ecological types using DNA markers and sequencing, and flowering times of these accessions at three sowing times were recorded.

Key Results

A new allele with an insertion of a long interspersed nuclear element (LINE) at the promoter of the E1 locus (e1-re) was identified. Insertion and deletion of 36 bases in the eighth intron (E2-in and E2-dl) were observed at the E2 locus. Systematic discrimination among the alleles at the E1–E3 loci was achieved using PCR-based markers. Allelic combinations at the E1–E4 loci were found to be associated with ecological types, and about 62–66 % of variation of flowering time could be attributed to these loci.

Conclusions

The study advances understanding of the combined roles of the E1–E4 loci in flowering and geographic adaptation, and suggests the existence of unidentified genes for flowering in soybean,     

燕麦属不同倍性种质资源抗旱性状评价及筛选

盆栽控水试验测定了燕麦属13个二倍体、7个四倍体和5个六倍体物种共106份材料的主要抗旱性状表现,用GGEbiplot软件的主成分分析法比较了各性状之间的关系及其对抗旱鉴定的贡献,综合评价燕麦属野生资源在燕麦抗旱育种中的潜能和利用价值。结果表明,干旱处理后植株的死亡率和萎蔫程度与可溶性糖含量的增加幅度呈显著正相关关系(r>0.5, P<0.05),而胁迫后植株的丙二醛(MDA)含量和植株相对电导率与抗旱能力也明显相关(r>0.5, P<0.01)。综合考虑抗旱的相关形态和生理指标,筛选到二倍体Avena atlantica、A. wiestii 和A. strigosa,四倍体种A. murphyi,以及六倍体栽培燕麦A. sativa和普通野燕麦A. fatua的部分居群具有优良的综合抗旱性。基于A. wiestii,A. strigosa和A. murphyi与栽培燕麦较近的亲缘关系,其抗旱性可通过远缘杂交的方式在普通燕麦育种中加以利用。而对于具有明显抗旱优势的野生二倍体材料A. atlantica,则可通过克隆其抗旱基因进而遗传转化的方法将其应用于栽培燕麦的抗旱性改良。同时该研究表明燕麦的抗旱性不具有种属和分布区域的特异性,因此其抗旱性并非简单的由基因或环境决定,在确定抗旱材料时需要对个体进行全面的抗旱性评价和鉴定,以期在利用抗旱材料或通过克隆抗旱基因来改善干旱地区生态环境的实践中能更准确和有效。     

A molecular analysis of some Eastern Atlantic grouper from the Epinephelus and Mycteroperca genus

Mitochondrial cytochrome b (397 bp) and 16S rDNA (516 bp) sequences analysis was used to investigate the phylogenetic relationships among some Eastern Atlantic Epinephelinae species. Six species of Epinephelus (E. aeneus, E. caninus, E. costae, E. haifensis, E. marginatus and E. tauvina) and two species of Mycteroperca (M. rubra and M. fusca) were analysed. Neighbour-joining and maximum-parsimony analysis support the paraphyletic grouping of the Epinephelus and Mycteroperca analysed. The maximum pairwise nucleotide divergence value in cyt b among all taxa was 0.196 between E. aeneus and E. marginatus and the minimum value was 0.006 between E. costae and M. rubra. Meanwhile, in 16S sequence analysis, the maximum value is 0.093 between E. aeneus and E. tauvina and the minimum value is 0.011 between E. marginatus and M. rubra. Molecular clock estimates for the species suggest a divergence time of 20-24 mya, which coincides with the Miocene period. A molecular analysis was also conducted, using other Epinephelinae sequences from GenBank in order to improve our understanding of the phyletic status of the Epinephelus and Mycteroperca species analysed.     

Nucleotide diversity and minisatellite in chloroplast Asp(GUC)–Thr(GGU) region in Elymus trachycaulus complex, Elymus alaskanus and Elymus caninus

Nucleotide variation in chloroplast Asp(GUC)–Thr(GGU) intergenic region and genetic relationships among this group were examined among Elymus trachycaulus complex, Elymus alaskanus and Elymus caninus. The estimates of nucleotide diversity (π) ranged from 0.00111 for Elymus virescens to 0.03086 for E. caninus. Highest nucleotide diversity was found for E. caninus among the taxa analyzed here and followed by Elymus hyperarcticus. E. virescens accessions are genetically very uniform. Phylogenetic analysis suggested that E. caninus is paraphyletic. Elymus violaceus is genetically distinct from both E. alaskanus and E. trachycaulus. Our result indicates that Asp (GUC)–Thr (GGU) intergenic region has a high rate of evolutionary in Elymus species. Large indels detected in this region appear to have a highly rate of evolution and are thus more prone to homoplasy. We also first reported a minisatellite discovered in Asp (GUC)–Thr (GGU) region in Elymus species. The minisatellite identified here is an excellent candidate marker for studying population structures of Elymus species.     

Botryosphaeriaceae from tuart (Eucalyptus gomphocephala) woodland, including descriptions of four new species

Eucalyptus gomphocephala (tuart) is a tree native to the southwest coast of Western Australia, where, in some areas, there is a significant decline in the health of tuart. Botryosphaeriaceous taxa have been isolated as endophytes and canker pathogens from numerous hosts in many parts of the world and have been implicated in the decline of E. gomphocephala. In the present study, endophytic fungi were isolated from a wide variety of native woody plant species (Acacia cochlearis, A. rostellifera, Allocasuarina fraseriana, Agonis flexuosa, Banksia grandis, E. gomphocephala, E. marginata and Santalum acuminatum), at two locations in native E. gomphocephala woodland; a site in decline at Yalgorup National Park and a healthy site at Woodman Point Regional Park. Of the 226 isolates obtained, 154 were botryosphaeriaceous taxa, 80 % of which were found to be Neofusicoccum australe, isolated from all hosts at both collection sites. Four new species are described, Dothiorella moneti, Dothiorella santali, Neofusicoccum pennatisporum, and a species belonging to a genus only recently included in the Botryosphaeriaceae, Aplosporella yalgorensis. The other species isolated were Botryosphaeria dothidea on the new hosts A. rostellifera, A. cochlearis and E. marginata and Dichomera eucalypti, on the new host E. marginata. None of the new species formed lesions on excised stems of their host species, E. gomphocephala, or a common plantation species, E. globulus. However, Neofusicoccum australe formed lesions on excised stems of E. globulus and E. gomphocephala.     

Genetic relationships between wild progenitor pear (Pyrus L.) species and local cultivars native to Georgia,South Caucasus

The genetic diversity of 108 individuals of wild pear species (Pyrus communis subsp. caucasica, P. balansae, P. salicifolia, P. syriaca, P. demetrii, P. bulgarica, P. ketzkhovelii, P. sachokiana) and 35 samples of local and introduced cultivated pears from the country of Georgia were compared to 73 individuals of wild P. communis subsp. caucasica and P. communis subsp. pyraster in the collection of USDA-ARS National Plant Germplasm System (NPGS). Pyrus communis subsp. caucasica from both Georgia and the NPGS, P. communis subsp. pyraster from the NPGS, and P. salicifolia from Georgia were differentiated, based on analysis of eleven microsatellite markers. In addition, accessions of P. communis subsp. caucasica from Georgia were genetically distinct from accessions of the same subspecies in the NPGS collection that originated from other European and Middle Eastern Asian countries. Local pear cultivars in Georgia were genetically similar to P. communis subsp. caucasica and P. balansae growing wild in Georgia suggesting that they may have originated from native pear trees that could serve as unique genetic resources for pear breeding programmes.     

Independent FLC Mutations as Causes of Flowering-Time Variation in Arabidopsis thaliana and Capsella rubella

Capsella rubella is an inbreeding annual forb closely related to Arabidopsis thaliana, a model species widely used for studying natural variation in adaptive traits such as flowering time. Although mutations in dozens of genes can affect flowering of A. thaliana in the laboratory, only a handful of such genes vary in natural populations. Chief among these are FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). Common and rare FRI mutations along with rare FLC mutations explain a large fraction of flowering-time variation in A. thaliana. Here we document flowering time under different conditions in 20 C. rubella accessions from across the species’ range. Similar to A. thaliana, vernalization, long photoperiods and elevated ambient temperature generally promote flowering. In this collection of C. rubella accessions, we did not find any obvious loss-of-function FRI alleles. Using mapping-by-sequencing with two strains that have contrasting flowering behaviors, we identified a splice-site mutation in FLC as the likely cause of early flowering in accession 1408. However, other similarly early C. rubella accessions did not share this mutation. We conclude that the genetic basis of flowering-time variation in C. rubella is complex, despite this very young species having undergone an extreme genetic bottleneck when it split from C. grandiflora a few tens of thousands of years ago.     

Essential oil composition of Hypericum L. species from Southeastern Serbia and their chemotaxonomy

The essential oils of the aerial parts of nine species of Hypericum (Hypericum barbatum, Hypericum hirsutum, Hypericum linarioides, Hypericum maculatum, Hypericum olympicum, Hypericum perforatum, Hypericum richeri, Hypericum rumeliacum and Hypericum tetrapterum), collected from different locations in Southeast Serbia, were obtained by steam distillation and analyzed by GC and GC–MS. The essential oils investigated were characterized by a high content of non-terpene compounds and a low content of monoterpenes. The contents of non-terpenes, monoterpenes and sesquiterpenes in oils of the species H. barbatum, H. richeri and H. rumeliacum (section Drosocaprium) were similar and these oils were characterized by high contents of fatty acids. The oils of H. hirsutum and H. linarioides (section Taeniocarpium) contained a high percentage of n-nonane. There were similarities in contents of non-terpenes and sesquiterpenes in oils of species that belong to the section Hypericum (H. maculatum, H. perforatum and H. tetrapterum). The oil of H. olympicum differed from others by higher terpene content. A comparison was also carried out of the chemical composition of the essential oils from flower, leaf and stem of H. perforatum and it revealed that the highest concentration of non-terpene compounds was found in the flower and stem oil, while a high concentration of sesquiterpenes was characteristic for leaf oil. There were significant differences in the concentrations of the same compounds in the essential oils of H. maculatum, H. olympicum and H. perforatum, collected in different years from the same location which could be explained by seasonal differences. All data were statistically processed with principal component analysis and cluster analysis. The main conclusion from the above data is that genetic and environmental factors both play a role in determining the composition of essential oils of the Hypericum species studied.     

Using genetic diversity information to establish core collections of Stylosanthes capitata and Stylosanthes macrocephala

Stylosanthes species are important forage legumes in tropical and subtropical areas. S. macrocephala and S. capitata germplasm collections that consist of 134 and 192 accessions, respectively, are maintained at the Brazilian Agricultural Research Corporation Cerrados (Embrapa-Cerrados). Polymorphic microsatellite markers were used to assess genetic diversity and population structure with the aim to assemble a core collection. The mean values of H_O and H_E for S. macrocephala were 0.08 and 0.36, respectively, whereas the means for S. capitata were 0.48 and 0.50, respectively. Roger’s genetic distance varied from 0 to 0.83 for S. macrocephala and from 0 to 0.85 for S. capitata. Analysis with STRUCTURE software distinguished five groups among the S. macrocephala accessions and four groups among those of S. capitata. Nei’s genetic diversity was 27% in S. macrocephala and 11% in S. capitata. Core collections were assembled for both species. For S. macrocephala, all of the allelic diversity was represented by 23 accessions, whereas only 13 accessions were necessary to represent all allelic diversity for S. capitata. The data presented herein evidence the population structure present in the Embrapa-Cerrados germplasm collections of S. macrocephala and S. capitata, which may be useful for breeding programs and germplasm conservation.     

Herbivore feeding preferences as measured by leaf damage and stomatal ingestion: a mangrove crab example

The diet of the mangrove crab, Aratus pisonii, was assessed by determining the percent of damaged leaves at selected mangrove communities and by examining herbivore gut contents. This study compared the utility of both methods and tested if comparable levels of damage and dietary preference occurred using the methods. Percent of damaged leaves was determined for the three species of mangroves within Tampa Bay, FL, USA, including: the red, black, and white mangroves (Rhizophora mangle, Avicennia germinans, and Laguncularia racemosa, respectively) in four 5×10-m quadrats during summer 2001. For each species, in each of the quadrats, 200 leaves per tree were assessed for the presence or absence of crab damage. A. pisonii were sampled from the same quadrats from which leaf damage data were collected. Stomach contents were dissected and food items were classified into a number of categories.Species damaged and preferred were determined by comparing relative numbers of mangrove leaf stomata from the three mangrove species in gut contents. Results suggested that both methods provide similar estimates of preference. R. mangle leaves were preferred over those of A. germinans and L. racemosa. The percent of R. mangle leaves with damage was about 20-30 times greater than the other species, and R. mangle leaf stomata were 3 to 20 times more abundant in crab guts compared to leaf stomata of the other species. Gut contents indicated that A. pisonii is omnivorous, that average-sized adult crabs (1.4-1.7-cm width) prefer R. mangle, and that the diet of males is more varied than of females. While use of both percent leaf damage and crab gut contents reliably indicates preference, gut contents may describe better the actual diet and elucidate trends for different size or sex classes within a population.     

Symbiotic diversity of Ensifer meliloti strains recovered from various legume species in Tunisia

Ensifer meliloti (formerly Sinorhizobium meliloti) was first considered as a specific microsymbiont of Medicago, Melilotus and Trigonella. However, strains of E. meliloti were recovered from root nodules of various legume species and their symbiotic status still remains unclear. Here, we further investigate the specificity of these strains. A collection of 47 E. meliloti strains isolated in Tunisia from root nodules of Medicago truncatula, Medicago sativa, Medicago ciliaris, Medicago laciniata, Medicago marina, Medicago scutellata, Phaseolus vulgaris, Cicer arietinum, Argyrolobium uniflorum, Lotus creticus, Lotus roudairei, Ononis natrix, Retama raetam, Genista saharae, Acacia tortilis, Hedysarum carnosum and Hippocrepis bicontorta were examined by REP-PCR fingerprinting, PCR-RFLPs of the 16S-23S rDNA IGS, the nifH gene and nifD-K intergenic spacer, and sequencing of 16S rRNA and nodA genes. Their nodulation range was also assessed by cross-inoculation experiments. No clear correlation was found between chromosomal backgrounds and host plants of origin. The nodulation polyvalence of the species E. meliloti was associated with a high symbiotic heterogeneity. On the basis of PCR-RFLP data from the nifH gene and nifD-K intergenic spacer, E. meliloti strains isolated from non-Medicago legumes harboured distinct genes and possessed wider host ranges. Some strains did not nodulate Medicago species. On the basis of nodA phylogeny, the majority of the Tunisian strains, including strains from Medicago, harboured distinct nodA alleles more related to those found in E. medicae than those found in E. meliloti. However, more work is still needed to characterize this group further. The diversity observed among M. laciniata isolates, which was supported by nodA phylogeny, nifH typing and the efficiency profile on M. ciliaris, indicated that what was thought to be bv. medicaginis is certainly heterogeneous.     

In Silico Identification and Experimental Validation of Insertion–Deletion Polymorphisms in Tomato Genome

Comparative analysis of the genome sequences of Solanum lycopersicum variety Heinz 1706 and S. pimpinellifolium accession LA 1589 using MUGSY software identified 145 695 insertion–deletion (InDel) polymorphisms. A selected set of 3029 candidate InDels (≥2 bp) across the entire tomato genome were subjected to PCR validation, and 82.4% could be verified. Of 2272 polymorphic InDels between LA 1589 and Heinz 1706, 61.6, 45.2, and 31.6% were polymorphic in 8 accessions of S. pimpinellifolium, 4 accessions of S. lycopersicum var. cerasiforme, and 10 varieties of S. lycopersicum, respectively. Genetic distance was 0.216 in S. pimpinellifolium, 0.202 in S. lycopersicum var. cerasiforme, and 0.108 in S. lycopersicum. The data suggested a reduction of genetic variation from S. pimpinellifolium to S. lycopersicum var. cerasiforme and S. lycopersicum. Cluster analysis showed that the 8 accessions of S. pimpinellifolium were in one group, whereas 4 accessions of S. lycopersicum var. cerasiforme and 10 varieties of S. lycopersicum were in the same group.     

Plastid DNA sequencing and nuclear SNP genotyping help resolve the puzzle of central American Platanus

Background and Aims

Recent research on the history of Platanus reveals that hybridization phenomena occurred in the central American species. This study has two goals: to help resolve the evolutive puzzle of central American Platanus, and to test the potential of real-time polymerase chain reaction (PCR) for detecting ancient hybridization.

Methods

Sequencing of a uniparental plastid DNA marker [psbA-trnH^(GUG) intergenic spacer] and qualitative and quantitative single nucleotide polymorphism (SNP) genotyping of biparental nuclear ribosomal DNA (nrDNA) markers [LEAFY intron 2 (LFY-i2) and internal transcribed spacer 2 (ITS2)] were used.

Key Results

Based on the SNP genotyping results, several Platanus accessions show the presence of hybridization/introgression, including some accessions of P. rzedowskii and of P. mexicana var. interior and one of P. mexicana var. mexicana from Oaxaca (= P. oaxacana). Based on haplotype analyses of the psbA-trnH spacer, five haplotypes were detected. The most common of these is present in taxa belonging to P. orientalis, P. racemosa sensu lato, some accessions of P. occidentalis sensu stricto (s.s.) from Texas, P. occidentalis var. palmeri, P. mexicana s.s. and P. rzedowskii. This is highly relevant to genetic relationships with the haplotypes present in P. occidentalis s.s. and P. mexicana var. interior.

Conclusions

Hybridization and introgression events between lineages ancestral to modern central and eastern North American Platanus species occurred. Plastid haplotypes and qualitative and quantitative SNP genotyping provide information critical for understanding the complex history of Mexican Platanus. Compared with the usual molecular techniques of sub-cloning, sequencing and genotyping, real-time PCR assay is a quick and sensitive technique for analysing complex evolutionary patterns.