Who is the mother of the potato? — restriction endonuclease analysis of chloroplast DNA of cultivated potatoes

Summary Chloroplast DNA from 44 lines of 16 wild and 7 cultivatedSolanum species were compared by restriction endonuclease analysis. Seven chloroplast genome types were identified among them by 5 restriction enzymes: Type A (S. tuberosum ssp.andigena andS. maglia); Type S (S. goniocalyx, S. phureja, S. stenotomum, S. ×chaucha and a line of ssp.andigena); Type C (S. acaule, S. bukasovii, S. canasense, S. multidissectum andS. ×juzepczukii); Type T (S. tuberosum ssp.tuberosum); Type W (other wild species); Type W (S. chacoense f.gibberulosum) and Type W (S. tarijense). From this cytoplasmic identification, it was concluded thatS. goniocalyx, S. phureja, S. ×chaucha and ssp.andigena were derived fromS. stenotomum or its primitive type, which may have originally evolved itself fromS. canasense. The chloroplast genome of the European potato, however, was introduced from the Chilean potato, which might have been primarily constructed with the nuclear genome from ssp.andigena and with cytoplasm from other species. The cytoplasmic donor of the Chilean potato could not be determined.Contribution from the Laboratory of Genetics, Faculty of Agriculture, Kyoto University, Japan, No. 479. This work was done at Kyoto University when the author was a graduate student at Kobe University     

Oxygen evolution and phosphorylation in Scenedesmus as influenced by the inhibitor-β complex from potato and by phloridzin

Summary Scenedesmus cells were tried as a photosynthesizing test system for the inhibitor- complex from potato (var. Majestic). The main effect on oxygen evolution is an inhibition of the second gush during the induction period. The formation of bound phosphate is increased by the inhibitor when the cell suspensions are shaken in the light, whereas no significant trend is observed in similar experiments in the dark. — Phloridzin inhibits the same part of oxygen evolution as inhibitor- from potato when cells pretreated in light are the test object. Concentrations of 1 mM increase the formation of bound phosphate in light, but at 2 mM there is a decrease in this action. Phloridzin and inhibitor- from potato have different R_f values. — The biochemical effects studied precede possible effects on cell division. — The results are discussed in relation to the localization of the site(s) of action.     

Rare recent natural hybridization in Hieracium s. str. – evidence from morphology, allozymes and chloroplast DNA

The first proven data on natural hybridization in the genus Hieracium s. str. are presented. Plants with intermediate morphological characters between the diploids H. alpinum and H. transsilvanicum were found in the Muntii Rodnei (Romanian Eastern Carpathians) in 2001 and in the Chornohora Mts (Ukrainian Eastern Carpathians) in 2003. While plants of intermediate morphology between usually so called basic species are usually tri- or tetraploid in Hieracium s. str., these plants were diploid (2n=18) like both parental species in this region. The Romanian plant did not produce fertile achenes in free pollination and in control backcrosses with H. transsilvanicum, two hybrids from Ukraine were completly seed sterile in free pollination and reciprocal crosses. Pollen stainability as an indirect measure of male fertility was quite high in the studied Ukrainian hybrid plants and similar to the parental taxa. Evidence from allozyme analysis also confirmed the hybrid origin of the studied plants. Sequencing and PCR-RFLP analyses of the trnT-trnL intergenic spacer revealed that all hybrid plants had the H. transsilvanicum chloroplast DNA haplotype. Maternal inheritance of chloroplast DNA in this particular cross was proved with artificial hybrids from reciprocal experimental crosses between H. alpinum and H. transsilvanicum. In both localities, the natural hybrid plants were found in disturbed habitats, exceptionally allowing contact of the otherwise ecologically vicariate parental species. Morphologically, the hybrid plants belong to H. × krasani Woł.     

Origins of cultivars of Chrysanthemum—Evidence from the chloroplast genome and nuclear LFY gene

The origins of cultivated chrysanthemums have attracted considerable attention, but they remain poorly known. Here, we reconstructed the phylogeny of representative well‐known cultivars and wild species of the genus Chrysanthemum using chloroplast genomes and the nuclear LEAFY gene. Our results suggest that geographic and ecological factors may determine the opportunities for wild species to be involved in the origin of the cultivars. The wild species C. indicum, C. zawadskii, C. dichrum, C. nankingense, C. argyrophyllum, and C. vestitum were likely directly or indirectly involved as paternal species of most of the chrysanthemum cultivars examined in this study. Yet, the maternal species is supported to be a lineage of an extinct wild Chrysanthemum species and its subsequent cultivars, as all accessions of chrysanthemum cultivars sampled formed a strongly supported clade, distinct from all other species of Chrysanthemum in the plastome tree. Thus, the cultivated chrysanthemums originated from multiple hybridizations involving several paternal species rather than only two or a few wild species, with an extinct species and its subsequent cultivars serving as the maternal parents. This finding is consistent with Chrysanthemum having high rates of hybridization and gene flow, which has been demonstrated within previous studies; nevertheless, it is important to unravel the role of an extinct wild Chrysanthemum species as the ultimate maternal parent species for all the chrysanthemum cultivars. Our results also suggest that C. vestitum from Tianzhu and Funiu Mountains in Anhui and Henan Provinces of China represent two distinct cryptic species.     

Narrow species concepts in the Frullania dilatata–appalachiana–eboracensis complex (Porellales, Jungermanniopsida): evidence from nuclear and chloroplast DNA markers

We investigated the phylogeny of a Holarctic-Asian group of Frullania species, the Frullania dilatata–F. appalachiana–F. eboracensis complex, using multiple accessions of morphologically circumscribed taxa and three molecular markers (nrITS region, cp DNA trnL-F and atpB-rbcL regions). Maximum parsimony and likelihood analyses indicated monophyly of morphologically defined taxa. Our phylogenies support a species rather than a subspecies concept within the complex, with four species in North America (F. appalachiana, F. eboracensis, F. parvistipula and F. virginica), and two species in Europe (F. dilatata and F. parvistipula). Accessions of F. dilatata from Southeast Europe and Asia are separated from other European accessions, indicating a former disjunct range of the species.     

Phylogenetic relationships between cultivated and wild species of the genusBeta revealed by DNA “fingerprinting”

Forty-one accessions of the genusBeta representing wild and cultivated species of all sections were analyzed by DNA fingerprinting. Four sugar beet minisatellite DNA probes revealed characteristic banding patterns with Southern-hybridizedBeta DNA restricted withHindIII. A total of 111 polymorphic RFLP bands were scored across all accessions. Cluster analysis based on genetic similarity estimates for all 820 combinations of accessions revealed the following results. (1) All accessions could unambiguously be identified by a characteristic RFLP banding pattern. (2) The sugar beet cultivars examined displayed a low level of genetic diversity; they showed high similarity toB. Vulgaris ssp.maritima but low genetic similarity to the other wild species of section I. (3) In most cases, the present taxonomic classification of the genusBeta was confirmed. Species of sections II, III, and IV were clearly distinguishable from those of section I except forB. Macrocarpa, which showed high similarity to wild species of section II. In a second experiment, 108 single-copy RFLP probes from sugar beet were Southern hybridized withB. procumbens DNA. A surprisingly low degree of homology (34%) was found. The results are discussed with regard to the taxonomic classification of the genusBeta.     

Phylogenomic evidence of bryophytes’ monophyly using complete and incomplete data sets from chloroplast proteomes

It is well recognized that bryophytes form the basal clade of land plants. However, the paraphyletic or monophyletic origin of bryophytes remains controversial. To get new insight into bryophytes’ relationship we analyzed four data sets, 1 complete (common orthologous protein sequences; COPs) and 3 incomplete (COPs + 1, COPs + 1?+?3 and COPs + 1?+?3?+?2 data sets with 0.16%, 3.2% and 3.77% missing data, respectively) from chloroplast proteomes, representing 1 charophycean alga (outgroup), 5 bryophytes, 4 pteridophytes and 6 gymnosperms. Maximum likelihood analyses under cpREV model of all four data sets showed monophyly of bryophytes with 100% bootstrap support. Further, sister relationship of mosses and liverworts has been inferred with strong bootstrap support in all data sets. Although all incomplete data sets have gradually increasing missing data, the trees obtained from them have higher levels of bootstrap support for most of the nodes in comparison to the tree from complete data set. This study also demonstrated the importance of using longer sequences even with missing data for phylogeny reconstruction.     

DNA targeting by the type I-G and type I-A CRISPR–Cas systems of Pyrococcus furiosus

CRISPR–Cas systems silence plasmids and viruses in prokaryotes. CRISPR–Cas effector complexes contain CRISPR RNAs (crRNAs) that include sequences captured from invaders and direct CRISPR-associated (Cas) proteins to destroy corresponding invader nucleic acids. Pyrococcus furiosus (Pfu) harbors three CRISPR–Cas immune systems: a Cst (Type I-G) system with an associated Cmr (Type III-B) module at one locus, and a partial Csa (Type I-A) module (lacking known invader sequence acquisition and crRNA processing genes) at another locus. The Pfu Cmr complex cleaves complementary target RNAs, and Csa systems have been shown to target DNA, while the mechanism by which Cst complexes silence invaders is unknown. In this study, we investigated the function of the Cst as well as Csa system in Pfu strains harboring a single CRISPR–Cas system. Plasmid transformation assays revealed that the Cst and Csa systems both function by DNA silencing and utilize similar flanking sequence information (PAMs) to identify invader DNA. Silencing by each system specifically requires its associated Cas3 nuclease. crRNAs from the 7 shared CRISPR loci in Pfu are processed for use by all 3 effector complexes, and Northern analysis revealed that individual effector complexes dictate the profile of mature crRNA species that is generated.     

Age-related changes in brain mitochondrial DNA deletion and oxidative stress are differentially modulated by dietary fat type and coenzyme Q₁₀

Mitochondria-related oxidative damage is a primary event in aging and age-related neurodegenerative disorders. Some dietary treatments, such as antioxidant supplementation or the enrichment of mitochondrial membranes with less oxidizable fatty acids, reduce lipid peroxidation and lengthen life span in rodents. This study compares life-long feeding on monounsaturated fatty acids (MUFAs), such as virgin olive oil, and n-6 polyunsaturated fatty acids, such as sunflower oil, with or without coenzyme Q₁₀ supplementation, with respect to age-related molecular changes in rat brain mitochondria. The MUFA diet led to diminished age-related phenotypic changes, with lipoxidation-derived protein markers being higher among the older animals, whereas protein carbonyl compounds were lower. It is noteworthy that the MUFA diet prevented the age-related increase in levels of mitochondrial DNA deletions in the brain mitochondria from aged animals. The findings of this study suggest that age-related oxidative stress is related, at the mitochondrial level, to other age-related features such as mitochondrial electron transport and mtDNA alterations, and it can be modulated by selecting an appropriate dietary fat type and/or by suitable supplementation with low levels of the antioxidant/electron carrier molecule coenzyme Q.     

Restriction data from chloroplast DNA for phylogenetic reconstruction: Is there only one accurate way of scoring?

Information from the same restriction analysis of chloroplast DNA of 33 taxa ofRubiaceae was scored in four different ways, two of which were based on fragments, and two on restriction sites, and they were subsequently analysed with Wagner parsimony. The methods resulted in different phylogenetic trees. The inherent differences between the methods relate to the amount of non-homologous characters and dependent characters, but none of the methods will systematically bias the resulting cladograms. The fragment analyses are much less time-consuming, but probably less accurate, than the site analyses. The choice of method is dependent on a trade-off between accuracy and resources (time). One important recommendation is made: all phylogenetic analyses of chloroplast DNA data should be accompanied by a data matrix and contain information on how the matrix was compiled.     

DNA damage in potato plants induced by cadmium,ethyl methanesulphonate and γ-rays

We have calibrated the alkaline protocol of the plant comet (Single Cell Gel Electrophoresis) assay as a method for detecting the extent of induced DNA damage in potato plants (Solanum tuberosum L. cultivar Korela). After 2 and 24 h treatments of the rooted cuttings with the heavy metal cadmium (Cd²⁺), a dose–response increase in DNA damage was noted versus controls in root nuclei. With a 24 h recovery period, the Cd²⁺-induced DNA damage in roots increased significantly. No significant increase in DNA damage was demonstrated in leaf nuclei after 24 h Cd²⁺ treatments, but continuous Cd²⁺ treatments for 2 weeks resulted in an increase in leaf DNA damage. This increase may be however associated with necrotic and apoptotic DNA fragmentation, as the affected plants had inhibited growth and distorted yellowish leaves. For comparison, the monofunctional alkylating agent ethyl methanesulphonate, and γ-rays were assessed for induced DNA damage. Analysis of the accumulation of cadmium by inductively coupled plasma optical emission spectrometry demonstrates that roots accumulate almost 9-fold more cadmium than aboveground parts of the rooted potato cuttings. This may explain the absence of Cd²⁺ genotoxicity in leaves after short-term treatments.     

Sea anemone collagen: Further evidence for the existence of only oneα-chain type

Summary Collagen from an inferior invertebrate, namely from the sea anemoneActinia equina L., appears to consist of three identical subunits (-chains). New evidence for this situation is reported on the basis of preparative-scale experiments.No fractionation of sea anemone collagen was obtained by CM-cellulose chromatography which is the method of choice for the isolation of vertebrate collagen subunits. On the other hand, the-component (mol. wt., 95.000) could be isolated by gel chromatography. It was homogenous when investigated by polyacrylamide gel electrophoresis (in the presence of sodium dodecyl sulphate) and by ion exchange chromatography on CM-cellulose. The amino acid composition of the-component was identical with that of unfractionated collagen.Divergent evolution of the collagen molecule appears likely since vertebrate collagen molecules are made up of different-chain types.     

In vivo evidence for translesion synthesis by the replicative DNA polymerase δ

The intolerance of DNA polymerase δ (Polδ) to incorrect base pairing contributes to its extremely high accuracy during replication, but is believed to inhibit translesion synthesis (TLS). However, chicken DT40 cells lacking the POLD3 subunit of Polδ are deficient in TLS. Previous genetic and biochemical analysis showed that POLD3 may promote lesion bypass by Polδ itself independently of the translesion polymerase Polζ of which POLD3 is also a subunit. To test this hypothesis, we have inactivated Polδ proofreading in pold3 cells. This significantly restored TLS in pold3 mutants, enhancing dA incorporation opposite abasic sites. Purified proofreading-deficient human Polδ holoenzyme performs TLS of abasic sites in vitro much more efficiently than the wild type enzyme, with over 90% of TLS events resulting in dA incorporation. Furthermore, proofreading deficiency enhances the capability of Polδ to continue DNA synthesis over UV lesions both in vivo and in vitro. These data support Polδ contributing to TLS in vivo and suggest that the mutagenesis resulting from loss of Polδ proofreading activity may in part be explained by enhanced lesion bypass.     

A phylogenetic study of the palm family (Palmae) based on chloroplast DNA sequences from thetrnL —trnF region

Phylogenies of the palm family based on DNA sequences from thetrnL —trnF region of the chloroplast genome are presented. Although the region is highly conserved in palms and relatively few sites in the aligned data matrix are parsimony informative, a variety of relationships among members of the family are revealed by the analyses, some of which are congruent with the current classification of the palms, and others which are not. However, consensus trees contain high levels of ambiguosity, partly due to the inadequate numbers of informative characters in the dataset. Additional data are required before well resolved palm phylogenies can be generated.     

African origins of modern asses as seen from paleontology and DNA: what about the Atlas wild ass?

As a contribution to the still open debate on the multiple african origins of the domesticated donkey, this work focuses on the wild ass of the Maghreb. It follows the recent paleontological review of the equids from Lac Karâr, a middle Pleistocene site in Northern Algeria, where most of the faunal remains were attributed to wild asses (Equus africanus Heuglin and Fitzinger, 1866). The morphometric resemblance between the equid of Lac Karâr, and Equus melkiensis Bagtach, Hadjouis and Eisenmann, 1984 which might correspond to the equid commonly referred to, as the Atlas wild ass (vernacular name) and, by descent, to Equus tabeti Arambourg, 1970, the only subspecies of ass from the early Pleistocene in Northern Africa, highlights the need for extensive biomolecular and radiometric studies on this wild and robust ass, endemic to the Maghreb. This is especially important given that progress in extracting ancient DNA from equids has been demonstrated by several recent studies and that remains of wild asses are still being uncovered in many late Pleistocene to Holocene (Neolithic) deposits in the Maghreb. The results from such studies could substantially improve the knowledge on the origin of asses. In particular, these analyses could shed light on the, as yet, undetermined clade 2 which may originate from the wild ass of the Maghreb as recently hypothesized by several authors. The archaeological and genetic data reviewed in this paper focuses on the ancient range of the Atlas wild ass mainly from sites in the northern part of the Maghreb; it contributes to current debates regarding this subspecies as one of the possible ancestors of modern asses. In addition, the paper identifies directions for further genetic researches on the extant donkey of the Maghreb.     

Changes in the activity of superoxide dismutase isoforms in the course of low-temperature adaptation in potato plants of wild type and transformed with Δ12-acyl-lipid desaturase gene

We investigated the changes in the total activity of superoxide dismutase (SOD) and the role of its isoforms in hardening potato (Solanum tuberosum L., cv. Desnitsa) plants of wild type and transformed with desA gene of Δ12-acyl-lipid desaturase from Synechocystis sp. PCC 6803. Hydroponically grown 8-week-old plants were exposed for six days to hardening temperature of 5°C. Before chilling, the total SOD activity in the transformed plants was somewhat greater than in the control plants. By the first day of hardening, SOD activity in both potato genotypes rose almost 1.5 times; however, the absolute value of SOD activity was considerably greater in the transformed plants. Subsequently, the total SOD activity in both genotypes decreased and by the end of the 6th day, it almost returned to the initial level. Electrophoretic and inhibitor analyses of potato plants revealed three types of SOD with one isoform of Mn-SOD, four isoforms of Fe-SOD, and two isoforms of Cu/Zn-SOD. In both genotypes, Fe-SOD3 manifested the greatest activity before chilling and in the course of hardening. Such changes in SOD activity corresponded to the rate of generation of superoxide anion radical and elevation of the content of products of peroxide oxidation of lipids (POL). Our data suggest that in the course of hardening of cold-resistant potato plants, the total SOD activity changed mostly due to Fe-SOD3 and to some extent as a result of elevated Cu/Zn-SOD2 activity, which was particularly evident at the beginning of hardening and more pronounced in the transformed plants. We assume that such temporal pattern is related to a greater rate of superoxide anion generation in the transformed plants as compared with control plants.     

DNase-I-like enzyme from the carp liver—Inhibition by muscle and endogenous actin

• 1.1. DNase-I-like activity occurs in the carp (Cyprinus carpio) liver cytosol (supernatant 105,000g).
• 2.2. The enzyme resembles DNase I from bovine pancreas in respect to the molecular mass (~31 kDa), pH (7.4) and ion requirements (Mg²⁺, Ca²⁺) and the ability to degrade native as well as denatured DNA.
• 3.3. As judged by comparison of DNase zymograms obtained after native- and SDS-PAGE, the enzyme occurs in the three molecular forms of similar molecular weight and different charges.
• 4.4. All these forms are inhibited by rabbit skeletal muscle actin as well as by endogenous actin isolated from the carp liver cytosol.
• 5.5. DNase from the carp liver cytosol does not interact with the antibodies directed against DNase I from bovine pancreas and against DNase I from the rat and bovine parotid glands.