Origins of Allium ampeloprasum horticultural groups and a molecular phylogeny of the section Allium (Allium: Alliaceae)

The subgenus Allium section Allium includes economically important species, such as garlic and leek, as well as other polyploid minor crops. Phylogenetic studies within this section, with a focus on horticultural groups within A. ampeloprasum, were performed on 31 accessions of 17 species using the nuclear ribosomal DNA internal transcribed spacer (ITS) region and the chloroplast trnL-F and trnD-T regions. The results confirmed the monophyly of section Allium. Four main clades were identified on all ITS analyses but the relationships among those and the remaining species studied within section Allium remained unresolved. Trees based on cpDNA recovered two major clades and a topology only partly congruent with that of the ITS tree. Intra-individual polymorphism of the ITS region proved useful in tracking putative parent species of polyploid taxa. The allopolyploid origin of great headed garlic (GHG), A. iranicum and A. polyanthum was confirmed. No signs of hybridization in leek or kurrat were detected but possible introgression events were identified in pearl onion and bulbous leek. Although GHG is often used as a garlic substitute, molecular analysis revealed only a distant relationship with garlic. We also clarified the previous incorrect classification of cultivated forms within A. ampeloprasum, by showing that leek, kurrat, pearl onion, and bulbous leek should be considered separately from GHG.     

Genetic diversity of the narrow endemic Allium aaseae (Alliaceae)

Low levels of genetic variability are common for a number of geographically restricted plants: these data are consistent with theoretical expectations that small populations should be genetically depauperate. However, in some species, high levels of variability have been found in rare species. Allium aaseae is a rare, narrow endemic in the foothills of the Boise Front of southwestern Idaho. Genetic variation in the rare endemic A. aaseae, and nearby populations of the more common species, A. simillimum, was examined with randomly amplified polymorphic DNA (RAPD) data. Eight populations of A. aaseae and six populations of A. simillimum (three near the range of A. aaseae, and three distant populations) of 25 individuals each were examined for this analysis. Genetic diversity as determined with RAPD markers of both species examined in this study is largely found within and not among populations. Levels of genetic diversity are high, especially for a narrow endemic species such as A. aaseae. Proportion of RAPD loci polymorphic was high in both species, although slightly higher in the more common A. simillimum. Because these higher levels of genetic variability run counter to theory, alternative explanations beyond population size must be invoked to explain the levels of genetic diversity found in this study. Possible explanations are (1) A. aaseae is only recently derived from A. simillimum, (2) hybridization between A. aaseae and A. simillimum is occurring, (3) multiple origins of A. aaseae, (4) populations of A. simillimum included in the analysis are all A. aaseae, (5) A. aaseae and A. simillimum are conspecific, and (6) an artifact of RAPD data.     

Ultralong telomeres shorten with age in nestling great tits but are static in adults and mask attrition of short telomeres

Telomere length (TL) is increasingly being used as a biomarker of senescence, but measuring telomeres remains a challenge. Within tissue samples, TL varies between cells and chromosomes. Class I telomeres are (presumably static) interstitial telomeric sequences, while terminal telomeres have been divided in shorter (Class II) telomeres and ultralong (Class III) telomeres, and the presence of the latter varies strongly between species. Class II telomeres typically shorten with age, but little is known of Class III telomere dynamics. Using multiple experimental approaches, we show great tits to have ultralong telomeres, and we investigated age effects on Class II and III telomeres using a longitudinal approach (our method excludes Class I telomeres). In adults, TL averaged over the whole distribution did not significantly change with age. However, more detailed analyses showed that Class II TL did shorten with age, and, as in other species, the longest Class II telomeres within individuals shortened more quickly with age. In contrast, Class III TL did not shorten with age within individual adults. Surprisingly, we found the opposite pattern in nestlings: Class III TL shortened significantly with age, while the age effect on Class II TL was close to zero. Thus, Class III TL may provide information on developmental history, while Class II TL provides information on telomere dynamics in adulthood. These findings have practical implications for telomere studies and raise the interesting question of what causes variation in TL dynamics between chromosomes within individuals and how this is related to development.     

Plastid transformation in greening scales of the onion bulb (Allium cepa,Alliaceae)

The greening of the upper part of the outerAllium cepa L. bulb scales, in particular along the vascular regions, is limited to the hypodermal cells in which typical leucoplasts are transformed to normal and functional chloroplasts. This process is light dependent and cannot afterwards be reversed or modified by darkness. The changes in fine structure are described and briefly discussed.Dedicated to Prof. DrLothar Geitler on the occasion of his 90th birthday and 55 years after the publication of his Grundriß der Cytologie.     

Variability in blood platelet inhibitory activity of Allium (Alliaceae) species accessions

In the past 20 yr, the presence of blood platelet inhibitory activity in plant species from the genus Allium has been confirmed by a range of clinical and in vitro investigations. Although a number of Allium species have been identified as possessing antiplatelet properties, little is known of the variability for this trait among accessions in these species. Experiments were conducted to assess variability in antiplatelet activity of 58 Allium (Alliaceae) accessions. Extracts were prepared from a diverse collection of 16 Allium species accessions, 33 cultivated accessions of Allium cepa including standard cultivars, inbred lines, and open-pollinated populations, and nine Allium cepa plant introductions of diverse origin. Platelet inhibitory activity was determined via a platelet aggregation assay with human platelet-rich plasma. Relative in vitro inhibition of platelet aggregation was measured for each accession and control samples, and inhibition constants (IC₅₀) were calculated. Dose-dependent inhibition was observed and measured for each Allium accession. Significant (P < 0.01) IC₅₀ variability was detected among accessions, with the lowest accession IC₅₀ values exhibiting nearly 50-fold greater inhibition of aggregation than the highest accession IC₅₀ values. IC₅₍₎ variability among Allium cepa accessions was ≈ 12 times less than among Allium species accessions. Results from this investigation demonstrate substantial variability for efficacy of the antiplatelet factor among Allium accessions.     

Pollen morphology of selected species of Allium (Alliaceae) distributed in Iran

Pollen morphology of 19 species of Allium representing six subgenera and 12 sections, were studied. The following characters were recognized as important for separating taxa at different taxonomic ranks: the sulcus, presence or absence of perforations on the pollen surface, density of perforations, size of perforations and size of the pollen grains. Rugulate, rugulate–striate, and simple–perforate exine ornamentation were distinguished. The type of sulcus is very characteristic in A. subgen. Allium sect. Allium . The extended sulcus was not observed in any species the other sections of subgen. Allium studied here, such as sect. Caerulea ( A. capitellatum ), sect. Codonprasum ( A. lenkoranicum and A. stamineum ) and sect. Avulsea ( A. rubellum and A. umblicatum ). Imperforated pollen grains were observed in representatives of A. subgen. Reticulatobulbosa and subgen. Polyprason .     

Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes

Prokaryotic chromosomes code for toxin–antitoxin (TA) loci, often in multiple copies. In E.coli, experimental evidence indicates that TA loci are stress-response elements that help cells survive unfavorable growth conditions. The first gene in a TA operon codes for an antitoxin that combines with and neutralizes a regulatory ‘toxin’, encoded by the second gene. RelE and MazF toxins are regulators of translation that cleave mRNA and function, in interplay with tmRNA, in quality control of gene expression. Here, we present the results from an exhaustive search for TA loci in 126 completely sequenced prokaryotic genomes (16 archaea and 110 bacteria). We identified 671 TA loci belonging to the seven known TA gene families. Surprisingly, obligate intracellular organisms were devoid of TA loci, whereas free-living slowly growing prokaryotes had particularly many (38 in Mycobacterium tuberculosis and 43 in Nitrosomonas europaea). In many cases, TA loci were clustered and closely linked to mobile genetic elements. In the most extreme of these cases, all 13 TA loci of Vibrio cholerae were bona fide integron elements located in the V.cholerae mega-integron. These observations strongly suggest that TA loci are mobile cassettes that move frequently within and between chromosomes and also lend support to the hypothesis that TA loci function as stress-response elements beneficial to free-living prokaryotes.     

TRIM retrotransposons occur in apple and are polymorphic between varieties but not sports

Retrotransposon markers have been demonstrated to be powerful tools for investigating linkage, evolution and genetics diversity in plants. In the present study, we identified and cloned three full-size TRIM (terminal-repeat retrotransposon in miniature) group retrotransposon elements from apple (Malus domestica) cv. ‘Antonovka’, the first from the Rosaceae. To investigate their utility as markers, we designed primers to match the long terminal repeats (LTRs) of the apple TRIM sequences. We found that PCR reactions with even a single primer produced multiple bands, suggesting that the copy number of these TRIM elements is relatively high, and that they may be locally clustered or nested in the genome. Furthermore, the apple TRIM primers employed in IRAP (inter-retrotransposon amplified polymorphism) or REMAP (retrotransposon-microsatellite amplified polymorphism) analyses produced unique, reproducible profiles for 12 standard apple cultivars. On the other hand, all seven of the sport mutations in this study were identical to their mother cultivar. Genetic similarity values calculated from the IRAP/REMAP analyses or the STMS (sequence tagged microsatellite sites) analysis were generally comparable. PAUP cluster analysis based on IRAP and REMAP markers in apple and Japanese quince generated an NJ tree that is in good accordance with both a tree based on SMTS markers and the origin of the studied samples. Our results demonstrate that, although they do not encode the proteins necessary to carry out a life cycle and are thereby non-autonomous, TRIMs are at least as polymorphic in their insertion patterns as conventional complete retrotransposons. Kristiina Antonius-Klemola, Ruslan Kalendar are the first two authors contributed equally to this work     

Flies (Diptera: Muscidae: Calliphoridae) are efficient pollinators of Allium ampeloprasum L. (Alliaceae) in field cages

In conjunction with efforts to identify efficient insect pollinators for seed multiplication of cross-pollinated plant species stored and maintained by USDA-ARS Western Regional Plant Introduction Station (WRPIS), experiments were conducted to assess and compare the efficiency of the house fly, Musca domestica L. (Diptera: Muscidae), and Calliphora vicina Robineau-Desvoidy (Diptera: Calliphoridae), and different densities of each fly species, to pollinate leek, Allium ampeloprasum L., plant inventory (PI) accessions in field cages for seed yield maximization and high germination. Cages with flowering plants were exposed to 0 flies or stocked with 100, 250, and 500 M. domestica or C. vicina pupae per week for 6 (2002) and 7 (2004) wk. Seed yield (weight per cage) increased linearly as fly densities (C. vicina or M. domestica) increased from 0 to 500 pupae per week, with 500 fly cages averaging 340.7 g (C. vicina) and 70.5 g (M. domestica) of seed in 2002 (PI 368343) and 615.3 g (PI 168977) and 357.5 g (PI 368343) in 2004 when only the C. vicina was used. For 0, 100, and 250 fly cages, seed yields averaged between 2.3 and 175.3 g in 2002 and 10.7 and 273.1 g in 2004. Mean 100-seed weights between treatments ranged narrowly between 0.4 and 0.5 g in 2002 and 0.3 and 0.4 g in 2004, and germination rates of seed lots from "fly cages" were mostly > or =80% in both years. The C. vicina is an efficient and cost-effective pollinator ($388.97 for pupae and shipping, compared with $2,400 for honey bee, Apis mellifera L. [Hymenoptera: Apidae], nuclei) for caged leek accessions, with 250 and 500 C. vicina pupae per week required to produce sufficient seed (130 g) to fill an accession storage bag in the WRPIS gene bank.     

Occurrence and taxonomic significance of cysteine sulphoxides in the genus Allium L. (Alliaceae)

Methiin was present in all investigated samples. In the genus Allium, methiin-dominated species (rarely used by man) were common, but the occurrence of the other cysteine sulphoxides was variable and was largely correlated with use as spices or vegetables. Two major chemical types (named according to the species where they occur) could be distinguished, and at least two more may be recognized. Isoalliin dominates in the widely used "onion-type", which includes chive (A. schoenoprasum) and top onion (A.xproliferum). Pearl onion and leek (A. ampeloprasum) have higher relative amounts of methiin and propiin, respectively. Alliin dominates in the widely used "garlic-type", which includes wild leek (A. obliquum) and sand leek (A. scorodoprasum). Alliin and isoalliin rarely co-dominate, being only found in the cultivated Chinese leek (A. tuberosum). A triple mix of almost equal amounts of methiin, alliin and isoalliin is present in ramson (A. ursinum). General trends in the three evolutionary lines of the genus Allium were apparent. In the first lineage, high amounts of methiin were more frequent, and propiin, although being a minor component in all three evolutionary lines, was present in the highest amounts. Most of the species in the second line showed only traces of cysteine sulphoxides. In the third line, the "onion-type" dominates, the "garlic type" is characteristic for subgenus Allium, and co-dominating alliin and isoalliin also occur. Generally, the total cysteine sulphoxide amount increased, and the complexity of cysteine sulphoxide patterns decreased in the transition from the first to the third evolutionary line.     

Genetic diversity in the top onion,Allium ×proliferum (Alliaceae), analysed by isozymes

Polymorphisms for six enzyme systems (GPI, IDH, PDG, PGM, SKD, and TPI) were analysed in the top onion,Allium ×proliferum. Five multilocus isozyme genotypes were found. The banding patterns of top onions were compared with those ofA. ×wakegi, A. cepa, A. fistulosum, A. altaicum, and artificial hybrids between these three species. One top onion type and one artificial hybrid had identical banding patterns. Shallots andA. altaicum, the wild progenitor ofA. fistulosum, cannot be distinguished from the common onion andA. fistulosum, respectively; these species are also potential contributors to the top onion's gene pool.     

Chinese hamster telomeres are comparable in size to mouse telomeres.

We report here the results of a telomere length analysis in four male Chinese hamsters by quantitative fluorescence in situ hybridization (Q-FISH). We were able to measure telomere length of 64 (73%) of 88 Chinese hamster telomeres. We could not measure telomere length in chromosome 10 or in the short arms of chromosomes 5, 6, 7 and 8 because of the overlaps between the interstitial and terminal telomeric signals. Our analysis in the 73% of Chinese hamster telomeres indicate that their average length is approximately 38 kb. Therefore, Chinese hamster telomeres are comparable in length to mouse telomeres, but are much longer than human telomeres. Similar to previous Q-FISH studies on human and mouse chromosomes, our results indicate that individual Chinese hamster chromosomes may have specific telomere lengths, suggesting that chromosome-specific factors may be involved in telomere length regulation.     

Short telomeres in yeast are highly recombinogenic

We report that recombination rates specifically increase by up to 10(3) near shortened telomeres in K. lactis cells. This occurs in cells lacking telomerase that undergo growth senescence as well as in cells with stably shortened telomeres that cause little effect on cell growth. The high rates of gene conversion allowed a subtelomeric marker, initially present at a single telomere, to efficiently spread to most or all other telomeres in the cell. We propose that short telomeres in K. lactis are not fully competent at capping chromosome ends and hence are occasionally processed by proteins that normally act to repair broken DNA ends through recombination. This helps explain how recombination can be frequent enough to permit maintenance of telomeres in yeast cells lacking telomerase.     

Multiple autopolyploidizations and range expansion of Allium przewalskianum Regel. (Alliaceae) in the Qinghai‐Tibetan Plateau

We used the Allium przewalskianum diploid–tetraploid complex on the Qinghai‐Tibetan Plateau (QTP) as a model to examine how this complex responded to the Quaternary climatic oscillations, and whether multiple autopolyploidizations have occurred. We sequenced five chloroplast DNA (cpDNA) fragments (accD‐psaI, trnH‐psbA, trnL‐trnF, trnS‐trnG and rpl16‐intron) in 306 individuals (all of known ploidy level) from 48 populations across the distribution of this species complex. We identified a total of 32 haplotypes—11 in diploids only, 13 in tetraploids only, and 8 found in both cytotypes. This, plus network analyses, indicated that tetraploids have arisen independently from diploids at least eight times. Most populations in the eastern QTP contained multiple haplotypes, but only a single haplotype was found for 17 tetraploid populations on the western QTP, suggesting a recent colonization of the western QTP. We further found that this species complex underwent an earlier range expansion around 5–150 thousand years ago (kya), after the largest glacial period (800–170 kya) in the QTP. In addition, the high frequencies of tetraploids in the QTP suggested that the tetraploid A. przewalskianum cytotype has evolutionary advantages over diploids in colonizing and/or surviving the arid habitats of the QTP.     

Cytology of the highly polyploid disjunct species, Allium dregeanum (Alliaceae), and of some Eurasian relatives

Chromosome numbers are given for 16 taxa in Allium Section Allium , three in Section Codonoprasum , two in each of Sections Molium and Rkizirideum and one in each of Sections K'aloprasum, Megaloprason and Melanocrommrum. The basic chromosome number is x = 8 in all except Section Molium , in which the studied species unusually have x = 7. Polyploid) is common in the genus, with over half of the studied taxa in Section Allium having polyploid representatives. The highest ploidy levels found so far in the genus occur in A. dregeanum (2n = 8x = 64 and 10x = 80), which is counted here for the first time. Although highly polyploid, this disjunct South African species forms only bivalents during meiosis. The chiasmata are proximal, an uncommon phenomenon reported also in hexaploid 1. nm-peloprasum. Although A. dregeanum is genetically related to A. ampeloprasum , the suggestion that it is a cultivated variant of that species introduced to South Africa by the early settlers is unlikely.     

Dyskeratosis congenita: short telomeres are not the rule

Telomeres are nucleoprotein structures at the end of linear chromosomes. Their length, structure, and integrity are regulated by the telomerase complex, the shelterins and components of the DNA damage response. In human subjects, defects in telomere maintenance are responsible for Dyskeratosis Congenita (DC), a rare genetic disorder characterized by aplastic anaemia, premature aging and predisposition to cancer. Recent data from the study of patients with Hoyeraal-Hreidarsson syndrome, a severe variant of DC, demonstrate the great molecular heterogeneity of this disease. While most cases of DC are associated with defects in factors involved in telomere length regulation, some severe forms of the disease seem to be rather associated with defects in telomere replication and protection.     

Human telomeres are attached to the nuclear matrix.

This report shows that human telomeres are tightly associated with the nuclear matrix. Telomere attachment is observed in several cell types and in all stages of interphase. Mapping experiments show that telomeres are anchored via their TTAGGG repeats; a subtelomeric repeat located immediately proximal to the telomeric TTAGGG repeats is quantitatively released from the nuclear matrix by restriction endonuclease cleavage. TTAGGG repeats introduced at chromosome-internal sites by DNA transfection do not behave as matrix attached loci, suggesting that the telomeric position of the repeats is required for their interaction with the nuclear matrix. These findings are consistent with the idea that telomeres function as a nucleoprotein complex.     

NSD1 mutations are the major cause of Sotos syndrome and occur in some cases of Weaver syndrome but are rare in other overgrowth phenotypes

Sotos syndrome is a childhood overgrowth syndrome characterized by a distinctive facial appearance, height and head circumference >97th percentile, advanced bone age, and developmental delay. Weaver syndrome is characterized by the same criteria but has its own distinctive facial gestalt. Recently, a 2.2-Mb chromosome 5q35 microdeletion, encompassing NSD1, was reported as the major cause of Sotos syndrome, with intragenic NSD1 mutations identified in a minority of cases. We evaluated 75 patients with childhood overgrowth, for intragenic mutations and large deletions of NSD1. The series was phenotypically scored into four groups, prior to the molecular analyses: the phenotype in group 1 (n=37) was typical of Sotos syndrome; the phenotype in group 2 (n=13) was Sotos-like but with some atypical features; patients in group 3 (n=7) had Weaver syndrome, and patients in group 4 (n=18) had an overgrowth condition that was neither Sotos nor Weaver syndrome. We detected three deletions and 32 mutations (13 frameshift, 8 nonsense, 2 splice-site, and 9 missense) that are likely to impair NSD1 functions. The truncating mutations were spread throughout NSD1, but there was evidence of clustering of missense mutations in highly conserved functional domains between exons 13 and 23. There was a strong correlation between presence of an NSD1 alteration and clinical phenotype, in that 28 of 37 (76%) patients in group 1 had NSD1 mutations or deletions, whereas none of the patients in group 4 had abnormalities of NSD1. Three patients with Weaver syndrome had NSD1 mutations, all between amino acids 2142 and 2184. We conclude that intragenic mutations of NSD1 are the major cause of Sotos syndrome and account for some Weaver syndrome cases but rarely occur in other childhood overgrowth phenotypes.