Interspecific hybrid between Allium cepa and Allium sativum

Summary Interspecific hybrids between Allium cepa and Allium sativum were obtained using the fertile clone A. sativum as the male parent. The nascent embryos which formed shortly in interspecific hybridization between A. cepa and A. sativum were rescued by ovule culture at an early stage. The zygotes or proembryos developed in Murashige and Skoog medium containing 5.7×10^-8 M indole-3-butyric acid (IBA). Once developed, the embryos were taken out of the ovule and cultured on embryo culture medium where they regenerated into whole plants. The hybridity of the plants obtained was examined by morphological observation, chromosome analysis, and ribosomal RNA gene analysis. The analyses proved that the plants were mature sexual hybrids between A. cepa and A. sativum. Each hybrid plant had keeled but fistulose leaves and formed a bulb resembling that of A. cepa. The hybrids produced not only S-propenyl-l-cysteine sulfoxide, which is the major flavor precursor in A. cepa, but also S-allyl-l-cysteine sulfoxide (alliin), which is characteristic of A. sativum.     

Taxonomic analysis of metagenomic data with kASA

The taxonomic analysis of sequencing data has become important in many areas of life sciences. However, currently available tools for that purpose either consume large amounts of RAM or yield insufficient quality and robustness. Here, we present kASA, a k-mer based tool capable of identifying and profiling metagenomic DNA or protein sequences with high computational efficiency and a user-definable memory footprint. We ensure both high sensitivity and precision by using an amino acid-like encoding of k-mers together with a range of multiple k’s. Custom algorithms and data structures optimized for external memory storage enable a full-scale taxonomic analysis without compromise on laptop, desktop, and HPCC.     

Taxonomic and biological trait differences of stream macroinvertebrate communities between mediterranean and temperate regions: implications for future climatic scenarios

Streams in mediterranean regions have highly seasonal discharge patterns, with predictable torrential floods and severe droughts. In contrast, discharge is less variable in temperate regions and intermittent flow conditions are uncommon. Hydroclimatic models predict that climate change would increase frequency and severity of floods and droughts across Europe, thus increasing the proportion of streams with mediterranean characteristics in actually temperate areas. Correspondingly, understanding actual ecological differences between mediterranean and temperate streams may help to anticipate large‐scale ecological impacts of climate change. Given that large‐scale factors determine local community composition, we hypothesized that climatic differences between mediterranean and temperate regions should affect the taxonomic and biological trait composition in streams. We assembled the abundance of stream macroinvertebrate genera of 265 sites each from the Mediterranean Basin and from temperate Europe and linked these abundances to published information on 61 categories of 11 biological traits reflecting the potential of resilience from and resistance to disturbances. Although regional taxonomic richness was higher in the mediterranean than in the temperate region, local taxonomic richness and diversity did not significantly differ between regions. Local trait richness and diversity were significantly higher in the mediterranean region. Both local taxonomic and trait‐community composition differed between regions, but the former varied much more than the latter, highlighting that climate change could produce large changes in the taxonomic but rather weak changes in the trait composition. The mediterranean region was characterized by macroinvertebrates with higher dispersion and colonization capabilities, suggesting that species loss in the temperate region, by extinction or northward emigration of taxa, would be compensated for by immigration of southern mediterranean taxa. Thus, climate change would likely have stronger implications for the local conservation of taxa than for the trait composition of stream macroinvertebrate communities.     

Further data supporting linkage between cystic fibrosis and the met oncogene and haplotype analysis with met and pJ3.11

The linkage of cystic fibrosis (CF) and the polymorphic DNA markers pJ3.11, met, 7C22, DOCR1-917, COL1A2, and TCRB have jointly localized the mutation causing CF to chromosome 7q2.1-3.1. We report further linkage data with two polymorphic markers at the met oncogene locus, pmetH and pmetD, which supports the tight linkage found by White et al. between CF and met. One family shows evidence for meiotic recombination between CF and met. Analysis of haplotypes in CF pedigrees collected for linkage studies combined with data from single affected families requesting prenatal diagnosis (Farrall et al., Lancet i:1402-1404, 1986) shows CF and met to be in linkage equilibrium in our population while pJ3.11-CF haplotypes show a deviation from the equilibrium frequencies.     

Phenotypic and genetic data supporting reclassification of Butyrivibrio fibrisolvens isolates

Among 55 Butyrivibrio fibrisolvens strains five ribotypes of B. fibrisolvens were described on the basis of RFLP profiles of 16S rDNA regions obtained with restriction endonuclease HaeIII. In the phylogenetic tree, these ribotypes were located in the XIVa cluster of Gram-positive bacteria. Phenotypic differences of selected ribotype groups became the basis for further reclassification of B. fibrisolvens.     

Gene pool differences between Northern and Southern Altaians inferred from the data on Y-chromosomal haplogroups

Y-chromosomal haplogroups composition and frequencies were analyzed in Northern and Southern Altaians. In the gene pool of Altaians a total of 18 Y-chromosomal haplogroups were identified, including C3xM77, C3c, DxM15, E, F^*, J2, I1a, I1b, K^*, N^*, N2, N3a, O3, P^*, Q^*, R1^*, R1a1, and R1b3. The structuring nature of the Altaic gene pool is determined by the presence of the Caucasoid and Mongoloid components, along with the ancient genetic substratum, marked by the corresponding Western and Eastern Eurasian haplogroups. Haplogroup R1a1 prevailed in both ethnic groups, accounting for about 53 and 38% of paternal lineages in Southern and Northern Altaians, respectively. This haplogroup is thought to be associated with the eastward expansion of early Indo-Europeans, and marks Caucasoid element in the gene pools of South Siberian populations. Similarly to haplogroup K^*, the second frequent haplogroup Q^* represents paleo-Asiatic marker, probably associated with the Ket and Samoyedic contributions to the Altaic gene pool. The presence of lineages N2 and N3a can be explained as the contribution of Finno-Ugric tribes, assimilated by ancient Turks. The presence of haplogroups C3xM77, C3c, N^*, and O3 reflects the contribution of Central Asian Mongoloid groups. These haplogroups, probably, mark the latest movements of Mongolian migrants from the territory of contemporary Tuva and Mongolia. The data of factor analysis, variance analysis, cluster analysis, and phylogenetic analysis point to substantial genetic differentiation of Northern and Southern Altaians. The differences between Northern and Southern Altaians in the haplogroup composition, as well as in the internal haplotype structure were demonstrated.     

Gene pool differences between northern and southern Altaians inferred from the data on Y-chromosomal haplogroups

Y-chromosomal haplogroups composition and frequencies were analyzed in Northern and Southern Altaians. In the gene pool of Altaians a total of 18 Y-chromosomal haplogroups were identified, including C3xM77, C3c, DxM15, E, F*, J2, I1a, I1b, K*, N*, N2, N3a, O3, P*, Q*, R1*, R1a1, and R1b3. The structured nature of the Altaic gene pool is determined by the presence of the Caucasoid and Mongoloid components, along with the ancient genetic substratum, marked by the corresponding Western and Eastern Eurasian haplogroups. Haplogroup R1a1 prevailed in both ethnic groups, accounting for about 53 and 38% of paternal lineages in Southern and Northern Altaians, respectively. This haplogroup is thought to be associated with the eastward expansion of early Indo-Europeans, and marks Caucasoid element in the gene pools of South Siberian populations. Similarly to haplogroup K*, the second frequent haplogroup Q* represents paleo-Asiatic marker, probably associated with the Ket and Samoyedic contributions to the Altaic gene pool. The presence of lineages N2 and N3a can be explained as the contribution of Finno--Ugric tribes, assimilated by ancient Turks. The presence of haplogroups C3xM77, C3c, N*, and 03 reflects the contribution of Central Asian Mongoloid groups. These haplogroups, probably, mark the latest movements of Mongolian migrants from the territory of contemporary Tuva and Mongolia. The data of factor analysis, variance analysis, cluster analysis, and phylogenetic analysis point to substantial genetic differentiation of Northern and Southern Altaians. The differences between Northern and Southern Altaians in the haplogroup composition, as well as in the internal haplotype structure were demonstrated.     

Interspecific hybrids between onion (Allium cepa L.) with S-cytoplasm and leek (Allium ampeloprasum L.)

 Interspecific hybrids between Allium cepa and A. ampeloprasum have been generated as a first step for the introduction of S-cytoplasm from onion into leek. Pre-zygotic barriers of crossability were observed after the arrival of pollen tubes at the end of the style when entering the cavity. Nevertheless, micropyle penetration of pollen tubes and the formation of hybrid embryos were also observed. After accomplishing in vitro culture of ovaries and ovules successively, triploid hybrid plants with 24 chromosomes were obtained. Their hybrid nature was confirmed by RAPD analysis, genomic in situ hybridization, and morphological analysis. Southern hybridization with a cytoplasmic probe indicated the transfer of unaltered S-cytoplasm into the hybrid plants. Received: 9 May 1996 / Accepted: 23 August 1996     

Medullary structure differences in Gelidium and Pterocladia (Gelidiales, Rhodophyceae): Taxonomic meaning

Study of the apical portions of vegetative thalli of 21 species of the genera Gelidium and Pterocladia (Gelidiales-Rhodophyta) revealed the existence of six patterns of medullary structure. Each pattern is characterized by the organization of the medullary tissue and the changes in cellular dimensions from apex to subapex. These characters can be used to separate groups of species within each genus.     

Gorillas of Bwindi-Impenetrable Forest and the Virunga Volcanoes: Taxonomic implications of morphological and ecological differences

Based on their geographic proximity to the Virunga Volcanoes (≈ 25 km), the Bwindi-Impenetrable Forest gorillas have been referred to the subspecies Gorilla gorilla beringei. Differences in anatomy, habitat, ecology, and behavior, however, suggest Bwindi gorillas are distinct from those in the Virungas. Relative to Virunga gorillas, Bwindi gorillas live at lower elevations, in warmer temperatures, are much more arboreal, have longer day ranges and larger home ranges, and eat much more fruit and pith, and less bamboo and leaves. Morphological differences reflect the differences in ecology, habitat, and behavior. Bwindi gorillas measured have smaller bodies, relatively longer limbs, hands, and feet, shorter trunks, thumbs, big toes, and tooth row lengths, and narrower trunks and orbital breadths than Virunga gorillas. These differences indicate Bwindi gorillas do not belong to G.g. beringei and should not be referred to as “mountain gorillas.” How unique the distinguishing features of Bwindi gorillas are, and whether or not they should be assigned to a new taxon, depends on the expression of these features in eastern lowland gorillas (G.g. graueri). © 1996 Wiley-Liss, Inc.     

Evidence for nuclear-cytoplasmic incompatibility between Allium fistulosum and A. cepa

An F₂ population (Allium fistulosum x A. cepa) of 20plants, 10 BC₁,[(A. fistulosum x A. cepa) x A. cepa], and 50 BC₂ plants, [(A. fistulosum x A. cepa) x A. cepa] x A. cepa were studied cytogenetically and characterized for four isozyme alleles plus various morphological characteristics. All of the progenies were in A. fistulosum (the bunching onion) cytoplasm. In the F₂ population we observed non-random chromosomal and allelic segregation, suppression of bulb onion allelic expression, and abnormalities in mitosis and meiosis. Most BC₂ plants resembled A. cepa (the bulbing onion) morphologically, but anthers, filaments, pistils, and petals were abnormal. Only 3 plants, and these were most nearly like the F₁ hybrid morphologically, produced any seeds.The data and observations support the hypothesis of nuclear-cytoplasmic incompatibility interactions between the bunching and bulb onion species.Use of trade names does not imply endorsement of the products named nor criticism of similar ones not named. This research was supported by the New Mexico Agricultural Experiment Station.     

Production and characterization of somatic hybrid plants between leek (Allium ampeloprasum L.) and onion (Allium cepa L.)

 Results are reported on the production and characterization of somatic hybrids between Allium ampeloprasum and A. cepa. Both symmetric and asymmetric protoplast fusions were carried out using a polyethylene-based mass fusion protocol. Asymmetric fusions were performed using gamma ray-treated donor protoplasts of A. cepa and iodoacetamide-treated A. ampeloprasum protoplasts. However, the use of gamma irradiation to eliminate or inactivate the donor DNA of A. cepa proved to be detrimental to the development of fusion calli, and thus it was not possible to obtain hybrids from asymmetric fusions. The symmetric fusions yielded a high number of hybrid calli and regenerated plants. The analysis of the nuclear DNA composition using interspecific variation of rDNA revealed that most of the regenerated plants were hybrids. Flow cytometric analysis of nuclear DNA showed that these hybrid plants contained a lower DNA content than the sum of the DNA amounts of the parental species, suggesting that they were aneuploid. A shortage of chromosomes in the hybrids was confirmed by genomic in situ hybridization. Chromosome counts in metaphase cells of six hybrids revealed that these plants lacked 2–7 leek chromosomes. One hybrid showed also the loss of onion chromosomes. The hybrids had an intermediate phenotype in leaf morphology. The application of these somatic hybrids in breeding is discussed. Received: 7 April 1997 / Accepted: 10 September 1997     

Taxonomic differences shape the responses of freshwater aerobic anoxygenic phototrophic bacterial communities to light and predation

Aerobic anoxygenic phototrophic (AAP) bacteria are a phylogenetically diverse and ubiquitous group of prokaryotes that use organic matter but can harvest light using bacteriochlorophyll a. Although the factors regulating AAP ecology have long been investigated through field surveys, the few available experimental studies have considered AAPs as a group, thus disregarding the potential differential responses between taxonomically distinct AAP assemblages. Here, we used sequencing of the pufM gene to describe the diversity of AAPs in 10 environmentally distinct temperate lakes, and to investigate the taxonomic responses of AAP communities in these lakes when subjected to similar experimental manipulations of light and predator removal. The studied communities were clearly dominated by Limnohabitans AAP but presented a clear taxonomic segregation between lakes presumably driven by local conditions, which was maintained after experimental manipulations. Predation reduction (but not light exposure) caused significant compositional shifts across most assemblages, but the magnitude of these changes could not be clearly related to changes in bulk AAP abundances or taxonomic richness of AAP assemblages during experiments. Only a few operational taxonomic units, which differed taxonomically between lakes, were found to respond positively during experimental treatments. Our results highlight that different freshwater AAP communities respond differently to similar control mechanisms, highlighting that in‐depth knowledge on AAP diversity is essential to understand the ecology and potential role of these photoheterotrophs.     

Body shape and differences between species

The variation of body shape among prosimians is reviewed. Special emphasis is placed on the selective advantages, that is the mechanical reasons, to which variants of the locomotor apparatus can be traced back. There are differences found in the cheiridia, but at present they cannot be explained in terms of mechanics; there is nearly no knowledge about the mechanical meaning of their diversity. Myological characteristics of taxa can be explained mechanically, but this has not yet been done. Well known are variations of body proportions. These discriminate higher taxa, and are largely coincident with the often-used locomotor categories. In spite of this, there are only few sound arguments about the real biomechanic value of characteristic proportions for a given locomotor mode. What is known on this field, is reviewed. Progress can be made only, if the mechanical conditions, set by postural behavior and locomotion, are understood completely. The subtle distinctions between lower taxonomic units can normally be identified only on the basis of detailed and quantified analyses of movements on one hand, and of biometrics on the other. In the few cases in which such studies have been made, the differences of morphology fit to the mechanical requirements of locomotion which also differ only in quantitative details.