Extensive sequence divergence in the 3' inverted repeat of the chloroplast rbcL gene in non-flowering land plants and algae

A stem-loop region is present at the 3' terminus of the chloroplast rbcL mRNA in all taxa surveyed to date. In spinach, this structure has been shown by others to be involved in modulating transcript stability and correct 3' terminus processing, and is a conserved feature of other flowering plant rbcL mRNAs. In Chlamydomonas reinhardtii, an analogous structure has been shown by others to serve as a transcription terminator. Our sequencing data have shown that this region is highly divergent in several non-flowering land plants, as evidenced by representatives from the ferns, conifers, `fern-allies' and liverworts. To extend our analysis, a computer-assisted survey of the stem-loop region of the 3' flanking region of published chloroplast rbcL genes was undertaken. The flowering plant rbcL inverted repeats (IR) were remarkably conserved in sequence, allowing for precise multiple alignments of both monocot and dicot sequences within a single matrix. Surprisingly, sequences obtained from non-flowering land plants, algae, photosynthetic protists and photosynthetic prokaryotes were extremely variant, in terms of both sequence composition and thermodynamic parameters.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/31333/1/0000243.pd

The consensus land plant chloroplast gene order is present, with two alterations, in the moss Physcomitrella patens

A restriction endonuclease cleavage site map for the enzymes Cla I and Bgl II, and a partial map for Sac I, has been constructed for the chloroplast genome of the moss Physcomitrella patens (Hedw.) BSG. The plastid chromosome contains approximately 122 kb organized into small (21 kb) and large (82 kb) single-copy regions separated by two copies of a repeat sequence (9.4 kb) oriented in an inverted arrangement. Genes for 17 proteins and 2 ribosomal RNAs have been mapped using heterologous probes from corn, spinach, pea, and petunia. The general order and arrangement of the moss chloroplast genes are similar to the consensus land plant genome typified by that of spinach, with two major exceptions. First, there is an inversion of approximately 20 kb, bordered internally by psbA and atpH , and also containing the genes atpF and atpA . Second, rpl 2 and rps 19 have been relocated to a different position within the large single-copy region, adjacent to the 20 kb inversion.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47565/1/438_2004_Article_BF00330462.pd

Pitcher Plants (Sarracenia) Provide a 21st-Century Perspective on Infraspecific Ranks and Interspecific Hybrids: A Modest Proposal for Appropriate Recognition and Usage

The taxonomic use of infraspecific ranks (subspecies, variety, subvariety, form, and subform), and the formal recognition of interspecific hybrid taxa, is permitted by the International Code of Nomenclature for algae, fungi, and plants. However, considerable confusion regarding the biological and systematic merits is caused by current practice in the use of infraspecific ranks, which obscures the meaningful variability on which natural selection operates, and by the formal recognition of those interspecific hybrids that lack the potential for inter-lineage gene flow. These issues also may have pragmatic and legal consequences, especially regarding the legal delimitation and management of Threatened and Endangered Species. A detailed comparison of three contemporary floras highlights the degree to which infraspecific and interspecific variation are treated inconsistently. An in depth analysis of taxonomy of the North American flowering plant genus Sarracenia (Sarraceniaceae) provides an ideal case study illustrating the confusion that can arise from inconsistent and apparently arbitrary designation of infraspecific ranks and hybrid taxa. To alleviate these problems, we propose the abandonment of infraspecific ranks of “variety” and “form”, and discourage naming of sterile interspecific hybrids except for use in the horticultural or agronomic trade. Our recommendations for taxonomic practice are in accord with the objectives proposed in the Systematics Agenda 2000, Systematics Agenda 2020, and the Global Strategy for Plant Conservation.Organismic and Evolutionary Biolog

Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci

The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some—including the infamous ergot alkaloids—have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses

Phylogeny and Biogeography of the Carnivorous Plant Family Sarraceniaceae

The carnivorous plant family Sarraceniaceae comprises three genera of wetland-inhabiting pitcher plants: Darlingtonia in the northwestern United States, Sarracenia in eastern North America, and Heliamphora in northern South America. Hypotheses concerning the biogeographic history leading to this unusual disjunct distribution are controversial, in part because genus- and species-level phylogenies have not been clearly resolved. Here, we present a robust, species-rich phylogeny of Sarraceniaceae based on seven mitochondrial, nuclear, and plastid loci, which we use to illuminate this family's phylogenetic and biogeographic history. The family and genera are monophyletic: Darlingtonia is sister to a clade consisting of Heliamphora+Sarracenia. Within Sarracenia, two clades were strongly supported: one consisting of S. purpurea, its subspecies, and S. rosea; the other consisting of nine species endemic to the southeastern United States. Divergence time estimates revealed that stem group Sarraceniaceae likely originated in South America 44–53 million years ago (Mya) (highest posterior density [HPD] estimate = 47 Mya). By 25–44 (HPD = 35) Mya, crown-group Sarraceniaceae appears to have been widespread across North and South America, and Darlingtonia (western North America) had diverged from Heliamphora+Sarracenia (eastern North America+South America). This disjunction and apparent range contraction is consistent with late Eocene cooling and aridification, which may have severed the continuity of Sarraceniaceae across much of North America. Sarracenia and Heliamphora subsequently diverged in the late Oligocene, 14–32 (HPD = 23) Mya, perhaps when direct overland continuity between North and South America became reduced. Initial diversification of South American Heliamphora began at least 8 Mya, but diversification of Sarracenia was more recent (2–7, HPD = 4 Mya); the bulk of southeastern United States Sarracenia originated co-incident with Pleistocene glaciation, <3 Mya. Overall, these results suggest climatic change at different temporal and spatial scales in part shaped the distribution and diversity of this carnivorous plant clade

Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the Clavicipitaceae reveals dynamics of alkaloid Loci

The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some—including the infamous ergot alkaloids—have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses

Effects of antibiotic resistance, drug target attainment, bacterial pathogenicity and virulence, and antibiotic access and affordability on outcomes in neonatal sepsis: an international microbiology and drug evaluation prospective substudy (BARNARDS)

Background Sepsis is a major contributor to neonatal mortality, particularly in low-income and middle-income countries (LMICs). WHO advocates ampicillin–gentamicin as first-line therapy for the management of neonatal sepsis. In the BARNARDS observational cohort study of neonatal sepsis and antimicrobial resistance in LMICs, common sepsis pathogens were characterised via whole genome sequencing (WGS) and antimicrobial resistance profiles. In this substudy of BARNARDS, we aimed to assess the use and efficacy of empirical antibiotic therapies commonly used in LMICs for neonatal sepsis. Methods In BARNARDS, consenting mother–neonates aged 0–60 days dyads were enrolled on delivery or neonatal presentation with suspected sepsis at 12 BARNARDS clinical sites in Bangladesh, Ethiopia, India, Pakistan, Nigeria, Rwanda, and South Africa. Stillborn babies were excluded from the study. Blood samples were collected from neonates presenting with clinical signs of sepsis, and WGS and minimum inhibitory concentrations for antibiotic treatment were determined for bacterial isolates from culture-confirmed sepsis. Neonatal outcome data were collected following enrolment until 60 days of life. Antibiotic usage and neonatal outcome data were assessed. Survival analyses were adjusted to take into account potential clinical confounding variables related to the birth and pathogen. Additionally, resistance profiles, pharmacokinetic–pharmacodynamic probability of target attainment, and frequency of resistance (ie, resistance defined by in-vitro growth of isolates when challenged by antibiotics) were assessed. Questionnaires on health structures and antibiotic costs evaluated accessibility and affordability. Findings Between Nov 12, 2015, and Feb 1, 2018, 36 285 neonates were enrolled into the main BARNARDS study, of whom 9874 had clinically diagnosed sepsis and 5749 had available antibiotic data. The four most commonly prescribed antibiotic combinations given to 4451 neonates (77·42%) of 5749 were ampicillin–gentamicin, ceftazidime–amikacin, piperacillin–tazobactam–amikacin, and amoxicillin clavulanate–amikacin. This dataset assessed 476 prescriptions for 442 neonates treated with one of these antibiotic combinations with WGS data (all BARNARDS countries were represented in this subset except India). Multiple pathogens were isolated, totalling 457 isolates. Reported mortality was lower for neonates treated with ceftazidime–amikacin than for neonates treated with ampicillin–gentamicin (hazard ratio [adjusted for clinical variables considered potential confounders to outcomes] 0·32, 95% CI 0·14–0·72; p=0·0060). Of 390 Gram-negative isolates, 379 (97·2%) were resistant to ampicillin and 274 (70·3%) were resistant to gentamicin. Susceptibility of Gram-negative isolates to at least one antibiotic in a treatment combination was noted in 111 (28·5%) to ampicillin–gentamicin; 286 (73·3%) to amoxicillin clavulanate–amikacin; 301 (77·2%) to ceftazidime–amikacin; and 312 (80·0%) to piperacillin–tazobactam–amikacin. A probability of target attainment of 80% or more was noted in 26 neonates (33·7% [SD 0·59]) of 78 with ampicillin–gentamicin; 15 (68·0% [3·84]) of 27 with amoxicillin clavulanate–amikacin; 93 (92·7% [0·24]) of 109 with ceftazidime–amikacin; and 70 (85·3% [0·47]) of 76 with piperacillin–tazobactam–amikacin. However, antibiotic and country effects could not be distinguished. Frequency of resistance was recorded most frequently with fosfomycin (in 78 isolates [68·4%] of 114), followed by colistin (55 isolates [57·3%] of 96), and gentamicin (62 isolates [53·0%] of 117). Sites in six of the seven countries (excluding South Africa) stated that the cost of antibiotics would influence treatment of neonatal sepsis

HIGH RESOLUTION GIS MAPPING AND CURRENT STATUS OF THE TEN VIABLE POPULATIONS OF SHORT\u27S GOLDENROD (SOLIDAGO SHORTII-ASTERACEAE) IN KENTUCKY

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Geographic distribution of Sarraceniaceae.

<p><i>Darlingtonia</i> (A) is restricted to western North America, <i>Sarracenia</i> (B) is widespread in Eastern North America, and <i>Heliamphora</i> (C) occurs in northern South America <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039291#pone.0039291-Juniper1" target="_blank">[17]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039291#pone.0039291-Schnell1" target="_blank">[27]</a>. Photographs by the authors.</p

BEAST chronogram for the combined data and hypothesized biogeographic history of Sarraceniaceae.

<p>(A) Mean divergence times estimates are shown at the nodes of the cladogram. 95% posterior probability distribution shown with thick blue lines. Ancestral areas reconstructions from LAGRANGE <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039291#pone.0039291-Drummond1" target="_blank">[70]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039291#pone.0039291-Swofford1" target="_blank">[71]</a> shown in boxes near nodes. SA = South America; ENA = Eastern North America; WNA = Western North America; SAf = South Africa; and As = Asia. (B) We hypothesize that Sarraceniaceae originated in the Middle Eocene, perhaps in South America, and achieved its widespread distribution in North and South America by the Late Eocene. An early migration of Sarraceniaceae out of South America during the Eocene may have been facilitated via land connections in the proto-Caribbean. This connection would likely have been unavailable for direct overland migration by the mid-Oligocene, which is consistent with the early Oligocene disjunction of northern (<i>Sarracenia</i>, <i>Darlingtonia</i>) and southern (<i>Heliamphora</i>) members of Sarraceniacace. An East (<i>Sarracenia</i>+<i>Heliamphora</i>)/West (<i>Darlingtonia</i>) disjunction occurred in the very latest Oligocene, and may have been attributable to broad scale cooling and aridification during the late Oligocene.</p