scholarly journals Impatiens glandulifera (Himalayan balsam) chloroplast genome sequence as a promising target for populations studies

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8739 ◽  
Author(s):  
Giovanni Cafa ◽  
Riccardo Baroncelli ◽  
Carol A. Ellison ◽  
Daisuke Kurose
Keyword(s):  
Rust Fungus ◽  
Molecular Study ◽  
Plant Evolution ◽  
Native Range ◽  
Impatiens Glandulifera ◽  
Promising Target ◽  
Himalayan Balsam ◽  
Chloroplast Genome Sequence ◽  
Genome Skimming ◽  
Low Coverage

Background Himalayan balsam Impatiens glandulifera Royle (Balsaminaceae) is a highly invasive annual species native of the Himalayas. Biocontrol of the plant using the rust fungus Puccinia komarovii var. glanduliferae is currently being implemented, but issues have arisen with matching UK weed genotypes with compatible strains of the pathogen. To support successful biocontrol, a better understanding of the host weed population, including potential sources of introductions, of Himalayan balsam is required. Methods In this molecular study, two new complete chloroplast (cp) genomes of I. glandulifera were obtained with low coverage whole genome sequencing (genome skimming). A 125-year-old herbarium specimen (HB92) collected from the native range was sequenced and assembled and compared with a 2-year-old specimen from UK field plants (HB10). Results The complete cp genomes were double-stranded molecules of 152,260 bp (HB92) and 152,203 bp (HB10) in length and showed 97 variable sites: 27 intragenic and 70 intergenic. The two genomes were aligned and mapped with two closely related genomes used as references. Genome skimming generates complete organellar genomes with limited technical and financial efforts and produces large datasets compared to multi-locus sequence typing. This study demonstrates the suitability of genome skimming for generating complete cp genomes of historic herbarium material. It also shows that complete cp genomes are solid genetic markers for population studies that could be linked to plant evolution and aid with targeting native range and natural enemy surveys for biocontrol of invasive species.

Chrysomyxa abietis (needle rust of fir).

2021 ◽  
Author(s):  
Keyword(s):  
Life Cycle ◽  
New Zealand ◽  
North America ◽  
Rust Fungus ◽  
Significant Problem ◽  
Northern Europe ◽  
Native Range ◽  
Obligate Parasite ◽  
The Usa ◽  
Accidental Introduction

Abstract C. abietis is a microcyclic rust fungus; an obligate parasite completing its life cycle on species of Picea (spruce). Only the current year's needles of Picea are infected and those needles are shed early. Reported from northern Europe and Asia, the fungus is a Regulated Pest for the USA. It is absent from North America, where susceptible species are native, and Australia and New Zealand, where they are introduced. Although usually not a significant problem in its native range, because conditions are not favourable for heavy infections every year (Smith et al., 1988; Hansen, 1997), this rust could be more damaging as an invasive in other temperate areas. Due to the fact that small amounts of infection may be overlooked, accidental introduction could occur through importation of infected seedlings or young trees.

scholarly journals Chloroplast DNA analysis of the invasive weed, Himalayan balsam (Impatiens glandulifera), in the British Isles

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Daisuke Kurose ◽  
Kathryn M. Pollard ◽  
Carol A. Ellison
Keyword(s):  
Chloroplast Dna ◽  
Dna Analysis ◽  
British Isles ◽  
Impatiens Glandulifera ◽  
Invasive Weed ◽  
Himalayan Balsam

scholarly journals On the impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters

2019 ◽  
Author(s):  
Eleonora Rachtman ◽  
Metin Balaban ◽  
Vineet Bafna ◽  
Siavash Mirarab
Keyword(s):  
Whole Genome ◽  
Ecological Research ◽  
Target Species ◽  
Free Sample ◽  
A Genome ◽  
Genome Skimming ◽  
Low Coverage ◽  
The Impact ◽  
Contamination Problem ◽  
Sample Identification

AbstractThe ability to detect the identity of a sample obtained from its environment is a cornerstone of molecular ecological research. Thanks to the falling price of shotgun sequencing, genome skimming, the acquisition of short reads spread across the genome at low coverage, is emerging as an alternative to traditional barcoding. By obtaining far more data across the whole genome, skimming has the promise to increase the precision of sample identification beyond traditional barcoding while keeping the costs manageable. While methods for assembly-free sample identification based on genome skims are now available, little is known about how these methods react to the presence of DNA from organisms other than the target species. In this paper, we show that the accuracy of distances computed between a pair of genome skims based on k-mer similarity can degrade dramatically if the skims include contaminant reads; i.e., any reads originating from other organisms. We establish a theoretical model of the impact of contamination. We then suggest and evaluate a solution to the contamination problem: Query reads in a genome skim against an extensive database of possible contaminants (e.g., all microbial organisms) and filter out any read that matches. We evaluate the effectiveness of this strategy when implemented using Kraken-II, in detailed analyses. Our results show substantial improvements in accuracy as a result of filtering but also point to limitations, including a need for relatively close matches in the contaminant database.

scholarly journals Puccinia abrupta var. partheniicola on Parthenium hysterophorus in Southern Africa

Plant Disease ◽  
2002 ◽  
Vol 86 (3) ◽  
pp. 327-327 ◽  
Author(s):  
A. R. Wood ◽  
M. Scholler
Keyword(s):  
South Africa ◽  
Biological Control ◽  
High Altitude ◽  
Southern Africa ◽  
Plant Protection ◽  
Rust Fungus ◽  
Parthenium Hysterophorus ◽  
International Institute ◽  
Native Range ◽  
Research Institute

Parthenium weed (Parthenium hysterophorus L., family Asteraceae), an annual herb of neotropic origin, is an invasive noxious weed with a pantropical distribution (1). It is particularly undesirable because of the serious health risks it poses to people living close to infestations (1). In January 1995, S. Neser (ARC-Plant Protection Research Institute, Pretoria, South Africa) collected a rust fungus on this plant near Brits, Northwest Province, South Africa (25°35′S, 27°46′E). Only uredinia were present. The same rust fungus was collected in the same area in January, March, and June of 2001, and again only uredinia were observed. In its native range, P. hysterophorus is infected by two rust fungus species, Puccinia abrupta Diet. & Holw. var. partheniicola (Jackson) Parmelee and Puccinia melampodii Diet. & Holw., but the latter species is microcyclic with telia only. The morphology of the urediniospores in the South African collections corresponds to Puccinia abrupta var. partheniicola (3): obovoid to almost triangular, 22 to 27 × 18 to 25 µm, echinulate, two subequatorial and one apical germ pores, spines absent around germ pores, wall 1 to 2.5 µm thick. The native range of Puccinia abrupta var. partheniicola is Mexico and northern South America (3). In addition, it has been recorded from Mauritius (3), Kenya, and India (H. C. Evans and C. A. Ellison, International Institute of Biological Control, CAB, 1987, unpublished data). It was intentionally introduced into Australia for the biological control of P. hysterophorus (2). Thirteen specimens in the Arthur Herbarium were examined, and only two had telia in addition to uredinia. The other 11 had only uredinia, indicating that nonformation of telia is common. Telia and uredinia are produced in high altitude, semiarid areas of Mexico, whereas in low altitude, more humid areas only uredinia are produced (1). The production of telia appears to depend on environmental conditions, and their absence is not unexpected at the Brits site, which is a high altitude (1,120 m) area with high summer rainfall (400 to 600 mm per year from November to February) and dry winters. Voucher specimens were deposited at the National Collection of Fungi, Plant Protection Research Institute, Pretoria (PREM 57298) and the Arthur Herbarium, West Lafayette, IN (PUR N1117). To our knowledge, this is the second report of this rust fungus in Africa and the first in southern Africa. References: (1) H. C. Evans. Trans. Br. Mycol. Soc. 88:105, 1987. (2) A. Parker et. al. Plant Pathol. 43:1, 1994. (3) J. A. Parmelee. Can. J. Bot. 45:2267, 1967.

scholarly journals Sewage Pollution Promotes the Invasion-Related Traits of Impatiens glandulifera in an Oligotrophic Habitat of the Sharr Mountain (Western Balkans)

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2814
Author(s):  
Milos Stanojevic ◽  
Maja Trailovic ◽  
Tijana Dubljanin ◽  
Zoran Krivošej ◽  
Miroslav Nikolic ◽  
...  
Keyword(s):  
Soil Nutrient ◽  
Ecological Knowledge ◽  
Western Balkans ◽  
Structured Interviews ◽  
Impatiens Glandulifera ◽  
Himalayan Balsam ◽  
Competitive Species ◽  
Vegetation Species ◽  
Very High ◽  
Impatiens Glandulifera Royle

An annual plant, Himalayan balsam (Impatiens glandulifera Royle) is globally widespread and one of Europe’s top invaders. We focused on two questions: does this species indeed not invade the southern areas and does the environment affect some of its key invisibility traits. In an isolated model mountainous valley, we jointly analyzed the soil (21 parameters), the life history traits of the invader (height, stem diameter, aboveground dw), and the resident vegetation (species composition and abundances, Ellenberg indicator values), and supplemented it with local knowledge (semi-structured interviews). Uncontrolled discharge of fecal wastewaters directly into the local dense hydrological network fostered mass infestation of an atypical habitat. The phenotypic plasticity of the measured invasion-related traits was very high in the surveyed early invasion (30–50% invader cover) stages. Different microhabitat conditions consistently correlated with its growth performance. The largest individuals were restricted to the deforested riparian habitats, with extreme soil nutrient enrichment (primarily by P and K) and low-competitive, species-poor resident vegetation. We showed that ecological context can modify invasion-related traits and what could affect a further invasion process. Finally, this species is likely underreported in the wider region; public attitude and loss of traditional ecological knowledge are further management risks.

scholarly journals Characteristics of the Completed Chloroplast Genome Sequence of Xanthium Spinosum: Comparative Analyses, Identification of Mutational Hotspots and Phylogenetic Implications

2020 ◽  
Author(s):  
Gurusamy Raman ◽  
KyuTae Park ◽  
Joo Hwan Kim ◽  
SeonJoo Park
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Plant Evolution ◽  
Rrna Genes ◽  
Trna Genes ◽  
Mutational Hotspots ◽  
Phylogenetic Implications ◽  
Intergenic Regions ◽  
Chloroplast Genome Sequence ◽  
Cp Genome

Abstract Background: The invasive alien species, Xanthium spinosum has been used as a traditional Chinese medicine for many years. Unfortunately, there are no extensive molecular studies for this plant. Results: Here, the complete chloroplast genome sequence of X. spinosum was assembled and analyzed. The cp genome of X. spinosum was 152,422 bp and possessed quadripartite circular structure. The cp genome contained 115 unique genes, including 80 protein-coding genes, 31 tRNA genes and 4 rRNA genes. Comparative analysis revealed that X. spinosum encoded a higher number of repeats (999 repeats) and 701 SSRs in their cp genome. Also, fourteen divergences (Pi > 0.03) were found in the intergenic regions. The accD gene underwent positive selection within Heliantheae, which contributes to further investigation of the adaptive plant evolution in the ecosystem. Additionally, the phylogenetic analysis revealed that Parthenium is a sister clade to both Xanthium and Ambrosia and it is an early-diverging lineage of subtribe Ambrosiinae though it supports with very weak bootstrap value. Conclusion: The identified hotspot regions were thought to be useful molecular markers for resolving phylogenetic relationships and species validation of Xanthium.

PhyloHerb: A phylogenomic pipeline for processing genome skimming data for plants

2021 ◽  
Author(s):  
Liming Cai ◽  
Hongrui Zhang ◽  
CHARLES C DAVIS
Keyword(s):  
Genomic Dna ◽  
High Throughput Sequencing ◽  
Data Partitioning ◽  
Published Data ◽  
Herbarium Specimens ◽  
Bioinformatic Pipeline ◽  
Biodiversity Research ◽  
Blast Search ◽  
Genome Skimming ◽  
Low Coverage

Premise of the study: The application of high throughput sequencing, especially to herbarium specimens, is greatly accelerating biodiversity research. Among various techniques, low coverage Illumina sequencing of total genomic DNA (genome skimming) can simultaneously recover the plastid, mitochondrial, and nuclear ribosomal regions across hundreds of species. Here, we introduce PhyloHerb -- a bioinformatic pipeline to efficiently and effectively assemble phylogenomic datasets derived from genome skimming. Methods and Results: PhyloHerb uses either a built-in database or user-specified references to extract orthologous sequences using BLAST search. It outputs FASTA files and offers a suite of utility functions to assist with alignment, data partitioning, concatenation, and phylogeny inference. The program is freely available at https://github.com/lmcai/PhyloHerb/. Conclusions: Using published data from Clusiaceae, we demonstrated that PhyloHerb can accurately identify genes using highly fragmented assemblies derived from sequencing older herbarium specimens. Our approach is effective at all taxonomic depths and is scalable to thousands of species.

Thekopsora areolata (cherry spruce rust).

2021 ◽  
Author(s):  
Keyword(s):  
Life Cycle ◽  
New Zealand ◽  
North America ◽  
Rust Fungus ◽  
Native Range ◽  
Obligate Parasite ◽  
The Usa ◽  
The One ◽  
Accidental Introduction

Abstract T. areolata is a heteroecious rust fungus; an obligate parasite with stages of its life cycle on cones of Picea species and leaves of Prunus spp. Reported from Europe and Asia, the fungus is a Regulated Pest for the USA. It is absent from North America, where susceptible species are native or introduced, and Australia and New Zealand, where such species are introduced. Although usually not a major problem in its native range, this rust could be more damaging as an invasive in other temperate areas. Due to the fact that small amounts of infection may be overlooked, accidental introduction could occur through importation of infected cones carrying aeciospores. The one known introduction to North America involved a tree of Prunus sp. in a garden, from which there was no documented spread.

scholarly journals Differing impacts of two major plant invaders on urban plant-dwelling spiders (Araneae) during flowering season

2021 ◽  
Author(s):  
Tobias Bauer ◽  
Daria Alison Bäte ◽  
Fabian Kempfer ◽  
Jens Schirmel
Keyword(s):  
Prey Item ◽  
Large Scale ◽  
Plant Invasions ◽  
Potential Prey ◽  
Impatiens Glandulifera ◽  
Flowering Season ◽  
General Flowering ◽  
Himalayan Balsam ◽  
Spider Abundance ◽  
Crab Spider

AbstractPlant invasions can have major impacts on ecosystems and influence global species diversity. In Central Europe, Himalayan balsam (Impatiens glandulifera) and American goldenrods (Solidago canadensis and S. gigantea) are important invaders often establishing dense and homogeneous stands, especially in urban and other disturbed habitats. We investigated their impacts on plant-dwelling spiders (abundance, family structure, guild structure) and potential spider prey items during flowering season within an urbanized landscape using a paired design comparing invaded and native reference vegetation plots. In general, flowering American goldenrods and Himalayan balsam had no significant impacts on the spider family composition. Invasion of American goldenrods further had no effect on total spider abundance and potential prey item abundance. In contrast, goldenrods showed a significantly increased crab spider (Thomisidae) abundance while being less inhabited by web builders. Himalayan balsam negatively influenced free hunters and running crab spider (Philodromidae) abundance, while we found no effects on other groups and total spider abundance. For Himalayan balsam, potential prey item abundance was higher than in native vegetation stands. Notwithstanding that our results only represent a snapshot of the system, they suggest that large-scale removal of urban goldenrod stands during flowering season might negatively influence local spider abundance, especially of crab spiders. Management efforts should therefore be accompanied by compensation measures to avoid disruptive effects on local plant-dwelling spider communities.

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