6 research outputs found
First draft genome assembly of the desert locust, Schistocerca Gregaria
BACKGROUND: At the time of publication, the most devastating desert
locust crisis in decades is affecting East Africa, the Arabian Peninsula
and South-West Asia. The situation is extremely alarming in East
Africa, where Kenya, Ethiopia and Somalia face an unprecedented
threat to food security and livelihoods. Most of the time, however,
locusts do not occur in swarms, but live as relatively harmless solitary
insects. The phenotypically distinct solitarious and gregarious locust
phases differ markedly in many aspects of behaviour, physiology and
morphology, making them an excellent model to study how
environmental factors shape behaviour and development. A better
understanding of the extreme phenotypic plasticity in desert locusts
will offer new, more environmentally sustainable ways of fighting
devastating swarms.
METHODS: High molecular weight DNA derived from two adult males
was used for Mate Pair and Paired End Illumina sequencing and
PacBio sequencing. A reliable reference genome of Schistocerca
gregaria was assembled using the ABySS pipeline, scaffolding was
improved using LINKS.
RESULTS: In total, 1,316 Gb Illumina reads and 112 Gb PacBio reads were produced and assembled. The resulting draft genome consists
of 8,817,834,205 bp organised in 955,015 scaffolds with an N50 of
157,705 bp, making the desert locust genome the largest insect
genome sequenced and assembled to date. In total, 18,815 proteinencoding genes are predicted in the desert locust genome, of which
13,646 (72.53%) obtained at least one functional assignment based on
similarity to known proteins.
CONCLUSIONS: The desert locust genome data will contribute greatly to
studies of phenotypic plasticity, physiology, neurobiology, molecular
ecology, evolutionary genetics and comparative genomics, and will
promote the desert locustâs use as a model system. The data will also
facilitate the development of novel, more sustainable strategies for
preventing or combating swarms of these infamous insects.The Special Research Fund of KU Leuven, the Research Foundation of Flanders, the Special Research Fund of Ghent University, the Department of Research and Innovation of the University of Pretoria, the U.S. National Science Foundation, the U.S. Department of Agriculture and the Biotechnology and Biological Sciences Research Council UK.http://f1000research.compm2021BiochemistryGeneticsMicrobiology and Plant Patholog
A chromosome-level Amaranthus cruentus genome assembly highlights gene family evolution and biosynthetic gene clusters that may underpin the nutritional value of this traditional crop
Traditional crops historically provided accessible and affordable nutrition to millions of rural dwellers but have been neglected, with most modern agricultural systems over reliant on a small number of internationally-traded crops. Traditional crops are typically well-adapted to local agro-ecological conditions and many are nutrient-dense. They can play a vital role in local food systems through enhanced nutrition (especially where diets are dominated by starch crops), food security and livelihoods for smallholder farmers, and a climate-resilient and biodiverse agriculture. Using short-read, long-read and phased sequencing technologies we generated a high-quality chromosome-level genome assembly for Amaranthus cruentus, an under-researched crop with micronutrient- and protein-rich leaves and gluten-free seed, but lacking improved varieties, with respect to productivity and quality traits. The 370.9 MB genome demonstrates a shared whole genome duplication with a related species, Amaranthus hypochondriacus. Comparative genome analysis indicates chromosomal loss and fusion events following genome duplication that are common to both species, as well as fission of chromosome 2 in A. cruentus alone, giving rise to a haploid chromosome number of 17 (versus 16 in A. hypochondriacus). Genomic features potentially underlying the nutritional value of this crop include two A. cruentus-specific genes with a likely role in phytic acid synthesis (an anti-nutrient), expansion of ion transporter gene families, and identification of biosynthetic gene clusters conserved within the amaranth lineage. The A. cruentus genome assembly will underpin much-needed research and global breeding efforts to develop improved varieties for economically viable cultivation and realisation of the benefits to global nutrition security and agrobiodiversity
Agaric acid reduces Salmonella biofilm formation by inhibiting flagellar motility
Salmonella biofilms are a common cause of contaminations in the food or feed industry. In a screening for novel compounds to combat biofilm-associated foodborne outbreaks, we identified agaric acid as a Salmonella Typhimurium biofilm inhibitor that does not affect planktonic growth. Importantly, the remaining biofilm cells after preventive treatment with agaric acid were significantly more sensitive to the common disinfectant hydrogen peroxide. Screening of a GFP-promoter fusion library of biofilm related genes revealed that agaric acid downregulates the transcription of genes responsible for flagellar motility. Concurrently, swimming motility was completely abrogated in the presence of agaric acid, indicating that biofilm inhibition occurs via interference with the motility phenotype. Moreover, agaric acid also reduced biofilm formation of Pseudomonas aeruginosa, Staphylococcus aureus and Escherichia coli. Agaric acid thus shows potential as an anti-virulence compound that inhibits both motility and biofilm formation.KU Leuven Research Fund;
Leuven Research and Development (LRD) reserve fund;
Institute for the Promotion of Innovation through Science and Technology in Flanders (IWT) and FWO-Vlaanderen.http://www.elsevier.com/locate/bioflmhj2021BiochemistryGeneticsMicrobiology and Plant Patholog
Complete genome sequence of collection strain acinetobacter baumannii ATCC BAA-1790, used as a model to study the antibiotic resistance reversion induced by iodine-containing complexes
The strain Acinetobacter baumannii ATCC BAA-1790 was sequenced as a
model for nosocomial multidrug-resistant infections. Long-read PacBio sequencing
revealed a circular chromosome of 3,963,235 bp with two horizontally transferred
genomic islands and a 67,023-bp plasmid. Multiple antibiotic resistance genes and
genome methylation patterns were identified.The Industrial Development and Industrial Safety Committee of the Ministry of Industry and Infrastructural Development of the Republic of Kazakhstan, South African National Research Foundation (NRF) and the University of Pretoria.https://mra.asm.orgam2021BiochemistryGeneticsMicrobiology and Plant Patholog
Complete genome sequence of a multidrug-resistant strain, Escherichia coli ATCC BAA-196, as a model for studying induced antibiotic resistance reversion
Here, we report the complete genome sequence of the multidrugresistant
Escherichia coli strain ATCC BAA-196, a model organism used for studying
possible antibiotic resistance reversion induced by FS-1, an iodine-containing complex.
Two genomes, representing FS-1-treated and negative-control variants and composed of
a chromosome and several plasmids, were assembled.The Industrial Development and
Industrial Safety Committee of the Ministry of Industry and Infrastructural Development
of the Republic of Kazakhstan, the South African
National Research Foundation and the University of
Pretoria.https://mra.asm.orgam2020BiochemistryGeneticsMicrobiology and Plant Patholog