Publications by authors named "Lotte Pronk"
With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC.
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- Microbiomes are crucial for plant growth, but the genetic factors influencing their development are not well understood.
- The study analyzes the rhizosphere microbiome in a variety of wild and domesticated tomatoes, identifying gene regions that influence which bacteria are recruited, including important genes related to iron and water regulation.
- By combining microbiome research with plant genetics, the research highlights potential traits that could be used to improve plant-microbiome interactions in future breeding efforts.
Article Synopsis
- Metagenomics is a powerful tool for examining microbial communities, but most research currently focuses on bacteria, neglecting eukaryotic microbes.
- A new classifier called Whokaryote was developed to effectively distinguish between eukaryotic and prokaryotic contigs by analyzing gene structure, achieving high accuracy rates (94% recall, 96% precision).
- The enhanced version, Whokaryote+Tiara, combines features from Whokaryote with predictions from another classifier and significantly improves performance, leading to better identification of important gene clusters in microbial community studies.
Root-colonizing bacteria have been intensively investigated for their intimate relationship with plants and their manifold plant-beneficial activities. They can inhibit growth and activity of pathogens or induce defence responses. In recent years, evidence has emerged that several plant-beneficial rhizosphere bacteria do not only associate with plants but also with insects.
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