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Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies.
Plant Biotechnol J
January 2025
College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
Transposable elements (TEs) are significant drivers of genome evolution, yet their recent dynamics and impacts within and among species, as well as the roles of host genes and non-coding RNAs in the transposition process, remain elusive. With advancements in large-scale pan-genome sequencing and the development of open data sharing, large-scale comparative genomics studies have become feasible. Here, we performed complete de novo TE annotations and identified active TEs in 310 plant genome assemblies across 119 species and seven crop populations.
View Article and Find Full Text PDFThe genome of the sapphire damselfish : a new resource to support further investigation of the evolution of Pomacentrids.
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Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology, 904-0495, Onna-son, Okinawa, Japan.
The number of high-quality genomes is rapidly increasing across taxa. However, it remains limited for coral reef fish of the Pomacentrid family, with most research focused on anemonefish. Here, we present the first assembly for a Pomacentrid of the genus .
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National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Hubei, China. Electronic address:
In the face of climate change and the growing global population, there is an urgent need to accelerate the development of high-yielding crop varieties. To this end, vast amounts of genotype-to-phenotype data have been collected, and many machine learning (ML) models have been developed to predict phenotype from a given genotype. However, the requirement for high densities of single-nucleotide polymorphisms (SNPs) and the labor-intensive collection of phenotypic data are hampering the use of these models to advance breeding.
View Article and Find Full Text PDFA High-Throughput Screening Pipeline to Identify Methyltransferase and Exonuclease Inhibitors of SARS-CoV-2 NSP14.
Biochemistry
January 2025
National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States.
SARS-CoV-2 infections led to a worldwide pandemic in 2020. As of 2024, therapeutics against SARS-CoV-2 have continued to be desirable. NSP14 is a dual-function methyltransferase (MTase) and exonuclease (ExoN) with key roles in SARS-CoV-2 genome propagation and host immune system evasion.
View Article and Find Full Text PDFDeep sequencing-derived Metagenome Assembled Genomes from the gut microbiome of liver transplant patients.
Sci Data
January 2025
Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
Recurrence of metabolic dysfunction-associated steatotic liver disease (MASLD) after liver transplantation (LT) is a continuing concern. The role of gut microbiome dysbiosis in MASLD initiation and progression has been well established. However, there is a lack of comprehensive gut microbiome shotgun sequence data for patients experiencing MASLD recurrence after LT.
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