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| http://dx.doi.org/10.3389/fmolb.2017.00089 | DOI Listing |
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A High-Quality Phased Genome Assembly of Stinging Nettle ( ssp. ).
Plants (Basel)
January 2025
Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada.
Stinging nettles () have a long history of association with human civilization, having been used as a source of textile fibers, food and medicine. Here, we present a chromosome-level, phased genome assembly for a diploid female clone of from Romania. Using a combination of PacBio HiFi, Oxford Nanopore, and Illumina sequencing, as well as Hi-C long-range interaction data (using a novel Hi-C protocol presented here), we assembled two haplotypes of 574.
View Article and Find Full Text PDFPrediction of transcript isoforms and identification of tissue-specific genes in cucumber.
BMC Genomics
January 2025
Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China.
Background: Identification of global transcriptional events is crucial for genome annotation, as accurate annotation enhances the efficiency and comparability of genomic information across species. However, the annotation of transcripts in the cucumber genome remains to be improved, and many transcriptional events have not been well studied.
Results: We collected 1,904 high-quality public cucumber transcriptome samples from the National Center for Biotechnology Information (NCBI) to identify and annotate transcript isoforms in the cucumber genome.
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 PDFNuclear and mitochondrial genome assemblies for the endangered wood-decaying fungus Somion occarium.
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Earlham Institute, Norwich, UK.
Somion occarium is a wood-decaying bracket fungus belonging to an order known to be rich in useful chemical compounds. Despite its widespread distribution, S. occarium has been assessed as endangered on at least one national Red List, presumably due to loss of old-growth forest habitat.
View Article and Find Full Text PDFThe genome of the sapphire damselfish : a new resource to support further investigation of the evolution of Pomacentrids.
GigaByte
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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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