Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
Sequencing whole plant genomes provides a solid foundation for applied and basic studies. Genome sequences of agricultural plants attract special attention, as they reveal information on the regulation of beneficial plant traits. Flax is a valuable crop cultivated for oil and fiber. Genome sequences of its representatives are rich sources of genetic information for the improvement of cultivated forms of the plant. In our work, we sequenced the first genome of flax with the dehiscence of capsules- convar. (Boenn.) Dumort-on the Oxford Nanopore Technologies (ONT) and Illumina platforms. We obtained 23 Gb of raw ONT data and 89 M of 150 + 150 paired-end Illumina reads and tested different tools for genome assembly and polishing. The genome assembly produced according to the Canu-Racon ×2-medaka-POLCA scheme had optimal contiguity and completeness: assembly length-412.6 Mb, N50-5.2 Mb, L50-28, and complete BUSCO-94.6% (64.0% duplicated, eudicots_odb10). The obtained high-quality genome assembly of convar. provides opportunities for further studies of evolution, domestication, and genome regulation in the section .
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10702972 | PMC |
| http://dx.doi.org/10.3389/fgene.2023.1269837 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
sp. nov. and sp. nov., isolated from forest soil in Ireland.
Int J Syst Evol Microbiol
September 2025
School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
Two yeast strains, PYCC 10015 and PYCC 10016, were isolated from soil from an Irish forest. Sequence analysis of the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) of the rRNA gene repeat, and the D1/D2 domain of the LSU rRNA gene, showed that they belong to the and genera of the order , but they did not exactly match any known species.
View Article and Find Full Text PDFWhole-genome assembly and comparative genomic analyses provide insight into the endophytic lifestyle of Trichoderma lixii.
Curr Genet
September 2025
Fermentation and Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu-Tawi, 180001, India.
Trichoderma species exhibit remarkable versatility in adaptability and in occupying habitats with lifestyles ranging from mycoparasitism and saprotrophy to endophytism. In this study, we present the first high-quality whole-genome assembly and annotation of T. lixii using Illumina HiSeq technology to explore the mechanisms of endophytic lifestyle and plant colonization.
View Article and Find Full Text PDFATG16L1 controls mammalian vacuolar proton ATPase.
J Cell Biol
October 2025
Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.
The mechanisms governing mammalian proton pump V-ATPase function are of fundamental and medical interest. The assembly and disassembly of cytoplasmic V1 domain with the membrane-embedded V0 domain of V-ATPase is a key aspect of V-ATPase localization and function. Here, we show that the mammalian protein ATG16L1, primarily appreciated for its role in canonical autophagy and in noncanonical membrane atg8ylation processes, controls V-ATPase.
View Article and Find Full Text PDFNUMTsearcher: advancing detection and evolutionary insights of nuclear mitochondrial DNA segments across human, rabbit, and fish genomes.
J Hered
September 2025
Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China.
Nuclear mitochondrial DNA segments (NUMTs), which are mitochondrial DNA fragments integrated into the nuclear genome, serve as markers of evolutionary history. This study aims to enhance the detection and analysis of NUMTs by developing a script named NUMTsearcher. Utilizing the latest chromosome-level genome assemblies from various species, including human, rabbit, and six fish species, the study compares NUMTsearcher's performance against traditional methods such as LAST (Local Alignment Search Tool), BLAST (Basic Local Alignment Search Tool), BLAT (BLAST-Like Alignment Tool), and the pan-mitogenome approach, which integrates mitogenomes from diverse sources to identify fixed NUMTs in the nuclear genome.
View Article and Find Full Text PDFCharacterization of the Kaposi's sarcoma-associated herpesvirus terminase complex component ORF29.
Microbiol Spectr
September 2025
Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto, Japan.
Kaposi's sarcoma-associated herpesvirus (KSHV) belongs to the Gammaherpesvirinae subfamily. During the lytic phase of herpesviruses, viral capsids form in the host cell nucleus, and the replicated viral genome is packaged into these capsids. The herpesviral genome is replicated as a precursor head-to-tail concatemer consisting of tandemly repeated genomic units, each flanked by terminal repeats (TRs).
View Article and Find Full Text PDF