First draft reference genome and annotation of the alternative oil species Physaria fendleri.

Autor: Johnston CR; BioDiscovery Institute, Department of Biological Sciences, University of North Texas, Denton, TX 76201, USA., Horn PJ; BioDiscovery Institute, Department of Biological Sciences, University of North Texas, Denton, TX 76201, USA., Alonso AP; BioDiscovery Institute, Department of Biological Sciences, University of North Texas, Denton, TX 76201, USA.
Jazyk: angličtina
Zdroj: G3 (Bethesda, Md.) [G3 (Bethesda)] 2024 Sep 04; Vol. 14 (9).
DOI: 10.1093/g3journal/jkae114
Abstrakt: In the wake of increasing demand for renewable energy sources, plant-based sources including alternative oilseeds have come to the forefront of interest. Hydroxy fatty acids (HFAs), produced in a few oilseed species, are important chemical feed stocks for industrial applications. An integrated approach was taken to assemble the first draft genome of the alternative HFA producer Physaria fendleri (n = 6), an outcrossing species with high heterozygosity. Both de novo transcriptome assemblies and genome assemblies were produced with public and generated sequencing reads. Resulting intermediate assemblies were then scaffolded and patched with multiple data sources, followed by super-scaffolding onto a masked genome of Camelina laxa (n = 6). Despite a current lack of available resources for the physical mapping of genomic scaffolds of P. fendleri, topography of the genome with respect to repeat and gene content was preserved at the scaffold level and not significantly lost via super-scaffolding. Read representation, gene and genome completion statistics, and annotation results illustrated the creation of a functional draft genome and a tool for future research on alternative oil species.
Competing Interests: Conflicts of interest The author(s) declare no conflict of interest.
(© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)
Databáze: MEDLINE
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