@article{df1332841ee642d695c490966b845fc3,
title = "Metagenomics approach for Polymyxa betae genome assembly enables comparative analysis towards deciphering the intracellular parasitic lifestyle of the plasmodiophorids",
abstract = "Genomic knowledge of the tree of life is biased to specific groups of organisms. For example, only six full genomes are currently available in the rhizaria clade. Here, we have applied metagenomic techniques enabling the assembly of the genome of Polymyxa betae (Rhizaria, Plasmodiophorida) RES F41 isolate from unpurified zoospore holobiont and comparison with the A26–41 isolate. Furthermore, the first P. betae mitochondrial genome was assembled. The two P. betae nuclear genomes were highly similar, each with just ~10.2 k predicted protein coding genes, ~3% of which were unique to each isolate. Extending genomic comparisons revealed a greater overlap with Spongospora subterranea than with Plasmodiophora brassicae, including orthologs of the mammalian cation channel sperm-associated proteins, raising some intriguing questions about zoospore physiology. This work validates our metagenomics pipeline for eukaryote genome assembly from unpurified samples and enriches plasmodiophorid genomics; providing the first full annotation of the P. betae genome.",
keywords = "Ankyrin repeats, CatSper, Plasmodiophora, Polymyxa betae, Rhizaria, Spongospora",
author = "Alain Decro{\"e}s and Li, {Jun Min} and Lorna Richardson and Euphemia Mutasa-Gottgens and Gipsi Lima-Mendez and Mathieu Mahillon and Claude Bragard and Finn, {Robert D.} and Anne Legr{\`e}ve",
note = "Funding Information: This work was supported by UCLouvain, Belgium and China Agriculture Research System from the Ministry of Agriculture of the P. R. China ( CARS-03 ). RF is supported by EMBL core funds, UK. Funding Information: Spongospora subterranea predicted proteins set used in the S. subterranea genome announcement [ 37 ] was kindly provided by Stephan Ciaghi and Arne Schwelm. We express our gratitude to Britta Schulz (KWS SAAT SE, Einbeck, Germany) for kindly providing seeds from the KWS2320 sugar beet. Computational resources have been partially provided by the Consortium des {\'E}quipements de Calcul Intensif (C{\'E}CI), funded by the Fonds de la Recherche Scientifique de Belgique (F.R.S.-FNRS) under Grant No. 2.5020.11 and by the Walloon Region. Publisher Copyright: {\textcopyright} 2021 The Authors",
year = "2022",
month = jan,
doi = "10.1016/j.ygeno.2021.11.018",
language = "English",
volume = "114",
pages = "9--22",
journal = "Genomics",
issn = "0888-7543",
publisher = "Academic Press Inc.",
number = "1",
}