High quality genome assembly and annotation (v1) of the eukaryotic freshwater microalga Coccomyxa elongata SAG 216-3b

Anton Kraege; Edgar Chavarro-Carrero; Eva Schnell; Stefanie Heilmann-Heimbach; Kerstin Becker; Karl Köhrer; Bruno Hüettel; Nafiseh Sargheini; Philipp Schiffer; Ann-Marie Waldvogel; Bart P H J Thomma; Hanna Rovenich

doi:10.1093/g3journal/jkae294

High quality genome assembly and annotation (v1) of the eukaryotic freshwater microalga Coccomyxa elongata SAG 216-3b

G3 (Bethesda). 2024 Dec 13:jkae294. doi: 10.1093/g3journal/jkae294. Online ahead of print.

Authors

Affiliations

¹ Institute of Plant Sciences, University of Cologne, Zülpicher Straße 47b, 50674 Cologne, Germany.
² Institute of Human Genetics, University Hospital of Bonn, University of Bonn, Venusberg, Sigmund-Freund, Straße 25, 53127 Bonn, Germany.
³ NGS Core Facility, Medical Faculty of the University of Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany.
⁴ Cologne Center for Genomics (CCG), Medical Faculty, University of Cologne, Weyertal 115b, 50931 Cologne, Germany.
⁵ Biological and Medical Research Centre (BMFZ), Genomics & Transcriptomics Laboratory, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany.
⁶ Max Planck Genome Centre, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829 Cologne, Germany.
⁷ Institute of Zoology, University of Cologne, Zülpicher Straße 47b, 50674 Cologne, Germany.
⁸ Cluster of Excellence on Plant Sciences (CEPLAS), Zülpicher Straße 47b, 50674 Cologne, Germany.

PMID: 39671565
DOI: 10.1093/g3journal/jkae294

Abstract

Unicellular green algae of the genus Coccomyxa are recognized for their worldwide distribution and ecological versatility. Coccomyxa elongata is a freshwater species of the Coccomyxa simplex clade, which also includes lichen symbionts. To facilitate future molecular and phylogenomic studies of this versatile clade of algae, we generated a high-quality genome assembly for Coccomyxa elongata Chodat & Jaag SAG 216-3b within the framework of the Biodiversity Genomics Center Cologne (BioC2) initiative. A combination of long-read PacBio HiFi and Oxford Nanopore Technologies with chromatin conformation capture (Hi-C) sequencing led to the assembly of the genome into 21 scaffolds with a total length of 51.4 Mb and an N50 of 2.8 Mb. Nineteen of the scaffolds represent highly complete nuclear chromosomes delimited by telomeric repeats, while the two additional scaffolds represent the mitochondrial and plastid genomes. Transcriptome-guided gene annotation resulted in the identification of 14,811 protein-coding genes, of which 61% have annotated PFAM domains and 841 are predicted to be secreted. BUSCO analysis against the Chlorophyta database identified a total of 1,494 (98.4 %) complete gene models, suggesting a highly complete genome annotation.

Keywords: Coccomyxa; Trebouxiophyceae; genome annotation; genome assembly; long-read sequencing; unicellular algae.