Section: Genomics
Topic: Biology of interactions, Genetics/genomics, Plant biology

High quality genome assembly and annotation (v1) of the eukaryotic terrestrial microalga Coccomyxa viridis SAG 216-4

Kraege, Anton1 ; Chavarro-Carrero, Edgar A.1 ; Guiglielmoni, Nadège2 ; Schnell, Eva1; Kirangwa, Joseph2; Heilmann-Heimbach, Stefanie3, 4 ; Becker, Kerstin5, 6 ; Köhrer, Karl6 ; Schiffer, Philipp2 ; Thomma, Bart P. H. J.1, 7 ; Rovenich, Hanna1  
1 Institute for Plant Sciences, University of Cologne, Germany
2 Institute of Zoology, University of Cologne, Germany
3 Institute of Human Genetics, University Hospital of Bonn & University of Bonn, Germany
4 NGS Core Facility, Medical Faculty of the University of Bonn, Germany
5 Cologne Center for Genomics (CCG), Medical Faculty, University of Cologne, Germany
6 Biological and Medical Research Centre (BMFZ), Genomics & Transcriptomics Laboratory, Heinrich-Heine-University Düsseldorf, Germany
7 Cluster of Excellence on Plant Sciences (CEPLAS), Germany

10.24072/pcjournal.447 - Peer Community Journal, Volume 4 (2024), article no. e72.

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Unicellular green algae of the genus Coccomyxa are recognized for their worldwide distribution and ecological versatility. Most species described to date live in close association with various host species, such as in lichen associations. However, little is known about the molecular mechanisms that drive such symbiotic lifestyles. We generated a high-quality genome assembly for the lichen photobiont Coccomyxa viridis SAG 216-4 (formerly C. mucigena). Using long-read PacBio HiFi and Oxford Nanopore Technologies in combination with chromatin conformation capture (Hi-C) sequencing, we assembled the genome into 21 scaffolds with a total length of 50.9 Mb, an N50 of 2.7 Mb and a BUSCO score of 98.6%. While 19 scaffolds represent full-length nuclear chromosomes, two additional scaffolds represent the mitochondrial and plastid genomes. Transcriptome-guided gene annotation resulted in the identification of 13,557 protein-coding genes, of which 68% have annotated PFAM domains and 962 are predicted to be secreted.

Published online:
DOI: 10.24072/pcjournal.447
Type: Research article

Kraege, Anton 1; Chavarro-Carrero, Edgar A. 1; Guiglielmoni, Nadège 2; Schnell, Eva 1; Kirangwa, Joseph 2; Heilmann-Heimbach, Stefanie 3, 4; Becker, Kerstin 5, 6; Köhrer, Karl 6; Schiffer, Philipp 2; Thomma, Bart P. H. J. 1, 7; Rovenich, Hanna 1

1 Institute for Plant Sciences, University of Cologne, Germany
2 Institute of Zoology, University of Cologne, Germany
3 Institute of Human Genetics, University Hospital of Bonn & University of Bonn, Germany
4 NGS Core Facility, Medical Faculty of the University of Bonn, Germany
5 Cologne Center for Genomics (CCG), Medical Faculty, University of Cologne, Germany
6 Biological and Medical Research Centre (BMFZ), Genomics & Transcriptomics Laboratory, Heinrich-Heine-University Düsseldorf, Germany
7 Cluster of Excellence on Plant Sciences (CEPLAS), Germany
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
@article{10_24072_pcjournal_447,
     author = {Kraege, Anton and Chavarro-Carrero, Edgar A. and Guiglielmoni, Nad\`ege and Schnell, Eva and Kirangwa, Joseph and Heilmann-Heimbach, Stefanie and Becker, Kerstin and K\"ohrer, Karl and Schiffer, Philipp and Thomma, Bart P. H. J. and Rovenich, Hanna},
     title = {High quality genome assembly and annotation (v1) of the eukaryotic terrestrial microalga {\protect\emph{Coccomyxa} viridis} {SAG} 216-4},
     journal = {Peer Community Journal},
     eid = {e72},
     publisher = {Peer Community In},
     volume = {4},
     year = {2024},
     doi = {10.24072/pcjournal.447},
     language = {en},
     url = {https://peercommunityjournal.org/articles/10.24072/pcjournal.447/}
}
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%A Schiffer, Philipp
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Kraege, Anton; Chavarro-Carrero, Edgar A.; Guiglielmoni, Nadège; Schnell, Eva; Kirangwa, Joseph; Heilmann-Heimbach, Stefanie; Becker, Kerstin; Köhrer, Karl; Schiffer, Philipp; Thomma, Bart P. H. J.; Rovenich, Hanna. High quality genome assembly and annotation (v1) of the eukaryotic terrestrial microalga Coccomyxa viridis SAG 216-4. Peer Community Journal, Volume 4 (2024), article  no. e72. doi : 10.24072/pcjournal.447. https://peercommunityjournal.org/articles/10.24072/pcjournal.447/

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.genomics.100300

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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