High quality genome assembly and annotation (v1) of the eukaryotic terrestrial microalga Coccomyxa viridis SAG 216-4
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...
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2024-08-01
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| Online Access: | https://peercommunityjournal.org/articles/10.24072/pcjournal.447/ |
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| author | 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 |
| author_facet | 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 |
| author_sort | Kraege, Anton |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-a2514841d18d433d809cfd10cd9da913 |
| institution | Kabale University |
| issn | 2804-3871 |
| language | English |
| publishDate | 2024-08-01 |
| publisher | Peer Community In |
| record_format | Article |
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| spelling | doaj-art-a2514841d18d433d809cfd10cd9da9132025-02-07T10:17:18ZengPeer Community InPeer Community Journal2804-38712024-08-01410.24072/pcjournal.44710.24072/pcjournal.447High quality genome assembly and annotation (v1) of the eukaryotic terrestrial microalga Coccomyxa viridis SAG 216-4 Kraege, Anton0https://orcid.org/0000-0002-4741-5671Chavarro-Carrero, Edgar A.1https://orcid.org/0000-0003-0837-6830Guiglielmoni, Nadège2https://orcid.org/0000-0002-6185-1592Schnell, Eva3Kirangwa, Joseph4Heilmann-Heimbach, Stefanie5https://orcid.org/0000-0003-1057-465XBecker, Kerstin6https://orcid.org/0009-0009-7897-7181Köhrer, Karl7https://orcid.org/0000-0003-3644-2022Schiffer, Philipp8https://orcid.org/0000-0001-6776-0934Thomma, Bart P. H. J.9https://orcid.org/0000-0003-4125-4181Rovenich, Hanna10https://orcid.org/0000-0001-6138-4480Institute for Plant Sciences, University of Cologne, GermanyInstitute for Plant Sciences, University of Cologne, GermanyInstitute of Zoology, University of Cologne, GermanyInstitute for Plant Sciences, University of Cologne, GermanyInstitute of Zoology, University of Cologne, GermanyInstitute of Human Genetics, University Hospital of Bonn & University of Bonn, Germany; NGS Core Facility, Medical Faculty of the University of Bonn, GermanyCologne Center for Genomics (CCG), Medical Faculty, University of Cologne, Germany; Biological and Medical Research Centre (BMFZ), Genomics & Transcriptomics Laboratory, Heinrich-Heine-University Düsseldorf, GermanyBiological and Medical Research Centre (BMFZ), Genomics & Transcriptomics Laboratory, Heinrich-Heine-University Düsseldorf, GermanyInstitute of Zoology, University of Cologne, GermanyInstitute for Plant Sciences, University of Cologne, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), GermanyInstitute for Plant Sciences, University of Cologne, GermanyUnicellular 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.https://peercommunityjournal.org/articles/10.24072/pcjournal.447/ |
| spellingShingle | 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 |
| title | High quality genome assembly and annotation (v1) of the eukaryotic terrestrial microalga Coccomyxa viridis SAG 216-4
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| title_full | High quality genome assembly and annotation (v1) of the eukaryotic terrestrial microalga Coccomyxa viridis SAG 216-4
|
| title_fullStr | High quality genome assembly and annotation (v1) of the eukaryotic terrestrial microalga Coccomyxa viridis SAG 216-4
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| title_full_unstemmed | High quality genome assembly and annotation (v1) of the eukaryotic terrestrial microalga Coccomyxa viridis SAG 216-4
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| title_short | High quality genome assembly and annotation (v1) of the eukaryotic terrestrial microalga Coccomyxa viridis SAG 216-4
|
| title_sort | high quality genome assembly and annotation v1 of the eukaryotic terrestrial microalga coccomyxa viridis sag 216 4 |
| url | https://peercommunityjournal.org/articles/10.24072/pcjournal.447/ |
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