ABSTRACT
In this study, the genome of the microalgal strain Coelastrella sp. UAM-C/S07 was analyzed to assess its potential as a strain capable of producing high-value carotenoids and fatty acids. A total of 9,319 coding sequences (CDSs) were identified, distributed across 1,065 contigs assembled using a de novo approach.
KEYWORDS: chlorophyte genomics, microalgae, Coelastrella, carotenoids, biofuels, long-read sequencing
ANNOUNCEMENT
Mitigating atmospheric CO₂ is a major environmental challenge, and microalgae act as efficient carbon sinks that often surpass terrestrial plants in carbon fixation (1). Microalgal biomass also provides a sustainable source of renewable energy and high-value metabolites (2, 3). The genus Coelastrella is promising due to its capacity to produce carotenoids, such as astaxanthin and canthaxanthin, and to accumulate lipids suitable for biodiesel (4–6). However, genomic resources for this genus remain limited.
A Coelastrella sp. strain previously isolated from Chalchoapan Lake, Veracruz, Mexico (18.41,611° N, 95.13,417° W) (7), was used for genomic analysis. The strain was established as a monoclonal culture from a single isolated cell and maintained in BG11 medium for 72 h at 35°C, 100 rpm, and 100 μmol photons m⁻² s⁻¹ prior to DNA extraction (8).
Genomic DNA was extracted using the DNeasy PowerSoil Kit (QIAGEN, Germany) following the manufacturer’s protocol with minor modifications. DNA quality was assessed with a Thermo Fisher Nanodrop One (OD260/280 and OD260/230), and integrity was verified by agarose gel electrophoresis (9).
Whole-genome sequencing was performed on a MinION R10.4.1 flow cell (mK1b device, FLO-MIN114) with the Rapid Barcoding Kit V14 (SQK-RBK114.24; Oxford Nanopore Technologies, Oxford, UK), generating 1,031,325 reads (200–173,656 bp). Read quality was evaluated with FastQC (v0.74) (10), and Filtlong (v0.3.1) (11) was used for Q20 filtering, yielding 598,477 reads with an N50 of 3,751 bp. Assembly was generated with Flye (v2.9.6) (12), polished with three rounds of Racon (v1.4.3) (13) and one round of Medaka (14), followed by removal of redundant contigs using purge_dups (v1.2.6) (15). Contaminant and chimeric sequences were removed using BlobToolkit (v4.4.6) (16), Kraken2 (Standard Database) (v2.17.0) (17), and FCS-GX (v0.5.5) (18). Assembly quality and completeness were assessed with QUAST (v5.2.0) (19) and BUSCO (v5.5.0) (20).
The final assembly comprised 1,065 contigs totaling 89.9 Mb, with an N50 of 218 kb, L50 of 127, GC content of 52.05%, and BUSCO completeness of 91%. Structural gene prediction was performed using GeMoMa (v1.9) (21), with genome annotations from Scenedesmus glucoliberatum PABB004 (22) and Scenedesmus sp. NREL 46B-D3 (23) as reference species for predicting protein-coding genes.
Functional annotation was performed using InterProScan (v5.76-107.0) (24), eggNOG-mapper (v2.1.13) (25), and BLASTp (v2.1.16) (26) searches against the UniProtKB/Swiss-Prot database. Detailed annotation coverage and completeness metrics are summarized in Table 1.
TABLE 1.
Assembly and annotation summary for Coelastrella sp. UAM-C/S07
| Category | Metric | Value |
|---|---|---|
| Genome assembly | Assembly size | 89.9 Mb |
| Number of contigs | 1,065 | |
| N50 | 218 kb | |
| L50 | 127 | |
| GC content | 52.05% | |
| Genome annotation | BUSCO completeness | Assembly: 91%; annotation: 87% |
| Predicted protein-coding genes | 9,319 | |
| Annotation coverage | InterProScan: 8,645 (92.8%) COG: 7,139 (76.6%) Swiss-Prot: 5,311 (57.0%) KEGG: 4,649 (49.9%) GO terms: 1,302 (14.0%) |
|
| Total ncRNA loci | 119 (54 tRNAs, 7 rRNAs, 3 snRNAs, 21 miRNA-family elements, 33 isrG-like small RNAs) |
Non-coding RNA annotation was performed with Infernal (v1.1.5) (27), and full-length rRNA genes were independently predicted with Barrnap (v0.9) (28). The annotation identified 11 genes involved in the carotenoid biosynthesis pathway, including beta-carotene 3-hydroxylase (EC 1.14.15.24) and 93 genes associated with lipid metabolism, such as malonyl-CoA S-malonyltransferase (EC 2.3.1.39) and delta-12 desaturase (EC 1.14.19.6). A summary of genome assembly and annotation metrics, including functional annotation coverage and completeness statistics, is provided in Table 1.
This draft genome assembly represents a valuable resource for future research on microalgae as producers of high-value compounds, such as pigments and lipids, and for advancing studies in genome biology and metabolic engineering.
ACKNOWLEDGMENTS
Mauricio Carrasco acknowledges the financial support provided by SECIHTI for the scholarship awarded (CVU 1253628). Adrian A Estrada-Graf acknowledges support from the Fulbright García-Robles Graduate Studies Fellowship. This work was supported by UAM-funded project 106 S264-24, awarded under the Call for Research Proposals Addressing Current Challenges, and by SECTEI (grant SECTEI/044/2024).
The authors also thank Mónica Rodríguez-Palacio for providing the biological material essential to this research.
Contributor Information
Marcia Morales-Ibarría, Email: mmorales@cua.uam.mx.
Jason E. Stajich, University of California Riverside, Riverside, California, USA
DATA AVAILABILITY
This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JBSVDD000000000. The version described in this paper is version JBSVDD010000000. Raw sequencing data have been deposited in the NCBI Sequence Read Archive (SRA) under the accession SRR36252716, BioProject accession PRJNA1369635, and Biosample SAMN53397293. The corresponding genome annotation (gene models, CDSs, and predicted proteins), including the 18S rRNA gene sequence used for molecular identification of the strain, has been uploaded to NCBI and is also available via Zenodo (https://doi.org/10.5281/zenodo.18555187).
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JBSVDD000000000. The version described in this paper is version JBSVDD010000000. Raw sequencing data have been deposited in the NCBI Sequence Read Archive (SRA) under the accession SRR36252716, BioProject accession PRJNA1369635, and Biosample SAMN53397293. The corresponding genome annotation (gene models, CDSs, and predicted proteins), including the 18S rRNA gene sequence used for molecular identification of the strain, has been uploaded to NCBI and is also available via Zenodo (https://doi.org/10.5281/zenodo.18555187).