Best practices for methylome characterization in novel species: a case study in the microalgae Microchloropsis
Abstract Microalgae remain an important feedstock in the circular bioeconomy. The discovery of new species combined with advanced biotechnology drives optimization of performance predicated on deep knowledge of algal genomics and phenotype. Understanding the contribution of epigenetic processes to a...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-04-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-025-08027-6 |
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| author | Christina R. Steadman Eric M. Small Shounak Banerjee C. Raul Gonzalez-Esquer Sara Pacheco Scott N. Twary |
| author_facet | Christina R. Steadman Eric M. Small Shounak Banerjee C. Raul Gonzalez-Esquer Sara Pacheco Scott N. Twary |
| author_sort | Christina R. Steadman |
| collection | DOAJ |
| description | Abstract Microalgae remain an important feedstock in the circular bioeconomy. The discovery of new species combined with advanced biotechnology drives optimization of performance predicated on deep knowledge of algal genomics and phenotype. Understanding the contribution of epigenetic processes to algal function provides insight and better approaches for achieving production goals. Here, we provide a methodological framework for investigating epigenetic modifications in new species, including analysis of state-of-the-art techniques, and best practices for discerning novel modifications, focusing on variants of DNA methylation. Further, we demonstrate that specific forms of DNA methylation are overlooked by traditional epigenetic analysis strategies. Using high-throughput, lower cost techniques, we provide several pieces of evidence demonstrating Microchloropsis gaditana and M. salina (formerly Nannochloropsis), two candidate feedstock species, lack the most ubiquitous forms of eukaryotic DNA methylation (5mC and 5hmC) and instead employ N6-adenine methylation (6mA), commonly found in bacteria, in their genomes. Interestingly, transcriptionally diverse physiological conditions do not elicit differential 6mA methylation, suggesting the presence of 6mA may provide stability and protection of the genome. These collective discoveries illuminate not only an exciting avenue for improving feedstock genetic drift, stability, and culture health for bioproduction but also an ideal model species to study other epigenetic processes in microalgae. |
| format | Article |
| id | doaj-art-e70143e2003a4ea8b59ded1d7c865c62 |
| institution | OA Journals |
| issn | 2399-3642 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj-art-e70143e2003a4ea8b59ded1d7c865c622025-08-20T02:19:57ZengNature PortfolioCommunications Biology2399-36422025-04-018111310.1038/s42003-025-08027-6Best practices for methylome characterization in novel species: a case study in the microalgae MicrochloropsisChristina R. Steadman0Eric M. Small1Shounak Banerjee2C. Raul Gonzalez-Esquer3Sara Pacheco4Scott N. Twary5Genomics & Bioanalytics Group, Los Alamos National LaboratoryGenomics & Bioanalytics Group, Los Alamos National LaboratoryGenomics & Bioanalytics Group, Los Alamos National LaboratoryMicrobial & Biome Science Group, Los Alamos National LaboratoryMicrobial & Biome Science Group, Los Alamos National LaboratoryMicrobial & Biome Science Group, Los Alamos National LaboratoryAbstract Microalgae remain an important feedstock in the circular bioeconomy. The discovery of new species combined with advanced biotechnology drives optimization of performance predicated on deep knowledge of algal genomics and phenotype. Understanding the contribution of epigenetic processes to algal function provides insight and better approaches for achieving production goals. Here, we provide a methodological framework for investigating epigenetic modifications in new species, including analysis of state-of-the-art techniques, and best practices for discerning novel modifications, focusing on variants of DNA methylation. Further, we demonstrate that specific forms of DNA methylation are overlooked by traditional epigenetic analysis strategies. Using high-throughput, lower cost techniques, we provide several pieces of evidence demonstrating Microchloropsis gaditana and M. salina (formerly Nannochloropsis), two candidate feedstock species, lack the most ubiquitous forms of eukaryotic DNA methylation (5mC and 5hmC) and instead employ N6-adenine methylation (6mA), commonly found in bacteria, in their genomes. Interestingly, transcriptionally diverse physiological conditions do not elicit differential 6mA methylation, suggesting the presence of 6mA may provide stability and protection of the genome. These collective discoveries illuminate not only an exciting avenue for improving feedstock genetic drift, stability, and culture health for bioproduction but also an ideal model species to study other epigenetic processes in microalgae.https://doi.org/10.1038/s42003-025-08027-6 |
| spellingShingle | Christina R. Steadman Eric M. Small Shounak Banerjee C. Raul Gonzalez-Esquer Sara Pacheco Scott N. Twary Best practices for methylome characterization in novel species: a case study in the microalgae Microchloropsis Communications Biology |
| title | Best practices for methylome characterization in novel species: a case study in the microalgae Microchloropsis |
| title_full | Best practices for methylome characterization in novel species: a case study in the microalgae Microchloropsis |
| title_fullStr | Best practices for methylome characterization in novel species: a case study in the microalgae Microchloropsis |
| title_full_unstemmed | Best practices for methylome characterization in novel species: a case study in the microalgae Microchloropsis |
| title_short | Best practices for methylome characterization in novel species: a case study in the microalgae Microchloropsis |
| title_sort | best practices for methylome characterization in novel species a case study in the microalgae microchloropsis |
| url | https://doi.org/10.1038/s42003-025-08027-6 |
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