Chromosome-level genome assembly for an edible protein microalgae Auxenochlorella pyrenoidosa

1. United Nations Department of Economic and Social Affairs. Population Division (Ed.). World Population 9, 1–54 (2022).

   Google Scholar 

2. Williamson, E., Ross, I. L., Wall, B. T. & Hankamer, B. Microalgae: Potential novel protein for sustainable human nutrition. Trends Plant Sci. 29, 370–382 (2024).

   Google Scholar 

3. Torres-Tiji, Y., Fields, F. J. & Mayfield, S. P. Microalgae as a future food source. Biotechnol Adv. 41, 107536 (2020).

   Google Scholar 

4. Becker, E. W. Micro-algae as a source of protein. Biotechnol Adv. 25, 207–210 (2007).

   Google Scholar 

5. Krienitz, L., Huss, V. A. & Bock, C. Chlorella: 125 years of the green survivalist. Trends Plant Sci. 20, 67–69 (2015).

   Google Scholar 

6. Barbosa, M. J., Janssen, M., Sudfeld, C., D’Adamo, S. & Wijffels, R. H. Hypes, hopes, and the way forward for microalgal biotechnology. Trends Biotechnol. 41, 452–471 (2023).

   Google Scholar 

7. Fan, J. et al. Genomic foundation of starch-to-lipid switch in oleaginous Chlorella spp. Plant Physiol. 169, 2444–2461 (2015).

   Google Scholar 

8. Zou, S. et al. Combining and comparing coalescent, distance and character-based approaches for barcoding microalgaes: A test with Chlorella-like species (Chlorophyta). PLoS One 11, e0153833 (2016).

   Google Scholar 

9. Zhu, T. et al. Transcriptomic and metabolomic analysis reveal the effects of light quality on the growth and lipid biosynthesis in Chlorella pyrenoidosa. Biomolecules. 14, 1144 (2024).

   Google Scholar 

10. Chen, L., Zhang, L. & Liu, T. Concurrent production of carotenoids and lipid by a filamentous microalga Trentepohlia arborum. Bioresource Technol. 214, 567–573 (2016).

    Google Scholar 

11. Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 18, 170–175 (2021).

    Google Scholar 

12. Do, V. H. et al. Pasa: leveraging population pangenome graph to scaffold prokaryote genome assemblies. Nucleic Acids Res. 52, e15 (2024).

    Google Scholar 

13. Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Current protocols in bioinformatics Chapter 4, Unit 4.10 (2004).

    Google Scholar 

14. Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573–580 (1999).

    Google Scholar 

15. Chan, P. P., Lin, B. Y., Mak, A. J. & Lowe, T. M. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res. 49, 9077–9096 (2021).

    Google Scholar 

16. Kalvari, I. et al. Rfam 14: expanded coverage of metagenomic, viral and microRNA families. Nucleic Acids Res. 49, D192–D200 (2021).

    Google Scholar 

17. Gene Ontology Consortium. The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Res. 47, D330–D338 (2019).

    Google Scholar 

18. Kanehisa, M. & Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27–30 (2000).

    Google Scholar 

19. Saier, M. H. et al. The Transporter Classification Database (TCDB): 2021 update. Nucleic Acids Res. 49, D461–D467 (2021).

    Google Scholar 

20. Boeckmann, B. et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31, 365–70 (2003).

    Google Scholar 

21. Blin, K. et al. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res. 51, W46–W50 (2023).

    Google Scholar 

22. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP613830 (2025).

23. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP637498 (2025).

24. Zhang, S. et al. The GSA Family in 2025: A broadened sharing platform for multi-omics and multimodal data. Genom Proteom Bioinf. 23, qzaf072 (2025).

    Google Scholar 

25. CNCB-NGDC Members and Partners. Database resources of the National Genomics Data Center, China National Center for Bioinformation in 2025. Nucleic Acids Res. 53, D30–D44 (2025).

    Google Scholar 

26. CNCB Genome Sequence Archive https://ngdc.cncb.ac.cn/gsa/browse/CRA033078 (2025).

27. Luo, X. M. GenBank https://identifiers.org/ncbi/insdc.gca:GCA_047663505.1 (2025).

28. Luo, X. M. Auxenochlorella pyrenoidosa genome annotation and protein sequences. figshare https://doi.org/10.6084/m9.figshare.28498355 (2025).

Download references

Authors and Affiliations

1. Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences; Chengdu Agricultural Science and Technology Center, Chengdu, 610000, China

   Xiumei Luo, Ge Guan & Maozhi Ren

2. School of Agricultural Science of Zhengzhou University, Zhengzhou, Henan, 450000, China

   Haotian Su, Ge Guan & Maozhi Ren

Contributions

X.L.: Funding acquisition, Conceptualization, Methodology/Study design, Resources, Investigation, Formal analysis, Writing-original draft. H.S.: Formal analysis, Data curation, Investigation, Writing-original draft. G.G.: Formal analysis, Data curation, Investigation, Writing-original draft. M.R.: Funding acquisition, Data curation, Conceptualization, Supervision, Writing-review and editing.

Corresponding authors

Correspondence to Xiumei Luo or Maozhi Ren.

Competing interests

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.

Reprints and permissions