ArticleBMC genomics2013
Nannochloropsis plastid and mitochondrial phylogenomes reveal organelle diversification mechanism and intragenus phylotyping strategy in microalgae.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26 citing papers in PubMed, 63 citations in OpenAlex.
- Insights into the Phylogeny and Enigmatic Mitochondrial Biology of Eustigmatophyte Algae From Over 50 Newly Sequenced Organellar Genomes.Genome biology and evolution · 2026Article
- Charting the landscape of organellar genome evolution in eustigmatophyte algae.bioRxiv : the preprint server for biology · 2026Article
- Conjunctive BSA-Seq and BSR-Seq to Map the Genes of Yellow Leaf Mutations in Hot Peppers (Genes · 2024Article
- Comparative structure and evolution of the organellar genomes of Padina usoehtunii (Dictyotales) with the brown algal crown radiation clade.BMC genomics · 2024Article
- Complete mitochondrial genome of an oleaginous microalgaMitochondrial DNA. Part B, Resources · 2024Article
- Identification and characterization ofHorticulture research · 2022Article
- Occurrence, Evolution and Specificities of Iron-Sulfur Proteins and Maturation Factors in Chloroplasts from Algae.International journal of molecular sciences · 2021Review
- Large Differences in the HaptophyteFrontiers in microbiology · 2021Article
- Comparative Plastid Genomics of Cryptomonas Species Reveals Fine-Scale Genomic Responses to Loss of Photosynthesis.Genome biology and evolution · 2020Article
- Optimal Growth Temperature and Intergenic Distances in Bacteria, Archaea, and Plastids of Rhodophytic Branch.BioMed research international · 2020Article
- Plastid Genomes and Proteins Illuminate the Evolution of Eustigmatophyte Algae and Their Bacterial Endosymbionts.Genome biology and evolution · 2019Article
- Advanced genetic tools enable synthetic biology in the oleaginous microalgae Nannochloropsis sp.Plant cell reports · 2018Review
- Recurrent Loss, Horizontal Transfer, and the Obscure Origins of Mitochondrial Introns in Diatoms (Bacillariophyta).Genome biology and evolution · 2018Article
- Complete Genome Sequence of the Model Oleaginous AlgaGenome announcements · 2018Article
- Engineering the Chloroplast Genome of Oleaginous Marine MicroalgaFrontiers in plant science · 2018Article
- Membrane Proteomic Insights into the Physiology and Taxonomy of an Oleaginous Green Microalga.Plant physiology · 2017Article
- The plastid genome of some eustigmatophyte algae harbours a bacteria-derived six-gene cluster for biosynthesis of a novel secondary metabolite.Open biology · 2016Article
- Comparative genomics of mitochondria in chlorarachniophyte algae: endosymbiotic gene transfer and organellar genome dynamics.Scientific reports · 2016Article
- A Comparative Analysis of Mitochondrial Genomes in Eustigmatophyte Algae.Genome biology and evolution · 2016Article
- Algorithms for reconstruction of chromosomal structures.BMC bioinformatics · 2016Article
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Authors and funding
11 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMicroalgae are promising feedstock for production of lipids, sugars, bioactive compounds and in particular biofuels, yet development of sensitive and reliable phylotyping strategies for microalgae has been hindered by the paucity of phylogenetically closely-related finished genomes.
resultsUsing the oleaginous eustigmatophyte Nannochloropsis as a model, we assessed current intragenus phylotyping strategies by producing the complete plastid (pt) and mitochondrial (mt) genomes of seven strains from six Nannochloropsis species. Genes on the pt and mt genomes have been highly conserved in content, size and order, strongly negatively selected and evolving at a rate 33% and 66% of nuclear genomes respectively. Pt genome diversification was driven by asymmetric evolution of two inverted repeats (IRa and IRb): psbV and clpC in IRb are highly conserved whereas their counterparts in IRa exhibit three lineage-associated types of structural polymorphism via duplication or disruption of whole or partial genes. In the mt genomes, however, a single evolution hotspot varies in copy-number of a 3.5 Kb-long, cox1-harboring repeat. The organelle markers (e.g., cox1, cox2, psbA, rbcL and rrn16_mt) and nuclear markers (e.g., ITS2 and 18S) that are widely used for phylogenetic analysis obtained a divergent phylogeny for the seven strains, largely due to low SNP density. A new strategy for intragenus phylotyping of microalgae was thus proposed that includes (i) twelve sequence markers that are of higher sensitivity than ITS2 for interspecies phylogenetic analysis, (ii) multi-locus sequence typing based on rps11_mt-nad4, rps3_mt and cox2-rrn16_mt for intraspecies phylogenetic reconstruction and (iii) several SSR loci for identification of strains within a given species.
conclusionThis first comprehensive dataset of organelle genomes for a microalgal genus enabled exhaustive assessment and searches of all candidate phylogenetic markers on the organelle genomes. A new strategy for intragenus phylotyping of microalgae was proposed which might be generally applicable to other microalgal genera and should serve as a valuable tool in the expanding algal biotechnology industry.
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