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Nannochloropsis plastid and mitochondrial phylogenomes reveal organelle diversification mechanism and intragenus phylotyping strategy in microalgae.

Wei L, Xin Y, Wang D, Jing X, Zhou Q, Su X, Jia J, Ning K, Chen F, Hu Q, Xu J - BMC Genomics (2013)

Bottom Line: 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.This 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: BioEnergy Genome Center and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.

ABSTRACT

Background: Microalgae 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.

Results: Using 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.

Conclusion: This 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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Comparison of functional complements of organelle genomes. Among Nannochloropsis, brown algae and diatoms, shared and lineage-specific genes from plastid and mitochondrial genomes are compared via Venn diagrams. (A) Shared and lineage-specific genes of different plastid genomes. (B) Shared and lineage-specific genes of different mitochondrial genomes.
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Figure 2: Comparison of functional complements of organelle genomes. Among Nannochloropsis, brown algae and diatoms, shared and lineage-specific genes from plastid and mitochondrial genomes are compared via Venn diagrams. (A) Shared and lineage-specific genes of different plastid genomes. (B) Shared and lineage-specific genes of different mitochondrial genomes.

Mentions: Organelle genomes were thought to have undergone size- and functional reduction [29,30], and frequent genetic exchange via endosymbiotic gene transfer (EGT) and homologous recombination [31,32]. The present-day microalgal pt genomes mainly encode the components of photosystems, carbon assimilation, photosynthetic electron transport and gene translation machinery [33], while the mt genomes encode genes mostly involved in respiratory electron transport, oxidative phosphorylation, ATP synthesis and ribosome biosynthesis [5,34]. In Nannochloropsis, brown algae and diatoms, nearly all the photosystem I and photosystem II genes encoded by the pt genomes were retained in a high degree of consistency (FigureĀ 2). However, a photosystem I gene (psaM) was lost in Nannochloropsis pt genome. A photosystem II gene (psbM) was also absent in the pt genomes of Nannochloropsis as in other red algae, but was present in the green algae lineage [35-39]. In addition, all of the cytochrome components found in other stramenopiles and the red lineage of algae (with the exception of petL) have been retained in Nannochloropsis pt genomes [40-46].


Nannochloropsis plastid and mitochondrial phylogenomes reveal organelle diversification mechanism and intragenus phylotyping strategy in microalgae.

Wei L, Xin Y, Wang D, Jing X, Zhou Q, Su X, Jia J, Ning K, Chen F, Hu Q, Xu J - BMC Genomics (2013)

Comparison of functional complements of organelle genomes. Among Nannochloropsis, brown algae and diatoms, shared and lineage-specific genes from plastid and mitochondrial genomes are compared via Venn diagrams. (A) Shared and lineage-specific genes of different plastid genomes. (B) Shared and lineage-specific genes of different mitochondrial genomes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750441&req=5

Figure 2: Comparison of functional complements of organelle genomes. Among Nannochloropsis, brown algae and diatoms, shared and lineage-specific genes from plastid and mitochondrial genomes are compared via Venn diagrams. (A) Shared and lineage-specific genes of different plastid genomes. (B) Shared and lineage-specific genes of different mitochondrial genomes.
Mentions: Organelle genomes were thought to have undergone size- and functional reduction [29,30], and frequent genetic exchange via endosymbiotic gene transfer (EGT) and homologous recombination [31,32]. The present-day microalgal pt genomes mainly encode the components of photosystems, carbon assimilation, photosynthetic electron transport and gene translation machinery [33], while the mt genomes encode genes mostly involved in respiratory electron transport, oxidative phosphorylation, ATP synthesis and ribosome biosynthesis [5,34]. In Nannochloropsis, brown algae and diatoms, nearly all the photosystem I and photosystem II genes encoded by the pt genomes were retained in a high degree of consistency (FigureĀ 2). However, a photosystem I gene (psaM) was lost in Nannochloropsis pt genome. A photosystem II gene (psbM) was also absent in the pt genomes of Nannochloropsis as in other red algae, but was present in the green algae lineage [35-39]. In addition, all of the cytochrome components found in other stramenopiles and the red lineage of algae (with the exception of petL) have been retained in Nannochloropsis pt genomes [40-46].

Bottom Line: 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.This 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: BioEnergy Genome Center and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.

ABSTRACT

Background: Microalgae 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.

Results: Using 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.

Conclusion: This 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.

Show MeSH
Related in: MedlinePlus