title: Nannochloropsis plastid and mitochondrial phylogenomes reveal organelle diversification mechanism and intragenus phylotyping strategy in microalgae.
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.
  
  
  CONCLUSIONS
  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.
authors.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.
authors.forename: Li
authors.initials: L
authors.lastname: Wei
authors.forename: Yi
authors.initials: Y
authors.lastname: Xin
authors.forename: Dongmei
authors.initials: D
authors.lastname: Wang
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Jing
authors.forename: Qian
authors.initials: Q
authors.lastname: Zhou
authors.forename: Xiaoquan
authors.initials: X
authors.lastname: Su
authors.forename: Jing
authors.initials: J
authors.lastname: Jia
authors.forename: Kang
authors.initials: K
authors.lastname: Ning
authors.forename: Feng
authors.initials: F
authors.lastname: Chen
authors.forename: Qiang
authors.initials: Q
authors.lastname: Hu
authors.forename: Jian
authors.initials: J
authors.lastname: Xu
mesh_terms: D019143:Evolution, Molecular; D005819:Genetic Markers / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics*; D054629:Genome, Mitochondrial / Q000235:genetics*; D023281:Genomics; D058086:Microalgae / Q000166:cytology* / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D018087:Plastids / Q000235:genetics*; D011110:Polymorphism, Genetic / Q000235:genetics
chemical_list: D005819:Genetic Markers
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