A pangenomic analysis of the Nannochloropsis organellar genomes reveals novel genetic variations in key metabolic genes

BMC Genomics

Rose Ann Cattolico²  Gabrielle Rocap¹  Scott Twary³  Olga Chertkov³  Michael Jacobs²  Cedar McKay¹  Ramesh K Jha³  Kyungyoon J Kwon⁴  Shawn R Starkenburg³ 

[1]School of Oceanography, University of Washington, Seattle 98195, WA, USA

[2]Biology Department, University of Washington, Seattle 98195, WA, USA

[3]Bioscience Division, Los Alamos National Laboratory, Los Alamos 87545, NM, USA

[4]Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley 94720, CA, USA

关键词: Gene divergence;    Genome evolution;    Stramenopiles;    Genome;    Mitochondria;    Chloroplast;    Nannochloropsis;   

Others  :  1217668
DOI  :  10.1186/1471-2164-15-212

 received in 2013-04-24, accepted in 2014-03-11,  发布年份 2014

【 摘 要 】

Background

Microalgae in the genus Nannochloropsis are photosynthetic marine Eustigmatophytes of significant interest to the bioenergy and aquaculture sectors due to their ability to efficiently accumulate biomass and lipids for utilization in renewable transportation fuels, aquaculture feed, and other useful bioproducts. To better understand the genetic complement that drives the metabolic processes of these organisms, we present the assembly and comparative pangenomic analysis of the chloroplast and mitochondrial genomes from Nannochloropsis salina CCMP1776.

Results

The chloroplast and mitochondrial genomes of N. salina are 98.4% and 97% identical to their counterparts in Nannochloropsis gaditana. Comparison of the Nannochloropsis pangenome to other algae within and outside of the same phyla revealed regions of significant genetic divergence in key genes that encode proteins needed for regulation of branched chain amino synthesis (acetohydroxyacid synthase), carbon fixation (RuBisCO activase), energy conservation (ATP synthase), protein synthesis and homeostasis (Clp protease, ribosome).

Conclusions

Many organellar gene modifications in Nannochloropsis are unique and deviate from conserved orthologs found across the tree of life. Implementation of secondary and tertiary structure prediction was crucial to functionally characterize many proteins and therefore should be implemented in automated annotation pipelines. The exceptional similarity of the N. salina and N. gaditana organellar genomes suggests that N. gaditana be reclassified as a strain of N. salina.

【 授权许可】

   
2014 Starkenburg et al.; licensee BioMed Central Ltd.

【 图 表 】

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