Nannochloropsis genomes reveal evolution of microalgal oleaginous traits

PLoS Genet. 2014 Jan;10(1):e1004094. doi: 10.1371/journal.pgen.1004094. Epub 2014 Jan 9.

Abstract

Oleaginous microalgae are promising feedstock for biofuels, yet the genetic diversity, origin and evolution of oleaginous traits remain largely unknown. Here we present a detailed phylogenomic analysis of five oleaginous Nannochloropsis species (a total of six strains) and one time-series transcriptome dataset for triacylglycerol (TAG) synthesis on one representative strain. Despite small genome sizes, high coding potential and relative paucity of mobile elements, the genomes feature small cores of ca. 2,700 protein-coding genes and a large pan-genome of >38,000 genes. The six genomes share key oleaginous traits, such as the enrichment of selected lipid biosynthesis genes and certain glycoside hydrolase genes that potentially shift carbon flux from chrysolaminaran to TAG synthesis. The eleven type II diacylglycerol acyltransferase genes (DGAT-2) in every strain, each expressed during TAG synthesis, likely originated from three ancient genomes, including the secondary endosymbiosis host and the engulfed green and red algae. Horizontal gene transfers were inferred in most lipid synthesis nodes with expanded gene doses and many glycoside hydrolase genes. Thus multiple genome pooling and horizontal genetic exchange, together with selective inheritance of lipid synthesis genes and species-specific gene loss, have led to the enormous genetic apparatus for oleaginousness and the wide genomic divergence among present-day Nannochloropsis. These findings have important implications in the screening and genetic engineering of microalgae for biofuels.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Evolution, Molecular
  • Gene Transfer, Horizontal
  • Genetic Variation
  • Genome*
  • Microalgae / genetics*
  • Molecular Sequence Annotation
  • Phylogeny*
  • Sequence Analysis, DNA
  • Species Specificity
  • Transcriptome
  • Triglycerides / biosynthesis
  • Triglycerides / genetics*

Substances

  • Triglycerides

Associated data

  • SRA/SRP032930

Grant support

This work was supported by Ministry of Science and Technology of China (2012CB721101; 2012AA02A707; 2011CB200902), National Natural Science Foundation of China (31010103907, 91231205, 61103167) and International Innovation Partnership Program from Chinese Academy of Sciences. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.