Fast forward genetics to identify mutations causing a high light tolerant phenotype in Chlamydomonas reinhardtii by whole-genome-sequencingReport as inadecuate

Fast forward genetics to identify mutations causing a high light tolerant phenotype in Chlamydomonas reinhardtii by whole-genome-sequencing - Download this document for free, or read online. Document in PDF available to download.

BMC Genomics

, 16:57

First Online: 06 February 2015Received: 18 March 2014Accepted: 12 January 2015DOI: 10.1186-s12864-015-1232-y

Cite this article as: Schierenbeck, L., Ries, D., Rogge, K. et al. BMC Genomics 2015 16: 57. doi:10.1186-s12864-015-1232-y


BackgroundHigh light tolerance of microalgae is a desired phenotype for efficient cultivation in large scale production systems under fluctuating outdoor conditions. Outdoor cultivation requires the use of either wild-type or non-GMO derived mutant strains due to safety concerns. The identification and molecular characterization of such mutants derived from untagged forward genetics approaches was limited previously by the tedious and time-consuming methods involving techniques such as classical meiotic mapping. The combination of mapping with next generation sequencing technologies offers alternative strategies to identify genes involved in high light adaptation in untagged mutants.

ResultsWe used the model alga Chlamydomonas reinhardtii in a non-GMO mutation strategy without any preceding crossing step or pooled progeny to identify genes involved in the regulatory processes of high light adaptation. To generate high light tolerant mutants, wildtype cells were mutagenized only to a low extent, followed by a stringent selection. We performed whole-genome sequencing of two independent mutants hit1 and hit2 and the parental wildtype. The availability of a reference genome sequence and the removal of shared bakground variants between the wildtype strain and each mutant, enabled us to identify two single nucleotide polymorphisms within the same gene Cre02.g085050, hereafter called LRS1 putative Light Response Signaling protein 1. These two independent single amino acid exchanges are both located in the putative WD40 propeller domain of the corresponding protein LRS1. Both mutants exhibited an increased rate of non-photochemical-quenching NPQ and an improved resistance against chemically induced reactive oxygen species. In silico analyses revealed homology of LRS1 to the photoregulatory protein COP1 in plants.

ConclusionsIn this work we identified the nuclear encoded gene LRS1 as an essential factor for high light adaptation in C. reinhardtii. The causative random mutation within this gene was identified by a rapid and efficient method, avoiding any preceding crossing step, meiotic mapping, or pooled progeny. Our results open up new insights into mechanisms of high light adaptation in microalgae and at the same time provide a simplified strategy for non-GMO forward genetics, a crucial precondition that could result in the identification of key factors for economically relevant biological processes within algae.

KeywordsWhole-genome-sequencing Chlamydomonas reinhardtii Forward genetics Mutation identification SNPs High light AbbreviationsHLHigh light

SNPsSingle nucleotide polymorphisms

GMOGenetically modified organisms



hit1 and hit2high light tolerant mutants 1 and 2

JGIDOE Joint Genome Institute

GATKGenome Analysis Toolkit

BWABurrows-Wheeler Aligner

AFAllele frequency

LRSPutative Light Response Signaling protein 1

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Author: Lisa Schierenbeck - David Ries - Kristin Rogge - Sabrina Grewe - Bernd Weisshaar - Olaf Kruse


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