Comparative transcriptome of wild type and selected strains of the microalgae Tisochrysis lutea provides insights into the genetic basis, lipid metabolism and the life cycle.
The applied exploitation of microalgae cultures has to date almost exclusively involved the use of wild type strains, deposited over decades in dedicated culture collections. Concomitantly, the concept of improving algae with selection programs for particular specific purposes is slowly emerging. Studying since a decade an economically and ecologically important haptophyte Tisochrysis lutea (Tiso), we took advantage of the availability of wild type (Tiso-Wt) and selected (Tiso-S2M2) strains to conduct a molecular variations study. This endeavour presented substantial challenges: the genome assembly was not yet available, the life cycle unknown and genetic diversity of Tiso-Wt poorly documented. This study brings the first molecular data in order to set up a selection strategy for that microalgae. Following high-throughput Illumina sequencing, transcriptomes of Tiso-Wt and Tiso-S2M2 were de novo assembled and annotated. Genetic diversity between both strains was analyzed and revealed a clear conservation, while a comparison of transcriptomes allowed identification of polymorphisms resulting from the selection program. Of 34,374 transcripts, 291 were differentially expressed and 165 contained positional polymorphisms (SNP, Indel). We focused on lipid over-accumulation of the Tiso-S2M2 strain and 8 candidate genes were identified by combining analysis of positional polymorphism, differential expression levels, selection signature and by study of putative gene function. Moreover, genetic analysis also suggests the existence of a sexual cycle and genetic recombination in Tisochrysis lutea.
IFREMER-PBA, Nantes, France.
Gregory
G
Carrier
IFREMER-PBA, Nantes, France.
Matthieu
M
Garnier
UMT Geno-Vigne®, Montpellier, France.
Loïc
L
Le Cunff
IFREMER-PBA, Nantes, France.
Gaël
G
Bougaran
CNRS-UPMC, UMR 7144, Station Biologique de Roscoff, Roscoff, France.
Ian
I
Probert
CNRS-UPMC, UMR 7144, Station Biologique de Roscoff, Roscoff, France.
Colomban
C
De Vargas
CNRS-UPMC, ABiMS, Station Biologique de Roscoff, Roscoff, France.
Erwan
E
Corre
IFREMER-PBA, Nantes, France.
Jean-Paul
JP
Cadoret
IFREMER-PBA, Nantes, France.
Bruno
B
Saint-Jean
D020418:Algal Proteins / Q000235:genetics* / Q000378:metabolism; D020869:Gene Expression Profiling; D014644:Genetic Variation; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D008018:Life Cycle Stages / Q000235:genetics*; D050356:Lipid Metabolism / Q000235:genetics*; D058086:Microalgae / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D059467:Transcriptome
D020418:Algal Proteins