Genetic and phenotypic intra-species diversity of alga Tisochrysis lutea reveals original genetic structure and domestication potential

Oceanic phytoplankton species are generally composed of many strains, with intra-species diversity consisting of genetic and phenotypic variability. Despite its importance in ecological and biotechnological contexts, this intra-species diversity and variation among strains has been little studied. We investigated the intra-species diversity of the microalga Tisochrysis lutea, a haptophyte of the Isochrysidales order. Inter-strain diversity of T. lutea was studied because of the economic importance of the species as a feed in aquaculture and for antioxidant metabolite production, particularly fucoxanthin and other carotenoids, which have health benefits. We analysed Tara Ocean datasets which revealed that T. lutea was present in the Pacific, Atlantic and Indian Oceans but not in the Arctic or Austral Oceans. We next made phenotypic and genotypic comparisons of 11 strains of T. lutea from worldwide algal collections. All strains were cultivated in the same controlled conditions for one week, and several phenotypic traits were measured, notably antioxidant content. In parallel, the genomes of each strain were sequenced, and genetic variants identified. At the genetic and phenotypic levels, the strains were distinct from each other and our analysis revealed natural trait variations of interest in relation to further exploitation in domestication programmes. A large number of genetic variations were identified among the strains, but no major differences in genome size were observed. Moreover, limited genetic structure was observed among these strains, which could be a consequence of the complex life history of species within the Isochrysidales. Our study provides new knowledge on the intra-species diversity that should be considered in future environmental studies and breeding programmes. Tisochrysis lutea is found in many parts of the world’s oceans.T. lutea has high inter-strain phenotypic and genomic variation.Genetic structure of strains from culture collections is limited. Tisochrysis lutea is found in many parts of the world’s oceans. T. lutea has high inter-strain phenotypic and genomic variation. Genetic structure of strains from culture collections is limited.海洋浮游植物物种通常由多个菌株构成，其种内多样性体现为遗传变异与表型变异的结合。尽管种内多样性及菌株间差异在生态学与生物技术领域具有重要意义，但相关研究却相对匮乏。本研究针对等鞭金藻目（Isochrysidales）的定鞭藻（haptophyte）——泰氏拟定鞭金藻（Tisochrysis lutea）的种内多样性展开探究。之所以开展该物种的菌株间多样性研究，是因为其作为水产养殖饵料以及抗氧化代谢产物生产原料的经济价值，其中尤以岩藻黄素（fucoxanthin）与其他类胡萝卜素（carotenoids）最为突出，这类物质均具有健康益处。本研究分析了塔拉海洋（Tara Ocean）数据集，结果显示泰氏拟定鞭金藻分布于太平洋、大西洋与印度洋，并未见于北冰洋与南大洋。随后，研究人员对来自全球藻类保藏中心的11株泰氏拟定鞭金藻开展表型与基因型比较分析。所有菌株均在统一可控的培养条件下培育一周，并测定了多项表型性状，其中尤以抗氧化物质含量为重点检测指标。与此同时，对每一株菌株的基因组进行测序并鉴定遗传变异位点。从遗传与表型层面来看，各菌株间存在显著差异；本研究分析发现了具有应用价值的自然性状变异，可用于后续的驯化培育项目。研究在菌株间鉴定出大量遗传变异，但未发现基因组大小存在显著差异。此外，这些菌株间的遗传结构分化程度有限，这一现象可能与等鞭金藻目物种复杂的生活史有关。本研究为种内多样性研究提供了新的认知，该成果可为后续环境研究与育种项目提供参考依据。泰氏拟定鞭金藻广泛分布于全球多处海域；该物种的菌株间存在显著的表型与基因组变异；来自保藏中心的菌株其遗传结构分化程度有限。泰氏拟定鞭金藻广泛分布于全球多处海域；该物种的菌株间存在显著的表型与基因组变异；来自保藏中心的菌株其遗传结构分化程度有限。