Laboratoire d'Océanographie Microbienne (LOMIC), CNRS/Sorbonne University, Observatoire Océanologique, UMR 7621, Banyuls s/ Mer, 66650, France.
Diversité, Adaptation Et Développement Des Plantes (DIADE) UMR 232, University of Montpellier, IRD, CIRAD, 911 Avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France.
BMC Genomics. 2024 Nov 6;25(1):1045. doi: 10.1186/s12864-024-10896-w.
Although metabarcoding and metagenomic approaches have generated large datasets on worldwide phytoplankton species diversity, the intraspecific genetic diversity underlying the genetic adaptation of marine phytoplankton to specific environmental niches remains largely unexplored. This is mainly due to the lack of biological resources and tools for monitoring the dynamics of this diversity in space and time.
To gain insight into population diversity, a novel method based on INDEL markers was developed on Bathycoccus prasinos (Mamiellophyceae), an abundant and cosmopolitan species with strong seasonal patterns. Long read sequencing was first used to characterize structural variants among the genomes of six B. prasinos strains sampled from geographically distinct regions in the world ocean. Markers derived from identified insertions/deletions were validated by PCR then used to genotype 55 B. prasinos strains isolated during the winter bloom 2018-2019 in the bay of Banyuls-sur-Mer (Mediterranean Sea, France). This led to their classification into eight multi-loci genotypes and the sequencing of strains representative of local diversity, further improving the available genetic diversity of B. prasinos. Finally, selected markers were directly tracked on environmental DNA sampled during 3 successive blooms from 2018 to 2021, showcasing a fast and cost-effective approach to follow local population dynamics.
This method, which involves (i) pre-identifying the genetic diversity of B. prasinos in environmental samples by PCR, (ii) isolating cells from selected environmental samples and (iii) identifying genotypes representative of B. prasinos diversity for sequencing, can be used to comprehensively describe the diversity and population dynamics not only in B. prasinos but also potentially in other generalist phytoplankton species.
尽管代谢组学和宏基因组学方法已经生成了关于世界范围内浮游植物物种多样性的大量数据集，但海洋浮游植物对特定环境小生境的遗传适应性的种内遗传多样性在很大程度上仍未得到探索。这主要是由于缺乏监测这种多样性在空间和时间上动态的生物资源和工具。
为了深入了解种群多样性，我们针对广泛分布且具有强烈季节性模式的物种泡叶藻（Mamiellophyceae）属巴氏藻，开发了一种基于 INDEL 标记的新方法。首先使用长读测序技术来描述从世界大洋不同地理区域采集的六个巴氏藻菌株的基因组结构变异。从鉴定出的插入/缺失中衍生出的标记通过 PCR 进行验证，然后用于对 2018-2019 年冬季在法国巴纽尔斯-苏尔-梅尔湾（地中海）爆发的 55 株巴氏藻进行基因分型。这将它们分为 8 个多基因座基因型，并对当地多样性具有代表性的菌株进行测序，进一步提高了巴氏藻的可用遗传多样性。最后，在所采集的 2018 年至 2021 年的 3 个连续水华期间的环境 DNA 中直接追踪了选定的标记，展示了一种快速且具有成本效益的方法来跟踪当地种群动态。
该方法包括（i）通过 PCR 预先识别环境样本中巴氏藻的遗传多样性，（ii）从选定的环境样本中分离细胞，以及（iii）鉴定代表巴氏藻多样性的基因型进行测序，不仅可以全面描述巴氏藻的多样性和种群动态，而且可能还可以描述其他广食性浮游植物物种的多样性和种群动态。
