Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.
Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.
Environ Microbiol. 2022 Dec;24(12):6086-6099. doi: 10.1111/1462-2920.16171. Epub 2022 Aug 24.
For more than a decade, high-throughput sequencing has transformed the study of marine planktonic communities and has highlighted the extent of protist diversity in these ecosystems. Nevertheless, little is known relative to their genomic diversity at the species-scale as well as their major speciation mechanisms. An increasing number of data obtained from global scale sampling campaigns is becoming publicly available, and we postulate that metagenomic data could contribute to deciphering the processes shaping protist genomic differentiation in the marine realm. As a proof of concept, we developed a findable, accessible, interoperable and reusable (FAIR) pipeline and focused on the Mediterranean Sea to study three a priori abundant protist species: Bathycoccus prasinos, Pelagomonas calceolata and Phaeocystis cordata. We compared the genomic differentiation of each species in light of geographic, environmental and oceanographic distances. We highlighted that isolation-by-environment shapes the genomic differentiation of B. prasinos, whereas P. cordata is impacted by geographic distance (i.e. isolation-by-distance). At present time, the use of metagenomics to accurately estimate the genomic differentiation of protists remains challenging since coverages are lower compared to traditional population surveys. However, our approach sheds light on ecological and evolutionary processes occurring within natural marine populations and paves the way for future protist population metagenomic studies.
十多年来，高通量测序技术已经改变了海洋浮游生物群落的研究方式，并突出了这些生态系统中原生生物多样性的程度。然而，相对于其在物种尺度上的基因组多样性以及主要的物种形成机制，我们知之甚少。越来越多的从全球范围采样活动中获得的数据正在变得公开可用，我们假设宏基因组数据有助于揭示塑造海洋原生生物基因组分化的过程。作为概念验证，我们开发了一个可发现、可访问、可互操作和可重复使用的（FAIR）管道，并专注于地中海，研究三种事先确定的丰富的原生生物物种：Bathycoccus prasinos、Pelagomonas calceolata 和 Phaeocystis cordata。我们比较了每种物种在地理、环境和海洋距离方面的基因组分化。我们强调，环境隔离塑造了 B. prasinos 的基因组分化，而 P. cordata 则受到地理距离（即隔离距离）的影响。目前，由于与传统的种群调查相比，覆盖率较低，使用宏基因组学来准确估计原生生物的基因组分化仍然具有挑战性。然而，我们的方法揭示了自然海洋种群中发生的生态和进化过程，并为未来的原生生物种群宏基因组学研究铺平了道路。
