An INDEL genomic approach to explore population diversity of phytoplankton.

IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY BMC Genomics Pub Date : 2024-11-06 DOI:10.1186/s12864-024-10896-w
Martine Devic, Louis Dennu, Jean-Claude Lozano, Cédric Mariac, Valérie Vergé, Philippe Schatt, François-Yves Bouget, François Sabot
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Abstract

Background: 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.

Results: 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.

Conclusions: 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.

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探索浮游植物种群多样性的 INDEL 基因组方法。
背景:尽管代谢编码和元基因组学方法已经产生了有关全球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生态位的遗传适应所依赖的种内遗传多样性在很大程度上仍未得到探索。这主要是由于缺乏生物资源和工具来监测这种多样性在空间和时间上的动态变化:为了深入了解种群多样性,研究人员开发了一种基于 INDEL 标记的新方法,该方法适用于 Bathycoccus prasinos(Mamiellophyceae),这是一种丰富的世界性物种,具有很强的季节性。首先使用长读数测序来描述从世界海洋不同地理区域采样的六个 B. prasinos 菌株基因组的结构变异特征。通过 PCR 验证了从已识别的插入/缺失中提取的标记,然后用于对 2018-2019 年冬季水华期间在 Banyuls-sur-Mer 海湾(法国地中海)分离的 55 株 B. prasinos 菌株进行基因分型。这使得它们被划分为八个多基因型,并对代表当地多样性的菌株进行了测序,进一步提高了普拉西诺斯蚕的现有遗传多样性。最后,在 2018 年至 2021 年连续 3 次水华期间,对环境 DNA 取样直接跟踪所选标记,展示了一种快速、经济有效的方法来跟踪当地种群动态:该方法包括:(i)通过 PCR 预先确定环境样本中棱皮藻的遗传多样性;(ii)从选定的环境样本中分离细胞;(iii)确定代表棱皮藻多样性的基因型进行测序。
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来源期刊
BMC Genomics
BMC Genomics 生物-生物工程与应用微生物
CiteScore
7.40
自引率
4.50%
发文量
769
审稿时长
6.4 months
期刊介绍: BMC Genomics is an open access, peer-reviewed journal that considers articles on all aspects of genome-scale analysis, functional genomics, and proteomics. BMC Genomics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.
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