Predicting global distributions of eukaryotic plankton communities from satellite data

プランクトンを宇宙から観測する --衛星データを入力データとする海洋真核微生物群集予測モデルの開発--. 京都大学プレスリリース. 2023-10-19.Satellite remote sensing is a powerful tool to monitor the global dynamics of marine plankton. Previous research has focused on developing models to predict the size or taxonomic groups of phytoplankton. Here, we present an approach to identify community types from a global plankton network that includes phytoplankton and heterotrophic protists and to predict their biogeography using global satellite observations. Six plankton community types were identified from a co-occurrence network inferred using a novel rDNA 18 S V4 planetary-scale eukaryotic metabarcoding dataset. Machine learning techniques were then applied to construct a model that predicted these community types from satellite data. The model showed an overall 67% accuracy in the prediction of the community types. The prediction using 17 satellite-derived parameters showed better performance than that using only temperature and/or the concentration of chlorophyll a. The constructed model predicted the global spatiotemporal distribution of community types over 19 years. The predicted distributions exhibited strong seasonal changes in community types in the subarctic–subtropical boundary regions, which were consistent with previous field observations. The model also identified the long-term trends in the distribution of community types, which suggested responses to ocean warming

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems

de novode\ novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

International audienceBackground: Oxford Nanopore Technologies Ltd (Oxford, UK) have recently commercialized MinION, a small single-molecule nanopore sequencer, that offers the possibility of sequencing long DNA fragments from small genomes in a matter of seconds. The Oxford Nanopore technology is truly disruptive; it has the potential to revolutionize genomic applications due to its portability, low cost, and ease of use compared with existing long reads sequencing technologies. The MinION sequencer enables the rapid sequencing of small eukaryotic genomes, such as the yeast genome. Combined with existing assembler algorithms, near complete genome assemblies can be generated and comprehensive population genomic analyses can be performed. Results: Here, we resequenced the genome of the Saccharomyces cerevisiae S288C strain to evaluate the performance of nanopore-only assemblers. Then we de novo sequenced and assembled the genomes of 21 isolates representative of the S. cerevisiae genetic diversity using the MinION platform. The contiguity of our assemblies was 14 times higher than the Illumina-only assemblies and we obtained one or two long contigs for 65 % of the chromosomes. This high contiguity allowed us to accurately detect large structural variations across the 21 studied genomes. Conclusion: Because of the high completeness of the nanopore assemblies, we were able to produce a complete cartography of transposable elements insertions and inspect structural variants that are generally missed using a short-read sequencing strategy. Our analyses show that the Oxford Nanopore technology is already usable for de novo sequencing and assembly; however, non-random errors in homopolymers require polishing the consensus using an alternate sequencing technology

Global observation of plankton communities from space

Abstract Satellite remote sensing from space is a powerful way to monitor the global dynamics of marine plankton. Previous research has focused on developing models to predict the size or taxonomic groups of phytoplankton. Here we present an approach to identify representative communities from a global plankton network that included both zooplankton and phytoplankton and using global satellite observations to predict their biogeography. Six representative plankton communities were identified from a global co-occurrence network inferred using a novel rDNA 18S V4 planetary-scale eukaryotic metabarcoding dataset. Machine learning techniques were then applied to train a model that predicted these representative communities from satellite data. The model showed an overall 67% accuracy in the prediction of the representative communities. The prediction based on 17 satellite-derived parameters showed better performance than based only on temperature and/or the concentration of chlorophyll a . The trained model allowed to predict the global spatiotemporal distribution of communities over 19-years. Our model exhibited strong seasonal changes in the community compositions in the subarctic-subtropical boundary regions, which were consistent with previous field observations. This network-oriented approach can easily be extended to more comprehensive models including prokaryotes as well as viruses

European mink (Mustela lutreola) reference genome and population genomics

International audienceThe European mink (Mustela lutreola) is considered as critically endangered in the IUCN red list, and is already extinct in large parts of its ancestral range. A chromosome-scale reference genome has been recently produced during the ERGA (European Reference Genome Atlas) pilot project, from an individual sampled in 2006 in Dordogne (France) in the framework of the first National Action Plan for European Mink. A fibroblast cell culture was derived from a skin biopsy on this animal, and then cryopreserved in liquid nitrogen in the Paris National Museum of Natural History cell collection. This frozen sample was used to generate fresh cell cultures for the production of high-quality DNA that was subsequently sequenced and assembled into a high-quality reference genome. This reference can now be used for genomic studies of this species that presents a very high risk of inbreeding depression especially in the western part of its geographic distribution. Inbreeding depression is a critical concern for conservation efforts as it is common in small, declining or fragmented populations. Demographic history of a population can also have an impact on inbreeding depression and shape the levels of genetic load. Interestingly, small populations with extremely low genetic diversity do not always present evidence of Inbreeding depression and may persist thanks to the purging of strong deleterious variants. One way to measure the extent of inbreeding is to scan genomes for runs of homozygosity (ROH). This method is becoming more commonly used to estimate inbreeding and could become a new index for conservation status in wild animals. For this study, we selected two European mink from France (LIFE VISON et PNA Vison), two from Romania, two from Estonia and two from Spain for whole genome re-sequencing (> 25x), each genomic sequence being compared to the reference genome. We expect to find long stretches of ROH that would indicate recent events of inbreeding. The results might have a direct impact on the current conservation program for the European mink

European mink (Mustela lutreola) reference genome and population genomics

International audienceThe European mink (Mustela lutreola) is considered as critically endangered in the IUCN red list, and is already extinct in large parts of its ancestral range. A chromosome-scale reference genome has been recently produced during the ERGA (European Reference Genome Atlas) pilot project, from an individual sampled in 2006 in Dordogne (France) in the framework of the first National Action Plan for European Mink. A fibroblast cell culture was derived from a skin biopsy on this animal, and then cryopreserved in liquid nitrogen in the Paris National Museum of Natural History cell collection. This frozen sample was used to generate fresh cell cultures for the production of high-quality DNA that was subsequently sequenced and assembled into a high-quality reference genome. This reference can now be used for genomic studies of this species that presents a very high risk of inbreeding depression especially in the western part of its geographic distribution. Inbreeding depression is a critical concern for conservation efforts as it is common in small, declining or fragmented populations. Demographic history of a population can also have an impact on inbreeding depression and shape the levels of genetic load. Interestingly, small populations with extremely low genetic diversity do not always present evidence of Inbreeding depression and may persist thanks to the purging of strong deleterious variants. One way to measure the extent of inbreeding is to scan genomes for runs of homozygosity (ROH). This method is becoming more commonly used to estimate inbreeding and could become a new index for conservation status in wild animals. For this study, we selected two European mink from France (LIFE VISON et PNA Vison), two from Romania, two from Estonia and two from Spain for whole genome re-sequencing (> 25x), each genomic sequence being compared to the reference genome. We expect to find long stretches of ROH that would indicate recent events of inbreeding. The results might have a direct impact on the current conservation program for the European mink

From genome wide SNPs to genomic islands of differentiation: the quest for species diagnostic markers in two scleractinian corals,<i>Pocillopora</i>and<i>Porites</i>

Abstract Coral reefs are of paramount importance in marine ecosystems, where they provide support for a large part of the biodiversity. Being quite sensitive to global changes, they are therefore the prime targets for biodiversity conservation policies. However, such conservation goals require accurate species identification, which are notoriously difficult to get in these highly morphologically variable organisms, rich in cryptic species. There is an acute need for easy-to-use and resolutive species diagnostic molecular markers. The present study builds on the huge sequencing effort developed during the TARA Pacific expedition to develop a genotyping strategy to assign coral samples to the correct species within two coral genera ( Porites and Pocillopora ). For this purpose, we developed a technique that we called “Divergent Fragment” based on the sequencing of a less than 2kb long diagnostic genomic fragment determined from the metagenomic data of a subset of the corals collected. This method has proven to be rapid, resolvable and cost-effective. Sequencing of PCR fragments nested along the species diagnostic fragment allowed us to assign 232 individuals of the genus Pocillopora and 247 individuals of the genus Porites to previously identified independent genetic lineages ( i . e . species). This genotyping method will allow to fully analyze the coral samples collected across the Pacific during the Tara Pacific expedition and opens technological perspectives in the field of population genomics-guided conservation

Predicting global distributions of eukaryotic plankton communities from satellite data

International audienceAbstract Satellite remote sensing is a powerful tool to monitor the global dynamics of marine plankton. Previous research has focused on developing models to predict the size or taxonomic groups of phytoplankton. Here, we present an approach to identify community types from a global plankton network that includes phytoplankton and heterotrophic protists and to predict their biogeography using global satellite observations. Six plankton community types were identified from a co-occurrence network inferred using a novel rDNA 18 S V4 planetary-scale eukaryotic metabarcoding dataset. Machine learning techniques were then applied to construct a model that predicted these community types from satellite data. The model showed an overall 67% accuracy in the prediction of the community types. The prediction using 17 satellite-derived parameters showed better performance than that using only temperature and/or the concentration of chlorophyll a . The constructed model predicted the global spatiotemporal distribution of community types over 19 years. The predicted distributions exhibited strong seasonal changes in community types in the subarctic–subtropical boundary regions, which were consistent with previous field observations. The model also identified the long-term trends in the distribution of community types, which suggested responses to ocean warming

Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

International audienceAbstract Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e . the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene