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

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

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

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

International audienc