The extremely rich palaeontological record of the horse family, also known as equids, has provided many examples of macroevolutionary change over the last ~55 Mya. This family is also one of the most documented at the palaeogenomic level, with hundreds of ancient genomes sequenced. While these data have advanced understanding of the domestication history of horses and donkeys, the palaeogenomic record of other equids remains l...

Whole genome characterizations of crop plants based on ancient DNA have provided unique keys for a better understanding of the evolutionary origins of modern cultivars, the pace and mode of selection underlying their adaptation to new environments and the production of phenotypes of interest. Although forests are among the most biologically rich ecosystems on earth and represent a fundamental resource for human societies, no a...

Hydrothermal vents form archipelagos of ephemeral deep‐sea habitats that raise interesting questions about the evolution and dynamics of the associated endemic fauna, constantly subject to extinction‐recolonization processes. These metal‐rich environments are coveted for the mineral resources they harbour, thus raising recent conservation concerns. The evolutionary fate and demographic resilience of hydrothermal species strong...

Aim Intensive studies since the beginning of the 21st century have provided vast amounts of knowledge about soil microbial diversity at local and global scales. However, microbial habitats have been poorly investigated at large scale. This study aims to characterize soil bacterial habitats across France for the first time by integrating the description of numerous environmental factors and human activities. Location We focus o...

The planktonic tunicates appendicularians and thaliaceans are highly efficient filter feeders on a wide range of prey size including bacteria and have shorter generation times than any other marine grazers. These traits allow some tunicate species to reach high population densities and ensure their success in a favourable environment. However, there are still few studies focusing on which genes and gene pathways are associated...

Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high‐throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis...

In the epipelagic ocean, the genus Oithona is considered as one of the most abundant and widespread copepods and plays an important role in the trophic food web. Despite its ecological importance, little is known about Oithona and cyclopoid copepods genomics. Therefore, we sequenced, assembled and annotated the genome of Oithona nana . The comparative genomic analysis integrating available copepod genomes highlighted the expan...

Summary Dinoflagellates (Alveolata) are one of the ecologically most important groups of modern phytoplankton. Their biological complexity makes assessment of their global diversity and community structure difficult. We used massive V 9 18 S rDNA sequencing from 106 size‐fractionated plankton communities collected across the world's surface oceans during the T ara O ceans expedition (2009–2012) to assess patterns of pelagic di...

Summary Sequencing of 16S rDNA polymerase chain reaction ( PCR ) amplicons is the most common approach for investigating environmental prokaryotic diversity, despite the known biases introduced during PCR . Here we show that 16S rDNA fragments derived from Illumina‐sequenced environmental metagenomes ( mi tag s) are a powerful alternative to 16S rDNA amplicons for investigating the taxonomic diversity and structure of prokaryo...

Summary Heavy metals are pollutants which affect all organisms. Since a small number of eukaryotes have been investigated with respect to metal resistance, we hypothesize that many genes that control this phenomenon remain to be identified. This was tested by screening soil eukaryotic metatranscriptomes which encompass RNA from organisms belonging to the main eukaryotic phyla. Soil‐extracted polyadenylated mRNAs were converted...