Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence

Abstract

Eukaryotic phytoplankton are key actors in marine ecosystems, they contribute to atmospheric CO2 sequestration and supply organic matter to the trophic network. Among them, Pelagophytes (Stramenopiles) algae are a diverse class with coastal species causative of harmful algal blooms while others are cosmopolites and abundant in open ocean ecosystems. Despite their ecological importance, only a few genomic references exist limiting our capacity to identify them and study their adaptation mechanisms in a changing environment. Here, we report the complete chromosome-scale assembled genome sequence of Pelagomonas calceolata. We identified unusual large low-GC and gene-rich regions potentially hosting centromeres. These particular genomic structures could be explained by the absence of genes necessary for an important recombination pathway in this species. We identified a large repertoire of genes involved in inorganic nitrogen sensing and uptake as well as many genes replacing iron-required proteins potentially explaining its ecological success in oligotrophic waters. Finally, based on this high-quality assembly, we evaluated P. calceolata relative abundance in all oceans using environmental Tara datasets. Our results suggest that P. calceolata is one of the most abundant eukaryote species in the oceans with a relative abundance driven by the high temperature and iron-poor conditions. Collectively, these findings bring new insights into the biology and ecology of P. calceolata and lay the foundation for the analysis of the adaptation and acclimation strategy of this picophytoplankton.

Changes in functional composition and gene expression in eukaryotic plankton at the Atlantic-Arctic Polar front

“…Many studies based either on satellite ( 6, 7 ) or genomic data ( 4, 8, 9 ) revealed a mainly latitudinal and temperature driven biogeographical partitioning of the oceans. While some species have strictly defined environmental niches ( 4, 10 ), some display cosmopolitan biogeographies, such as Bathycoccus prasinos which is present in both polar and temperate oceans ( 11 ) or Pelagomonas calceolata that is cosmopolitan in all except polar oceans ( 12 ).…”