Population genomics of picophytoplankton unveils novel chromosome hypervariability

Abstract

Phytoplanktonic eukaryotes form huge panmictic populations and have evolved original hypervariability mechanisms to resist viral attack.

Development of CRISPR-Cas systems for genome editing and beyond

“…As a Junior Fellow at Harvard in 2009, I had experienced firsthand the challenges of working with zinc finger nucleases. After reading studies describing the DNA recognition mechanism of microbial TALE proteins (Boch et al, 2009;Moscou and Bogdanove, 2009), I asked Le Cong, a rotation graduate student, to join me to develop TALEs for use in mammalian cells (Zhang et al, 2011). In 2010, I accepted a faculty position at MIT and the Broad Institute, planning to build a research program around genome and transcriptome editing.…”

“…It has been particularly exciting to witness how this technology has flourished through the contributions of so many talented scientists who share the same spirit of openness and generosity. This is a time of plenty for curious biologistswe have only glimpsed a tiny sliver of the diversity of life at the molecular level, and every few months, new genetic 'wonders' are reported: plankton with shattered chromosomes (Blanc-Mathieu et al, 2017), lamprey genome rearrangements , phage-encoded diversity generating retroelements (Doulatov et al, 2004;Benler et al, 2018), and marine microorganisms that use novel DNA repair systems (Deng et al, 2018). Each natural system tempts us to explore new paths, determining the mechanism and function behind these systems, and opening new opportunities to tinker, ultimately leading to a healthier and more sustainable future.…”

Virus-host coexistence in phytoplankton through the genomic lens

“…To resolve the highly repetitive SOC sequence, genomic DNA from RCC2590 and the evolved line MA3 were re-sequenced with the SMRT Technology PacBio RS II by the GetPlaGe sequencing platform in Toulouse, France as previously described [14]. The raw data was assembled using HGAP3 [28].…”

“…The O. mediterraneus RCC2590 genome assembly comprised 20 large scaffolds, in agreement with the number and sizes of chromosomes estimated from Pulsed Field Gel Electrophoresis (PFGE) (Figure 1). Probes designed to unique regions of three chromosomes: the big outlier chromosome (BOC), carrying the candidate sexual mating type locus [58] [14], the predicted small outlier chromosome (SOC), involved in viral resistance [13] [14], and chromosome 17, carrying the 18S rRNA gene, hybridised to chromosomal bands in the gel corresponding to their assembled sizes. Sixteen scaffolds were bordered by two telomeric sequences, providing further validation that this genome assembly comprised a majority of complete chromosome sequences.…”

“…prasinoviruses [11][12] [10], and fostered the discovery of one structurally unstable [13] and hypervariable [14] small outlier chromosome implicated in the resistance of the microalga to prasinoviruses. Ostreococcus mediterraneus is the most recently described Ostreococcus species and gene phylogeny of the 18S rRNA indicated it is the earliest branching member of the genus [15].…”