An Extremely Streamlined Macronuclear Genome in the Free-Living Protozoan Fabrea salina

Abstract

Ciliated protists are among the oldest unicellular organisms with a heterotrophic lifestyle and share a common ancestor with Plantae. Unlike any other eukaryotes, there are two distinct nuclei in ciliates with separate germline and somatic cell functions. Here, we assembled a near complete macronuclear genome of Fabrea salina, which belongs to one of the oldest clades of ciliates. Its extremely minimized genome (18.35 Mb) is the smallest among all free-living heterotrophic eukaryotes and exhibits typical streamlined genomic features, including high gene density, tiny introns and shrinkage of gene paralogs. Gene families involved in hypersaline stress resistance, DNA replication proteins and mitochondrial biogenesis are expanded, and the accumulation of phosphatidic acid may play an important role in resistance to high osmotic pressure. We further investigated the morphological and transcriptomic changes in the macronucleus during sexual reproduction and highlighted the potential contribution of macronuclear residuals to this process. We believe that the minimized genome generated in this study provides novel insights into the genome streamlining theory and will be an ideal model to study the evolution of eukaryotic heterotrophs.

iGDP: An integrated genome decontamination pipeline for wild ciliated microeukaryotes

“…This excellent performance might be a result of high assembly continuity of the reference genome (N50 = 469.6 kb) with more than half of the contigs capped with telomere sequence repeats at both ends, which can benefit homology search and telomere reads‐assisted approaches. Similar results (100% recall rate and 99.98% precision) were obtained when running iGDP on the recently published genome of the ciliate Fabrea salina with algal and bacterial contaminants assembled using long‐read sequencing technology (Zhang et al, 2022). However, it is not always possible to isolate sufficient high‐quality DNA material from a realistic wild ciliate sample to perform third‐generation sequencing.…”

“…were obtained when running iGDP on the recently published genome of the ciliate Fabrea salina with algal and bacterial contaminants assembled using long-read sequencing technology (Zhang et al, 2022). However, it is not always possible to isolate sufficient high-quality DNA material from a realistic wild ciliate sample to perform third-generation sequencing.…”

Stop or Not: Genome-Wide Profiling of Reassigned Stop Codons in Ciliates

“…1 c ). Although most ciliate species are AT-rich ( Aeschlimann et al 2014 ; Wang et al 2016 ; Zhang et al 2022 ), the GC content of these seven species ranges from 29.1% to 50.1%, and four of them have a GC content of more than 45% ( fig. 1 a ).…”

Adaptation in Unstable Environments and Global Gene Losses: Small but Stable Gene Networks by the May–Wigner Theory

“…The gene number reductions have often been observed in unicellular organisms, probably because of their cells’ direct contact with environments. The streamlined and compact genomes of many marine bacteria, such as Prochlorococcus and Pelagibacterales, and the eukaryotic Fabrea salina were proposed to promote the adaptation to a wider range of stresses ( Giovannoni et al 2014 ; Zhang et al 2022 ). Furthermore, genomes streamline as the optimal temperature increase in bacteria and archaea ( Sabath et al 2013 ).…”