The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell

Abstract

Summary The giant, single-celled organism Stentor coeruleus has a long history as a model system for studying pattern formation and regeneration in single cells. Stentor (Figure 1A,B [1,2]) is a heterotrichous ciliate distantly related to familiar ciliate models such as Tetrahymena or Paramecium. The primary distinguishing feature of Stentor is its incredible size: a single cell is 1 millimeter long. Early developmental biologists, including T.H. Morgan[3], were attracted to the system because of its regenerative abilities -- if large portions of a cell are surgically removed, the remnant reorganizes into a normal-looking but smaller cell with correct proportionality [2,3]. These biologists were also drawn to Stentor because it exhibits a rich repertoire of behaviors, including light avoidance, mechanosensitive contraction, food selection, and even the ability to habituate to touch, a simple form of learning usually seen in higher organisms [4]. While early microsurgical approaches demonstrated a startling array of regenerative and morphogenetic processes in this single-celled organism, Stentor was never developed as a molecular model system. We report the sequencing of the Stentor coeruleus macronuclear genome and reveal key features of the genome: First, we find that Stentor uses the standard genetic code, suggesting that ciliate specific genetic codes arose after Stentor branched from other ciliates. We also discover that ploidy correlates with Stentor’s cell size. Finally, in the Stentor genome, we discover the smallest spliceosomal introns reported for any species. The sequenced genome opens the door to molecular analysis of single-cell regeneration in Stentor.

Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors

“…Phylogenomic analysis was performed using the supertree method (Chen, Wang, Sheng, Warren, & Gao, ). Predicted protein sequences from Euplotes vannus identified in this work, from 31 other ciliates collected from previous studies (Aeschlimann et al, ; Keeling et al, ; Slabodnick et al, ; Wang et al, ), and from transcriptome sequencing by the Marine Microbial Eukaryote Transcriptome Sequencing Project (data available on iMicrobe: http://imicrobe.us/, accession number and gene ID see Table S1), were used to generate a concatenated data set (Chen et al, ; Gentekaki, Kolisko, Gong, & Lynn, ). A Maximum Likelihood tree based on the concatenated data set covering 157 genes was reconstructed by using gpsit version 1.0 (relaxed masking, E‐value cutoff = 1e‐10, sequence identity cutoff = 50%) (Chen et al, ) and raxml‐hpc2 version 8.2.9 (on CIPRES Science Gateway, LG model of amino acid substitution + Γ distribution + F, four rate categories, 500 bootstrap replicates) (Stamatakis, ).…”

The Transcriptional Program of Regeneration in the Giant Single Cell,Stentor coeruleus

“…Although Stentor regeneration was the focus of study that began over more than 100 years ago and then continuing into the early 1980s, the lack of genetic tools in the organism prevented detailed molecular analysis of its processes. Taking advantage of our recently completed genome of Stentor coeruleus [19] and using RNA-seq, we can for the first time provide molecular details of the factors involved in regeneration of the oral apparatus. Key genes which display significant changes in expression over time include highly conserved genes involved in centriole biogenesis and ciliogenesis.…”

Demonstration of RNA interference by bacterial feeding in Stentor polymorphus

“…Stentor is a genus in the ciliate phylum that is renowned for its morphology and ability to regenerate. The most well-studied species in this genus, Stentor coeruleus, has recently been established as a model with tools such as a sequenced genome and ability to perform RNA interference (RNAi) by feeding [10,11], but other Stentor species lack similar tools. S. polymorphus was first reported as a distinct species in 1773, although at the time it was called Vorticella polymorpha [12].…”