Bergerac Strains of C. elegans Revisited: Expansion of Tc1 elements Impose a Significant Genomic and Fitness Cost

Abstract

The DNA transposon Tc 1 was the first transposable element (TE) to be characterized in Caenorhabditis elegans and to date, remains the best-studied TE in Caenorhabditis worms. While Tc 1 copy-number is regulated at approximately 30 copies in the laboratory N2/Bristol and the vast majority of C. elegans strains, the Bergerac strain and its derivatives have experienced a marked Tc 1 proliferation. Given the historical importance of the Bergerac strain in the development of the C. elegans model, we implemented a modern genomic analysis of three Bergerac strains (CB4851, RW6999, and RW7000) in conjunction with multiple phenotypic assays to better elucidate the (i) genomic distribution of Tc 1 , and (ii) phenotypic consequences of TE deregulation for the host organism. The median estimates of Tc 1 copy-number in the Bergerac strains ranged from 451 to 748, which is both (i) greater than previously estimated, and (ii) likely to be an underestimate of the actual copy-numbers since coverage-based estimates and ddPCR results both suggest higher Tc 1 numbers. All three Bergerac strains had significantly reduced trait means compared to the N2 control for each of four fitness-related traits, with specific traits displaying significant differences between Bergerac strains. T c1 proliferation was genome-wide, specific to Tc 1 , and particularly high on chromosomes V and X. There were fewer Tc 1 insertions in highly expressed chromatin environments than expected by chance. Furthermore, Tc 1 integration motifs were also less frequent in exon than non-coding sequences. The source of the proliferation of Tc 1 in the Bergerac strains is specific to Tc 1 and independent of other TEs. The Bergerac strains contain none of the alleles that have previously been found to derepress TE activity in C. elegans. However, the Bergerac strains had several Tc 1 insertions near or within highly germline-transcribed genes which could account for the recent germline proliferation.

Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast

“…Despite these issues, one emerging theme from current evaluation studies is that considerable variation in performance exists among different short-read TE detectors, across organisms and evaluation frameworks [8,14,15,16]. As such, there is not yet any clear basis to select the best short-read TE detector for a new organism, and thus researchers must base tool choice by extrapolation from performance on other taxa or employ multiple methods to ensure robust biological conclusions [17,18,19].…”

“…The original McClintock system automated installation of these six "component" TE detection methods, provided a common interface to run all components, reduced the number of shared input files, and generated a standard set of output files [15]. Since its initial development, the McClintock system has been used to support detection of TE insertions and enable biological discoveries in a variety of organisms and biological contexts [15,16,17,18,19,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44] and to facilitate comparative evaluation of multiple TE detectors [15,16,45].…”