The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development

Abstract

SUMMARY Programmed DNA rearrangements in the single-celled eukaryote Oxytricha trifallax completely rewire its germline into a somatic nucleus during development. This elaborate, RNA-mediated pathway eliminates noncoding DNA sequences that interrupt gene loci and reorganizes the remaining fragments by inversions and permutations to produce functional genes. Here, we report the Oxytricha germline genome and compare it to the somatic genome to present a global view of its massive scale of genome rearrangements. The remarkably encrypted genome architecture contains >3,500 scrambled genes, as well as >800 predicted germline-limited genes expressed, and some posttranslationally modified, during genome rearrangements. Gene segments for different somatic loci often interweave with each other. Single gene segments can contribute to multiple, distinct somatic loci. Terminal precursor segments from neighboring somatic loci map extremely close to each other, often overlapping. This genome assembly provides a draft of a scrambled genome and a powerful model for studies of genome rearrangement.

Origin, structure and function of millions of chromosomes present in the macronucleus of unicellular eukaryotic ciliate, Oxytricha trifallax: a model organism for transgenerationally programmed genome rearrangements

“…Majority of MAC chromosomes contain only one transcribable and translatable gene and their average size is 3.7 kb Chen et al 2014). With some frequency (∼10%), certain alternate forms of these small chromosomes arise; these are isoforms that share some chromosomal sequences.…”

“…MIC diploid genome has about 810 genes that have normal eukaryotic gene structure and are expressed in MIC during conjugal reproduction . Remaining MIC genome specifies transposons, internally eliminated sequences (IESs), satellite sequences and about 18,400 MAC-expressed genes Chen et al 2014). Among these 18,400 MAC destined genes, about 17,850 are interrupted mostly in their exons by at least one IES; and about 550 genes are IES-less .…”

“…In a gene, the MDSs are not always located contiguously at a locus. Many MDSs are inverted or translocated to distinct gene loci on the same or different chromosome Swart et al 2013;Chen et al 2014). The process of differentiation of MIC into MAC involves deletion of IESs, unscrambling and correctly ordering of MDSs specific genewise and loss of transposons.…”

New Advances in NGS Technologies

“…Although, in previous decades, the development of the Sanger method has brought many findings in chemistry, automation and miniaturization of the process, only the advent of NGS technologies has led to a significant improvement of quality and speed of the genome analysis [19]. The release of new sequencing platforms and the reduction of costs associated with the NGS technology is the consequence of three factors:…”

Small RNA-mediated regulation of DNA dosage in the ciliate Oxytricha

“…On the other hand, 21,134 sRNA reads (0.31%) map to MDS-IES junctions, whereas 1.25% of a set of similarly produced, randomly generated 21 nt, 5 ′ U sequences from the complete MIC assembly overlap MDS-IES junctions. The published MAC and MIC genome assemblies were used for this analysis (Swart et al 2013;Chen et al 2014). A similar analysis was done for the 30-to 50-nt sRNAs, which also primarily map to MAC-specific regions, as shown in Supplemental Figure S3E.…”