Recurring patterns among scrambled genes in the encrypted genome of the ciliate Oxytricha trifallax

Abstract

Some genera of ciliates, such as Oxytricha and Stylonychia, undergo massive genome reorganization during development and provide model organisms to study DNA rearrangement. A common feature of these ciliates is the presence of two types of nuclei: a germline micronucleus and a transcriptionally-active somatic macronucleus containing over 16,000 gene sized “nanochromosomes”. During conjugation the old parental macronucleus disintegrates and a new macronucleus forms from a copy of the zygotic micronucleus. During this process, macronuclear chromosomes assemble through DNA processing events that delete 90-98% of the DNA content of the micronucleus. This includes the deletion of noncoding DNA segments that interrupt precursor DNA regions in the micronucleus, as well as transposons and other germline-limited DNA. Each macronuclear locus may be present in the micronucleus as several nonconsecutive, permuted, and/or inverted DNA segments. Here we investigate the genome-wide range of scrambled gene architectures that describe all precursor-product relationships in Oxytricha trifallax, the first completely sequenced scrambled genome. We find that five general, recurrent patterns in the sets of scrambled micronuclear precursor pieces can describe over 80% of Oxytricha's scrambled genes. These include instances of translocations and inversions, and other specific patterns characterized by alternating stretches of consecutive odd and even DNA segments. Moreover, we find that iterating patterns of alternating odd-even segments up to four times can describe over 96% of the scrambled precursor loci. Recurrence of these highly structured genetic architectures within scrambled genes presumably reflects recurrent evolutionary events that gave rise to over 3,000 of scrambled loci in the germline genome.

Russian doll genes and complex chromosome rearrangements inOxytricha trifallax

“…Figure 4 shows an example of one the 22 contigs, with nested pairs of repeat and return words in blue and green, respectively. The reduction process leaves 6 scrambled pointers with DOW 4,10,11,8,12,11,9,8,4,9,10,12 (commas added to separate the symbols). This word has no appearances of a repeat or return pattern.…”

“…Most arise from gene duplication and insertion of young genes or transposons into long introns [18,20,9]. In this study, we follow up on previous analyses in [4], that described the most commonly recurring scrambled patterns across the genome. Here, we present the most elaborate cases of genome rearrangement in O. trifallax, which highlight the extraordinary degree of topological complexity that can arise from such a highly plastic genomic architecture.…”

“…Highly scrambled loci. We previously reported that most scrambled loci in O. trifallax contain various combinations of recurrent scrambled patterns, and that recurrent patterns can account for a large majority (96%) of all scrambled genes [4]. For example, the MAC contig represented by red MDSs in Figure 1 is scrambled, with the MDS order in the MIC locus M 1 M 3 M 5 M 7 · · · M 6 M 4 M 2 , a cluster of odd MDSs in consecutive order, separated from the corresponding even numbered segments in reverse consecutive order.…”

“…Genome sequences from Oxytricha trifallax MIC and MAC sequences from Oxytricha trifallax were obtained from the <mds_ies_db> website (Burns et al 2016b), in the form of annotated tables, and processed as described in Burns et al (2016a), available from http://knot.math.usf.edu/data/scrambled_ patterns/processed_annotation_of_oxy_tri.gff. These were parsed to produce the various types of graphical representations described below using a combination of in-house Python and SQL scripts.…”

“…IES). MDSs fuse together by recombination at short (2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20) repeats, called pointers, at the ends of MDSs, retaining one copy of the pointer in the MAC. The accuracy of this process is guided by a suite of long and small RNAs ( [16,8], reviewed in [2] and [21]).…”