SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping.

Yi Feng,Leslie Y Beh,Wei-Jen Chang,Laura F Landweber

doi:10.1093/gbe/evaa147

Abstract

Ciliates are microbial eukaryotes with distinct somatic and germline genomes. Postzygotic development involves extensive remodeling of the germline genome to form somatic chromosomes. Ciliates therefore offer a valuable model for studying the architecture and evolution of programed genome rearrangements. Current studies usually focus on a few model species, where rearrangement features are annotated by aligning reference germline and somatic genomes. Although many high-quality somatic genomes have been assembled, a high-quality germline genome assembly is difficult to obtain due to its smaller DNA content and abundance of repetitive sequences. To overcome these hurdles, we propose a new pipeline, SIGAR (Split-read Inference of Genome Architecture and Rearrangements) to infer germline genome architecture and rearrangement features without a germline genome assembly, requiring only short DNA sequencing reads. As a proof of principle, 93% of rearrangement junctions identified by SIGAR in the ciliate Oxytricha trifallax were validated by the existing germline assembly. We then applied SIGAR to six diverse ciliate species without germline genome assemblies, including Ichthyophthirius multifilii, a fish pathogen. Despite the high level of somatic DNA contamination in each sample, SIGAR successfully inferred rearrangement junctions, short eliminated sequences, and potential scrambled genes in each species. This pipeline enables pilot surveys or exploration of DNA rearrangements in species with limited DNA material access, thereby providing new insights into the evolution of chromosome rearrangements.

Highlights

Ciliates are model organisms for studying genome rearrangement
SIGAR infers MIC genome structure and DNA rearrangement features by identifying short MIC reads that partially map to MAC chromosomes
SIGAR verifies that split-read junctions correspond to rearrangement breakpoints by searching within the split read for short sequence motifs, called “pointers,” which are microhomologous repeated sequences in the MIC that are retained as a single copy in the MAC after rearrangement

Summary

Introduction

Ciliates are model organisms for studying genome rearrangement. They exhibit nuclear dimorphism: Each cell contains a somatic macronucleus (MAC) and a germline micronucleus (MIC). The MAC consists of high-copy number chromosomes that are transcriptionally active in vegetative growth. The MIC genome is inert, and only involved in sexual conjugation. A new MAC genome rearranges from a copy of the zygotic MIC, together with massive DNA elimination (Chen et al 2014; Hamilton et al 2016). The retained, macronuclear destined sequences (MDS) must be properly ordered and oriented, and sometimes even descrambled (Chen et al 2014; Sheng et al 2020), to form functional MAC chromosomes The retained, macronuclear destined sequences (MDS) must be properly ordered and oriented, and sometimes even descrambled (Chen et al 2014; Sheng et al 2020), to form functional MAC chromosomes (fig. 1A)

Methods

Results

Conclusion