Bridging the Gap between Vertebrate Cytogenetics and Genomics with Single-Chromosome Sequencing (ChromSeq)

Abstract

The study of vertebrate genome evolution is currently facing a revolution, brought about by next generation sequencing technologies that allow researchers to produce nearly complete and error-free genome assemblies. Novel approaches however do not always provide a direct link with information on vertebrate genome evolution gained from cytogenetic approaches. It is useful to preserve and link cytogenetic data with novel genomic discoveries. Sequencing of DNA from single isolated chromosomes (ChromSeq) is an elegant approach to determine the chromosome content and assign genome assemblies to chromosomes, thus bridging the gap between cytogenetics and genomics. The aim of this paper is to describe how ChromSeq can support the study of vertebrate genome evolution and how it can help link cytogenetic and genomic data. We show key examples of ChromSeq application in the refinement of vertebrate genome assemblies and in the study of vertebrate chromosome and karyotype evolution. We also provide a general overview of the approach and a concrete example of genome refinement using this method in the species Anolis carolinensis.

Keywords: Anolis; DOPseq; chromosomics; cytogenomics; de novo assembly; flow sorting; karyotype; microdissection; reference genomes.

Figure 1

Schematic representation of ChromSeq workflow. Briefly, chromosomes are isolated via either flow sorting or microdissection (only mechanical microdissection is shown). After isolation, Whole-Genome Amplification (WGA) is performed on chromosomal DNA. Eventually, chromosomal DNA can be labeled with fluorochromes and hybridized onto the target species metaphases to confirm the identity of isolated chromosomes. WGA products are then sequenced with next generation sequencing technologies. Sequencing data can be mapped on the target species reference genome or assembled de novo. The latter approach has proven successful when a combination of high throughput chromosome isolation (millions of copies) and long-read sequencing approaches are implemented.