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

Alessio Iannucci,Marta Svartman,Artem P Lisachov,Vladimir A Trifonov,Roscoe Stanyon,Claudio Ciofi,Alexey I Makunin

doi:10.3390/genes12010124

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.

Highlights

Reference genomes are crucial to investigate many biological aspects of a species.Rough drafts are often sufficient to provide an overview of genome organization, chromosome-level assemblies are essential for a more detailed investigation of evolutionary processes and functional annotation, for complex organisms [1].For vertebrates, in particular, the availability of high-quality chromosome-level reference genomes has led to significant outcomes in comparative and functional genomics (e.g., [2,3,4,5,6,7])
Genomics has proven to be fundamental in the study of vertebrate genome evolution
An impressive and admirable effort is currently underway to generate high-quality, complete reference genomes for all ~70,000 extant vertebrate species to enable a new era of discovery across this field [17]

Summary

Introduction

Reference genomes are crucial to investigate many biological aspects of a species. Rough drafts are often sufficient to provide an overview of genome organization, chromosome-level assemblies are essential for a more detailed investigation of evolutionary processes and functional annotation, for complex organisms [1]. A correct direction read of the assembly from p terminus to q terminus is not guaranteed This lack of coordination between assembly and previous cytogenetic results leads to a loss of information about genome organization and evolution, and it may generate misunderstandings among investigators. The method is based on generation sequencing of DNA from microdissected or flow-sorted chromosomes It has been widely employed in plants for the chromosome assignment of assembled genomes, leading to highly significant results (e.g., [30,31,32,33,34,35,36,37]). Genes 2021, 12, 124 as ChromSeq in plant genome studies [35] and we will adopt this term throughout the manuscript

ChromSeq Workflow

Application in Vertebrate Genome Projects

Application in Vertebrate Karyotype Evolution Studies

ChromSeq to Refine Anolis carolinensis Genome Assembly

Findings

Conclusions