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.

Lizards as Model Organisms of Sex Chromosome Evolution: What We Really Know from a Systematic Distribution of Available Data?

“…Single-chromosome sequencing (ChromSeq) is a further promising method in the study of sex chromosome system. By combining chromosome isolation (via microdissection or flow sorting), whole-genome amplification (WGA), hybridization and bioinformatic techniques ChromSeq has the power to the gap between cytogenetic and genomic studies [ 116 , 117 , 118 ]. So far, ChromSeq has been performed on just a handful of lizard species, but its application on a wider selection of taxa would help to uncover poorly study features of the lizard genome and karyotype [ 116 , 117 , 118 ].…”

“…In these clades, repeated fusions between the Y chromosome and non-homologous autosomes have been identified in different closely related lineages, further promoting their high karyological variability [ 71 ]. In some cases (e.g., Norops, Dactyloidae, Sceloporus and Phrynosomatidae), fusions between autosomes and sex chromosomes, rather than producing multiple sex chromosome systems may generate single, albeit enlarged pairs, containing distinct pseudoautosomal regions [ 116 , 117 , 118 ]. In rare cases, sex chromosome diversification can be observed also at intraspecific level in lizards, as in the case of Carinascincus ocellatus, where ecologically distinct populations exhibit different heterochromatinization levels of the Y chromosome [ 88 ].…”

Cytogenetic Analysis of the Bimodal Karyotype of the Common European Adder, Vipera berus (Viperidae)

“…Molecular cytogenetic techniques such as whole chromosome painting and comparative genomic hybridization are powerful methods for comparing and identifying specific microchromosomes of interest in the preparation of mitotic metaphase plates [ 76 , 77 ]. Basic karyological information is crucial to link cytogenetic and genomic data [ 78 , 79 , 80 ].…”

Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern

“…PacBio, Pacific Biosciences; ONT, Oxford Nanopore Technologies. 1 Choi et al ( 2009 ); 2 Iannucci et al ( 2021 )…”