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

Iannucci, Alessio; Makunin, Alex; Lisachov, Artem; Ciofi, Claudio; Stanyon, Roscoe; Svartman, Marta; Trifonov, Vladimir A.

doi:10.3390/genes12010124

Cited by 13 publications

(15 citation statements)

References 89 publications

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“…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 ].…”

Section: Cytogenetic and Molecular Methods For The Identification Of Sex Chromosome Systemsmentioning

confidence: 99%

“…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 ].…”

Section: Rise and Diversification Of Gsd And Sex Chromosome Systemsmentioning

confidence: 99%

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

Mezzasalma

Guarino

Odierna

2021

Genes

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Lizards represent unique model organisms in the study of sex determination and sex chromosome evolution. Among tetrapods, they are characterized by an unparalleled diversity of sex determination systems, including temperature-dependent sex determination (TSD) and genetic sex determination (GSD) under either male or female heterogamety. Sex chromosome systems are also extremely variable in lizards. They include simple (XY and ZW) and multiple (X1X2Y and Z1Z2W) sex chromosome systems and encompass all the different hypothesized stages of diversification of heterogametic chromosomes, from homomorphic to heteromorphic and completely heterochromatic sex chromosomes. The co-occurrence of TSD, GSD and different sex chromosome systems also characterizes different lizard taxa, which represent ideal models to study the emergence and the evolutionary drivers of sex reversal and sex chromosome turnover. In this review, we present a synthesis of general genome and karyotype features of non-snakes squamates and discuss the main theories and evidences on the evolution and diversification of their different sex determination and sex chromosome systems. We here provide a systematic assessment of the available data on lizard sex chromosome systems and an overview of the main cytogenetic and molecular methods used for their identification, using a qualitative and quantitative approach.

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Section: Cytogenetic and Molecular Methods For The Identification Of Sex Chromosome Systemsmentioning

confidence: 99%

Section: Rise and Diversification Of Gsd And Sex Chromosome Systemsmentioning

confidence: 99%

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

Mezzasalma

Guarino

Odierna

2021

Genes

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“…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 ].…”

Section: Discussionmentioning

confidence: 99%

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

Spangenberg

Redekop

Simanovsky

et al. 2022

Animals

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Vipera berus is the species with the largest range of snakes on Earth and one of the largest among reptiles in general. It is also the only snake species found in the Arctic Circle. Vipera berus is the most involved species of the genus Vipera in the process of interspecific hybridization in nature. The taxonomy of the genus Vipera is based on molecular markers and morphology and requires clarification using SC-karyotyping. This work is a detailed comparative study of the somatic and meiotic karyotypes of V. berus, with special attention to DNA and protein markers associated with synaptonemal complexes. The karyotype of V. berus is a remarkable example of a bimodal karyotype containing both 16 large macrochromosomes and 20 microchromosomes. We traced the stages of the asynchronous assembly of both types of bivalents. The number of crossing-over sites per pachytene nucleus, the localization of the nucleolar organizer, and the unique heterochromatin block on the autosomal bivalent 6—an important marker—were determined. Our results show that the average number of crossing-over sites per pachytene nucleus is 49.5, and the number of MLH1 sites per bivalent 1 reached 11, which is comparable to several species of agamas.

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

Section: Structural Variant Discover and Genotyping In Threatened Spe...mentioning

confidence: 99%

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

et al. 2021

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Structural variants (SVs) are large rearrangements (>50 bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, that is, variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While there are increasing opportunities to investigate functional genomic variation in threatened species via single nucleotide polymorphism (SNP) data sets, SVs remain understudied despite their potential influence on fitness traits of conservation interest. In this future-focused Opinion, we contend that characterizing SVs offers the conservation genomics community an exciting opportunity to complement SNP-based approaches to enhance species recovery. We also leverage the existing literature-predominantly in human health, agriculture and ecoevolutionary biology-to identify approaches for readily characterizing SVs and consider how integrating these into the conservation genomics toolbox may transform the way we manage some of the world's most threatened species.

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

Cited by 13 publications

References 89 publications

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

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

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

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

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