Chromosomics

Bridging the Gap between Genomes and Chromosomes

Janine E Deakin, Sally Potter, Rachel O'Neill, Aurora Ruiz-Herrera, Marcelo B Cioffi, Mark D B Eldridge, Kichi Fukui, Jennifer A Marshall Graves, Darren Griffin, Frank Grutzner, Lukáš Kratochvíl, Ikuo Miura, Michail Rovatsos, Kornsorn Srikulnath, Erik Wapstra, Tariq Ezaz

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Abstract

The recent advances in DNA sequencing technology are enabling a rapid increase in the number of genomes being sequenced. However, many fundamental questions in genome biology remain unanswered, because sequence data alone is unable to provide insight into how the genome is organised into chromosomes, the position and interaction of those chromosomes in the cell, and how chromosomes and their interactions with each other change in response to environmental stimuli or over time. The intimate relationship between DNA sequence and chromosome structure and function highlights the need to integrate genomic and cytogenetic data to more comprehensively understand the role genome architecture plays in genome plasticity. We propose adoption of the term 'chromosomics' as an approach encompassing genome sequencing, cytogenetics and cell biology, and present examples of where chromosomics has already led to novel discoveries, such as the sex-determining gene in eutherian mammals. More importantly, we look to the future and the questions that could be answered as we enter into the chromosomics revolution, such as the role of chromosome rearrangements in speciation and the role more rapidly evolving regions of the genome, like centromeres, play in genome plasticity. However, for chromosomics to reach its full potential, we need to address several challenges, particularly the training of a new generation of cytogeneticists, and the commitment to a closer union among the research areas of genomics, cytogenetics, cell biology and bioinformatics. Overcoming these challenges will lead to ground-breaking discoveries in understanding genome evolution and function.

Original languageEnglish
Pages (from-to)1-17
Number of pages17
JournalGenes
Volume10
Issue number8
DOIs
Publication statusPublished - 20 Aug 2019

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Chromosomes
Genome
Cytogenetics
Cell Biology
Chromosome Structures
Centromere
Genomics
Computational Biology
DNA Sequence Analysis
Mammals
Technology
Research
Genes

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Deakin, J. E., Potter, S., O'Neill, R., Ruiz-Herrera, A., Cioffi, M. B., Eldridge, M. D. B., ... Ezaz, T. (2019). Chromosomics: Bridging the Gap between Genomes and Chromosomes. Genes, 10(8), 1-17. https://doi.org/10.3390/genes10080627
Deakin, Janine E ; Potter, Sally ; O'Neill, Rachel ; Ruiz-Herrera, Aurora ; Cioffi, Marcelo B ; Eldridge, Mark D B ; Fukui, Kichi ; Marshall Graves, Jennifer A ; Griffin, Darren ; Grutzner, Frank ; Kratochvíl, Lukáš ; Miura, Ikuo ; Rovatsos, Michail ; Srikulnath, Kornsorn ; Wapstra, Erik ; Ezaz, Tariq. / Chromosomics : Bridging the Gap between Genomes and Chromosomes. In: Genes. 2019 ; Vol. 10, No. 8. pp. 1-17.
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abstract = "The recent advances in DNA sequencing technology are enabling a rapid increase in the number of genomes being sequenced. However, many fundamental questions in genome biology remain unanswered, because sequence data alone is unable to provide insight into how the genome is organised into chromosomes, the position and interaction of those chromosomes in the cell, and how chromosomes and their interactions with each other change in response to environmental stimuli or over time. The intimate relationship between DNA sequence and chromosome structure and function highlights the need to integrate genomic and cytogenetic data to more comprehensively understand the role genome architecture plays in genome plasticity. We propose adoption of the term 'chromosomics' as an approach encompassing genome sequencing, cytogenetics and cell biology, and present examples of where chromosomics has already led to novel discoveries, such as the sex-determining gene in eutherian mammals. More importantly, we look to the future and the questions that could be answered as we enter into the chromosomics revolution, such as the role of chromosome rearrangements in speciation and the role more rapidly evolving regions of the genome, like centromeres, play in genome plasticity. However, for chromosomics to reach its full potential, we need to address several challenges, particularly the training of a new generation of cytogeneticists, and the commitment to a closer union among the research areas of genomics, cytogenetics, cell biology and bioinformatics. Overcoming these challenges will lead to ground-breaking discoveries in understanding genome evolution and function.",
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Deakin, JE, Potter, S, O'Neill, R, Ruiz-Herrera, A, Cioffi, MB, Eldridge, MDB, Fukui, K, Marshall Graves, JA, Griffin, D, Grutzner, F, Kratochvíl, L, Miura, I, Rovatsos, M, Srikulnath, K, Wapstra, E & Ezaz, T 2019, 'Chromosomics: Bridging the Gap between Genomes and Chromosomes', Genes, vol. 10, no. 8, pp. 1-17. https://doi.org/10.3390/genes10080627

Chromosomics : Bridging the Gap between Genomes and Chromosomes. / Deakin, Janine E; Potter, Sally; O'Neill, Rachel; Ruiz-Herrera, Aurora; Cioffi, Marcelo B; Eldridge, Mark D B; Fukui, Kichi; Marshall Graves, Jennifer A; Griffin, Darren; Grutzner, Frank; Kratochvíl, Lukáš; Miura, Ikuo; Rovatsos, Michail; Srikulnath, Kornsorn; Wapstra, Erik; Ezaz, Tariq.

In: Genes, Vol. 10, No. 8, 20.08.2019, p. 1-17.

Research output: Contribution to journalReview article

TY - JOUR

T1 - Chromosomics

T2 - Bridging the Gap between Genomes and Chromosomes

AU - Deakin, Janine E

AU - Potter, Sally

AU - O'Neill, Rachel

AU - Ruiz-Herrera, Aurora

AU - Cioffi, Marcelo B

AU - Eldridge, Mark D B

AU - Fukui, Kichi

AU - Marshall Graves, Jennifer A

AU - Griffin, Darren

AU - Grutzner, Frank

AU - Kratochvíl, Lukáš

AU - Miura, Ikuo

AU - Rovatsos, Michail

AU - Srikulnath, Kornsorn

AU - Wapstra, Erik

AU - Ezaz, Tariq

PY - 2019/8/20

Y1 - 2019/8/20

N2 - The recent advances in DNA sequencing technology are enabling a rapid increase in the number of genomes being sequenced. However, many fundamental questions in genome biology remain unanswered, because sequence data alone is unable to provide insight into how the genome is organised into chromosomes, the position and interaction of those chromosomes in the cell, and how chromosomes and their interactions with each other change in response to environmental stimuli or over time. The intimate relationship between DNA sequence and chromosome structure and function highlights the need to integrate genomic and cytogenetic data to more comprehensively understand the role genome architecture plays in genome plasticity. We propose adoption of the term 'chromosomics' as an approach encompassing genome sequencing, cytogenetics and cell biology, and present examples of where chromosomics has already led to novel discoveries, such as the sex-determining gene in eutherian mammals. More importantly, we look to the future and the questions that could be answered as we enter into the chromosomics revolution, such as the role of chromosome rearrangements in speciation and the role more rapidly evolving regions of the genome, like centromeres, play in genome plasticity. However, for chromosomics to reach its full potential, we need to address several challenges, particularly the training of a new generation of cytogeneticists, and the commitment to a closer union among the research areas of genomics, cytogenetics, cell biology and bioinformatics. Overcoming these challenges will lead to ground-breaking discoveries in understanding genome evolution and function.

AB - The recent advances in DNA sequencing technology are enabling a rapid increase in the number of genomes being sequenced. However, many fundamental questions in genome biology remain unanswered, because sequence data alone is unable to provide insight into how the genome is organised into chromosomes, the position and interaction of those chromosomes in the cell, and how chromosomes and their interactions with each other change in response to environmental stimuli or over time. The intimate relationship between DNA sequence and chromosome structure and function highlights the need to integrate genomic and cytogenetic data to more comprehensively understand the role genome architecture plays in genome plasticity. We propose adoption of the term 'chromosomics' as an approach encompassing genome sequencing, cytogenetics and cell biology, and present examples of where chromosomics has already led to novel discoveries, such as the sex-determining gene in eutherian mammals. More importantly, we look to the future and the questions that could be answered as we enter into the chromosomics revolution, such as the role of chromosome rearrangements in speciation and the role more rapidly evolving regions of the genome, like centromeres, play in genome plasticity. However, for chromosomics to reach its full potential, we need to address several challenges, particularly the training of a new generation of cytogeneticists, and the commitment to a closer union among the research areas of genomics, cytogenetics, cell biology and bioinformatics. Overcoming these challenges will lead to ground-breaking discoveries in understanding genome evolution and function.

KW - cytogenetics

KW - sex chromosomes

KW - chromosome rearrangements

KW - genome plasticity

KW - centromere

KW - genome biology

KW - evolution

U2 - 10.3390/genes10080627

DO - 10.3390/genes10080627

M3 - Review article

VL - 10

SP - 1

EP - 17

JO - Genes

JF - Genes

SN - 2073-4425

IS - 8

ER -

Deakin JE, Potter S, O'Neill R, Ruiz-Herrera A, Cioffi MB, Eldridge MDB et al. Chromosomics: Bridging the Gap between Genomes and Chromosomes. Genes. 2019 Aug 20;10(8):1-17. https://doi.org/10.3390/genes10080627