Overview of currently available approaches used in cytogenomics

Liehr, Thomas

doi:10.1016/b978-0-12-823579-9.00002-3

Cited by 2 publications

(2 citation statements)

References 49 publications

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“…Despite the continuous development of modern cytogenetic techniques, shrimp chromosome research has not made corresponding progress using new techniques, such as electron microscopy, laser scanning microscopy, multiple fluorescent in situ hybridization (M-FISH), spectral karyotyping (SKY), laser microdissection (LM), and optical genome mapping (OGM), as reported in model organisms, livestock, poultry, and crops [35][36][37]. However, in the field of shrimp genomics, some significant breakthroughs have been made.…”

Section: Chromosome Number Morphology and Evolution In Penaeid Shrimpmentioning

confidence: 99%

Penaeid Shrimp Chromosome Studies Entering the Post-Genomic Era

Zhang,

Xiang,

Yuan

et al. 2023

Genes

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Chromosome studies provide the foundation for comprehending inheritance, variation, systematics, and evolution. Penaeid shrimps are a group of crustaceans with great economic importance. Basic cytogenetic information obtained from these shrimps can be used to study their genome structure, chromosome relationships, chromosome variation, polyploidy manipulation, and breeding. The study of shrimp chromosomes experienced significant growth in the 1990s and has been closely linked to the progress of genome research since the application of next-generation sequencing technology. To date, the genome sequences of five penaeid shrimp species have been published. The availability of these genomes has ushered the study of shrimp chromosomes into the post-genomic era. Currently, research on shrimp cytogenetics not only involves chromosome counting and karyotyping, but also extends to investigating submicroscopic changes; exploring genome structure and regulation during various cell divisions; and contributing to the understanding of mechanisms related to growth, sexual control, stress resistance, and genome evolution. In this article, we provide an overview of the progress made in chromosome research on penaeid shrimp. We emphasize the mutual promotion between studies on chromosome structure and genome research and highlight the impact of chromosome-level assembly on studies of genome structure and function. Additionally, we summarize the emerging trends in post-genomic-era shrimp chromosome research.

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Section: Chromosome Number Morphology and Evolution In Penaeid Shrimpmentioning

confidence: 99%

Penaeid Shrimp Chromosome Studies Entering the Post-Genomic Era

Zhang,

Xiang,

Yuan

et al. 2023

Genes

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“…knowledge acquired from combining genomic, epigenomic, proteomic/interactomic and metabolomics data/information) and gene ontologies are naturally limited due to impossibility of synchronous processing of data on all tissues/cells of a human organism [28,42,48]. This becomes even more sophisticated in cases of CNVs and chromosomal imbalances (cytopostgenomic aspects), which are featured by simultaneous involvement of multiple genes [46,48,49]. Still, there are technological solutions for processing large genomic data sets [8,10,28,48].…”

Section: Practicementioning

confidence: 99%

Knowledge-Based Prioritization of Genomic Variations: A Quest for Detailed Understanding the Genetic Architecture of Diseases

Iourov

2023

Preprint

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Understanding the genetic architecture of a disease is crucial for development of valid diagnostic and therapeutic interventions. The analysis of genomic variations associated with pathological conditions is the starting point for uncovering disease-causing pathways (candidate processes). However, the complexity of intergenic and genetic-environmental interactions hinders the identification of pathogenic values of genomic changes. Furthermore, heredity, epigenetics and somatic mosaicism make the interpretation of genomic data even more sophisticated. To succeed, a variety of bioinformatic techniques are applied. Here, reviewing own and literature data, knowledge-based prioritization of genomic variations is described. Theoretical basis of the knowledge-based prioritization is given with a special regard to gene ontology, heuristics, hermeneutics (genomic hermeneutics) and analytics. Practical and methodological issues of prioritization using ontology- or pathway-based systems analysis are considered in the light of optimistic and realistic scenarios of cumulative phenotypic effects of the variome (the whole set of genomic variations in an individual or specific set of genomic variations for a phenotypic outcome). In the present communication, copy number variants (CNVs) in children with neurodevelopmental diseases are used as a practical foundation for the prioritization, inasmuch as these genome variations are systematically overlooked in the so-called NGS era. Nonetheless, it is highly likely that the prioritization is applicable to almost all types of genomic variations (e.g. chromosome abnormalities, gene mutations, functional synonymous variants etc.). The present methodology seems to be a valuable addition to current biomedical science widening the opportunities for medical genomics and genetics.

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Overview of currently available approaches used in cytogenomics

Cited by 2 publications

References 49 publications

Penaeid Shrimp Chromosome Studies Entering the Post-Genomic Era

Penaeid Shrimp Chromosome Studies Entering the Post-Genomic Era

Knowledge-Based Prioritization of Genomic Variations: A Quest for Detailed Understanding the Genetic Architecture of Diseases

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