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Fish genomics and its impact on fundamental and applied research of vertebrate biology

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Abstract

The living fishes span a unique and interesting set of animals because of their vast diversity, morphology, ecology, genetics and genomics, and higher importance to biology, economy and culture. During the past decade, the remarkable increase in fish genome sequencing has revolutionized comparative and evolutionary genomics, with the outcome of stimulating insights into vertebrate genome biology. Fish genomics has been transformed rapidly, with the availability of high-quality chromosome level genome assemblies and large collections of sequencing datasets, which are roadmaps for striking discoveries. Landmark achievements are being made; such as the accomplishment of fully assembled lungfish genome which is biggest genome ever sequenced. Here, we highlight current developments in vertebrate’s comparative genomics and discuss how fish genomes could be considered as vital resources for genomic studies. We present a recent overview of genomics data, address different approaches applicable to comparative genomics analyses, and illustrate these comparisons to better understand the complex mechanisms under the vertebrate genomes. We also summarize the applications in chromosomes research and cytogenomics.

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Funding

We acknowledge São Paulo Research Foundation (FAPESP)—grant number 2015/16661–1 (to C.M.), a Postdoctoral Researcher award at Kasetsart University (to S.F.A. and K.S.), and National Counsel of Technological and Scientific Development (CNPq)—grant numbers 304111/2020–1 (to M.J.) and 304111/2020–1 (to C.M.).

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SFA and CM drafted the manuscript; conceived the ideas and reviewed the literature; SFA and MJ performed the data analysis, including comparative repeatomic abundance and phylogeny, plotted graphics, and designed all figures; SFA, MJ, KS and CM reviewed the data and revised the manuscript. All authors approved the manuscript for publication. All authors have read and agreed to the published version of the manuscript.

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Correspondence to Cesar Martins.

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Ahmad, S.F., Jehangir, M., Srikulnath, K. et al. Fish genomics and its impact on fundamental and applied research of vertebrate biology. Rev Fish Biol Fisheries 32, 357–385 (2022). https://doi.org/10.1007/s11160-021-09691-7

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  • DOI: https://doi.org/10.1007/s11160-021-09691-7

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