Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure

Black flounder (Paralichthys orbignyanus, Pleuronectiformes) is a commercially significant marine fish with promising aquaculture potential in Argentina. Despite extensive studies on Black flounder aquaculture, its limited genetic information available hampers the crucial role genetics plays in the...

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Autores: Villarreal, Fernando, Burguener, Germán F., Sosa, Ezequiel J., Stocchi, Nicolas, Somoza, Gustavo M., Turjanski, Adrián G., Blanco, Andrés, Viñas de Puig, Jordi, Mechaly, Alejandro S.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2024
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10256/27818
Acceso en línea:http://hdl.handle.net/10256/27818
Access Level:acceso abierto
Palabra clave:ADN mitocondrial
Genomes
Mitochondrial DNA
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spelling Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structureVillarreal, FernandoBurguener, Germán F.Sosa, Ezequiel J.Stocchi, NicolasSomoza, Gustavo M.Turjanski, Adrián G.Blanco, AndrésViñas de Puig, JordiMechaly, Alejandro S.ADN mitocondrialGenomesMitochondrial DNAGenomesBlack flounder (Paralichthys orbignyanus, Pleuronectiformes) is a commercially significant marine fish with promising aquaculture potential in Argentina. Despite extensive studies on Black flounder aquaculture, its limited genetic information available hampers the crucial role genetics plays in the development of this activity. In this study, we first employed Illumina sequencing technology to sequence the entire genome of Black flounder. Utilizing two independent libraries one from a female and another from a male with 150 bp paired-end reads, a mean insert length of 350 bp, and over 35 X-fold coverage, we achieved assemblies resulting in a genome size of ~ 538 Mbp. Analysis of the assemblies revealed that more than 98% of the core genes were present, with more than 78% of them having more than 50% coverage. This indicates a somehow complete and accurate genome at the coding sequence level. This genome contains 25,231 protein-coding genes, 445 tRNAs, 3 rRNAs, and more than 1,500 non-coding RNAs of other types. Black flounder, along with pufferfishes, seahorses, pipefishes, and anabantid fish, displays a smaller genome compared to most other teleost groups. In vertebrates, the number of transposable elements (TEs) is often correlated with genome size. However, it remains unclear whether the sizes of introns and exons also play a role in determining genome size. Hence, to elucidate the potential factors contributing to this reduced genome size, we conducted a comparative genomic analysis between Black flounder and other teleost orders to determine if the small genomic size could be explained by repetitive elements or gene features, including the whole genome genes and introns sizes. We show that the smaller genome size of flounders can be attributed to several factors, including changes in the number of repetitive elements, and decreased gene size, particularly due to lower amount of very large and small introns. Thus, these components appear to be involved in the genome reduction in Black flounder. Despite these insights, the full implications and potential benefits of genome reduction in Black flounder for reproduction and aquaculture remain incompletely understood, necessitating further researchThis study was funded by projects grants by the Agencia Nacional de Promoción Científica y Tecnológica (ANPCYT, Argentina) to ASM (PICT-2017–2839 and PICT-2020 SERIE-0696) and partially funded by JV (MPCUdG2016/130)BioMed Central2024info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10256/27818http://hdl.handle.net/10256/27818BMC Genomics, 2024, vol. 25, num. 297Articles publicats (D-B)Villarreal, Fernando Burguener, Germán F. Sosa, Ezequiel J. Stocchi, Nicolas Somoza, Gustavo M. Turjanski, Adrián G. Blanco, Andrés Viñas de Puig, Jordi Mechaly, Alejandro S. 2024 Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure BMC Genomics 25 297reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)Inglésinfo:eu-repo/semantics/altIdentifier/doi/10.1186/s12864-024-10081-zinfo:eu-repo/semantics/altIdentifier/issn/1471-2164info:eu-repo/semantics/altIdentifier/eissn/1471-2164Attribution 4.0 International (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10256/278182026-05-29T05:05:01Z
dc.title.none.fl_str_mv Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure
title Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure
spellingShingle Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure
Villarreal, Fernando
ADN mitocondrial
Genomes
Mitochondrial DNA
Genomes
title_short Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure
title_full Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure
title_fullStr Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure
title_full_unstemmed Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure
title_sort Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure
dc.creator.none.fl_str_mv Villarreal, Fernando
Burguener, Germán F.
Sosa, Ezequiel J.
Stocchi, Nicolas
Somoza, Gustavo M.
Turjanski, Adrián G.
Blanco, Andrés
Viñas de Puig, Jordi
Mechaly, Alejandro S.
author Villarreal, Fernando
author_facet Villarreal, Fernando
Burguener, Germán F.
Sosa, Ezequiel J.
Stocchi, Nicolas
Somoza, Gustavo M.
Turjanski, Adrián G.
Blanco, Andrés
Viñas de Puig, Jordi
Mechaly, Alejandro S.
author_role author
author2 Burguener, Germán F.
Sosa, Ezequiel J.
Stocchi, Nicolas
Somoza, Gustavo M.
Turjanski, Adrián G.
Blanco, Andrés
Viñas de Puig, Jordi
Mechaly, Alejandro S.
author2_role author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv ADN mitocondrial
Genomes
Mitochondrial DNA
Genomes
topic ADN mitocondrial
Genomes
Mitochondrial DNA
Genomes
description Black flounder (Paralichthys orbignyanus, Pleuronectiformes) is a commercially significant marine fish with promising aquaculture potential in Argentina. Despite extensive studies on Black flounder aquaculture, its limited genetic information available hampers the crucial role genetics plays in the development of this activity. In this study, we first employed Illumina sequencing technology to sequence the entire genome of Black flounder. Utilizing two independent libraries one from a female and another from a male with 150 bp paired-end reads, a mean insert length of 350 bp, and over 35 X-fold coverage, we achieved assemblies resulting in a genome size of ~ 538 Mbp. Analysis of the assemblies revealed that more than 98% of the core genes were present, with more than 78% of them having more than 50% coverage. This indicates a somehow complete and accurate genome at the coding sequence level. This genome contains 25,231 protein-coding genes, 445 tRNAs, 3 rRNAs, and more than 1,500 non-coding RNAs of other types. Black flounder, along with pufferfishes, seahorses, pipefishes, and anabantid fish, displays a smaller genome compared to most other teleost groups. In vertebrates, the number of transposable elements (TEs) is often correlated with genome size. However, it remains unclear whether the sizes of introns and exons also play a role in determining genome size. Hence, to elucidate the potential factors contributing to this reduced genome size, we conducted a comparative genomic analysis between Black flounder and other teleost orders to determine if the small genomic size could be explained by repetitive elements or gene features, including the whole genome genes and introns sizes. We show that the smaller genome size of flounders can be attributed to several factors, including changes in the number of repetitive elements, and decreased gene size, particularly due to lower amount of very large and small introns. Thus, these components appear to be involved in the genome reduction in Black flounder. Despite these insights, the full implications and potential benefits of genome reduction in Black flounder for reproduction and aquaculture remain incompletely understood, necessitating further research
publishDate 2024
dc.date.none.fl_str_mv 2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10256/27818
http://hdl.handle.net/10256/27818
url http://hdl.handle.net/10256/27818
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1186/s12864-024-10081-z
info:eu-repo/semantics/altIdentifier/issn/1471-2164
info:eu-repo/semantics/altIdentifier/eissn/1471-2164
dc.rights.none.fl_str_mv Attribution 4.0 International (CC BY 4.0)
https://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv Attribution 4.0 International (CC BY 4.0)
https://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv BMC Genomics, 2024, vol. 25, num. 297
Articles publicats (D-B)
Villarreal, Fernando Burguener, Germán F. Sosa, Ezequiel J. Stocchi, Nicolas Somoza, Gustavo M. Turjanski, Adrián G. Blanco, Andrés Viñas de Puig, Jordi Mechaly, Alejandro S. 2024 Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure BMC Genomics 25 297
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instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
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