Academic Journal
View in EDS
HTML Full Text

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

Bibliographic Details
Title: Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure.
Authors: Villarreal, Fernando, Burguener, Germán F., Sosa, Ezequiel J., Stocchi, Nicolas, Somoza, Gustavo M., Turjanski, Adrián G., Blanco, Andrés, Viñas, Jordi, Mechaly, Alejandro S.
Source: BMC Genomics; 3/20/2024, Vol. 25 Issue 1, p1-17, 17p
Subject Terms: PARALICHTHYS, MARINE fishes, FLATFISHES, WHOLE genome sequencing, FISH farming, NUCLEOTIDE sequencing, TRANSFER RNA, GENOMES
Geographic Terms: ARGENTINA
Abstract: 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. [ABSTRACT FROM AUTHOR]
Copyright of BMC Genomics is the property of BioMed Central and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Complementary Index
Full text is not displayed to guests.
FullText Links:
  – Type: pdflink
Text:
  Availability: 1
CustomLinks:
  – Url: https://resolver.ebsco.com/c/xy5jbn/result?sid=EBSCO:edb&genre=article&issn=14712164&ISBN=&volume=25&issue=1&date=20240320&spage=1&pages=1-17&title=BMC Genomics&atitle=Genome%20sequencing%20and%20analysis%20of%20black%20flounder%20%28Paralichthys%20orbignyanus%29%20reveals%20new%20insights%20into%20Pleuronectiformes%20genomic%20size%20and%20structure.&aulast=Villarreal%2C%20Fernando&id=DOI:10.1186/s12864-024-10081-z
    Name: Full Text Finder (for New FTF UI) (s8985755)
    Category: fullText
    Text: Find It @ SCU Libraries
    MouseOverText: Find It @ SCU Libraries
Header DbId: edb
DbLabel: Complementary Index
An: 176181690
RelevancyScore: 1007
AccessLevel: 6
PubType: Academic Journal
PubTypeId: academicJournal
PreciseRelevancyScore: 1007.03820800781
IllustrationInfo
Items – Name: Title
  Label: Title
  Group: Ti
  Data: Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure.
– Name: Author
  Label: Authors
  Group: Au
  Data: <searchLink fieldCode="AR" term="%22Villarreal%2C+Fernando%22">Villarreal, Fernando</searchLink><br /><searchLink fieldCode="AR" term="%22Burguener%2C+Germán+F%2E%22">Burguener, Germán F.</searchLink><br /><searchLink fieldCode="AR" term="%22Sosa%2C+Ezequiel+J%2E%22">Sosa, Ezequiel J.</searchLink><br /><searchLink fieldCode="AR" term="%22Stocchi%2C+Nicolas%22">Stocchi, Nicolas</searchLink><br /><searchLink fieldCode="AR" term="%22Somoza%2C+Gustavo+M%2E%22">Somoza, Gustavo M.</searchLink><br /><searchLink fieldCode="AR" term="%22Turjanski%2C+Adrián+G%2E%22">Turjanski, Adrián G.</searchLink><br /><searchLink fieldCode="AR" term="%22Blanco%2C+Andrés%22">Blanco, Andrés</searchLink><br /><searchLink fieldCode="AR" term="%22Viñas%2C+Jordi%22">Viñas, Jordi</searchLink><br /><searchLink fieldCode="AR" term="%22Mechaly%2C+Alejandro+S%2E%22">Mechaly, Alejandro S.</searchLink>
– Name: TitleSource
  Label: Source
  Group: Src
  Data: BMC Genomics; 3/20/2024, Vol. 25 Issue 1, p1-17, 17p
– Name: Subject
  Label: Subject Terms
  Group: Su
  Data: <searchLink fieldCode="DE" term="%22PARALICHTHYS%22">PARALICHTHYS</searchLink><br /><searchLink fieldCode="DE" term="%22MARINE+fishes%22">MARINE fishes</searchLink><br /><searchLink fieldCode="DE" term="%22FLATFISHES%22">FLATFISHES</searchLink><br /><searchLink fieldCode="DE" term="%22WHOLE+genome+sequencing%22">WHOLE genome sequencing</searchLink><br /><searchLink fieldCode="DE" term="%22FISH+farming%22">FISH farming</searchLink><br /><searchLink fieldCode="DE" term="%22NUCLEOTIDE+sequencing%22">NUCLEOTIDE sequencing</searchLink><br /><searchLink fieldCode="DE" term="%22TRANSFER+RNA%22">TRANSFER RNA</searchLink><br /><searchLink fieldCode="DE" term="%22GENOMES%22">GENOMES</searchLink>
– Name: SubjectGeographic
  Label: Geographic Terms
  Group: Su
  Data: <searchLink fieldCode="DE" term="%22ARGENTINA%22">ARGENTINA</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: 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. [ABSTRACT FROM AUTHOR]
– Name: Abstract
  Label:
  Group: Ab
  Data: <i>Copyright of BMC Genomics is the property of BioMed Central and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
PLink https://login.libproxy.scu.edu/login?url=https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&scope=site&db=edb&AN=176181690
RecordInfo BibRecord:
  BibEntity:
    Identifiers:
      – Type: doi
        Value: 10.1186/s12864-024-10081-z
    Languages:
      – Code: eng
        Text: English
    PhysicalDescription:
      Pagination:
        PageCount: 17
        StartPage: 1
    Subjects:
      – SubjectFull: ARGENTINA
        Type: general
      – SubjectFull: PARALICHTHYS
        Type: general
      – SubjectFull: MARINE fishes
        Type: general
      – SubjectFull: FLATFISHES
        Type: general
      – SubjectFull: WHOLE genome sequencing
        Type: general
      – SubjectFull: FISH farming
        Type: general
      – SubjectFull: NUCLEOTIDE sequencing
        Type: general
      – SubjectFull: TRANSFER RNA
        Type: general
      – SubjectFull: GENOMES
        Type: general
    Titles:
      – TitleFull: Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure.
        Type: main
  BibRelationships:
    HasContributorRelationships:
      – PersonEntity:
          Name:
            NameFull: Villarreal, Fernando
      – PersonEntity:
          Name:
            NameFull: Burguener, Germán F.
      – PersonEntity:
          Name:
            NameFull: Sosa, Ezequiel J.
      – PersonEntity:
          Name:
            NameFull: Stocchi, Nicolas
      – PersonEntity:
          Name:
            NameFull: Somoza, Gustavo M.
      – PersonEntity:
          Name:
            NameFull: Turjanski, Adrián G.
      – PersonEntity:
          Name:
            NameFull: Blanco, Andrés
      – PersonEntity:
          Name:
            NameFull: Viñas, Jordi
      – PersonEntity:
          Name:
            NameFull: Mechaly, Alejandro S.
    IsPartOfRelationships:
      – BibEntity:
          Dates:
            – D: 20
              M: 03
              Text: 3/20/2024
              Type: published
              Y: 2024
          Identifiers:
            – Type: issn-print
              Value: 14712164
          Numbering:
            – Type: volume
              Value: 25
            – Type: issue
              Value: 1
          Titles:
            – TitleFull: BMC Genomics
              Type: main
ResultId 1