Cytogenetics, genomics and biodiversity of the South American and African Arapaimidae fish family (Teleostei, Osteoglossiformes)

Ezequiel Aguiar de Oliveira, Luiz Antonio Carlos Bertollo, Petr Rab, Tariq Ezaz, Cassia Fernanda Yano, Terumi Hatanaka, Oladele Ilesanmi Jegede, Alongklod Tanomtong, Thomas Liehr, Alexandr Sember, Sandra Regina Maruyama, Eliana Feldberg, Patrik Ferreira Viana, Marcelo de Bello Cioffi

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Abstract

Osteoglossiformes represents one of the most ancestral teleost lineages, currently widespread over almost all continents, except for Antarctica. However, data involving advanced molecular cytogenetics or comparative genomics are yet largely limited for this fish group. Therefore, the present investigations focus on the osteoglossiform family Arapaimidae, studying a unique fish model group with advanced molecular cytogenetic genomic tools. The aim is to better explore and clarify certain events and factors that had impact on evolutionary history of this fish group. For that, both South American and African representatives of Arapaimidae, namely Arapaima gigas and Heterotis niloticus, were examined. Both species differed markedly by diploid chromosome numbers, with 2n = 56 found in A. gigas and 2n = 40 exhibited by H. niloticus. Conventional cytogenetics along with fluorescence in situ hybridization revealed some general trends shared by most osteoglossiform species analyzed thus far, such as the presence of only one chromosome pair bearing 18S and 5S rDNA sites and karyotypes dominated by acrocentric chromosomes, resembling thus the patterns of hypothetical ancestral teleost karyotype. Furthermore, the genomes of A. gigas and H. niloticus display remarkable divergence in terms of repetitive DNA content and distribution, as revealed by comparative genomic hybridization (CGH). On the other hand, genomic diversity of single copy sequences studied through principal component analyses (PCA) based on SNP alleles genotyped by the DArT seq procedure demonstrated a very low genetic distance between the South American and African Arapaimidae species; this pattern contrasts sharply with the scenario found in other osteoglossiform species. Underlying evolutionary mechanisms potentially explaining the obtained data have been suggested and discussed.

Original languageEnglish
Article numbere0214225
Pages (from-to)1-19
Number of pages19
JournalPLoS One
Volume14
Issue number3
DOIs
Publication statusPublished - 25 Mar 2019

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Osteoglossiformes
Arapaima gigas
Biodiversity
Chromosomes
Genomics
cytogenetics
Cytogenetics
African Americans
Fish
Fishes
biodiversity
Karyotype
genomics
karyotyping
Bearings (structural)
fish
comparative genomic hybridization
acrocentric chromosomes
Comparative Genomic Hybridization
Ribosomal DNA

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de Oliveira, E. A., Bertollo, L. A. C., Rab, P., Ezaz, T., Yano, C. F., Hatanaka, T., ... de Bello Cioffi, M. (2019). Cytogenetics, genomics and biodiversity of the South American and African Arapaimidae fish family (Teleostei, Osteoglossiformes). PLoS One, 14(3), 1-19. [e0214225]. https://doi.org/10.1371/journal.pone.0214225
de Oliveira, Ezequiel Aguiar ; Bertollo, Luiz Antonio Carlos ; Rab, Petr ; Ezaz, Tariq ; Yano, Cassia Fernanda ; Hatanaka, Terumi ; Jegede, Oladele Ilesanmi ; Tanomtong, Alongklod ; Liehr, Thomas ; Sember, Alexandr ; Maruyama, Sandra Regina ; Feldberg, Eliana ; Viana, Patrik Ferreira ; de Bello Cioffi, Marcelo. / Cytogenetics, genomics and biodiversity of the South American and African Arapaimidae fish family (Teleostei, Osteoglossiformes). In: PLoS One. 2019 ; Vol. 14, No. 3. pp. 1-19.
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de Oliveira, EA, Bertollo, LAC, Rab, P, Ezaz, T, Yano, CF, Hatanaka, T, Jegede, OI, Tanomtong, A, Liehr, T, Sember, A, Maruyama, SR, Feldberg, E, Viana, PF & de Bello Cioffi, M 2019, 'Cytogenetics, genomics and biodiversity of the South American and African Arapaimidae fish family (Teleostei, Osteoglossiformes)', PLoS One, vol. 14, no. 3, e0214225, pp. 1-19. https://doi.org/10.1371/journal.pone.0214225

Cytogenetics, genomics and biodiversity of the South American and African Arapaimidae fish family (Teleostei, Osteoglossiformes). / de Oliveira, Ezequiel Aguiar; Bertollo, Luiz Antonio Carlos; Rab, Petr; Ezaz, Tariq; Yano, Cassia Fernanda; Hatanaka, Terumi; Jegede, Oladele Ilesanmi; Tanomtong, Alongklod; Liehr, Thomas; Sember, Alexandr; Maruyama, Sandra Regina; Feldberg, Eliana; Viana, Patrik Ferreira; de Bello Cioffi, Marcelo.

In: PLoS One, Vol. 14, No. 3, e0214225, 25.03.2019, p. 1-19.

Research output: Contribution to journalArticle

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T1 - Cytogenetics, genomics and biodiversity of the South American and African Arapaimidae fish family (Teleostei, Osteoglossiformes)

AU - de Oliveira, Ezequiel Aguiar

AU - Bertollo, Luiz Antonio Carlos

AU - Rab, Petr

AU - Ezaz, Tariq

AU - Yano, Cassia Fernanda

AU - Hatanaka, Terumi

AU - Jegede, Oladele Ilesanmi

AU - Tanomtong, Alongklod

AU - Liehr, Thomas

AU - Sember, Alexandr

AU - Maruyama, Sandra Regina

AU - Feldberg, Eliana

AU - Viana, Patrik Ferreira

AU - de Bello Cioffi, Marcelo

PY - 2019/3/25

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N2 - Osteoglossiformes represents one of the most ancestral teleost lineages, currently widespread over almost all continents, except for Antarctica. However, data involving advanced molecular cytogenetics or comparative genomics are yet largely limited for this fish group. Therefore, the present investigations focus on the osteoglossiform family Arapaimidae, studying a unique fish model group with advanced molecular cytogenetic genomic tools. The aim is to better explore and clarify certain events and factors that had impact on evolutionary history of this fish group. For that, both South American and African representatives of Arapaimidae, namely Arapaima gigas and Heterotis niloticus, were examined. Both species differed markedly by diploid chromosome numbers, with 2n = 56 found in A. gigas and 2n = 40 exhibited by H. niloticus. Conventional cytogenetics along with fluorescence in situ hybridization revealed some general trends shared by most osteoglossiform species analyzed thus far, such as the presence of only one chromosome pair bearing 18S and 5S rDNA sites and karyotypes dominated by acrocentric chromosomes, resembling thus the patterns of hypothetical ancestral teleost karyotype. Furthermore, the genomes of A. gigas and H. niloticus display remarkable divergence in terms of repetitive DNA content and distribution, as revealed by comparative genomic hybridization (CGH). On the other hand, genomic diversity of single copy sequences studied through principal component analyses (PCA) based on SNP alleles genotyped by the DArT seq procedure demonstrated a very low genetic distance between the South American and African Arapaimidae species; this pattern contrasts sharply with the scenario found in other osteoglossiform species. Underlying evolutionary mechanisms potentially explaining the obtained data have been suggested and discussed.

AB - Osteoglossiformes represents one of the most ancestral teleost lineages, currently widespread over almost all continents, except for Antarctica. However, data involving advanced molecular cytogenetics or comparative genomics are yet largely limited for this fish group. Therefore, the present investigations focus on the osteoglossiform family Arapaimidae, studying a unique fish model group with advanced molecular cytogenetic genomic tools. The aim is to better explore and clarify certain events and factors that had impact on evolutionary history of this fish group. For that, both South American and African representatives of Arapaimidae, namely Arapaima gigas and Heterotis niloticus, were examined. Both species differed markedly by diploid chromosome numbers, with 2n = 56 found in A. gigas and 2n = 40 exhibited by H. niloticus. Conventional cytogenetics along with fluorescence in situ hybridization revealed some general trends shared by most osteoglossiform species analyzed thus far, such as the presence of only one chromosome pair bearing 18S and 5S rDNA sites and karyotypes dominated by acrocentric chromosomes, resembling thus the patterns of hypothetical ancestral teleost karyotype. Furthermore, the genomes of A. gigas and H. niloticus display remarkable divergence in terms of repetitive DNA content and distribution, as revealed by comparative genomic hybridization (CGH). On the other hand, genomic diversity of single copy sequences studied through principal component analyses (PCA) based on SNP alleles genotyped by the DArT seq procedure demonstrated a very low genetic distance between the South American and African Arapaimidae species; this pattern contrasts sharply with the scenario found in other osteoglossiform species. Underlying evolutionary mechanisms potentially explaining the obtained data have been suggested and discussed.

KW - karyotypes

KW - comparative genomics

KW - probe hybridization

KW - chromosome pairs

KW - freshwater fish

KW - molecular genetics

KW - Principal Component Analysis

KW - cytogenetics

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UR - http://www.mendeley.com/research/cytogenetics-genomics-biodiversity-south-american-african-arapaimidae-fish-family-teleostei-osteoglo

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