Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata)

O. Prakhongcheep, W. Thapana, A. Suntronpong, W. Singchat, K. Pattanatanang, R. Phatcharakullawarawat, N. Muangmai, S. Peyachoknagul, K. Matsubara, T. Ezaz, K. Srikulnath

    Research output: Contribution to journalArticle

    2 Citations (Scopus)
    4 Downloads (Pure)

    Abstract


    Background

    Satellite DNAs (stDNAs) are highly repeated sequences that constitute large portions of any genome. The evolutionary dynamics of stDNA (e.g. copy number, nucleotide sequence, location) can, therefore, provide an insight into genome organization and evolution. We investigated the evolutionary origin of VSAREP stDNA in 17 monitor lizards (seven Asian, five Australian, and five African) at molecular and cytogenetic level.


    Results

    Results revealed that VSAREP is conserved in the genome of Asian and Australian varanids, but not in African varanids, suggesting that these sequences are either differentiated or lost in the African varanids. Phylogenetic and arrangement network analyses revealed the existence of at least four VSAREP subfamilies. The similarity of each sequence unit within the same VSAREP subfamily from different species was higher than those of other VSAREP subfamilies belonging to the same species. Additionally, all VSAREP subfamilies isolated from the three Australian species (Varanus rosenbergi, V. gouldii, and V. acanthurus) were co-localized near the centromeric or pericentromeric regions of the macrochromosomes, except for chromosomes 3 and 4 in each Australian varanid. However, their chromosomal arrangements were different among species.


    Conclusions

    The VSAREP stDNA family lack homogenized species-specific nucleotide positions in varanid lineage. Most VSAREP sequences were shared among varanids within the four VSAREP subfamilies. This suggests that nucleotide substitutions in each varanid species accumulated more slowly than homogenization rates in each VSAREP subfamily, resulting in non-species-specific evolution of stDNA profiles. Moreover, changes in location of VSAREP stDNA in each Australian varanid suggests a correlation with chromosomal rearrangements, leading to karyotypic differences among these species.
    Original languageUndefined
    Pages (from-to)1-14
    Number of pages14
    JournalBMC Evolutionary Biology
    Volume17
    Issue number1
    DOIs
    Publication statusPublished - 2017

    Cite this

    Prakhongcheep, O., Thapana, W., Suntronpong, A., Singchat, W., Pattanatanang, K., Phatcharakullawarawat, R., ... Srikulnath, K. (2017). Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata). BMC Evolutionary Biology, 17(1), 1-14. https://doi.org/10.1186/s12862-017-1044-6
    Prakhongcheep, O. ; Thapana, W. ; Suntronpong, A. ; Singchat, W. ; Pattanatanang, K. ; Phatcharakullawarawat, R. ; Muangmai, N. ; Peyachoknagul, S. ; Matsubara, K. ; Ezaz, T. ; Srikulnath, K. / Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata). In: BMC Evolutionary Biology. 2017 ; Vol. 17, No. 1. pp. 1-14.
    @article{c0b7a8e2ca8f4154b4d443ae2e469d81,
    title = "Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata)",
    abstract = "BackgroundSatellite DNAs (stDNAs) are highly repeated sequences that constitute large portions of any genome. The evolutionary dynamics of stDNA (e.g. copy number, nucleotide sequence, location) can, therefore, provide an insight into genome organization and evolution. We investigated the evolutionary origin of VSAREP stDNA in 17 monitor lizards (seven Asian, five Australian, and five African) at molecular and cytogenetic level.ResultsResults revealed that VSAREP is conserved in the genome of Asian and Australian varanids, but not in African varanids, suggesting that these sequences are either differentiated or lost in the African varanids. Phylogenetic and arrangement network analyses revealed the existence of at least four VSAREP subfamilies. The similarity of each sequence unit within the same VSAREP subfamily from different species was higher than those of other VSAREP subfamilies belonging to the same species. Additionally, all VSAREP subfamilies isolated from the three Australian species (Varanus rosenbergi, V. gouldii, and V. acanthurus) were co-localized near the centromeric or pericentromeric regions of the macrochromosomes, except for chromosomes 3 and 4 in each Australian varanid. However, their chromosomal arrangements were different among species.ConclusionsThe VSAREP stDNA family lack homogenized species-specific nucleotide positions in varanid lineage. Most VSAREP sequences were shared among varanids within the four VSAREP subfamilies. This suggests that nucleotide substitutions in each varanid species accumulated more slowly than homogenization rates in each VSAREP subfamily, resulting in non-species-specific evolution of stDNA profiles. Moreover, changes in location of VSAREP stDNA in each Australian varanid suggests a correlation with chromosomal rearrangements, leading to karyotypic differences among these species.",
    author = "O. Prakhongcheep and W. Thapana and A. Suntronpong and W. Singchat and K. Pattanatanang and R. Phatcharakullawarawat and N. Muangmai and S. Peyachoknagul and K. Matsubara and T. Ezaz and K. Srikulnath",
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    language = "Undefined",
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    Prakhongcheep, O, Thapana, W, Suntronpong, A, Singchat, W, Pattanatanang, K, Phatcharakullawarawat, R, Muangmai, N, Peyachoknagul, S, Matsubara, K, Ezaz, T & Srikulnath, K 2017, 'Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata)', BMC Evolutionary Biology, vol. 17, no. 1, pp. 1-14. https://doi.org/10.1186/s12862-017-1044-6

    Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata). / Prakhongcheep, O.; Thapana, W.; Suntronpong, A.; Singchat, W.; Pattanatanang, K.; Phatcharakullawarawat, R.; Muangmai, N.; Peyachoknagul, S.; Matsubara, K.; Ezaz, T.; Srikulnath, K.

    In: BMC Evolutionary Biology, Vol. 17, No. 1, 2017, p. 1-14.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata)

    AU - Prakhongcheep, O.

    AU - Thapana, W.

    AU - Suntronpong, A.

    AU - Singchat, W.

    AU - Pattanatanang, K.

    AU - Phatcharakullawarawat, R.

    AU - Muangmai, N.

    AU - Peyachoknagul, S.

    AU - Matsubara, K.

    AU - Ezaz, T.

    AU - Srikulnath, K.

    N1 - cited By 0

    PY - 2017

    Y1 - 2017

    N2 - BackgroundSatellite DNAs (stDNAs) are highly repeated sequences that constitute large portions of any genome. The evolutionary dynamics of stDNA (e.g. copy number, nucleotide sequence, location) can, therefore, provide an insight into genome organization and evolution. We investigated the evolutionary origin of VSAREP stDNA in 17 monitor lizards (seven Asian, five Australian, and five African) at molecular and cytogenetic level.ResultsResults revealed that VSAREP is conserved in the genome of Asian and Australian varanids, but not in African varanids, suggesting that these sequences are either differentiated or lost in the African varanids. Phylogenetic and arrangement network analyses revealed the existence of at least four VSAREP subfamilies. The similarity of each sequence unit within the same VSAREP subfamily from different species was higher than those of other VSAREP subfamilies belonging to the same species. Additionally, all VSAREP subfamilies isolated from the three Australian species (Varanus rosenbergi, V. gouldii, and V. acanthurus) were co-localized near the centromeric or pericentromeric regions of the macrochromosomes, except for chromosomes 3 and 4 in each Australian varanid. However, their chromosomal arrangements were different among species.ConclusionsThe VSAREP stDNA family lack homogenized species-specific nucleotide positions in varanid lineage. Most VSAREP sequences were shared among varanids within the four VSAREP subfamilies. This suggests that nucleotide substitutions in each varanid species accumulated more slowly than homogenization rates in each VSAREP subfamily, resulting in non-species-specific evolution of stDNA profiles. Moreover, changes in location of VSAREP stDNA in each Australian varanid suggests a correlation with chromosomal rearrangements, leading to karyotypic differences among these species.

    AB - BackgroundSatellite DNAs (stDNAs) are highly repeated sequences that constitute large portions of any genome. The evolutionary dynamics of stDNA (e.g. copy number, nucleotide sequence, location) can, therefore, provide an insight into genome organization and evolution. We investigated the evolutionary origin of VSAREP stDNA in 17 monitor lizards (seven Asian, five Australian, and five African) at molecular and cytogenetic level.ResultsResults revealed that VSAREP is conserved in the genome of Asian and Australian varanids, but not in African varanids, suggesting that these sequences are either differentiated or lost in the African varanids. Phylogenetic and arrangement network analyses revealed the existence of at least four VSAREP subfamilies. The similarity of each sequence unit within the same VSAREP subfamily from different species was higher than those of other VSAREP subfamilies belonging to the same species. Additionally, all VSAREP subfamilies isolated from the three Australian species (Varanus rosenbergi, V. gouldii, and V. acanthurus) were co-localized near the centromeric or pericentromeric regions of the macrochromosomes, except for chromosomes 3 and 4 in each Australian varanid. However, their chromosomal arrangements were different among species.ConclusionsThe VSAREP stDNA family lack homogenized species-specific nucleotide positions in varanid lineage. Most VSAREP sequences were shared among varanids within the four VSAREP subfamilies. This suggests that nucleotide substitutions in each varanid species accumulated more slowly than homogenization rates in each VSAREP subfamily, resulting in non-species-specific evolution of stDNA profiles. Moreover, changes in location of VSAREP stDNA in each Australian varanid suggests a correlation with chromosomal rearrangements, leading to karyotypic differences among these species.

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    U2 - 10.1186/s12862-017-1044-6

    DO - 10.1186/s12862-017-1044-6

    M3 - Article

    VL - 17

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    EP - 14

    JO - BMC Evolutionary Biology

    JF - BMC Evolutionary Biology

    SN - 1471-2148

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