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 - Funding Information:
This study was financially supported by grants from Professor Motivation (PM) (No. PM4/2558) and Science Research Fund (ScRF) (No. ScRF-S19–2558) from the Faculty of Science, Kasetsart University to K.S., the Fellowship of Capacity Building for Kasetsart University on Internationalization (No. 0513.10109/ 1757) to O.P., the Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU, Thailand) (No. 6/2558) to O.P., the National Research Council of Thailand (NRCT), the Science Achievement Scholarship of Thailand (SAST) (No.5717400381) from the Office of the Higher Education Commission, Thailand to O.P., and partially supported by an Australian Research Council Future Fellowship (FT110100733) to T.E.
Publisher Copyright:
© 2017 The Author(s).
PY - 2017/8/16
Y1 - 2017/8/16
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.
KW - Homogenization
KW - Lizard
KW - Macrochromosome
KW - Nucleotide sequence conservation
KW - Repeated sequence
UR - http://www.scopus.com/inward/record.url?scp=85027499572&partnerID=8YFLogxK
U2 - 10.1186/s12862-017-1044-6
DO - 10.1186/s12862-017-1044-6
M3 - Article
SN - 1471-2148
VL - 17
SP - 1
EP - 14
JO - BMC Evolutionary Biology
JF - BMC Evolutionary Biology
IS - 1
M1 - 193
ER -