Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata)
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...
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| Format: | Article |
| Language: | English |
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BMC
2017-08-01
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| Series: | BMC Evolutionary Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s12862-017-1044-6 |
| _version_ | 1819007879331446784 |
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| author | Ornjira Prakhongcheep Watcharaporn Thapana Aorarat Suntronpong Worapong Singchat Khampee Pattanatanang Rattanin Phatcharakullawarawat Narongrit Muangmai Surin Peyachoknagul Kazumi Matsubara Tariq Ezaz Kornsorn Srikulnath |
| author_facet | Ornjira Prakhongcheep Watcharaporn Thapana Aorarat Suntronpong Worapong Singchat Khampee Pattanatanang Rattanin Phatcharakullawarawat Narongrit Muangmai Surin Peyachoknagul Kazumi Matsubara Tariq Ezaz Kornsorn Srikulnath |
| author_sort | Ornjira Prakhongcheep |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-21T00:31:35Z |
| format | Article |
| id | doaj.art-bd992904485b46a89acd959fe571fdb2 |
| institution | Directory Open Access Journal |
| issn | 1471-2148 |
| language | English |
| last_indexed | 2024-12-21T00:31:35Z |
| publishDate | 2017-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Evolutionary Biology |
| spelling | doaj.art-bd992904485b46a89acd959fe571fdb22022-12-21T19:21:53ZengBMCBMC Evolutionary Biology1471-21482017-08-0117111410.1186/s12862-017-1044-6Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata)Ornjira Prakhongcheep0Watcharaporn Thapana1Aorarat Suntronpong2Worapong Singchat3Khampee Pattanatanang4Rattanin Phatcharakullawarawat5Narongrit Muangmai6Surin Peyachoknagul7Kazumi Matsubara8Tariq Ezaz9Kornsorn Srikulnath10Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart UniversityLaboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart UniversityLaboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart UniversityLaboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart UniversityDepartment of Parasitology, Faculty of Veterinary Medicine, Kasetsart UniversityMildpets Animal HospitalDepartment of Fishery Biology, Faculty of Fisheries, Kasetsart UniversityLaboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart UniversityWildlife Genetics Laboratory, Institute for Applied Ecology, University of CanberraWildlife Genetics Laboratory, Institute for Applied Ecology, University of CanberraLaboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart UniversityAbstract 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.http://link.springer.com/article/10.1186/s12862-017-1044-6Nucleotide sequence conservationRepeated sequenceLizardHomogenizationMacrochromosome |
| spellingShingle | Ornjira Prakhongcheep Watcharaporn Thapana Aorarat Suntronpong Worapong Singchat Khampee Pattanatanang Rattanin Phatcharakullawarawat Narongrit Muangmai Surin Peyachoknagul Kazumi Matsubara Tariq Ezaz Kornsorn Srikulnath Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata) BMC Evolutionary Biology Nucleotide sequence conservation Repeated sequence Lizard Homogenization Macrochromosome |
| title | Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata) |
| title_full | Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata) |
| title_fullStr | Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata) |
| title_full_unstemmed | Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata) |
| title_short | Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata) |
| title_sort | lack of satellite dna species specific homogenization and relationship to chromosomal rearrangements in monitor lizards varanidae squamata |
| topic | Nucleotide sequence conservation Repeated sequence Lizard Homogenization Macrochromosome |
| url | http://link.springer.com/article/10.1186/s12862-017-1044-6 |
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