Comparative genomics reveals insights into anuran genome size evolution
Abstract Background Amphibians, particularly anurans, display an enormous variation in genome size. Due to the unavailability of whole genome datasets in the past, the genomic elements and evolutionary causes of anuran genome size variation are poorly understood. To address this, we analyzed whole-g...
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| Format: | Article |
| Language: | English |
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BMC
2023-07-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09499-8 |
| _version_ | 1797784799337775104 |
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| author | Bin Zuo Lotanna Micah Nneji Yan-Bo Sun |
| author_facet | Bin Zuo Lotanna Micah Nneji Yan-Bo Sun |
| author_sort | Bin Zuo |
| collection | DOAJ |
| description | Abstract Background Amphibians, particularly anurans, display an enormous variation in genome size. Due to the unavailability of whole genome datasets in the past, the genomic elements and evolutionary causes of anuran genome size variation are poorly understood. To address this, we analyzed whole-genome sequences of 14 anuran species ranging in size from 1.1 to 6.8 Gb. By annotating multiple genomic elements, we investigated the genomic correlates of anuran genome size variation and further examined whether the genome size relates to habitat types. Results Our results showed that intron expansions or contraction and Transposable Elements (TEs) diversity do not contribute significantly to genome size variation. However, the recent accumulation of transposable elements (TEs) and the lack of deletion of ancient TEs primarily accounted for the evolution of anuran genome sizes. Our study showed that the abundance and density of simple repeat sequences positively correlate with genome size. Ancestral state reconstruction revealed that genome size exhibits a taxon-specific pattern of evolution, with families Bufonidae and Pipidae experiencing extreme genome expansion and contraction events, respectively. Our result showed no relationship between genome size and habitat types, although large genome-sized species are predominantly found in humid habitats. Conclusions Overall, our study identified the genomic element and their evolutionary dynamics accounting for anuran genome size variation, thus paving a path to a greater understanding of the size evolution of the genome in amphibians. |
| first_indexed | 2024-03-13T00:45:02Z |
| format | Article |
| id | doaj.art-ecf32335d30243f989cbecfe9fc77f90 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-13T00:45:02Z |
| publishDate | 2023-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-ecf32335d30243f989cbecfe9fc77f902023-07-09T11:07:19ZengBMCBMC Genomics1471-21642023-07-0124111210.1186/s12864-023-09499-8Comparative genomics reveals insights into anuran genome size evolutionBin Zuo0Lotanna Micah Nneji1Yan-Bo Sun2Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan UniversityDepartment of Ecology and Evolutionary Biology, Princeton UniversityMinistry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan UniversityAbstract Background Amphibians, particularly anurans, display an enormous variation in genome size. Due to the unavailability of whole genome datasets in the past, the genomic elements and evolutionary causes of anuran genome size variation are poorly understood. To address this, we analyzed whole-genome sequences of 14 anuran species ranging in size from 1.1 to 6.8 Gb. By annotating multiple genomic elements, we investigated the genomic correlates of anuran genome size variation and further examined whether the genome size relates to habitat types. Results Our results showed that intron expansions or contraction and Transposable Elements (TEs) diversity do not contribute significantly to genome size variation. However, the recent accumulation of transposable elements (TEs) and the lack of deletion of ancient TEs primarily accounted for the evolution of anuran genome sizes. Our study showed that the abundance and density of simple repeat sequences positively correlate with genome size. Ancestral state reconstruction revealed that genome size exhibits a taxon-specific pattern of evolution, with families Bufonidae and Pipidae experiencing extreme genome expansion and contraction events, respectively. Our result showed no relationship between genome size and habitat types, although large genome-sized species are predominantly found in humid habitats. Conclusions Overall, our study identified the genomic element and their evolutionary dynamics accounting for anuran genome size variation, thus paving a path to a greater understanding of the size evolution of the genome in amphibians.https://doi.org/10.1186/s12864-023-09499-8Genome size variationSimple repeat sequencesAnuransTransposable elements |
| spellingShingle | Bin Zuo Lotanna Micah Nneji Yan-Bo Sun Comparative genomics reveals insights into anuran genome size evolution BMC Genomics Genome size variation Simple repeat sequences Anurans Transposable elements |
| title | Comparative genomics reveals insights into anuran genome size evolution |
| title_full | Comparative genomics reveals insights into anuran genome size evolution |
| title_fullStr | Comparative genomics reveals insights into anuran genome size evolution |
| title_full_unstemmed | Comparative genomics reveals insights into anuran genome size evolution |
| title_short | Comparative genomics reveals insights into anuran genome size evolution |
| title_sort | comparative genomics reveals insights into anuran genome size evolution |
| topic | Genome size variation Simple repeat sequences Anurans Transposable elements |
| url | https://doi.org/10.1186/s12864-023-09499-8 |
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