Abstract
Satellite DNA is a class of tandemly repetitive sequences characterized by rapid evolution and high intra- and inter-specific diversification and is usually the major component of the constitutive heterochromatin. We investigated the abundance of the satDNA in 77 species of Asclepias from Americas, a genus of the Apocynaceae family. De novo identification of the most abundant satDNA sequences was performed using Tandem Repeat Analyzer and Repeat Explorer pipelines. The abundance of satDNA in 77 species was determined using mapping reads, and the correlation between the abundance of satDNAs and clades on the phylogeny tree was estimated by lambda statistics using phytools R package. The repetitive sequences in Asclepias were mostly constitutive by transposable elements, ranged 11.11 to 16.32%. The satDNA ranged 0.985 to 7.732% and we obtained 12 satDNA sequences (call Sat1 to Sat12), being for the Sat1 we obtained seven families distributed across all species. The Sat2, Sat3, and families of Sat1 showed significant correlations with the topologies of the phylogenetic tree, among which some families of satDNAs displayed varying abundances across the main clades. We concluded that Asclepias is characterized by many satDNAs, and that the abundance of satDNAs is in accordance with the phylogeny and geographical distribution.
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All data analyzed during this study are included in Online Resource 3 supplementary information.
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Acknowledgements
We would like to thank the Federal University of Alagoas for the access to laboratories and scientific support, the Fundação de Amparo à Pesquisa de Alagoas (FAPEAL) for funding this project, and the National Council for the Improvement of Higher Education (CAPES).
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G.C.C. conceived the project and the experiments. C.A. drafted the manuscript. All authors contributed to the final manuscript draft.
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Online Resource 1. Throughput sequencing data of the Asclepias used in the study.
Online Resource 2. Maximum likelihood phylogeny obtained using concatenated chloroplast regions and support estimated by bootstraps (in percentages).
Online Resource 3. Monomer sequences of satellite DNA in Asclepias.
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Costa, G.C., Almeida, C. Identification of differential abundance of satellite DNA sequences in Asclepias (Apocynaceae): in-depth characterization of species-specific sequences. Plant Syst Evol 308, 41 (2022). https://doi.org/10.1007/s00606-022-01832-0
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DOI: https://doi.org/10.1007/s00606-022-01832-0