Abstract
Twenty-nine DNA regions of plastid origin have been previously identified in the mitochondrial genome of Cucurbita pepo (pumpkin; Cucurbitaceae). Four of these regions harbor homolog sequences of rbcL, matK, rpl20–rps12 and trnL–trnF, which are widely used as molecular markers for phylogenetic and phylogeographic studies. We extracted the mitochondrial copies of these regions based on the mitochondrial genome of C. pepo and, along with published sequences for these plastome markers from 13 Cucurbita taxa, we performed phylogenetic molecular analyses to identify inter-organellar transfer events in the Cucurbita phylogeny and changes in their nucleotide substitution rates. Phylogenetic reconstruction and tree selection tests suggest that rpl20 and rbcL mitochondrial paralogs arose before Cucurbita diversification whereas the mitochondrial matK and trnL–trnF paralogs emerged most probably later, in the mesophytic Cucurbita clade. Nucleotide substitution rates increased one order of magnitude in all the mitochondrial paralogs compared to their original plastid sequences. Additionally, mitochondrial trnL–trnF sequences obtained by PCR from nine Cucurbita taxa revealed higher nucleotide diversity in the mitochondrial than in the plastid copies, likely related to the higher nucleotide substitution rates in the mitochondrial region and loss of functional constraints in its tRNA genes.
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Acknowledgements
This manuscript includes in part the results of the Bachelor’s degree thesis of FTA, LMPT, PH, and KYRM, and postdoctoral work of XAD at Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México. We are grateful to D. Piñero and V. Souza for supporting the project, and Laura Espinosa-Asuar for her help in laboratory work. Funds were provided by Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (Conabio) Project KE004 “Diversidad genética de las especies de Cucurbita en México e hibridación entre plantas genéticamente modificadas y especies silvestres de Cucurbita” and Project Conabio PE001 “Diversidad genética de las especies de Cucurbita en México. Fase II. Genómica evolutiva y de poblaciones, recursos genéticos y domesticación”, as well as Consejo Nacional de Ciencia y Tecnología (CONACyT) Problemas Nacionales grant number 247730 to Daniel Piñero (Instituto de Ecología, UNAM). XAD had a fellowship from Programa de Becas Posdoctorales de la Dirección General de Asuntos del Personal Académico (DGAPA), Universidad Nacional Autónoma de México.
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Aguirre-Dugua, X., Castellanos-Morales, G., Paredes-Torres, L.M. et al. Evolutionary Dynamics of Transferred Sequences Between Organellar Genomes in Cucurbita. J Mol Evol 87, 327–342 (2019). https://doi.org/10.1007/s00239-019-09916-1
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DOI: https://doi.org/10.1007/s00239-019-09916-1