Abstract
The economically and nutritionally important genus Citrus belongs to the subfamily Aurantioideae in the family Rutaceae. Here, we analyzed the phylogenetic relationships of the subfamily Aurantioideae based on RAD-Seq. The RAD-Seq data produced phylogenetic trees with high support values, clear discriminations based on branch length, and elucidations of early branching events. Our genetic classification corresponded well with the classical morphological classification system and supported the subdivision of Citreae, one of two tribes of the Aurantioideae, into three subtribes—Triphasiinae, Citrinae, and Balsamocitrinae. Additionally, it was largely consistent with the subdivision of Clauseneae, the other tribe of the Aurantioideae, into three subtribes—Micromelinae, Clauseninae, and Merrillinae; the exception was Murraya paniculata. With the exception of members of primitive citrus fruit trees, namely, Severinia buxifolia and Hesperethusa crenulata, lower-level morphological groupings under subtribes based on genetic and morphological classifications corresponded well. The phylogenetic relationship between Asian “true citrus fruit trees” (genera Citrus, Poncirus, and Fortunella) and Australian/New Guinean citrus fruit trees (genera Microcitrus, Eremocitrus, and Clymenia) was inconsistent between present classification based mainly on the nuclear genome and the previous classification based on the chloroplast genome. This inconsistency may be explained by chloroplast capture. Our findings provide a valuable insight into the genetic relationships of the subfamily Aurantioideae in the family Rutaceae.
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Acknowledgements
We thank Ms. Akiko Sakai for technical assistance. Part of this work was supported by a Grant-in-Aid for Scientific Research (26450039 to Y.N., 19405019 to M.Y) from the Japan Society for the Promotion of Science. The RAD-Seq analysis was supported by the Joint Usage/Research Program of the Center for Ecological Research, Kyoto University. We would like to thank Editage for English language editing.
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Y.N., N.K., R.M., and M.Y. designed the research; T.M., N.K., R.M., and M.Y. preserved the plants; T.M. extracted the DNA; A.N., M.H., and H.K. prepared the RAD-Seq library; Y.N. performed the bioinformatic analysis; Y.N., N.K., R.M., and M.Y. analyzed the results; Y.N. wrote the manuscript; and N.K., R.M., and M.Y. revised the manuscript; all authors approved the final version to be published.
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Communicated by W.-W. Guo
Data archiving statement
Sequences are available at the DDBJ Sequence Read Archive (http://trace.ddbj.nig.ac.jp/dra/index_e.shtml; Accession no. DRA005954). The Citrus species data were used in another study, and the accession number is DRA004200 (Penjor et al. 2016).
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Nagano, Y., Mimura, T., Kotoda, N. et al. Phylogenetic relationships of Aurantioideae (Rutaceae) based on RAD-Seq. Tree Genetics & Genomes 14, 6 (2018). https://doi.org/10.1007/s11295-017-1223-z
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DOI: https://doi.org/10.1007/s11295-017-1223-z