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The evolution and utility of ribosomal ITS sequences in Bambusinae and related species: divergence, pseudogenes, and implications for phylogeny

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Abstract

Ribosomal internal transcribed spacer (ITS) sequences are commonly used for phylogenetic reconstruction because they are highly reiterated as components of rDNA repeats, and hence are often subject to rapid homogenization through concerted evolution. Concerted evolution leads to intragenomic uniformity of repeats even between loci on nonhomologous chromosomes. However, a number of studies have shown that the ITS polymorphism within individuals is quite common. The molecular systematics of Bambusinae and related species were recently assessed by different teams using independently generated ITS sequences, and the results disagreed in some remarkable features. Here we compared the ITS sequences of the members of Bambusa s. l., the genera Dendrocalamus, Dinochloa, Gigantochloa, Guadua, Melocalamus, Monocladus, Oxytenanthera, Thyrsostachys, Pleioblastus, Pseudosasa and Schizostachyum. We have reanalysed the ITS sequences used by different research teams to reveal the underlying patterns of their different results. After excluding the sequences suspected to represent paralogous loci, a phylogenetic analysis of the subtribe Bambusinae species were performed using maximum parsimony and maximum-likelihood methods. The implications of the findings are discussed. The risk of incorporating ITS paralogues in plant evolutionary studies that can distort the phylogenetic signal should caution molecular systematists.

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Acknowledgements

This work was funded by the Agricultural Science and Technology Achievements Transformation Funds Project of the Ministry of Science and Technology of China (2010GB24320621) and Key Technology Research and Development Program of Sichuan Province (no. 10ZC1136). Hui-Xing Song was supported by Foundation of Sichuan Educational Committee (no. 11ZA083). We wish to thank two anonymous reviewers for helpful comments that improved the manuscript. This paper benefited from the careful review of Bernard R. Baum, Agriculture and Agri-Food Canada, Ottawa.

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  1. School of Landscape Architecture, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People’s Republic of China

    HUI-XING SONG, SU-PING GAO, MING-YAN JIANG, GUANG-LI LIU, XIAO-FANG YU & QI-BING CHEN

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  1. HUI-XING SONG
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  2. SU-PING GAO
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Correspondence to QI-BING CHEN.

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[Song H.-X., Gao S.-P., Jiang M.-Y., Liu G.-L., Yu X.-F. and Chen Q.-B. 2012 The evolution and utility of ribosomal ITS sequences in Bambusinae and related species: divergence, pseudogenes, and implications for phylogeny. J. Genet. 91, xx–xx]

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SONG, HX., GAO, SP., JIANG, MY. et al. The evolution and utility of ribosomal ITS sequences in Bambusinae and related species: divergence, pseudogenes, and implications for phylogeny. J Genet 91, 129–139 (2012). https://doi.org/10.1007/s12041-012-0170-6

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