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Evolution of the Chloroplast trnL-trnF Region in the Gymnosperm Lineages Taxaceae and Cephalotaxaceae

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Abstract

The trnL-trnF region is located in the large single-copy region of the chloroplast genome. It consists of the trnL gene, a group I intron, and the trnL-F intergenic spacer. We analyzed the evolution of the region in three gymnosperm families, Taxaceae, Cephalotaxaceae, and Podocarpaceae, with especially dense sampling in Taxaceae and Cephalotaxaceae, for which we sequenced 43 accessions, representing all species. The trnL intron has a conserved secondary structure and contains elements that are homologous across land plants, and the spacer is highly variable in length and composition. The spatial distribution of nucleotide diversity along the trnL-F region suggests that different portions of this region have different evolutionary patterns. Tandem repeats that form stem–loop structures were detected in both the trnL intron and the trnL-F spacer, and the spacer sequences contain promoter elements for the trnF gene. The presence of promoters and stem–loop structures in the trnL-F spacer and high sequence variation in this region suggest that trnL and trnF are independently transcribed. Stem–loop regions P6, P8, and P9 of the trnL intron and the trnL-F spacer (except the promoter elements) might undergo neutral evolution with respect to their escape from functional constraints.

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Acknowledgments

We thank the following experts for providing plant materials: Yunfen Geng (Yunnan Academy of Forestry, Kunming, China), Qing Wang (Wuhan Botanical Garden, Chinese Academy of Sciences, China), Yinke Zhang (Hangzhou Botanical Garden, Zhejiang, China), Li Xu (Chinese Academy of Tropical Agriculture, Danzhou, Hainan, China), Yan Liu (Guangxi Institute of Botany, Guilin, China), Didier Maerki (Arboretum de Villardebelle, France), Christopher Quinn (Royal Botanic Garden, Sydney, Australia), Ron Determann (Atlanta Botanical Garden, USA), Robert G. Nicolson (Smith College, USA), Duang Buddhasukh (Chiang Mai University, Thailand), Richard W. Spjut (World Botanical Associates, California, USA), Stephane Bailleul (Montreal Botanical Garden, Canada), Bob Ursem (Botanic Garden, Delft University of Technology, The Netherlands), and James Stevenson (University of Oxford Botanic Garden, UK). This study was supported by the Start-up doctoral fund of Dalian Jiaotong University.

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Authors and Affiliations

  1. Laboratory of Biotechnology, Dalian Jiaotong University, Dalian, 116028, People’s Republic of China

    Da Cheng Hao & Jun Mu

  2. Lushan Botanical Garden, Chinese Academy of Sciences, Jiangxi, 332900, People’s Republic of China

    Bei Li Huang

  3. Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China

    Shi Lin Chen

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  1. Da Cheng Hao
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  2. Bei Li Huang
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  4. Jun Mu
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Correspondence to Jun Mu.

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Fig. S1

Variation of length and secondary structure of the stem-loop region P8 of the trnL intron (648 KB).

Fig. S2

Examples of stem-loop structures observed upstream of trnF GAA, including elements of the putative sigma70-type promoter found in the trnL-F spacer (italicized). Transcription start sites are shown in boldface and larger font (2.69 MB).

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Hao, D.C., Huang, B.L., Chen, S.L. et al. Evolution of the Chloroplast trnL-trnF Region in the Gymnosperm Lineages Taxaceae and Cephalotaxaceae. Biochem Genet 47, 351–369 (2009). https://doi.org/10.1007/s10528-009-9233-7

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