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Evolutionary and Functional Analysis of LEAFY COTYLEDON1 in Isoetes L. from China

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Abstract

LEAFY COTYLEDON1 (LEC1) is a HAP3 subunit of CCAAT-binding transcription factor. The species in the genus Isoetes L. from China include I. hypsophila, I. yunguiensis, I. sinensis, I. orientalis, and I. taiwenensis. In this study, we initially gathered substantial samples from wide geographic ranges in China. Then we explored the evolutionary characteristics and expression profiles of LEC1 in Isoetes from China. We amplified 57 unique LEC1 nucleotide sequences from 94 individuals. The value of nucleotide diversity was 0.01693 for all samples, and neutrality tests indicated that LEC1 is under purifying negative selection in the evolutionary process. AMOVA analysis revealed that the genetic variation occurred mainly among populations within species. Moreover, the non-synonymous to synonymous substitution rates for 41 unique LEC1 protein sequences further demonstrated the presence of negative selection acting on the species from China to fix amino acid residues. Phylogenetic analyses of nucleotide and protein sequences showed consistently that the trees consisted of two well-supported main clades, and that the haplotypes from H42 to H57 in I. hypsophila were exclusive. In addition, expression profile analysis revealed that LEC1 transcripts accumulated primarily in reproductive organs. Looking at drought tolerance, LEC1 transcripts increased markedly at 24 h after drought treatment and reached a peak at 48 h. RNA accumulation reoccurred at relatively low levels and was slightly elevated at 48 h after rehydration. Altogether, our analyses provide insight into the evolutionary process of LEC1, and our results might promote further studies of functional genes in Isoetes.

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Acknowledgments

The authors would like to thank Junneng Wang for presenting the samples from Taiwan and Guangqian Ge for the samples from Nayong, Guizhou. The research was supported by “National Natural Science Foundation of China” (30870168 and 31170203) and “the Fundamental Research Funds for the Central Universities” (2014204020206).

Contributions

T.Y. cultured the plant tissue and isolated RNA, performed the experiments, analyzed the data, and drafted the manuscript. W.Z., M.D. and F.T. performed the experiments and analyzed the data. X.D. analyzed partial data. X.L. and Y.G. revised the manuscript. All authors reviewed the final manuscript.

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Authors and Affiliations

  1. Laboratory of Plant Systematics and Evolutionary Biology, College of Life Science, Wuhan University, Wuhan, Hubei, China

    Tao Yang, Wei-wei Zan, Ming-fang Du, Feng-qing Tian, Xiao-kang Dai, You-hao Guo & Xing Liu

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  1. Tao Yang
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  2. Wei-wei Zan
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Corresponding authors

Correspondence to You-hao Guo or Xing Liu.

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Fig. S1

Median joining network for all 57 haplotypes. The pie charts are proportional in size to the contained haplotypes and the colors in the pie charts are according to species. (GIF 186 kb)

High resolution image (TIF 238 kb)

Fig. S2

Alignment of 41 LEC1 amino acid sequences obtained in this study. (GIF 307 kb)

High resolution image (TIF 448 kb)

Fig. S3

Three-dimensional structures of LEC1 proteins for a I. hypsophila, b I. yunguiensis, c I. sinensis, d I. orientalis, and e I. taiwanensis. (GIF 178 kb)

High resolution image (TIF 176 kb)

Table S1

Accession numbers for all obtained LEC1 sequences in this study (DOCX 20 kb)

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Yang, T., Zan, Ww., Du, Mf. et al. Evolutionary and Functional Analysis of LEAFY COTYLEDON1 in Isoetes L. from China. Plant Mol Biol Rep 35, 154–165 (2017). https://doi.org/10.1007/s11105-016-1009-8

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