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Comparative Analysis of Asteraceae Chloroplast Genomes: Structural Organization, RNA Editing and Evolution

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Abstract

Comparative chloroplast genome analysis presents new opportunities for performing molecular phylogeny studies and revealing the significant evolutionary features in higher plants, which has been widely documented from conifers to grass family. However, a systematic analysis of chloroplast genomes in Asteraceae family has not been conducted up to now. In this study, we compared and analyzed the gene content, genomic organization, and RNA editing sites of eight representative Asteraceae chloroplast genomes. Results showed that Asteraceae chloroplast had relatively conservative gene content. No gain or loss events occurred in the protein-coding genes, while some differences were found to be present in the gene structure and transfer RNA (tRNA) abundance. Genome structure analysis found some Asteraceae-specific or species-specific structure variations, and sequence rearrangement events were present in these genomes, suggesting specific evolutionary processes have occurred in this family. Some DNA regions containing parsimony-informative characters higher than 5 % were also identified, which could be used as the new molecular markers for phylogenetic analysis and plant identification of Asteraceae species. Furthermore, RNA editing in these genomes was investigated through computational analysis, and some species-specific sites were identified. Finally, phylogenetic analysis of 81 genes from 70 species supported the monophyly of the Asteraceae. Our study for the first time compared the organization, structure, and sequence divergence of eight Asteraceae chloroplast genomes, which will provide the valuable resource for molecular phylogeny of Asteraceae species and also facilitate the genetic and evolutionary studies in this family.

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Acknowledgments

This research was mainly funded by the National Basic Research Program of China (973 Program) (Grant No. 2009CB119200) and the National Natural Science Foundation of China (Grant No. 31471825) and partially supported by 948 Program (Grant No. 2010-S1), Ministry of Agriculture of China and the Open Project Program (Grant No. SKLOF201314), State Key Laboratory for Biology of Plant Diseases and Insect Pest.

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    Authors and Affiliations

    1. State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China

      Mengxing Wang, Licao Cui, Kewei Feng, Pingchuan Deng, Xianghong Du, Song Weining & Xiaojun Nie

    2. State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China

      Fanghao Wan

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    1. Mengxing Wang
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    2. Licao Cui
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    Correspondence to Song Weining or Xiaojun Nie.

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    Mengxing Wang and Licao Cui contributed equally to this work.

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    ESM 1

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    ESM_4

    Dot-plot comparison showing conserved and inverted regions found in two Chrysanthemum species, Ageratina, Guizotia, Helianthus, Jacobaea and Lactuca cp genomes (JPEG 941 kb)

    ESM_5

    Phylogenetic tree reconstruction of 70 taxa using maximum likelihood (ML) based on concatenated sequence from 81 cp genes. The position of the Asteraceae family is indicated by a red box (JPEG 1697 kb)

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    Wang, M., Cui, L., Feng, K. et al. Comparative Analysis of Asteraceae Chloroplast Genomes: Structural Organization, RNA Editing and Evolution. Plant Mol Biol Rep 33, 1526–1538 (2015). https://doi.org/10.1007/s11105-015-0853-2

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