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Identification of transposons near predicted lncRNA and mRNA pools of Prunus mume using an integrative transposable element database constructed from Rosaceae plant genomes

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Abstract

This study focused on the construction of a database of transposable elements (TEs) from Rosaceae plants, the third most economically important plant family in temperate regions, and its transcriptomics applications. The evolutionary effects of TEs on gene regulation have been explored, and TE insertions can be the molecular bases of changes in gene structure and function. However, a specific Rosaceae plant TE database (RPTEdb) is lacking. The genomes of several Rosaceae plants have been sequenced, providing the opportunity to mine TE data at a whole-genome level. Therefore, we constructed the RPTEdb, a collective and comprehensive database of 19,596 annotated TEs in the genomes of Rosaceae plants using previously described identification and annotation methods and published genome sequences. The user-friendly web-based database provides access to research tools through hyperlinks, including Browse, TE tree, tools, JBrowse, and search sections, and through the inputting of sequences on the main webpage. Next, we performed one advanced application in which TEs near predicted long non-coding RNA (lncRNA) and mRNA domains within white and red petal-tissue transcriptomes of Prunus mume ‘Fuban Tiaozhi’ were identified, revealing 16 TEs that overlapped or were near 16 differentially expressed lncRNA domains, and 54 TEs that overlapped or were near 54 differentially expressed mRNA domains, and the TEs’ possible functions were also discussed. We believe that the RPTEdb will contribute to the understanding of TE roles in the structural, functional and evolutionary dynamics of Rosaceae plant genomes.

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Abbreviations

TE:

Transposable element

lncRNA:

Long non-coding RNA

mRNA:

Messenger RNA

LTR:

Long terminal repeat

MITE:

Miniature inverted repeat transposable element

RPTEdb:

Rosaceae plant transposable elements database

HMM:

Hidden Markov model

WT:

White petal tissues

RT:

Red petal tissues

FPKM:

Fragments per kilobase of transcript per million fragments

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Acknowledgements

This study was funded by the National Natural Science Foundation of China (No. 31501787), the Fundamental Research Funds for the Central Universities (No. 2016ZCQ02), and the Special Fund for Beijing Common Construction Project.

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Authors and Affiliations

  1. Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China

    Kaifeng Ma, Qixiang Zhang, Tangren Cheng & Jia Wang

  2. Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China

    Qixiang Zhang

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  1. Kaifeng Ma
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  2. Qixiang Zhang
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Correspondence to Qixiang Zhang.

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Ma, K., Zhang, Q., Cheng, T. et al. Identification of transposons near predicted lncRNA and mRNA pools of Prunus mume using an integrative transposable element database constructed from Rosaceae plant genomes. Mol Genet Genomics 293, 1301–1316 (2018). https://doi.org/10.1007/s00438-018-1449-y

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