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Integrated analysis of mRNA-seq and miRNA-seq in calyx abscission zone of Korla fragrant pear involved in calyx persistence.

Abstract

BACKGROUND

The objective of this study was to characterize molecular mechanism of calyx persistence in Korla fragrant pear by transcriptome and small RNA sequencing. Abscission zone tissues of flowers at three stages (the first, fifth and ninth days of the late bloom stage), with 50 mg/L GA3 (calyx persistence treatment, C_1, C_5, C_9) or 500 mg/L PP333 (calyx abscission treatment, T_1, T_5, T_9), were collected and simultaneously conducted transcriptome and small RNA sequencing.

RESULTS

Through association analysis of transcriptome and small RNA sequencing, mRNA-miRNA network was conducted. Compared calyx persistence groups with calyx abscission groups during the same stage, 145, 56 and 150 mRNA-miRNA pairs were obtained in C_1 vs T_1, C_5 vs T_5 and C_9 vs T_9, respectively; When C_1 compared with C_5 and C_9, 90 and 506 mRNA-miRNA pairs were screened respectively, and 255 mRNA-miRNA pairs were obtained from the comparison between C_5 and C_9; When T_1 compared with the T_5 and T_9, respectively, 206 and 796 mRNA-miRNA pairs were obtained, and 383 mRNA-miRNA pairs were obtained from the comparison between T_5 and T_9. These mRNAs in miRNA-mRNA pairs were significantly enriched into the terpenoid backbone biosynthesis, photosynthesis - antenna proteins, porphyrin and chlorophyll metabolism, carotenoid biosynthesis, zeatin biosynthesis and plant hormone signal transduction. In addition, we obtained some key genes from miRNA-mRNA pairs that may be associated with calyx abscission, including protein phosphatase 2C (psi-miR394a-HAB1), receptor-like protein kinase (psi-miR396a-5p-HERK1), cellulose synthase-like protein D3 (psi-miR827-CSLD3), beta-galactosidase (psi-miR858b-β-galactosidase), SPL-psi-miR156j/157d, abscisic acid 8'-hydroxylase 1 (psi-miR396a-5p-CYP707A1) and auxin response factor (psi-miR160a-3p-ARF6, psi-miR167d-ARF18, psi-miR167a-5p-ARF25), etc. CONCLUSION: By integrated analysis mRNA and miRNA, our study gives a better understanding of the important genes and regulation pathway related to calyx abscission in Korla fragrant pear. We have also established the network of miRNA-mRNA pairs to learn about precise regulation of miRNA on calyx abscission.

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  • Authors+Show Affiliations

    ,

    Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, Xinjiang, China. Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003, Xinjiang, China.

    ,

    Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, Xinjiang, China. Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003, Xinjiang, China.

    ,

    Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, Xinjiang, China. Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003, Xinjiang, China.

    ,

    Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, Xinjiang, China. Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003, Xinjiang, China.

    ,

    Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, Xinjiang, China. Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003, Xinjiang, China.

    Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, Xinjiang, China. njx105@163.com. Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003, Xinjiang, China. njx105@163.com.

    Source

    BMC plant biology 19:1 2019 May 09 pg 192

    MeSH

    Conserved Sequence
    Flowers
    Gene Ontology
    Genes, Plant
    MicroRNAs
    Molecular Sequence Annotation
    Plant Proteins
    Pyrus
    RNA, Messenger
    Reproducibility of Results
    Sequence Analysis, RNA
    Transcriptome

    Pub Type(s)

    Journal Article

    Language

    eng

    PubMed ID

    31072362

    Citation

    Ma, Li, et al. "Integrated Analysis of mRNA-seq and miRNA-seq in Calyx Abscission Zone of Korla Fragrant Pear Involved in Calyx Persistence." BMC Plant Biology, vol. 19, no. 1, 2019, p. 192.
    Ma L, Zhou L, Quan S, et al. Integrated analysis of mRNA-seq and miRNA-seq in calyx abscission zone of Korla fragrant pear involved in calyx persistence. BMC Plant Biol. 2019;19(1):192.
    Ma, L., Zhou, L., Quan, S., Xu, H., Yang, J., & Niu, J. (2019). Integrated analysis of mRNA-seq and miRNA-seq in calyx abscission zone of Korla fragrant pear involved in calyx persistence. BMC Plant Biology, 19(1), p. 192. doi:10.1186/s12870-019-1792-0.
    Ma L, et al. Integrated Analysis of mRNA-seq and miRNA-seq in Calyx Abscission Zone of Korla Fragrant Pear Involved in Calyx Persistence. BMC Plant Biol. 2019 May 9;19(1):192. PubMed PMID: 31072362.
    * Article titles in AMA citation format should be in sentence-case
    TY - JOUR T1 - Integrated analysis of mRNA-seq and miRNA-seq in calyx abscission zone of Korla fragrant pear involved in calyx persistence. AU - Ma,Li, AU - Zhou,Li, AU - Quan,Shaowen, AU - Xu,Hang, AU - Yang,Jieping, AU - Niu,Jianxin, Y1 - 2019/05/09/ PY - 2018/09/07/received PY - 2019/04/22/accepted PY - 2019/5/11/entrez PY - 2019/5/11/pubmed PY - 2019/5/18/medline KW - Calyx abscission KW - Gene expression regulation KW - Korla fragrant pear KW - Transcriptome KW - miRNA SP - 192 EP - 192 JF - BMC plant biology JO - BMC Plant Biol. VL - 19 IS - 1 N2 - BACKGROUND: The objective of this study was to characterize molecular mechanism of calyx persistence in Korla fragrant pear by transcriptome and small RNA sequencing. Abscission zone tissues of flowers at three stages (the first, fifth and ninth days of the late bloom stage), with 50 mg/L GA3 (calyx persistence treatment, C_1, C_5, C_9) or 500 mg/L PP333 (calyx abscission treatment, T_1, T_5, T_9), were collected and simultaneously conducted transcriptome and small RNA sequencing. RESULTS: Through association analysis of transcriptome and small RNA sequencing, mRNA-miRNA network was conducted. Compared calyx persistence groups with calyx abscission groups during the same stage, 145, 56 and 150 mRNA-miRNA pairs were obtained in C_1 vs T_1, C_5 vs T_5 and C_9 vs T_9, respectively; When C_1 compared with C_5 and C_9, 90 and 506 mRNA-miRNA pairs were screened respectively, and 255 mRNA-miRNA pairs were obtained from the comparison between C_5 and C_9; When T_1 compared with the T_5 and T_9, respectively, 206 and 796 mRNA-miRNA pairs were obtained, and 383 mRNA-miRNA pairs were obtained from the comparison between T_5 and T_9. These mRNAs in miRNA-mRNA pairs were significantly enriched into the terpenoid backbone biosynthesis, photosynthesis - antenna proteins, porphyrin and chlorophyll metabolism, carotenoid biosynthesis, zeatin biosynthesis and plant hormone signal transduction. In addition, we obtained some key genes from miRNA-mRNA pairs that may be associated with calyx abscission, including protein phosphatase 2C (psi-miR394a-HAB1), receptor-like protein kinase (psi-miR396a-5p-HERK1), cellulose synthase-like protein D3 (psi-miR827-CSLD3), beta-galactosidase (psi-miR858b-β-galactosidase), SPL-psi-miR156j/157d, abscisic acid 8'-hydroxylase 1 (psi-miR396a-5p-CYP707A1) and auxin response factor (psi-miR160a-3p-ARF6, psi-miR167d-ARF18, psi-miR167a-5p-ARF25), etc. CONCLUSION: By integrated analysis mRNA and miRNA, our study gives a better understanding of the important genes and regulation pathway related to calyx abscission in Korla fragrant pear. We have also established the network of miRNA-mRNA pairs to learn about precise regulation of miRNA on calyx abscission. SN - 1471-2229 UR - https://www.unboundmedicine.com/medline/citation/31072362/Integrated_analysis_of_mRNA-seq_and_miRNA-seq_in_calyx_abscission_zone_of_Korla_fragrant_pear_involved_in_calyx_persistence L2 - https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-019-1792-0 DB - PRIME DP - Unbound Medicine ER -