Dataset Information

Genome-Wide Identification and Analysis of MicroRNAs Involved in Witches'-Broom Phytoplasma Response in Ziziphus jujuba.

ABSTRACT: MicroRNAs (miRNAs) play an important role in responding to biotic and abiotic stresses in plants. Jujube witches'-broom a phytoplasma disease of Ziziphus jujuba is prevalent in China and is a serious problem to the industry. However, the molecular mechanism of the disease is poorly understood. In this study, genome-wide identification and analysis of microRNAs in response to witches'-broom was performed. A total of 85 conserved miRNA unique sequences belonging to 32 miRNA families and 24 novel miRNA unique sequences, including their complementary miRNA* strands were identified from small RNA libraries derived from a uninfected and witches'-broom infected Z. jujuba plant. Differentially expressed miRNAs associated with Jujube witches'-broom disease were investigated between the two libraries, and 12 up-regulated miRNAs and 10 down- regulated miRNAs identified with more than 2 fold changes. Additionally, 40 target genes of 85 conserved miRNAs and 49 target genes of 24 novel miRNAs were predicted and their putative functions assigned. Using the modified 5'-RACE method, we confirmed that SPL and MYB were cleaved by miR156 and miR159, respectively. Our results provide insight into the molecular mechanisms of witches'-broom disease in Z. jujuba.

SUBMITTER: Shao F

PROVIDER: S-EPMC5100886 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Publications

Genome-Wide Identification and Analysis of MicroRNAs Involved in Witches'-Broom Phytoplasma Response in Ziziphus jujuba.

Shao Fenjuan F Zhang Qian Q Liu Hongwei H Lu Shanfa S Qiu Deyou D

PloS one 20161108 11

MicroRNAs (miRNAs) play an important role in responding to biotic and abiotic stresses in plants. Jujube witches'-broom a phytoplasma disease of Ziziphus jujuba is prevalent in China and is a serious problem to the industry. However, the molecular mechanism of the disease is poorly understood. In this study, genome-wide identification and analysis of microRNAs in response to witches'-broom was performed. A total of 85 conserved miRNA unique sequences belonging to 32 miRNA families and 24 novel m ...[more]

PMID: 27824938

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Project description:BACKGROUND:Mitogen-activated protein kinase (MAPK) cascades play vital roles in signal transduction in response to a wide range of biotic and abiotic stresses. In a previous study, we identified ten ZjMAPKs and five ZjMAPKKs in the Chinese jujube genome. We found that some members of ZjMAPKs and ZjMAPKKs may play key roles in the plant's response to phytoplasma infection. However, how these ZjMAPKKs are modulated by ZjMAPKKKs during the response process has not been elucidated. Little information is available regarding MAPKKKs in Chinese jujube. RESULTS:A total of 56 ZjMAPKKKs were identified in the jujube genome. All of these kinases contain the key S-TKc (serine/threonine protein kinase) domain, which is distributed among all 12 chromosomes. Phylogenetic analyses show that these ZjMAPKKKs can be classified into two subfamilies. Specifically, 41 ZjMAPKKKs belong to the Raf subfamily, and 15 belong to the MEKK subfamily. In addition, the ZjMAPKKKs in each subfamily share the same conserved motifs and gene structures. Only one pair of ZjMAPKKKs (15/16, on chromosome 5) was found to be tandemly duplicated. Using qPCR, the expression profiles of these MAPKKKs were investigated in response to infection with phytoplasma. In the three main infected tissues (witches' broom leaves, phyllody leaves, and apparently normal leaves), ZjMAPKKK26 and - 45 were significantly upregulated, and ZjMAPKKK3, - 43 and - 50 were significantly downregulated. ZjMAPKKK4, - 10, - 25 and - 44 were significantly and highly induced in sterile cultivated tissues infected by phytoplasma, while ZjMAPKKK6, - 7, - 17, - 18, - 30, - 34, - 35, - 37, - 40, - 41, - 43, - 46, - 52 and - 53 were significantly downregulated. CONCLUSIONS:For the first time, we present an identification and classification analysis of ZjMAPKKKs. Some ZjMAPKKK genes may play key roles in the response to phytoplasma infection. This study provides an initial understanding of the mechanisms through which ZjMAPKKKs are involved in the response of Chinese jujube to phytoplasma infection.

Dataset Information

Genome-Wide Identification and Analysis of MicroRNAs Involved in Witches'-Broom Phytoplasma Response in Ziziphus jujuba.

Publications

Genome-Wide Identification and Analysis of MicroRNAs Involved in Witches'-Broom Phytoplasma Response in Ziziphus jujuba.

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