Genome-wide identification and characterization of long non-coding RNAs responsive to<i>Dickeya zeae</i>in rice

Li, Wen Qi; Yu, Jie; Liu, Feng Quan; Wang, Fang Quan; Fan, Fang Jun; Wang, Jun; Zhu, Jin; Xu, Yongsheng; Wei, Zhong; Yang, Jie

doi:10.1039/c8ra04993a

Cited by 24 publications

(21 citation statements)

References 35 publications

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“…Among that number, experimental data of the possible functions were available for 14 genes ( Table S10 ). The largest group of genes was involved in response to biotic stresses, including fungi ( Os01g0701700 , MR = 41.952 [ 167 ], Os04g0637000 , MR = 15.1, [ 168 ], Os01g0117200 , MR = 57.35, [ 169 ]; Os05g0409500 , MR = 64.312 [ 170 ]; Os03g0798200 , MR = 90.111, [ 171 ]), bacteria ( Os05g0365300 , MR = 89.778, [ 172 ], Os04g0637000 [ 173 ]) and insects ( Os04g0637000 [ 168 ]) ( Table S3 , Table S10 ). A wide range of abiotic stresses was represented in CGN of Os02g0221900 , including response to cold ( Os01g0701700 [ 127 ]; Os05g0409500 [ 128 ]), drought ( Os05g0557700 [ 174 ], Os05g0409500 , [ 57 ]), phosphorus status ( Os03g0348200 , MR = 50.279, [ 175 ]; Os04g0650700, MR = 20, [ 175 ]; Os05g0557700 [ 176 , 177 ]; Os03g0647600 , MR = 74.162 [ 178 ], Os01g0882800 , MR = 98.122 [ 64 ]), nitrogen status ( Os01g0870300 , MR = 90.427, [ 179 ]; Os01g0882800 [ 180 ]) and silicone ( Os05g0409500 , [ 157 ]) ( Table 3 , Table S10 ).…”

Section: Resultsmentioning

confidence: 99%

Diverse Roles of MAX1 Homologues in Rice

Marzec

Situmorang

Brewer

et al. 2020

Genes

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Cytochrome P450 enzymes encoded by MORE AXILLARY GROWTH1 (MAX1)-like genes produce most of the structural diversity of strigolactones during the final steps of strigolactone biosynthesis. The diverse copies of MAX1 in Oryza sativa provide a resource to investigate why plants produce such a wide range of strigolactones. Here we performed in silico analyses of transcription factors and microRNAs that may regulate each rice MAX1, and compared the results with available data about MAX1 expression profiles and genes co-expressed with MAX1 genes. Data suggest that distinct mechanisms regulate the expression of each MAX1. Moreover, there may be novel functions for MAX1 homologues, such as the regulation of flower development or responses to heavy metals. In addition, individual MAX1s could be involved in specific functions, such as the regulation of seed development or wax synthesis in rice. Our analysis reveals potential new avenues of strigolactone research that may otherwise not be obvious.

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Section: Resultsmentioning

confidence: 99%

Diverse Roles of MAX1 Homologues in Rice

Marzec

Situmorang

Brewer

et al. 2020

Genes

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“…One of the most effective methods to control the disease in rice is the use of resistant varieties (Sect. 6.6;Li et al 2018a). A recent study recognized two clades within D. zeae strains (Pédron and Van Gijsegem 2019), one of which has been renamed D. oryzae following reanalysis of rice strains (Wang et al 2020).…”

Section: Other Cropsmentioning

confidence: 99%

Pectobacterium and Dickeya: Environment to Disease Development

Toth

Barny

Brurberg

et al. 2021

Plant Diseases Caused by Dickeya and Pectobacterium Species

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Article 25fa states that the author of a short scientific work funded either wholly or partially by Dutch public funds is entitled to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work.This publication is distributed under The Association of Universities in the Netherlands (VSNU) 'Article 25fa implementation' project. In this project research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication.

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“…Further investigations on lncRNAs have supported their roles in a variety of key biological processes of plants similar to mammalian lncRNAs. In recent years, numerous lncRNAs responsive to biotic and abiotic stresses have been identified in many plant species [27,31,32,33,34]. For instance, a large number of lncRNAs responsive to nitrogen stresses, phosphate deficiency, osmotic and salt stress, cold stress, and drought stress etc., were mined in many plants via high-throughput sequencing technology [1,26,32,35,36], while many lncRNAs might be related to plant defense against fungi, bacteria, and virus pathogens [31,37,38,39,40,41].…”

Section: Introductionmentioning

confidence: 99%

Identification of Long Non-Coding RNAs and the Regulatory Network Responsive to Arbuscular Mycorrhizal Fungi Colonization in Maize Roots

Han

Cheng

Zheng

et al. 2019

IJMS

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Recently, long noncoding RNAs (lncRNAs) have emerged as vital regulators of many biological processes in animals and plants. However, to our knowledge no investigations on plant lncRNAs which respond to arbuscular mycorrhizal (AM) fungi have been reported thus far. In this study, maize roots colonized with AM fungus were analyzed by strand-specific RNA-Seq to identify AM fungi-responsive lncRNAs and construct an associated regulatory network. A total of 1837 differentially expressed protein coding genes (DEGs) were identified from maize roots with Rhizophagus irregularis inoculation. Many AM fungi-responsive genes were homologs to MtPt4, STR, STR2, MtFatM, and enriched pathways such as fatty acid biosynthesis, response to phosphate starvation, and nitrogen metabolism are consistent with previous studies. In total, 5941 lncRNAs were identified, of which more than 3000 were new. Of those, 63 lncRNAs were differentially expressed. The putative target genes of differentially expressed lncRNAs (DELs) were mainly related to phosphate ion transmembrane transport, cellular response to potassium ion starvation, and lipid catabolic processes. Regulatory network analysis showed that DELs might be involved in the regulation of bidirectional nutrient exchange between plant and AM fungi as mimicry of microRNA targets. The results of this study can broaden our knowledge on the interaction between plant and AM fungi.

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Genome-wide identification and characterization of long non-coding RNAs responsive toDickeya zeaein rice

Abstract: Plant long non-coding RNA (lncRNA) is a type of newly emerging epigenetic regulator playing a critical role in plant growth, development, and biotic stress responses.

Cited by 24 publications

References 35 publications

Diverse Roles of MAX1 Homologues in Rice

Diverse Roles of MAX1 Homologues in Rice

Pectobacterium and Dickeya: Environment to Disease Development

Identification of Long Non-Coding RNAs and the Regulatory Network Responsive to Arbuscular Mycorrhizal Fungi Colonization in Maize Roots

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