Genome-wide identification and characterization of long non-coding RNAs conferring resistance to Colletotrichum gloeosporioides in walnut (Juglans regia)

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- 2 State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Tai ’ an 271018, Shandong Province, China.
- gloeosporioides in walnut overwinters in the diseased part with mycelium, and begins to move when the temperature reaches 11–.
- 15 °C in the following spring [11].
- Qin et al.
- A role for nine hub lncRNAs and 12 target genes in the resistance of Paulownia tomentosa to witches’broom was uncovered via a high-throughput sequencing experiment, and their func- tions were analyzed with an RNA-lncRNA co-expression network model [25].
- However, there are no reports regarding the role of lncRNAs in the walnut fruit resistance to anthracnose..
- Feng et al.
- Additionally and of the intergenic lncRNAs and genic lncRNAs were located in the antisense strand, respectively (Fig.
- Moreover, there was considerable diversity in the distribution of mRNA and lncRNA lengths (Fig.
- The number of upregulated and downregulated lncRNAs in the various comparisons were respectively as follows: 7668 and 1386 in the F26_0hpi vs F423_0hpi comparison.
- 6910 and 1165 in the F26_24hpi vs F423_.
- 1721 and 1593 in the F26_48hpi vs F423_48hpi comparison.
- 898 and 1133 in the F26_72 hpi vs F423_72 hpi comparison.
- and 4711 and 550 in the F26_120 hpi vs F423_120 hpi comparison (Fig.
- the number of upregulated and downregulated mRNAs in the various comparisons were respectively as follows: 6836 and 4622 in the F26_0 hpi vs F423_0 hpi comparison.
- 6392 and 3955 in the F26_24 hpi vs F423_24 hpi comparison.
- 3454 and 4347 in the F26_.
- 2709 and 3113 in the F26_72 hpi vs F423_72 hpi comparison.
- and 4976 and 3563 in the F26_120 hpi vs F423_120 hpi com- parison (Fig.
- These results revealed the similarities in the expres- sion of lncRNAs and mRNAs.
- Each step is described in detail in the Materials and Methods section.
- In the MEviolet module, a total of 208 GO terms were assigned, including 106, 8 and 94 GO terms in “bio- logical process”, “cellular component” and “molecular functions”, respectively (Additional file 9:Table_S9)..
- In the MElightyellow module, a total of 164 GO terms were assigned, including 79, 16 and 69 GO terms in.
- In the MEbrown2 module, a total of 126 GO terms were assigned, including 89, 5 and 32 GO terms in “bio- logical process”, “cellular component” and “molecular functions”, respectively (Additional file 9: Table_S9).
- In the MEwhite module, a total of 142 GO terms were assigned, including 95, 4 and 43 GO terms in “biological process”, “cellular component” and “molecular functions”, respectively (Additional file 9: Table_S9).
- In the MEorange module, a total of 128 GO terms were assigned, including 87, 8 and 33 GO terms in “biological process”, “cellular component” and “molecular functions”, respectively (Additional file 9: Table_S9).
- Each of the 10,645 lncRNAs is represented by a leaf in the tree, with each of the 19 modules presented as a major tree branch.
- In the MEviolet module, the 25 known target genes for 15 hub lncRNAs were found to be involved in multiple func- tions (Fig.
- In the MElightyellow module, 16 hub lncRNAs were generated and their 22 known target genes were involved in many functions (Fig.
- In the MEbrown2 module, 24 hub lncRNAs and their 15 known target genes were generated (Fig.
- In the MEwhite module, 23 hub lncRNAs were gener- ated and their 38 known target genes were involved in many functions (Fig.
- In the MEorange module, 18 hub lncRNAs were gen- erated and their 24 known target genes were involved in many functions (Fig.
- These results sug- gested that lncRNAs may participate in the resistance of.
- Most of the hub lncRNAs and its target genes in the five modules are enriched in the pathways of material metabolism and biosynthesis.
- In the white module, the function of hub lncRNA pathway map showed that cyclicnucleotide-gated channels and MPK4, the target genes of lncRNA MSTRG.94840.7,were upregu- lated at 72hpi, which were enriched in “plant pathogen in- teractions” pathway (Fig.
- In this study, we investigated the role of lncRNAs in the resist- ance of walnut fruit bracts to anthracnose based on se- quence analyses.
- The primary mycelium produced in plant cells exists as a biotroph, after which the secondary mycelium produced in the in- fected site switches to necrotrophic growth [39, 40].
- infestans are involved in the response to bi- otic stimulus (GO:0009607) and plant-pathogen.
- b MSTRG.103441.8 and the target gene LOC108979552 involved in the plant hormone signal transduction pathway enriched by KEGG analysis.
- In the current study, we obtained 10,645 upregu- lated lncRNAs and 15,247 upregulated mRNAs among the five comparisons (F26_0hpi vs F423_0hpi, F26_24 hpi vs F423_24 hpi, F26_48 hpi vs F423_48 hpi, F26_72 hpi vs F423_72 hpi, and F26_120 hpi vs F423_120 hpi)..
- The number of up-regulated lncRNAs and mRNAs in the F26 vs F423 was significantly higher at the early stages of C.
- “defense response to bacterium, incompatible inter- action ” in MEbrown2 module.
- “immune system process” in MEwhite module.
- These re- sults suggest that these genes may play important roles in the process of resistance to C.
- Phytohormones are known to be im- portant in the regulation of defense responses in plants [47 – 49].
- 32 genes were identified in the significantly enriched KEGG pathway “Plant hormone signal transduction”..
- Therefore, auxin may play a role in the resistance of wal- nut bracts to C.
- In addition, our result showed that the phenylpropanoid biosynthesis was one of the most significantly enriched pathways in the process of resistance to C.
- Lignin plays a structural role in the secondary cell walls formation [55], and flavonoids mediate plants against UV radiation and act as a visual signal for attracting pol- linators [56, 57].
- In the current study, we detected 10 R genes among the tar- get genes of 96 hub lncRNAs.
- gloeosporioides resistance and will facilitate the functional verification of the lncRNA in the future..
- Adapters and low-quality tags in the raw data were eliminated.
- The lncRNAs were analyzed regarding their correspond- ing positions in the reference genome and the positional relationships between lncRNAs and partner RNAs based on fragments.
- Additional file 3: Table S3.The expression level (reads counts) for each lncRNA genes detected in our study..
- The genes information of different modules in the WGCNA..
- Genes from the five modules in the F26..
- The funders had no role in the design of the study, collection, data analysis, data interpretation and manuscript writing..
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