High-throughput sequencing analysis revealed the regulation patterns of small RNAs on the development of A. comosus var. bracteatus leaves

Xiong, Yingyuan; Ma, Jun; He, Yehua; Lin, Zhen Yuan; Li, Xia; Yu, Shuang; Li, Ruixue; Jiang, Fuxing; Li, Xi; Huang, Zhuo; Sun, Lina

doi:10.1038/s41598-018-20261-z

Cited by 11 publications

(7 citation statements)

References 51 publications

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“…tool id=lefse upload) [39,40]. To correlate lung and intestine microbiota, analysis was performed using PICRUSt, including COG and KEGG function analysis [41,42]. The comparison between the two groups was conducted using t-test.…”

Section: Discussionmentioning

confidence: 99%

Bacterial association and comparison between lung and intestine in rats

et al. 2020

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The association between lung and intestine has already been reported, but the differences in community structures or functions between lung and intestine bacteria yet need to explore. To explore the differences in community structures or functions, the lung tissues and fecal contents in rats were collected and analyzed through 16S rRNA sequencing. It was found that intestine bacteria was more abundant and diverse than lung bacteria. In intestine bacteria, Firmicutes and Bacteroides were identified as major phyla while Lactobacillus was among the most abundant genus. However, in lung the major identified phylum was Proteobacteria and genus Pseudomonas was most prominent genus. On the other hand, in contrast the lung bacteria was more concentrated in cytoskeleton and function in energy production and conversion. While, intestine bacteria were enriched in RNA processing, modification chromatin structure, dynamics and amino acid metabolism. The study provides the basis for understanding the relationships between lung and intestine bacteria.

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Section: Discussionmentioning

confidence: 99%

Bacterial association and comparison between lung and intestine in rats

et al. 2020

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“…bracteatus shoots have revealed that transcriptional differences play vital roles in the biosynthesis of photosynthetic pigments and in the development of chloroplasts, which might cause differences in photosynthesis and leaf color (Li et al., 2017). miRNAs involved in the development of CGr and CWh leaves have been identified and the regulatory functions of miRNAs in albino leaf cells examined (Xiong et al., 2018).…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptomic and proteomic analyses of the green and white parts of chimeric leaves in Ananas comosus var. bracteatus

Xue

et al. 2019

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Background Ananas comosus var. bracteatus has high ornamental value due to its chimeric leaves. However, the chimeric trait is very unstable in red pineapple plants, and transcriptional variation between the two types of cells (white/green cells) and the molecular mechanism responsible for their albino phenotype remain poorly understood. Methods Comparative transcriptomic and proteomic analyses of the white parts (Whs) and green parts (Grs) of chimeric leaves were performed. Results In total, 1,685 differentially expressed genes (DEGs) (712 upregulated and 973 downregulated) and 1,813 differentially abundant proteins (DAPs) (1,018 with low abundance and 795 with high abundance) were identified. Based on Gene Ontology (Go) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, the DEGs were mostly involved in carbon fixation in photosynthetic organisms, porphyrin and chlorophyll metabolism and oxidative phosphorylation, while proteomic analysis revealed that DAPs were mostly related to ribosomes, photosynthesis, photosynthesis antennas, and porphyrin and chlorophyll metabolism. Combined analysis showed increased mRNA levels but low abundance of nine proteins level in Whs /Grs related to photosynthetic pigment and photosynthesis. Transcriptional changes, posttranscriptional regulation and translational alterations of key enzymes involved in chlorophyll biosynthesis and photosynthesis may play important roles in the albino parts of chimeric leaves.

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“…bracteatus (Fig 1A) by tissue culture, in accordance with our previous protocol [28]. Three developmental stages were evaluated based on the number of expanded leaves on the shoots [30]. WS1 (Fig 1B) and GS1 (Fig 1C) were completely white and green shoots, respectively, with only unexpanded leaves; WS2 (Fig 1D) and GS2 (Fig 1E) were completely white and green shoots, respectively, with four to five expanded leaves; WS3 (Fig 1F) and GS3 (Fig 1G) were completely white and green shoots, respectively, with ten to twelve expanded leaves.…”

Section: Methodsmentioning

confidence: 99%

Screening and characterization of long noncoding RNAs involved in the albinism of Ananas comosus var. bracteatus leaves

et al. 2019

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Long noncoding RNAs (lncRNAs) have been reported to play key regulatory roles in plant growth, development, and biotic and abiotic stress physiology. Revealing the mechanism of lncRNA regulation in the albino portions of leaves is important for understanding the development of chimeric leaves in Ananas comosus var. bracteatus. In this study, a total of 3,543 candidate lncRNAs were identified, among which 1,451 were differentially expressed between completely green (CGr) and completely white (CWh) leaves. LncRNAs tend to have shorter transcripts, lower expression levels, and greater expression specificity than protein-coding genes. Predicted lncRNA targets were functionally annotated by the Gene Ontology (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. A lncRNA-mRNA interaction network was constructed, and 36 target mRNAs related to chlorophyll metabolism were predicted to interact with 86 lncRNAs. Among these, 25 significantly differentially expressed lncRNAs putatively interacted with 16 target mRNAs. Based on an expression pattern analysis of the lncRNAs and their target mRNAs, the lncRNAs targeting magnesium chelatase subunit H (ChlH), protochlorophyllide oxidoreductase (POR), and heme o synthase (COX10) were suggested as key regulators of chlorophyll metabolism. This study provides the first lncRNA database for A. comosus var. bracteatus and contributes greatly to understanding the mechanism of epigenetic regulation of leaf albinism.

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High-throughput sequencing analysis revealed the regulation patterns of small RNAs on the development of A. comosus var. bracteatus leaves

Cited by 11 publications

References 51 publications

Bacterial association and comparison between lung and intestine in rats

Bacterial association and comparison between lung and intestine in rats

Comparative transcriptomic and proteomic analyses of the green and white parts of chimeric leaves in Ananas comosus var. bracteatus

Screening and characterization of long noncoding RNAs involved in the albinism of Ananas comosus var. bracteatus leaves

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