Comparative transcriptome analysis uncovers the regulatory functions of long noncoding RNAs in fruit development and color changes of Fragaria pentaphylla

Bai, Lijun; Chen, Qing; Jiang, Long; Lin, Yuanxiu; Ye, Yuntian; Liu, Peng; Wang, Xiaorong; Tang, Haoru

doi:10.1038/s41438-019-0128-4

Cited by 35 publications

(23 citation statements)

References 91 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Of these, 63.29% were lincRNAs, which was similar to the proportion of lincRNAs in rice 48 . The lncRNAs were shorter than known mRNAs as previously reported in other plants 49 , also the average number of exons was less.…”

Section: Discussionsupporting

confidence: 71%

Integrated analysis of lncRNA and mRNA transcriptomes reveals the potential regulatory role of lncRNA in kiwifruit ripening and softening

Chen

Cheng

Feng

et al. 2021

Sci Rep

View full text Add to dashboard Cite

Kiwifruit has gained increasing attention worldwide for its unique flavor and high nutritional value. Rapid softening after harvest greatly shortens its shelf-life and reduces the commercial value. Therefore, it is imperative and urgent to identify and clarify its softening mechanism. This study aimed to analyze and compare the long noncoding RNA (lncRNA) and mRNA expression patterns in ABA-treated (ABA) and room temperature (RT)-stored fruits with those in freshly harvested fruits (CK) as control. A total of 697 differentially expressed genes (DEGs) and 81 differentially expressed lncRNAs (DELs) were identified while comparing ABA with CK, and 458 DEGs and 143 DELs were detected while comparing RT with CK. The Kyoto Encyclopedia of Genes and Genomes analysis of the identified DEGs and the target genes of DELs revealed that genes involved in starch and sucrose metabolism, brassinosteroid biosynthesis, plant hormone signal transduction, and flavonoid biosynthesis accounted for a large part. The co-localization networks, including 38 DEGs and 31 DELs in ABA vs. CK, and 25 DEGs and 25 DELs in RT vs. CK, were also performed. Genes related to fruit ripening, such as genes encoding β-galactosidase, mannan endo-1,4-β-mannosidase, pectinesterase/pectinesterase inhibitor, and NAC transcription factor, were present in the co-localization network, suggesting that lncRNAs were involved in regulating kiwifruit ripening. Notably, several ethylene biosynthesis- and signaling-related genes, including one 1-aminocyclopropane-1-carboxylic acid oxidase gene and three ethylene response factor genes, were found in the co-localization network of ABA vs. CK, suggesting that the promoting effect of ABA on ethylene biosynthesis and fruit softening might be embodied by increasing the expression of these lncRNAs. These results may help understand the regulatory mechanism of lncRNAs in ripening and ABA-induced fruit softening of kiwifruit.

show abstract

Section: Discussionsupporting

confidence: 71%

Integrated analysis of lncRNA and mRNA transcriptomes reveals the potential regulatory role of lncRNA in kiwifruit ripening and softening

Chen

Cheng

Feng

et al. 2021

Sci Rep

View full text Add to dashboard Cite

show abstract

“…In angiosperms, lncRNAs participate in fruit development and color change in strawberry [ 33 ], as well as aroma formation in black tea [ 34 ]. In gymnosperms, lncRNAs have an important role in the regulation of leaf development [ 27 ] and leaf color changes in G. biloba [ 25 ].…”

Section: Discussionmentioning

confidence: 99%

A full-length transcriptome and gene expression analysis reveal genes and molecular elements expressed during seed development in Gnetum luofuense

Deng¹,

Hou

et al. 2020

BMC Plant Biol

View full text Add to dashboard Cite

Background Gnetum is an economically important tropical and subtropical gymnosperm genus with various dietary, industrial and medicinal uses. Many carbohydrates, proteins and fibers accumulate during the ripening of Gnetum seeds. However, the molecular mechanisms related to this process remain unknown. Results We therefore assembled a full-length transcriptome from immature and mature G. luofuense seeds using PacBio sequencing reads. We identified a total of 5726 novel genes, 9061 alternative splicing events, 3551 lncRNAs, 2160 transcription factors, and we found that 8512 genes possessed at least one poly(A) site. In addition, gene expression comparisons of six transcriptomes generated by Illumina sequencing showed that 14,323 genes were differentially expressed from an immature stage to a mature stage with 7891 genes upregulated and 6432 genes downregulated. The expression of 14 differentially expressed transcription factors from the MADS-box, Aux/IAA and bHLH families was validated by qRT-PCR, suggesting that they may have important roles in seed ripening of G. luofuense. Conclusions These findings provide a valuable molecular resource for understanding seed development of gymnosperms.

show abstract

“…In addition, some lncRNAs interact with microRNAs (miRNAs), serving as miRNA precursors or competing endogenous RNAs (ceRNAs) to serve as decoys for specific miRNAs, thus protecting the target mRNAs from repression [29][30][31][32] . In recent years, several studies have indicated that lncRNAs play important roles in various biological processes in plants, including roles in organ development, nutrient metabolism, male sterility, and plant immunity [33][34][35][36][37] . In particular, lncRNAs are considered essential regulators of the response to biotic and abiotic stresses in plants 30,[38][39][40] .…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage

Song

et al. 2021

Hortic Res

View full text Add to dashboard Cite

Long noncoding RNAs (lncRNAs) are widely present in different species and play critical roles in response to abiotic stresses. However, the functions of lncRNAs in Chinese cabbage under heat stress remain unknown. Here, we first conducted a global comparative analysis of 247,242 lncRNAs among 37 species. The results indicated that lncRNAs were poorly conserved among different species, and only 960 lncRNAs were homologous to 524 miRNA precursors. We then carried out lncRNA sequencing for a genome-wide analysis of lncRNAs and their target genes in Chinese cabbage at different stages of heat treatment. In total, 18,253 lncRNAs were identified, of which 1229 differentially expressed (DE) lncRNAs were characterized as being heat-responsive. The ceRNA network revealed that 38 lncRNAs, 16 miRNAs, and 167 mRNAs were involved in the heat response in Chinese cabbage. Combined analysis of the cis- and trans-regulated genes indicated that the targets of DE lncRNAs were significantly enriched in the “protein processing in endoplasmic reticulum” and “plant hormone signal transduction” pathways. Furthermore, the majority of HSP and PYL genes involved in these two pathways exhibited similar expression patterns and responded to heat stress rapidly. Based on the networks of DE lncRNA-mRNAs, 29 and 22 lncRNAs were found to interact with HSP and PYL genes, respectively. Finally, the expression of several critical lncRNAs and their targets was verified by qRT-PCR. Overall, we conducted a comparative analysis of lncRNAs among 37 species and performed a comprehensive analysis of lncRNAs in Chinese cabbage. Our findings expand the knowledge of lncRNAs involved in the heat stress response in Chinese cabbage, and the identified lncRNAs provide an abundance of resources for future comparative and functional studies.

show abstract

Comparative transcriptome analysis uncovers the regulatory functions of long noncoding RNAs in fruit development and color changes of Fragaria pentaphylla

Cited by 35 publications

References 91 publications

Integrated analysis of lncRNA and mRNA transcriptomes reveals the potential regulatory role of lncRNA in kiwifruit ripening and softening

Integrated analysis of lncRNA and mRNA transcriptomes reveals the potential regulatory role of lncRNA in kiwifruit ripening and softening

A full-length transcriptome and gene expression analysis reveal genes and molecular elements expressed during seed development in Gnetum luofuense

Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage

Contact Info

Product

Resources

About