Genome-wide identification and characterization of long non-coding RNAs involved in fruit ripening and the climacteric in Cucumis melo

lncRNA1471 mediates tomato-ripening initiation by binding to the ASR transcription factor

The regulatory mechanisms underlying fruit ripening, including hormone regulation, transcription factor activity, and epigenetic modifications, have been discussed extensively. Nonetheless, the role of long non-coding RNAs (lncRNAs) in fruit ripening remains unclear. Here, we identified lncRNA1471 as a negative regulator of tomato fruit-ripening initiation. Knocking out lncRNA1471 via large fragment deletion resulted in accelerated initiation of fruit ripening, a shorter color-breaking stage (BR), deeper coloration, increased levels of ethylene, lycopene, and β-carotene, accelerated chlorophyll degradation, and reduced fruit firmness. These phenotypic changes were accompanied by alterations in the carotenoid pathway flux, ethylene biosynthesis, and cell wall metabolism, primarily mediated by the direct regulation of key genes involved in these processes. For example, in the CR-lncRNA1471 mutant, lycopene-related SlPSY1 and SlZISO were upregulated. Additionally, the expression levels of ethylene biosynthetic genes (SlACS2 and SlACS4), ripening-related genes (RIN, NOR, CNR, and SlDML2), and cell wall metabolism genes (SlPL, SlPG2a, SlEXP1, SlPMEI-like, and SlBG4) were significantly upregulated, which further strengthening the findings mentioned above. Furthermore, lncRNA1471 was identified to interact with the abscisic stress-ripening protein (ASR) transcription factor by chromatin isolation by RNA purification coupled with mass spectrometry (ChIRP-MS) and protein pull-down assay in vitro, which might regulate key genes involved in tomato ripening. The discovery of the significant non-coding regulator lncRNA1471 enhances our understanding of the complex regulatory landscape governing fruit ripening. These findings provide valuable insights into the mechanisms underlying ripening, particularly regarding the involvement of lncRNAs in ripening.

Genome-Wide Identification and Expression Analysis of the Melon Aldehyde Dehydrogenase (ALDH) Gene Family in Response to Abiotic and Biotic Stresses

Through the integration of genomic information, transcriptome sequencing data, and bioinformatics methods, we conducted a comprehensive identification of the ALDH gene family in melon. We explored the impact of this gene family on melon growth, development, and their expression patterns in various tissues and under different stress conditions. Our study discovered a total of 17 ALDH genes spread across chromosomes 1, 2, 3, 4, 5, 7, 8, 11, and 12 in the melon genome. Through a phylogenetic analysis, these genes were classified into 10 distinct subfamilies. Notably, genes within the same subfamily exhibited consistent gene structures and conserved motifs. Our study discovered a pair of fragmental duplications within the melon ALDH gene. Furthermore, there was a noticeable collinearity relationship between the melon's ALDH gene and that of Arabidopsis (12 times), and rice (3 times). Transcriptome data reanalysis revealed that some ALDH genes consistently expressed highly across all tissues and developmental stages, while others were tissue- or stage-specific. We analyzed the ALDH gene's expression patterns under six stress types, namely salt, cold, waterlogged, powdery mildew, Fusarium wilt, and gummy stem blight. The results showed differential expression of CmALDH2C4 and CmALDH11A3 under all stress conditions, signifying their crucial roles in melon growth and stress response. RT-qPCR (quantitative reverse transcription PCR) analysis further corroborated these findings. This study paves the way for future genetic improvements in melon molecular breeding.

Characterization of FchAGL9 and FchSHP, two MADS-boxes related to softening of Fragaria chiloensis fruit

Fragaria chiloensis is a Chilean native species that softens intensively during its ripening. Its softening is related to cell wall disassembly due to the participation of cell wall degrading enzymes. Softening of F. chiloensis fruit can be accelerated by ABA treatment which is accompanied by the increment in the expression of key cell wall degrading genes, however the molecular machinery involved in the transcriptional regulation has not been studied until now. Therefore, the participation of two MADS-box transcription factors belonging to different subfamilies, FchAGL9 and FchSHP, was addressed. Both TFs are members of type-II MADS-box family (MIKC-type) and localized in the nucleus. FchAGL9 and FchSHP are expressed only in flower and fruit tissues, rising as the fruit softens with the highest expression level at C3-C4 stages. EMSA assays demonstrated that FchAGL9 binds to CArG sequences of RIN and SQM, meanwhile FchSHP interacts only with RIN. Bimolecular fluorescence complementation and yeast two-hybrid assays confirmed FchAGL9-FchAGL9 and FchAGL9-FchSHP interactions. Hetero-dimer structure was built through homology modeling concluding that FchSHP monomer binds to DNA. Functional validation by Luciferase-dual assays indicated that FchAGL9 transactivates FchRGL and FchPG's promoters, meanwhile FchSHP transactivates those of FchEXP2, FchRGL and FchPG. Over-expression of FchAGL9 in C2 F. chiloensis fruit rises FchEXP2 and FchEXP5 transcripts, meanwhile the over-expression of FchSHP also increments FchXTH1 and FchPL; in both cases there is a down-regulation of FchRGL and FchPG. In summary, we provided evidence of FchAGL9 and FchSHP participating in the transcription regulation associated to F. chiloensis's softening.

A multispecies study reveals the diversity and potential regulatory role of long noncoding RNAs in cucurbits

Plant long noncoding RNAs (lncRNAs) exhibit features such as tissue-specific expression, spatiotemporal regulation, and stress responsiveness. Although diverse studies support the regulatory role of lncRNAs in model plants, our knowledge about lncRNAs in crops is limited. We employ a custom pipeline on a dataset of over 1000 RNA-seq samples across nine representative species of the family Cucurbitaceae to predict 91 209 nonredundant lncRNAs. The lncRNAs were characterized according to three confidence levels and classified by their genomic context into intergenic, natural antisense, intronic, and sense-overlapping. Compared with protein-coding genes, lncRNAs were, on average, expressed at low levels and displayed significantly higher specificity when considering tissue, developmental stages, and stress responsiveness. The evolutionary analysis indicates higher positional conservation than sequence conservation, probably linked to the conserved modular motifs within syntenic lncRNAs. Moreover, a positive correlation between the expression of intergenic/natural antisense lncRNAs and their closest/parental gene was observed. For those intergenic, the correlation decreases with the distance to the neighboring gene, supporting that their potential cis-regulatory effect is within a short-range. Furthermore, the analysis of developmental studies showed that a conserved NAT-lncRNA family is differentially expressed in a coordinated way with their cognate sense protein-coding genes. These genes code for proteins associated with phloem development, thus providing insights about the potential involvement of some of the identified lncRNAs in a developmental process. We expect that this extensive inventory will constitute a valuable resource for further research lines focused on elucidating the regulatory mechanisms mediated by lncRNAs in cucurbits.

Integrated Metabolome, Transcriptome and Long Non-Coding RNA Analysis Reveals Potential Molecular Mechanisms of Sweet Cherry Fruit Ripening

Long non-coding RNAs (lncRNAs), a class of important regulatory factors for many biological processes in plants, have received much attention in recent years. To explore the molecular roles of lncRNAs in sweet cherry fruit ripening, we conducted widely targeted metabolome, transcriptome and lncRNA analyses of sweet cherry fruit at three ripening stages (yellow stage, pink stage, and dark red stage). The results show that the ripening of sweet cherry fruit involves substantial metabolic changes, and the rapid accumulation of anthocyanins (cyanidin 3-rutinoside, cyanidin 3-O-galactoside, and cyanidin 3-O-glucoside) is the main cause of fruit coloration. These ripening-related alterations in the metabolic profile are driven by specific enzyme genes related to the synthesis and decomposition of abscisic acid (ABA), cell wall disintegration, and anthocyanin biosynthesis, as well as transcription factor genes, such as MYBs, bHLHs, and WD40s. LncRNAs can target these ripening-related genes to form regulatory modules, incorporated into the sweet cherry fruit ripening regulatory network. Our study reveals that the lncRNA-mRNA module is an important component of the sweet cherry fruit ripening regulatory network. During sweet cherry fruit ripening, the differential expression of lncRNAs will meditate the spatio-temporal specific expression of ripening-related target genes (encoding enzymes and transcription factors related to ABA metabolism, cell wall metabolism and anthocyanin metabolism), thus driving fruit ripening.

Genome-wide analysis of long non-coding RNAs involved in the fruit development process of Cucumis melo Baogua

Melon (Cucumis melo L.) is a horticultural crop that is planted globally. Cucumis melo L. cv. Baogua is a typical melon that is suitable for studying fruit development because of its ability to adapt to different climatic conditions. Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs longer than 200 nucleotides, which play important roles in a wide range of biological processes by regulating gene expression. In this study, the transcriptome of the Baogua melon was sequenced at three stages of the process of fruit development (14 days, 21 days, and 28 days) to study the role of lncRNAs in fruit development. The cis and trans lncRNAs were subsequently predicted and identified to determine their target genes. Notably, 1716 high-confidence lncRNAs were obtained in the three groups. A subsequent differential expression analysis of the lncRNAs between the three groups revealed 388 differentially expressed lncRNAs. A total of 11 genes were analyzed further to validate the transcriptome sequencing results. Interestingly, the MELO3C001376.2 and MSTRG.571.2 genes were found to be significantly (P < 0.05) downregulated in the fruits. This study provides a basis to better understand the functions and regulatory mechanisms of lncRNAs during the development of melon fruit.

Generation of New β-Conglycinin-Deficient Soybean Lines by Editing the lincRNA lincCG1 Using the CRISPR/Cas9 System

Soybean β-conglycinin is a major allergen that adversely affects the nutritional properties of soybean. Soybean deficient in β-conglycinin is associated with low allergenicity and high nutritional value. Long intergenic noncoding RNAs (lincRNAs) regulate gene expression and are considered important regulators of essential biological processes. Despite increasing knowledge of the functions of lincRNAs, relatively little is known about the effects of lincRNAs on the accumulation of soybean β-conglycinin. The current study presents the identification of a lincRNA lincCG1 that was mapped to the intergenic noncoding region of the β-conglycinin α-subunit locus. The full-length lincCG1 sequence was cloned and found to regulate the expression of soybean seed storage protein (SSP) genes via both cis- and trans-acting regulatory mechanisms. Loss-of-function lincCG1 mutations generated using the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system led to the deficiency of the allergenic α'-, α-, and β-subunits of soybean β-conglycinin as well as higher content of proteins, sulfur-containing amino acids, and free arginine. The dominant null allele LincCG1, and consequently, the β-conglycinin-deficient phenotype associated with the lincCG1-gene-edited line was stably inherited by the progenies in a Mendelian fashion. The dominant null allele LincCG1 may therefore be exploited for engineering/developing novel hypoallergenic soybean varieties. Furthermore, Cas9-free and β-conglycinin-deficient homozygous mutant lines were obtained in the T1 generation. This study is the first to employ the CRISPR/Cas9 technology for editing a lincRNA gene associated with the soybean allergenic protein β-conglycinin. Moreover, this study reveals that lincCG1 plays a crucial role in regulating the expression of the β-conglycinin subunit gene cluster, besides highlighting the efficiency of employing the CRISPR/Cas9 system for modulating lincRNAs, and thereby regulating soybean seed components.

A long noncoding RNA functions in pumpkin fruit development through S-adenosyl-L-methionine synthetase

Long noncoding RNAs (lncRNAs) play important roles in various biological processes. However, the regulatory roles of lncRNAs underlying fruit development have not been extensively studied. The pumpkin (Cucurbita spp.) is a preferred model for understanding the molecular mechanisms regulating fruit development because of its variable shape and size and large inferior ovary. Here, we performed strand-specific transcriptome sequencing on pumpkin (Cucurbita maxima "Rimu") fruits at 6 developmental stages and identified 5,425 reliably expressed lncRNAs. Among the 332 lncRNAs that were differentially expressed during fruit development, the lncRNA MSTRG.44863.1 was identified as a negative regulator of pumpkin fruit development. MSTRG.44863.1 showed a relatively high expression level and an obvious period-specific expression pattern. Transient overexpression and silencing of MSTRG.44863.1 significantly increased and decreased the content of 1-aminocyclopropane carboxylic acid (a precursor of ethylene) and ethylene production, respectively. RNA pull-down and microscale thermophoresis assays further revealed that MSTRG.44863.1 can interact with S-adenosyl-L-methionine synthetase (SAMS), an enzyme in the ethylene synthesis pathway. Considering that ethylene negatively regulates fruit development, these results indicate that MSTRG.44863.1 plays an important role in the regulation of pumpkin fruit development, possibly through interacting with SAMS and affecting ethylene synthesis. Overall, our findings provide a rich resource for further study of fruit-related lncRNAs while offering insights into the regulation of fruit development in plants.

Emerging roles and mechanisms of lncRNAs in fruit and vegetables

With the development of genome sequencing technologies, many long non-coding RNAs (lncRNAs) have been identified in fruit and vegetables. lncRNAs are primarily transcribed and spliced by RNA polymerase II (Pol II) or plant-specific Pol IV/V, and exhibit limited evolutionary conservation. lncRNAs intricately regulate various aspects of fruit and vegetables, including pigment accumulation, reproductive tissue development, fruit ripening, and responses to biotic and abiotic stresses, through diverse mechanisms such as gene expression modulation, interaction with hormones and transcription factors, microRNA regulation, and involvement in alternative splicing. This review presents a comprehensive overview of lncRNA classification, basic characteristics, and, most importantly, recent advances in understanding their functions and regulatory mechanisms.

Integrated Transcriptomics and Metabolomics Analysis Promotes the Understanding of Adventitious Root Formation in Eucommia ulmoides Oliver

As a primary approach to nutrient propagation for many woody plants, cutting roots is essential for the breeding and production of Eucommia ulmoides Oliver. In this study, hormone level, transcriptomics, and metabolomics analyses were performed on two E. ulmoides varieties with different adventitious root (AR) formation abilities. The higher JA level on the 0th day and the lower JA level on the 18th day promoted superior AR development. Several hub genes executed crucial roles in the crosstalk regulation of JA and other hormones, including F-box protein (EU012075), SAUR-like protein (EU0125382), LOB protein (EU0124232), AP2/ERF transcription factor (EU0128499), and CYP450 protein (EU0127354). Differentially expressed genes (DEGs) and metabolites of AR formation were enriched in phenylpropanoid biosynthesis, flavonoid biosynthesis, and isoflavonoid biosynthesis pathways. The up-regulated expression of PAL, CCR, CAD, DFR, and HIDH genes on the 18th day could contribute to AR formation. The 130 cis-acting lncRNAs had potential regulatory functions on hub genes in the module that significantly correlated with JA and DEGs in three metabolism pathways. These revealed key molecules, and vital pathways provided more comprehensive insight for the AR formation mechanism of E. ulmoides and other plants.

Genome-wide identification of long non-coding RNAs and their potential functions in radish response to salt stress

Long non-coding RNAs (lncRNAs) are increasingly recognized as cis- and trans-acting regulators of protein-coding genes in plants, particularly in response to abiotic stressors. Among these stressors, high soil salinity poses a significant challenge to crop productivity. Radish (Raphanus sativus L.) is a prominent root vegetable crop that exhibits moderate susceptibility to salt stress, particularly during the seedling stage. Nevertheless, the precise regulatory mechanisms through which lncRNAs contribute to salt response in radish remain largely unexplored. In this study, we performed genome-wide identification of lncRNAs using strand-specific RNA sequencing on radish fleshy root samples subjected to varying time points of salinity treatment. A total of 7,709 novel lncRNAs were identified, with 363 of them displaying significant differential expression in response to salt application. Furthermore, through target gene prediction, 5,006 cis- and 5,983 trans-target genes were obtained for the differentially expressed lncRNAs. The predicted target genes of these salt-responsive lncRNAs exhibited strong associations with various plant defense mechanisms, including signal perception and transduction, transcription regulation, ion homeostasis, osmoregulation, reactive oxygen species scavenging, photosynthesis, phytohormone regulation, and kinase activity. Notably, this study represents the first comprehensive genome-wide analysis of salt-responsive lncRNAs in radish, to the best of our knowledge. These findings provide a basis for future functional analysis of lncRNAs implicated in the defense response of radish against high salinity, which will aid in further understanding the regulatory mechanisms underlying radish response to salt stress.

Genome-wide identification and analysis of Lateral Organ Boundaries Domain (LBD) transcription factor gene family in melon (Cucumis melo L.)

Background

Lateral Organ Boundaries Domain (LBD) transcription factor (TF) gene family members play very critical roles in several biological processes like plant-spesific development and growth process, tissue regeneration, different biotic and abiotic stress responses in plant tissues and organs. The LBD genes have been analyzed in various species. Melon (Cucumis melo L.), a member of the Cucurbitaceae family, is economically important and contains important molecules for nutrition and human health such as vitamins A and C, β-carotenes, phenolic acids, phenolic acids, minerals and folic acid. However, no studies have been reported so far about LBD genes in melon hence this is the first study for LBD genes in this plant.

Results

In this study, 40 melon CmLBD TF genes were identified, which were separated into seven groups through phylogenetic analysis. Cis-acting elements showed that these genes were associated with plant growth and development, phytohormone and abiotic stress responses. Gene Ontology (GO) analysis revealed that of CmLBD genes especially function in regulation and developmental processes. The in silico and qRT-PCR expression patterns demonstrated that CmLBD01 and CmLBD18 are highly expressed in root and leaf tissues, CmLBD03 and CmLBD14 displayed a high expression in male-female flower and ovary tissues.

Conclusions

These results may provide important contributions for future research on the functional characterization of the melon LBD gene family and the outputs of this study can provide information about the evolution and characteristics of melon LBD gene family for next studies.

Integrated analyses of metabolomics and transcriptomics reveal the potential regulatory roles of long non-coding RNAs in gingerol biosynthesis

BACKGROUND

As the characteristic functional component in ginger, gingerols possess several health-promoting properties. Long non-coding RNAs (lncRNAs) act as crucial regulators of diverse biological processes. However, lncRNAs in ginger are not yet identified so far, and their potential roles in gingerol biosynthesis are still unknown. In this study, metabolomic and transcriptomic analyses were performed in three main ginger cultivars (leshanhuangjiang, tonglingbaijiang, and yujiang 1 hao) in China to understand the potential roles of the specific lncRNAs in gingerol accumulation.

RESULTS

A total of 744 metabolites were monitored by metabolomics analysis, which were divided into eleven categories. Among them, the largest group phenolic acid category contained 143 metabolites, including 21 gingerol derivatives. Of which, three gingerol analogs, [8]-shogaol, [10]-gingerol, and [12]-shogaol, accumulated significantly. Moreover, 16,346 lncRNAs, including 2,513, 1,225, and 2,884 differentially expressed (DE) lncRNA genes (DELs), were identified in all three comparisons by transcriptomic analysis. Gene ontology enrichment (GO) analysis showed that the DELs mainly enriched in the secondary metabolite biosynthetic process, response to plant hormones, and phenol-containing compound metabolic process. Correlation analysis revealed that the expression levels of 11 DE gingerol biosynthesis enzyme genes (GBEGs) and 190 transcription factor genes (TF genes), such as MYB1, ERF100, WRKY40, etc. were strongly correlation coefficient with the contents of the three gingerol analogs. Furthermore, 7 and 111 upstream cis-acting lncRNAs, 1,200 and 2,225 upstream trans-acting lncRNAs corresponding to the GBEGs and TF genes were identified, respectively. Interestingly, 1,184 DELs might function as common upstream regulators to these GBEGs and TFs genes, such as LNC_008452, LNC_006109, LNC_004340, etc. Furthermore, protein-protein interaction networks (PPI) analysis indicated that three TF proteins, MYB4, MYB43, and WRKY70 might interact with four GBEG proteins (PAL1, PAL2, PAL3, and 4CL-4).

CONCLUSION

Based on these findings, we for the first time worldwide proposed a putative regulatory cascade of lncRNAs, TFs genes, and GBEGs involved in controlling of gingerol biosynthesis. These results not only provide novel insights into the lncRNAs involved in gingerol metabolism, but also lay a foundation for future in-depth studies of the related molecular mechanism.

Promoter Variation of the Key Apple Fruit Texture Related Gene MdPG1 and the Upstream Regulation Analysis

MdPG1 encoding polygalacturonase in apple (Malus × domestica) is a key gene associated with fruit firmness and texture variations among apple cultivars. However, the causative variants of MdPG1 are still not known. In this study, we identified a SNP^A/C variant within an ERF-binding element located in the promoter region of MdPG1. The promoter containing the ERF-binding element with SNP^A, rather than the SNP^C, could be strongly bound and activated by MdCBF2, a member of the AP2/ERF transcription factor family, as determined by yeast-one-hybrid and dual-luciferase reporter assays. We also demonstrated that the presence of a novel long non-coding RNA, lncRNA_PG1, in the promoter of MdPG1 was a causative variant. lncRNA_PG1 was specifically expressed in fruit tissues postharvest. lncRNA_PG1 could reduce promoter activity when it was fused to the promoter of MdPG1 and a tobacco gene encoding Mg-chelatase H subunit (NtCHLH) in transgenic tobacco cells but could not reduce promoter activity when it was supplied in a separate gene construct, indicating a cis-regulatory effect. Our results provide new insights into genetic regulation of MdPG1 allele expression and are also useful for the development of elite apple cultivars.

Investigating nicotine pathway-related long non-coding RNAs in tobacco

Long non-coding RNAs (lncRNAs) are transcripts longer than 200 bp with low or no protein-coding ability, which play essential roles in various biological processes in plants. Tobacco is an ideal model plant for studying nicotine biosynthesis and metabolism, and there is little research on lncRNAs in this field. Therefore, how to take advantage of the mature tobacco system to profoundly investigate the lncRNAs involved in the nicotine pathway is intriguing. By exploiting 549 public RNA-Seq datasets of tobacco, 30,212 lncRNA candidates were identified, including 24,084 large intervening non-coding RNAs (lincRNAs), 5,778 natural antisense transcripts (NATs) and 350 intronic non-coding RNAs (incRNAs). Compared with protein-coding genes, lncRNAs have distinct properties in terms of exon number, sequence length, A/U content, and tissue-specific expression pattern. lincRNAs showed an asymmetric evolutionary pattern, with a higher proportion (68.71%) expressed from the Nicotiana sylvestris (S) subgenome. We predicted the potential cis/trans-regulatory effects on protein-coding genes. One hundred four lncRNAs were detected as precursors of 30 known microRNA (miRNA) family members, and 110 lncRNAs were expected to be the potential endogenous target mimics for 39 miRNAs. By combining the results of weighted gene co-expression network analysis with the differentially expressed gene analysis of topping RNA-seq data, we constructed a sub-network containing eight lncRNAs and 25 nicotine-related coding genes. We confirmed that the expression of seven lncRNAs could be affected by MeJA treatment and may be controlled by the transcription factor NtMYC2 using a quantitative PCR assay and gene editing. The results suggested that lncRNAs are involved in the nicotine pathway. Our findings further deepened the understanding of the features and functions of lncRNAs and provided new candidates for regulating nicotine biosynthesis in tobacco.

Coordinating Diverse Functions of miRNA and lncRNA in Fleshy Fruit

Non-coding RNAs play vital roles in the diverse biological processes of plants, and they are becoming key topics in horticulture research. In particular, miRNAs and long non-coding RNAs (lncRNAs) are receiving increased attention in fruit crops. Recent studies in horticulture research provide both genetic and molecular evidence that miRNAs and lncRNAs regulate biological function and stress responses during fruit development. Here, we summarize multiple regulatory modules of miRNAs and lncRNAs and their biological roles in fruit sets and stress responses, which would guide the development of molecular breeding techniques on horticultural crops.

Genome-wide identification and comprehensive analysis reveal potential roles of long non-coding RNAs in fruit development of southern highbush blueberry (Vaccinium corymbosum L.)

Introduction

Blueberries have a high antioxidant content and are produced as healthy food worldwide. Long non-coding RNAs (lncRNAs) are a type of regulatory RNAs that play a variety of roles in plants. Nonetheless, information on lncRNAs and their functions during blueberry fruit development is scarce in public databases.

Methods

In the present study, we performed genome-wide identification of lncRNAs in a southern highbush blueberry using strand-specific RNA sequencing (ssRNA-Seq). Differentially expressed lncRNAs (DE-lncRNAs) and their potential target genes were analyzed at four stages of fruit development. Cis-regulatory DE-lncRNAs were predicted using co-localization analysis.

Results

These findings included a total of 25,036 lncRNAs from 17,801 loci. Blueberry lncRNAs had shorter transcript lengths, smaller open reading frame (ORF) sizes, fewer exons, and fewer isoforms than protein-coding RNAs, as well as lower expression levels and higher stage-specificity during fruit development. A total of 105 DE-lncRNAs were identified among the comparison group of PAD vs. CUP, 443 DE-lncRNAs were detected when comparing CUP with PINK fruits, and 285 DE-lncRNAs were revealed when comparing PINK and BLUE fruits. According to Kyoto Encyclopedia of Genes and Genomes annotation, target genes of DE-lncRNAs were primarily enriched in the "Autophagy-other", "DNA replication", "Endocytosis", 'photosynthesis' and 'chlorophyll metabolism' pathways, suggesting that lncRNAs may pay potential roles in fruit expansion and ripening. Moreover, several lncRNAs have been proposed as cis-regulators of the key genes involved in flavonoid biosynthesis. MSTRG.107242.6, and its putative target gene, BTB/POZ and TAZ domain-containing protein, might play critical roles in anthocyanin accumulation in blueberries.

Discussion

These findings highlight the regulatory function of lncRNAs and aid in elucidating the molecular mechanism underlying blueberry fruit growth.

Identification and Functional Analysis of Long Non-Coding RNA (lncRNA) in Response to Seed Aging in Rice

Many lncRNAs have been shown to play a vital role in aging processes. However, how lncRNAs regulate seed aging remains unknown. In this study, we performed whole transcriptome strand-specific RNA sequencing of samples from rice embryos, analyzed the differences in expression of rice seed lncRNAs before and after artificial aging treatment (AAT), and systematically screened 6002 rice lncRNAs. During the AAT period, the expression levels of most lncRNAs (454) were downregulated and only four were upregulated among the 458 differentially expressed lncRNAs (DELs). Cis- or trans-regulated target genes of the four upregulated lncRNAs were mainly related to base repair, while 454 downregulated lncRNAs were related to plant-pathogen interaction, plant hormones, energy metabolism, and secondary metabolism. The pathways of DEL target genes were similar with those of differentially expressed mRNAs (DEGs). A competing endogenous RNA (ceRNA) network composed of 34 lncRNAs, 24 microRNAs (miRNA), and 161 mRNAs was obtained. The cDNA sequence of lncRNA LNC_037529 was obtained by rapid amplification of cDNA ends (RACE) cloning with a total length of 1325 bp, a conserved 5' end, and a non-conserved 3' end. Together, our findings indicate that genome-wide selection for lncRNA downregulation was an important mechanism for rice seed aging. LncRNAs can be used as markers of seed aging in rice. These findings provide a future path to decipher the underlying mechanism associated with lncRNAs in seed aging.

Transcriptional profiling of long non-coding RNAs regulating fruit cracking in Punica granatum L. under bagging

Fruit cracking tremendously damages the appearance of fruit, easily leads to pathogen invasion, greatly reduces the marketability and causes immense economic losses. The pivotal role of long non-coding RNAs (lncRNAs) in diverse biological processes has been confirmed, while the roles of lncRNAs underlying fruit cracking remain poorly understood. In this study, the incidence of fruit cracking was 7.26% under the bagging treatment, the control group was 38.11%, indicating that bagging considerably diminished the fruit cracking rate. LncRNA libraries for fruit cracking (FC), fruit non-cracking (FNC) and fruit non-cracking under bagging (FB) in pomegranate (Punica granatum L.) were performed and analysed via high-throughput transcriptome sequencing. A total of 3194 lncRNAs were obtained with a total length of 4898846 nt and an average length of 1533.77 nt in pomegranate. We identified 42 differentially expressed lncRNAs (DELs) and 137 differentially expressed mRNAs (DEGs) in FC vs FNC and 35 DELs and 160 DEGs in FB vs FC that formed co-expression networks respectively, suggesting that there are involved in phytohormone signaling pathway, lignin catabolic process, lipid transport/binding, cutin biosynthetic process and cell wall organization. We also found that 18 cis-acting DELs regulated 18 target genes, and 10 trans-acting DELs regulated 24 target genes in FC vs FNC, 23 DELs regulate 23 target genes for the cis-acting lncRNAs and 12 DELs regulated 36 target genes in FB vs FC, which provides an understanding for the regulation of the fruit cracking. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis results demonstrated that DELs participated in calcium ion binding, glycerophospholipid metabolism, flavonoid biosynthetic process, cell wall biogenesis, xyloglucan metabolic process, hormone signal transduction and starch and sucrose metabolism. Our findings provide new insights into the roles of lncRNAs in regulating the fruit cracking and lay the foundation for further improvement of pomegranate quality.

B, Iquebal MA, Bhattacharya RC, Rai A, Kumar D. Genome wide identification of lncRNAs and circRNAs having regulatory role in fruit shelf life in health crop cucumber (Cucumis sativus L.)

Cucumber is an extremely perishable vegetable; however, under room conditions, the fruits become unfit for consumption 2-3 days after harvesting. One natural variant, DC-48 with an extended shelf-life was identified, fruits of which can be stored up to 10-15 days under room temperature. The genes involved in this economically important trait are regulated by non-coding RNAs. The study aims to identify the long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) by taking two contrasting genotypes, DC-48 and DC-83, at two different fruit developmental stages. The upper epidermis of the fruits was collected at 5 days and 10 days after pollination (DAP) for high throughput RNA sequencing. The differential expression analysis was performed to identify differentially expressed (DE) lncRNAs and circRNAs along with the network analysis of lncRNA, miRNA, circRNA, and mRNA interactions. A total of 97 DElncRNAs were identified where 18 were common under both the developmental stages (8 down regulated and 10 upregulated). Based on the back-spliced reads, 238 circRNAs were found to be distributed uniformly throughout the cucumber genomes with the highest numbers (71) in chromosome 4. The majority of the circRNAs (49%) were exonic in origin followed by inter-genic (47%) and intronic (4%) origin. The genes related to fruit firmness, namely, polygalacturonase, expansin, pectate lyase, and xyloglucan glycosyltransferase were present in the target sites and co-localized networks indicating the role of the lncRNA and circRNAs in their regulation. Genes related to fruit ripening, namely, trehalose-6-phosphate synthase, squamosa promoter binding protein, WRKY domain transcription factors, MADS box proteins, abscisic stress ripening inhibitors, and different classes of heat shock proteins (HSPs) were also found to be regulated by the identified lncRNA and circRNAs. Besides, ethylene biosynthesis and chlorophyll metabolisms were also found to be regulated by DElncRNAs and circRNAs. A total of 17 transcripts were also successfully validated through RT PCR data. These results would help the breeders to identify the complex molecular network and regulatory role of the lncRNAs and circRNAs in determining the shelf-life of cucumbers.

Genome-wide identification and characterization of long noncoding RNAs during peach (Prunus persica) fruit development and ripening

LncRNAs represent a class of RNA transcripts of more than 200 nucleotides (nt) in length without discernible protein-coding potential. The expression levels of lncRNAs are significantly affected by stress or developmental cues. Recent studies have shown that lncRNAs participate in fruit development and ripening processes in tomato and strawberry; however, in other fleshy fruits, the association between lncRNAs and fruit ripening remains largely elusive. Here, we constructed 9 ssRNA-Seq libraries from three different peach (Prunus persica) fruit developmental stages comprising the first and second exponential stages and the fruit-ripening stage. In total, 1500 confident lncRNAs from 887 loci were obtained according to the bioinformatics analysis. The lncRNAs identified in peach fruits showed distinct characteristics compared with protein-coding mRNAs, including lower expression levels, lower complexity of alternative splicing, shorter isoforms and smaller numbers of exons. Expression analysis identified 575 differentially expressed lncRNAs (DELs) classified into 6 clusters, among which members of Clusters 1, 2, 4 and 5 were putatively associated with fruit development and ripening processes. Quantitative real-time PCR revealed that the DELs indeed had stage-specific expression patterns in peach fruits. GO and KEGG enrichment analysis revealed that DELs might be associated with fruit-ripening-related physiological and metabolic changes, such as flavonoid biosynthesis, fruit texture softening, chlorophyll breakdown and aroma compound accumulation. Finally, the similarity analysis of lncRNAs within different plant species indicated the low sequence conservation of lncRNAs. Our study reports a large number of fruit-expressed lncRNAs and identifies fruit development phase-specific expressed lncRNA members, which highlights their potential functions in fruit development and ripening processes and lays the foundations for future functional research.

Genome-wide characterization and expression analysis of SAUR gene family in Melon (Cucumis melo L.)

We identified 66 melon SAUR genes by bioinformatic analyses. CmSAUR19, 38, 58, 62 genes are specifically expressed in different stages of fruit growth, suggesting their participation in regulating fruit development. Auxin plays a crucial role in plant growth by regulating the multiple auxin response genes. However, in melon (Cucumis melo L.), the functions of the auxin early response gene family SAUR (Small auxin up RNA) genes in fruit development are still poorly understood. Through genome-wide characterization of CmSAUR family in melon, we identified a total of 66 CmSAUR genes. The open reading frames of the CmSAUR genes ranged from 234 to 525 bp, containing only one exon and lacking introns. Chromosomal position and phylogenetic tree analyses found that the two gene clusters in the melon chromosome are highly homologous in the Cucurbitaceae plants. Among the four conserved motifs in CmSAUR proteins, motif 1, motif 2, and motif 3 located in most of the family protein sequences, and motif 4 showed a close correlation with the two gene clusters. The CmSAUR28 and CmSAUR58 genes have auxin response elements located in the promoters, suggesting they may be involved in the auxin signaling pathway to regulate fruit development. Through transcriptomic profiling in the four developmental stages of fruit and different lateral organs, we selected 16 differentially-expressed SAUR genes for performing further expression analyses. qRT-PCR results showed that five SAUR genes are specifically expressed in flower organs and ovaries. CmSAUR19 and CmSAUR58 were significantly accumulated in the early developmental stage of the fruit. CmSAUR38 and CmAUR62 showed high expression in the climacteric and post-climacteric stages, suggesting their specific role in controlling fruit ripening. This work provides a foundation for further exploring the function of the SAUR gene in fruit development.

Whole-Transcriptome Analysis Reveals Long Noncoding RNAs Involved in Female Floral Development of Hickory (Carya cathayensis Sarg.)

Hickory, an endemic woody oil and fruit tree species in China, is of great economic value. However, hickory has a long juvenile period and an inconsistent flowering of males and females, thus influencing the bearing rates and further limiting fruits yield. Currently, it is reported that long noncoding RNAs (lncRNAs) play critical regulatory roles in biological processes. However, the role of lncRNAs in the development of hickory female flowers remains unclear. In this study, a total of 6,862 putative lncRNAs were identified from the female flower transcriptomes in three different growth stages of hickory. We proposed that lncRNAs might play an important role in phytohormone signaling processes for flower formation, especially in the abscisic acid and jasmonic acid pathways, according to the results of our Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. Moreover, we predicted the interactions among four microRNAs (miRNAs), three lncRNAs, and four genes. We proposed that facing the changing environment, LNC_002115 competes with PHOSPHATE2 (PHO2) for the binding sites on cca-miR399f, and protects PHO2 from suppression. In addition, cis-acting LNC_002115 regulates the expression of the SHORT VEGETATIVE PHASE (SVP) by influencing ABRE-binding factor (ABF). In brief, LNC_002115 regulates hickory female floral development by impacting both PHO2 and SVP. This study was the first to identify lncRNAs involved in hickory female floral development, and provided new insight to elucidate how lncRNAs and their targets play a role in female floral development in hickory, thus unfolding the opportunities for functional characterization of blossom-related lncRNAs in further studies.

Comparative transcriptome analysis of melon (Cucumis melo L.) reveals candidate genes and pathways involved in powdery mildew resistance

Powdery mildew is a major disease in melon, primarily caused by Podosphaera xanthii (Px). Some melon varieties were resistant to powdery mildew, while others were susceptible. However, the candidate genes associated with resistance and the mechanism of resistance/susceptibility to powdery mildew in melon remain unclear. In this study, disease-resistant melon cultivar TG-1 and disease-susceptible melon cultivar TG-5 were selected for comparative transcriptome analysis. The results suggested that the numbers of differentially expressed genes (DEGs) in TG-5 was always more than that in TG-1 at each of the four time points after Px infection, indicating that their responses to Px infection may be different and that the active response of TG-5 to Px infection may be earlier than that of TG-1. Transcription factors (TFs) analysis among the DEGs revealed that the bHLH, ERF, and MYB families in TG-1 may play a vital role in the interaction between melon and powdery mildew pathogens. GO enrichment analysis of these DEGs in TG-5 showed that the SBP, HSF, and ERF gene families may play important roles in the early stage of melon development after Px infection. Finally, we speculated on the regulatory pathways of melon powdery mildew and found PTI and ABA signaling genes may be associated with the response to Px infection in melon.

Genome-wide analysis uncovers tomato leaf lncRNAs transcriptionally active upon Pseudomonas syringae pv. tomato challenge

Plants rely on (in)direct detection of bacterial pathogens through plasma membrane-localized and intracellular receptor proteins. Surface pattern-recognition receptors (PRRs) participate in the detection of microbe-associated molecular patterns (MAMPs) and are required for the activation of pattern-triggered immunity (PTI). Pathogenic bacteria, such as Pseudomonas syringae pv. tomato (Pst) deploys ~ 30 effector proteins into the plant cell that contribute to pathogenicity. Resistant plants are capable of detecting the presence or activity of effectors and mount another response termed effector-triggered immunity (ETI). In order to investigate the involvement of tomato’s long non-coding RNAs (lncRNAs) in the immune response against Pst, we used RNA-seq data to predict and characterize those that are transcriptionally active in leaves challenged with a large set of treatments. Our prediction strategy was validated by sequence comparison with tomato lncRNAs described in previous works and by an alternative approach (RT-qPCR). Early PTI (30 min), late PTI (6 h) and ETI (6 h) differentially expressed (DE) lncRNAs were identified and used to perform a co-expression analysis including neighboring (± 100 kb) DE protein-coding genes. Some of the described networks could represent key regulatory mechanisms of photosynthesis, PRR abundance at the cell surface and mitigation of oxidative stress, associated to tomato-Pst pathosystem.

Identification of Long Non-Coding RNAs Associated with Tomato Fruit Expansion and Ripening by Strand-Specific Paired-End RNA Sequencing

As emerging essential regulators in plant development, long non-coding RNAs (lncRNAs) have been extensively investigated in multiple horticultural crops, as well as in different tissues of plants. Tomato fruits are an indispensable part of people’s diet and are consumed as fruits and vegetables. Meanwhile, tomato is widely used as a model to study the ripening mechanism in fleshy fruit. Although increasing evidence shows that lncRNAs are involved in lots of biological processes in tomato plants, the comprehensive identification of lncRNAs in tomato fruit during its expansion and ripening and their functions are partially known. Here, we performed strand-specific paired-end RNA sequencing (ssRNA-seq) of tomato Heinz1706 fruits at five different developmental stages, as well as flowers and leaves. We identified 17,674 putative lncRNAs by referencing the recently released SL4.0 and annotation ITAG4.0 in tomato plants. Many lncRNAs show different expression patterns in fleshy fruit at different developmental stages compared with leaves or flowers. Our results indicate that lncRNAs play an important role in the regulation of tomato fruit expansion and ripening, providing informative lncRNA candidates for further studies in tomato fruits. In addition, we also summarize the recent advanced progress in lncRNAs mediated regulation on horticultural fruits. Hence, our study updates the understanding of lncRNAs in horticultural plants and provides resources for future studies relating to the expansion and ripening of tomato fruits.

Integrative lncRNA landscape reveals lncRNA-coding gene networks in the secondary cell wall biosynthesis pathway of moso bamboo (Phyllostachys edulis)

Background

LncRNAs are extensively involved in plant biological processes. However, the lack of a comprehensive lncRNA landscape in moso bamboo has hindered the molecular study of lncRNAs. Moreover, the role of lncRNAs in secondary cell wall (SCW) biosynthesis of moso bamboo is elusive.

Results

For comprehensively identifying lncRNA throughout moso bamboo genome, we collected 231 RNA-Seq datasets, 1 Iso-Seq dataset, and 1 full-length cDNA dataset. We used a machine learning approach to improve the pipeline of lncRNA identification and functional annotation based on previous studies and identified 37,009 lncRNAs in moso bamboo. Then, we established a network of potential lncRNA-coding gene for SCW biosynthesis and identified SCW-related lncRNAs. We also proposed that a mechanism exists in bamboo to direct phenylpropanoid intermediates to lignin or flavonoids biosynthesis through the PAL/4CL/C4H genes. In addition, we identified 4 flavonoids and 1 lignin-preferred genes in the PAL/4CL/C4H gene families, which gained implications in molecular breeding.

Conclusions

We provided a comprehensive landscape of lncRNAs in moso bamboo. Through analyses, we identified SCW-related lncRNAs and improved our understanding of lignin and flavonoids biosynthesis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07953-z.

Noncoding RNAs in Medicinal Plants and their Regulatory Roles in Bioactive Compound Production

BACKGROUND

Noncoding RNAs (ncRNAs), such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and long noncoding RNAs (lncRNAs), play significant regulatory roles in plant development and secondary metabolism and are involved in plant response to biotic and abiotic stresses. They have been intensively studied in model systems and crops for approximately two decades and massive amount of information have been obtained. However, for medicinal plants, ncRNAs, particularly their regulatory roles in bioactive compound biosynthesis, are just emerging as a hot research field.

OBJECTIVE

This review aims to summarize current knowledge on herbal ncRNAs and their regulatory roles in bioactive compound production.

RESULTS

So far, scientists have identified thousands of miRNA candidates from over 50 medicinal plant species and 11794 lncRNAs from Salvia miltiorrhiza, Panax ginseng, and Digitalis purpurea. Among them, more than 30 miRNAs and five lncRNAs have been predicted to regulate bioactive compound production.

CONCLUSION

The regulation may achieve through various regulatory modules and pathways, such as the miR397-LAC module, the miR12112-PPO module, the miR156-SPL module, the miR828-MYB module, the miR858-MYB module, and other siRNA and lncRNA regulatory pathways. Further functional analysis of herbal ncRNAs will provide useful information for quality and quantity improvement of medicinal plants.

Identification of the specific long-noncoding RNAs involved in night-break mediated flowering retardation in Chenopodium quinoa

Background

Night-break (NB) has been proven to repress flowering of short-day plants (SDPs). Long-noncoding RNAs (lncRNAs) play key roles in plant flowering. However, investigation of the relationship between lncRNAs and NB responses is still limited, especially in Chenopodium quinoa, an important short-day coarse cereal.

Results

In this study, we performed strand-specific RNA-seq of leaf samples collected from quinoa seedlings treated by SD and NB. A total of 4914 high-confidence lncRNAs were identified, out of which 91 lncRNAs showed specific responses to SD and NB. Based on the expression profiles, we identified 17 positive- and 7 negative-flowering lncRNAs. Co-expression network analysis indicated that 1653 mRNAs were the common targets of both types of flowering lncRNAs. By mapping these targets to the known flowering pathways in model plants, we found some pivotal flowering homologs, including 2 florigen encoding genes (FT (FLOWERING LOCUS T) and TSF (TWIN SISTER of FT) homologs), 3 circadian clock related genes (EARLY FLOWERING 3 (ELF3), LATE ELONGATED HYPOCOTYL (LHY) and ELONGATED HYPOCOTYL 5 (HY5) homologs), 2 photoreceptor genes (PHYTOCHROME A (PHYA) and CRYPTOCHROME1 (CRY1) homologs), 1 B-BOX type CONSTANS (CO) homolog and 1 RELATED TO ABI3/VP1 (RAV1) homolog, were specifically affected by NB and competed by the positive and negative-flowering lncRNAs. We speculated that these potential flowering lncRNAs may mediate quinoa NB responses by modifying the expression of the floral homologous genes.

Conclusions

Together, the findings in this study will deepen our understanding of the roles of lncRNAs in NB responses, and provide valuable information for functional characterization in future.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07605-2.

Genome-wide identification and characterization of long non-coding RNAs involved in flag leaf senescence of rice

KEY MESSAGE

This study showed the systematic identification of long non-coding RNAs (lncRNAs) involving in flag leaf senescence of rice, providing the possible lncRNA-mRNA regulatory relationships and lncRNA-miRNA-mRNA ceRNA networks during leaf senescence. LncRNAs have been reported to play crucial roles in diverse biological processes. However, no systematic identification of lncRNAs associated with leaf senescence in plants has been studied. In this study, a genome-wide high throughput sequencing analysis was performed using rice flag leaves developing from normal to senescence. A total of 3953 lncRNAs and 38757 mRNAs were identified, of which 343 lncRNAs and 9412 mRNAs were differentially expressed. Through weighted gene co-expression network analysis (WGCNA), 22 continuously down-expressed lncRNAs targeting 812 co-expressed mRNAs and 48 continuously up-expressed lncRNAs targeting 1209 co-expressed mRNAs were considered to be significantly associated with flag leaf senescence. Gene Ontology results suggested that the senescence-associated lncRNAs targeted mRNAs involving in many biological processes, including transcription, hormone response, oxidation-reduction process and substance metabolism. Additionally, 43 senescence-associated lncRNAs were predicted to target 111 co-expressed transcription factors. Interestingly, 8 down-expressed lncRNAs and 29 up-expressed lncRNAs were found to separately target 12 and 20 well-studied senescence-associated genes (SAGs). Furthermore, analysis on the competing endogenous RNA (CeRNA) network revealed that 6 down-expressed lncRNAs possibly regulated 51 co-expressed mRNAs through 15 miRNAs, and 14 up-expressed lncRNAs possibly regulated 117 co-expressed mRNAs through 21 miRNAs. Importantly, by expression validation, a conserved miR164-NAC regulatory pathway was found to be possibly involved in leaf senescence, where lncRNA MSTRG.62092.1 may serve as a ceRNA binding with miR164a and miR164e to regulate three transcription factors. And two key lncRNAs MSTRG.31014.21 and MSTRG.31014.36 also could regulate the abscisic-acid biosynthetic gene BGIOSGA025169 (OsNCED4) and BGIOSGA016313 (NAC family) through osa-miR5809. The possible regulation networks of lncRNAs involving in leaf senescence were discussed, and several candidate lncRNAs were recommended for prior transgenic analysis. These findings will extend the understanding on the regulatory roles of lncRNAs in leaf senescence, and lay a foundation for functional research on candidate lncRNAs.

Genome-Wide Identification and Characterization of Long Noncoding RNAs Involved in Chinese Wheat Mosaic Virus Infection of Nicotiana benthamiana

Simple Summary

Recent studies have shown that a large number of long noncoding RNAs (lncRNAs) can regulate various biological processes in animals and plants. However, the roles of long non-coding RNAs (lncRNAs) in the interaction between plants and viruses is unclear, particularly for the Chinese wheat mosaic virus (CWMV) interaction. In this study, we used a deep RNA sequencing strategy to profile lncRNAs involved in the response to CWMV infection in Nicotiana benthamiana and analyzed differentially expressed lncRNAs that responded to CWMV infection, using a bioinformatics method. We identified 1175 new lncRNAs in N. benthamiana infected with CWMV, with 65 lncRNAs showing differential expression. These lncRNAs were mainly enriched in plant hormone signal transduction and other pathways according to GO and KEGG pathway enrichment analyses. In addition, differential expression of XLOC_006393 after CWMV infection may be the precursor of NbmiR168c, which can respond to CWMV infection by modulating the expression of its target gene NbAGO1. We believe that our study makes a significant contribution to the literature because these results provide a valuable resource for studying lncRNAs involved in CWMV infection and improving the understanding of the molecular mechanism of CWMV infection.

Abstract

Recent studies have shown that a large number of long noncoding RNAs (lncRNAs) can regulate various biological processes in animals and plants. Although lncRNAs have been identified in many plants, they have not been reported in the model plant Nicotiana benthamiana. Particularly, the role of lncRNAs in plant virus infection remains unknown. In this study, we identified lncRNAs in N. benthamiana response to Chinese wheat mosaic virus (CWMV) infection by RNA sequencing. A total of 1175 lncRNAs, including 65 differentially expressed lncRNAs, were identified during CWMV infection. We then analyzed the functions of some of these differentially expressed lncRNAs. Interestingly, one differentially expressed lncRNA, XLOC_006393, was found to participate in CWMV infection as a precursor to microRNAs in N. benthamiana. These results suggest that lncRNAs play an important role in the regulatory network of N. benthamiana in response to CWMV infection.

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

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.

Genome-wide identification of long non-coding RNAs and circular RNAs reveal their ceRNA networks in response to cucumber green mottle mosaic virus infection in watermelon

Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) play vital roles in plant defense responses against viral infections. However, there is no systematic understanding of lncRNAs and circRNAs and their competing endogenous RNA (ceRNA) networks in watermelon under cucumber green mottle mosaic virus (CGMMV) stress. Here, we present the characterization and expression profiles of lncRNAs and circRNAs in watermelon leaves 48-h post-inoculation (48 hpi) with CGMMV, with mock inoculation as a control. Deep sequencing analysis revealed 2373 lncRNAs and 606 circRNAs in the two libraries. Among them, 67 lncRNAs (40 upregulated and 27 downregulated) and 548 circRNAs (277 upregulated and 271 downregulated) were differentially expressed (DE) in the 48 hpi library compared with the control library. Furthermore, 263 cis-acting matched lncRNA-mRNA pairs were detected for 49 of the DE-lncRNAs. KEGG pathway analysis of the cis target genes of the DE-lncRNAs revealed significant associations with phenylalanine metabolism, the citrate cycle (TCA cycle), and endocytosis. Additionally, 30 DE-lncRNAs were identified as putative target mimics of 33 microRNAs (miRNAs), and 153 DE-circRNAs were identified as putative target mimics of 88 miRNAs. Furthermore, ceRNA networks of lncRNA/circRNA-miRNA-mRNA in response to CGMMV infection are described, with 12 DE-lncRNAs and 65 DE-circRNAs combining with 22 miRNAs and competing for the miRNA binding sites on 29 mRNAs. The qRT-PCR validation of selected lncRNAs and circRNAs showed a general correlation with the high-throughput sequencing results. This study provides a valuable resource of lncRNAs and circRNAs involved in the response to CGMMV infection in watermelon.

Identification of lncRNAs and their regulatory relationships with target genes and corresponding miRNAs in melon response to powdery mildew fungi

Melon (Cucumis melo L.), an economically beneficial crop widely cultivated around the world, is vulnerable to powdery mildew (PM). However, the studies on molecular mechanism of melon response to PM fungi is still limited. Long non coding RNAs (lncRNAs) have emerged as new regulators in plants response to biotic stresses. We predicted and identified the intricate regulatory roles of lncRNAs in melon response to PM fungi. A total of 539 lncRNAs were identified from PM-resistant (MR-1) and susceptible melon (Top Mark), in which 254 were significantly altered after PM fungi infection. Multiple target genes of lncRNAs were found to be involved in the hydrolysis of chitin, callose deposition and cell wall thickening, plant-pathogen interaction and plant hormone signal transduction pathway. Additionally, a total of 42 lncRNAs possess the various functions with microRNAs (miRNAs), including lncRNAs that are targeted by miRNAs and function as miRNA precursors or miRNA sponges. These findings provide a comprehensive view of potentially functional lncRNAs, corresponding target genes and related lncRNA-miRNA pairs, which will greatly increase our knowledge of the mechanism underlying susceptibility and resistance to PM in melon.