Analysis of long-non-coding RNAs associated with ethylene in tomato

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.

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.

Long non-coding RNAs and their potential function in response to postharvest senescence of Sparassis latifolia during cold storage

Long non-coding RNAs (lncRNAs) have been shown to play crucial roles in response to aging processes. However, how lncRNAs regulate postharvest senescence of Sparassis latifolia (S. latifolia) with oriented polypropylene (OPP) film packing during cold storage remains unclear. In this study, we performed RNA-seq using the fruiting bodies of S. latifolia stored at 4 ℃ for 0, 8, 16 and 24 days after harvest, and profiled the lncRNA and mRNA transcriptome, respectively. In total, 1003 putative lncRNAs were identified, and there were 495, 483 and 162 differentially expressed (DE) lncRNAs, and 3680, 3941 and 1870 differentially expressed mRNAs after 8, 16 and 24 days of storage, respectively, compared to 0 day of storage. Target genes of differentially expressed lncRNAs were found to significantly associate with carbon and energy metabolism, response to abiotic stimulus, amino acid biosynthesis and metabolism, and protein synthesis and transcription. In addition, DE-lncRNA-mRNA co-expression networks in response to aging stress were also constructed. Taken together, these results confirm the regulatory role of lncRNAs in postharvest senescence of S. latifolia and will facilitate for improving preservation method.

Insights into the roles of long noncoding RNAs in the communication between plants and the environment

In addition to coding proteins, RNA molecules, especially long noncoding RNAs (lncRNAs), have well-established functions in regulating gene expression. The number of studies focused on the roles played by different types of lncRNAs in a variety of plant biological processes has markedly increased. These lncRNA roles involve plant vegetative and reproductive growth and responses to biotic and abiotic stresses. In this review, we examine the classification, mechanisms, and functions of lncRNAs and then emphasize the roles played by these lncRNAs in the communication between plants and the environment mainly with respect to the following environmental factors: temperature, light, water, salt stress, and nutrient deficiencies. We also discuss the consensus among researchers and the remaining challenges and underscore the exciting ways lncRNAs may affect the biology of plants.

A lncRNA bra-miR156HG regulates flowering time and leaf morphology as a precursor of miR156 in Brassica campestris and Arabidopsis thaliana

Long non-coding RNAs (lncRNAs) are important regulators in plant growth and development. Here the function of a lncRNA fragment was studied, which was predicted as an endogenous target mimic (eTM) of miR156 in Brassica campesrtis. Unexpectedly, the transformation of this lncRNA into Arabidopsis thaliana neither inhibited the expression of miR156a nor resulted in any phenotypes that differed from the control plants (CK). The full-length sequence of the lncRNA (named bra-miR156HG) was then obtained using RACE and transferred into A. thaliana. The transgenic plants displayed a delay in flowering time, an increasing number of rosette leaves, and a changed morphology of cauline leaves, which was similar to the plants that expressed bra-miR156a. In contrast, the overexpression of bra-miR156HG in B. campestris resulted in an increased tip angle of leaves and changed the length-width ratio of leaves at different nodes, suggesting that bra-miR156HG may be involved in regulating the leaf morphology. Collectively, our study showed that bra-miR156HG functions as a precursor of bra-miR156a involved in regulating plant flowering time and leaf development under different biological backgrounds. The secondary structure of lncRNA is essential not only for the normal roles that it plays but also for expanding the functional diversities.

Comprehensive investigation of long non-coding RNAs in an endophytic fungus Calcarisporium arbuscula NRRL 3705

Long non-coding RNAs (lncRNAs) play an important role in eukaryotic cells. However, there is no report of lncRNAs in endophytic fungi Calcarisporium arbuscula. Here, in Calcarisporium arbuscula NRRL 3705, an endophytic fungus predominantly producing mycotoxins aurovertins, the genome-wide identification of lncRNAs was carried out based on RNA-Seq. Totally, 1332 lncRNAs were identified, including 1082 long intergenic noncoding RNAs, 64 long intronic noncoding RNAs and 186 long noncoding natural antisense transcripts. The average length of lncRNA and mRNA were 254 and 1102 bp, respectively. LncRNAs were shorter, with fewer exons and lower expression levels. Moreover, there were 39 up-regulated lncRNAs and 10 down-regulated lncRNAs in the ΔaurA mutant, which lacks the aurovertin biosynthetic enzyme AurA. Interestingly, expression of genes related to the metabolism of linoleic acid and methane were significantly down regulated in the ΔaurA mutant. This study enriches the endophytic fungal lncRNA database and provide a basis for further research.

miRNAs and lncRNAs in tomato: Roles in biotic and abiotic stress responses

Plants are continuously exposed to various biotic and abiotic stresses in the natural environment. To cope with these stresses, they have evolved a multitude of defenses mechanisms. With the rapid development of genome sequencing technologies, a large number of non-coding RNA (ncRNAs) have been identified in tomato, like microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Recently, more and more evidence indicates that many ncRNAs are involved in plant response to biotic and abiotic stresses in tomato. In this review, we summarize recent updates on the regulatory roles of ncRNAs in tomato abiotic/biotic responses, including abiotic (high temperature, drought, cold, salinization, etc.) and biotic (bacteria, fungi, viruses, insects, etc.) stresses. Understanding the molecular mechanisms mediated by ncRNAs in response to these stresses will help us to clarify the future directions for ncRNA research and resistance breeding in tomato.

From molecular basics to agronomic benefits: Insights into noncoding RNA-mediated gene regulation in plants

The development of plants is largely dependent on their growth environment. To better adapt to a particular habitat, plants have evolved various subtle regulatory mechanisms for altering gene expression. Non coding RNAs (ncRNAs) constitute a major portion of the transcriptomes of eukaryotes. Various ncRNAs have been recognized as important regulators of the expression of genes involved in essential biological processes throughout the whole life cycles of plants. In this review, we summarize the current understanding of the biogenesis and contributions of small nucle olar RNA (snoRNA)- and regulatory long non coding RNA (lncRNA)-mediated gene regulation in plant development and environmental responses. Many regulatory ncRNAs appear to be associated with increased yield, quality and disease resistance of various species and cultivars. These ncRNAs may potentially be used as genetic resources for improving agronomic traits and for molecular breeding. The challenges in understanding plant ncRNA biology and the possibilities to make better use of these valuable gene resources in the future are discussed in this review.

DNA and coding/non-coding RNA methylation analysis provide insights into tomato fruit ripening

Ripening is the last, irreversible developmental stage during which fruit become palatable, thus promoting seed dispersal by frugivory. In Alisa Craig fruit, mRNAs with increasing m5C levels, such as STPK and WRKY 40, were identified as being involved in response to biotic and abiotic stresses. Furthermore, two mRNAs involved in cell wall metabolism, PG and EXP-B1, also presented increased m5C levels. In the Nr mutant, several m5C-modified mRNAs involved in fruit ripening, including those encoding WRKY and MADS-box proteins, were found. Targets of long non-coding RNAs and circular RNAs with different m5C sites were also found; these targets included 2-alkenal reductase, soluble starch synthase 1, WRKY, MADS-box, and F-box/ketch-repeat protein SKIP11. A combined analysis of changes in 5mC methylation and mRNA revealed many differentially expressed genes with differentially methylated regions encoding transcription factors and key enzymes related to ethylene biosynthesis and signal transduction; these included ERF084, EIN3, AP2/ERF, ACO5, ACS7, EIN3/4, EBF1, MADS-box, AP2/ERF, and ETR1. Taken together, our findings contribute to the global understanding of the mechanisms underlying fruit ripening, thereby providing new information for both fruit and post-harvest behavior.

Population transcriptomic analysis identifies the comprehensive lncRNAs landscape of spike in wheat (Triticum aestivum L.)

BACKGROUND

Long noncoding RNAs (lncRNAs) are emerging as the important regulators involving in growth and development as well as stress response in plants. However, current lncRNA studies were mainly performed at the individual level and the significance of it is not well understood in wheat.

RESULTS

In this study, the lncRNA landscape of wheat spike was characterized through analysing a total of 186 spike RNA-seq datasets from 93 wheat genotypes. A total of 35,913 lncRNAs as well as 1,619 lncRNA-mRNA pairs comprised of 443 lncRNAs and 464 mRNAs were obtained. Compared to coding genes, these lncRNAs displayed rather low conservation among wheat and other gramineous species. Based on re-sequencing data, the genetic variations of these lncRNA were investigated and obvious genetic bottleneck were found on them during wheat domestication process. Furthermore, 122 lncRNAs were found to act as ceRNA to regulate endogenous competition. Finally, association and co-localization analysis of the candidate lncRNA-mRNA pairs identified 170 lncRNAs and 167 target mRNAs significantly associated with spike-related traits, including lncRNA.127690.1/TraesCS2A02G518500.1 (PMEI) and lncRNA.104854.1/TraesCS6A02G050300.1 (ATG5) associated with heading date and spike length, respectively.

CONCLUSIONS

This study reported the lncRNA landscape of wheat spike through the population transcriptome analysis, which not only contribute to better understand the wheat evolution from the perspective of lncRNA, but also lay the foundation for revealing roles of lncRNA playing in spike development.

Identification and Analysis of Long Non-Coding RNAs Related to UV-B-Induced Anthocyanin Biosynthesis During Blood-Fleshed Peach (Prunus persica) Ripening

Blood flesh is a key fruit trait in peaches (Prunus persica) and can be attributed to the accumulation of anthocyanins. The roles of long non-coding RNAs (lncRNAs) have been highlighted by multiple studies in regulating fruit ripening, anthocyanin accumulation, and abiotic stress responses in many flowering plants. Such regulatory functions of lncRNAs in Prunus persica, nonetheless, have not been reported. In this research, we sequenced and analyzed the complete transcriptome of C3-20 (a blood-fleshed peach) fruit at four developmental stages. Analyses of the correlated genes and differentially expressed lncRNA target genes helped to forecast lncRNAs’ possible functions. The RNA-seq data were generated using high-throughput sequencing. In total, 17,456 putative lncRNAs, including 4,800 intergenic lncRNAs, 2,199 antisense lncRNAs, and 10,439 intronic lncRNAs were discovered, of which 4,871 differentially expressed lncRNAs (DE-lncRNAs) were annotated in the fruit developmental processes. The target genes of these DE-lncRNAs and their regulatory relationship identifying 21,795 cis-regulated and 18,271 trans-regulated targets of the DE-lncRNAs were in a similar way predicted by us. The enriched GO terms for the target genes included anthocyanin biosynthesis. Flavonoid biosynthesis and plant hormone signal transduction were also included in the enriched KEGG pathways. Co-expression network construction demonstrated that the highly expressed genes might co-regulate multiple other genes associated with auxin signal transduction and take effect in equal pathways. We discovered that lncRNAs, including LNC_000987, LNC_000693, LNC_001323, LNC_003610, LNC_001263, and LNC_003380, correlated with fruit that ripened and could take part in ethylene biosynthesis and metabolism and the ABA signaling pathway. Several essential transcription factors, such as ERFs, WRKY70, NAC56, and NAC72, may in a similar way regulate fruit ripening. Three DE-lncRNAs, XLOC_011933, XLOC_001865, and XLOC_042291, are involved in UV-B-induced anthocyanin biosynthesis and positively regulating UVR8 and COP10, were identified and characterized. Our discovery and characterization of XLOC_011933, XLOC_001865, and XLOC_042291 provide a more precise understanding and preliminarily establishes a theoretical framework for UV-B-induced flesh anthocyanin biosynthesis. This phenomenon might encourage more in-depth investigations to study the molecular mechanisms underlying peach flesh coloring.

The Functional Interplay between Ethylene, Hydrogen Sulfide, and Sulfur in Plant Heat Stress Tolerance

Plants encounter several abiotic stresses, among which heat stress is gaining paramount attention because of the changing climatic conditions. Severe heat stress conspicuously reduces crop productivity through changes in metabolic processes and in growth and development. Ethylene and hydrogen sulfide (H2S) are signaling molecules involved in defense against heat stress through modulation of biomolecule synthesis, the antioxidant system, and post-translational modifications. Other compounds containing the essential mineral nutrient sulfur (S) also play pivotal roles in these defense mechanisms. As biosynthesis of ethylene and H2S is connected to the S-assimilation pathway, it is logical to consider the existence of a functional interplay between ethylene, H2S, and S in relation to heat stress tolerance. The present review focuses on the crosstalk between ethylene, H2S, and S to highlight their joint involvement in heat stress tolerance.

Comprehensive Transcriptome Analysis Uncovers Hub Long Non-coding RNAs Regulating Potassium Use Efficiency in Nicotiana tabacum

Potassium (K) is the essential element for plant growth. It is one of the critical factors that determine crop yield, quality, and especially leaf development in tobacco. However, the molecular mechanism of potassium use efficiency (KUE), especially non-coding RNA, is still unknown. In this study, tobacco seedlings were employed, and their hydro-cultivation with K treatments of low and sufficient concentrations was engaged. Physiological analysis showed that low potassium treatment could promote malondialdehyde (MDA) accumulation and antioxidant enzyme activities such as peroxidase (POD), ascorbate-peroxidase (APX). After transcriptomic analysis, a total of 10,585 LncRNA transcripts were identified, and 242 of them were significantly differently expressed under potassium starvation. Furthermore, co-expression networks were constructed and generated 78 potential regulation modules in which coding gene and LncRNAs are involved and functional jointly. By further module-trait analysis and module membership (MM) ranking, nine modules, including 616 coding RNAs and 146 LncRNAs, showed a high correlation with K treatments, and 20 hub K-responsive LncRNAs were finally predicted. Following gene ontology (GO) analysis, the results showed potassium starvation inducing the pathway of antioxidative stress which is consistent with the physiology result mentioned above. Simultaneously, a part of detected LncRNAs, such as MSTRG.6626.1, MSTRG.11330.1, and MSTRG.16041.1, were co-relating with a bench of MYB, C3H, and NFYC transcript factors in response to the stress. Overall, this research provided a set of LncRNAs that respond to K concentration from starvation and sufficient supply. Simultaneously, the regulation network and potential co-functioning genes were listed as well. This massive dataset would serve as an outstanding clue for further study in tobacco and other plant species for nutrient physiology and molecular regulation mechanism.

Mechanisms of Oogenesis-Related Long Non-coding RNAs in Porcine Ovaries Treated With Recombinant Pig Follicle-Stimulating Hormone

Reproductive efficiency is of significant importance in pork production for it has a great impact on economic success. Ovulation rate is an early component of reproduction efficiency of pigs, and it contributes to the upper limit of litter size. In this study, we used the newly developed recombinant pig follicle stimulating hormone (rpFSH) instead of traditional PMSG to increase ovulation rate of pigs in order to achieve higher litter size, for it was better at stimulating ovulation, and showed more cheaper and greener. However, relatively little is known about the underlying genetic bases and molecular mechanisms. Consequently, an experiment was carried out in ovaries of replacement gilts to screen the key genes and lncRNAs that affect the fecundity of pigs by RNA-seq technology. Twenty gilts were divided into two groups, including 10 rpFSH treatment pigs and 10 control animals. After slaughtering and collecting the phenotypic data, ovaries of five pigs in each group were selected for RNA-seq. Total RNA was extracted to construct the library and then sequence on an Illumina Hiseq 4000 system. A comprehensive analysis of mRNAs and long non-coding RNAs (lncRNAs) from 10 samples was performed with bioinformatics. The phenotypic data showed that rpFSH treatment groups had the higher (P < 0.01) ovarian weight and more mature follicles. The RNA-seq results showed that a total of 43,499 mRNAs and 21,703 lncRNAs were identified, including 21,300 novel lncRNAs and 403 known lncRNAs, of which 585 mRNAs and 398 lncRNAs (P < 0.05) were significantly differentially expressed (DE) between the two groups of rpFSH treatment group and controlled group. GO and KEGG annotation analysis indicated that the target genes of DE lncRNAs and DE mRNAs were related to prolactin receptor activity, mitophagy by induced vacuole formation, and meiotic spindle. Moreover, we found that NR5A2 (nuclear receptor subfamily 5, group A, member 2), a target gene of lncRNA MSTRG.3902.1, was involved in regulating follicular development, ovulation, and estrogen production. Our study provided a catalog of lncRNAs and mRNAs associated with ovulation of rpFSH treatment, and they deserve further study to deepen the understanding of biological processes in the regulation of ovaries of rpFSH treatment pigs.

Comparison of lncRNA Expression in the Uterus between Periods of Embryo Implantation and Labor in Mice

Simple Summary

Progesterone has been proven to play an important role in female mammals during pregnancy. In this study, the uteri of pregnant mice were collected to compare mRNA and lncRNA expression between periods of embryo implantation and labor. The results show that 19 known differentially expressed lncRNAs and 31 novel differentially lncRNAs were commonly expressed between the two stages, indicating that these lncRNAs’ function is related to progesterone.

Abstract

Uterine function during pregnancy is regulated mainly by progesterone (P4) and estrogen (E2). Serum P4 levels are known to fluctuate significantly over the course of pregnancy, especially during embryo implantation and labor. In this study, pregnant mice at E0.5, E4.5, E15.5, and E18.5 (n = 3/E) were used for an RNA-Seq-based analysis of mRNA and lncRNA expression. In this analysis, 1971 differentially expressed (DE) mRNAs, 493 known DE lncRNAs, and 1041 novel DE lncRNAs were found between E0.5 and E4.5 at the embryo implantation stage, while 1149 DE mRNAs, 192 known DE lncRNAs, and 218 novel DE lncRNAs were found between E15.5 and E18.5 at the labor stage. The expression level of lncRNA-MMP11 was significantly downregulated by P4 treatment on MSM cells, while lncRNA-ANKRD37 was significantly upregulated. Notably, 117 DE mRNAs, 19 known DE lncRNAs, and 31 novel DE lncRNAs were commonly expressed between the two stages, indicating that these mRNAs and lncRNAs may be directly or indirectly regulated by P4.

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.

Genome-wide profiling of long noncoding RNAs involved in wheat spike development

BACKGROUND

Long noncoding RNAs (lncRNAs) have been shown to play important roles in the regulation of plant growth and development. Recent transcriptomic analyses have revealed the gene expression profiling in wheat spike development, however, the possible regulatory roles of lncRNAs in wheat spike morphogenesis remain largely unclear.

RESULTS

Here, we analyzed the genome-wide profiling of lncRNAs during wheat spike development at six stages, and identified a total of 8,889 expressed lncRNAs, among which 2,753 were differentially expressed lncRNAs (DE lncRNAs) at various developmental stages. Three hundred fifteen differentially expressed cis- and trans-regulatory lncRNA-mRNA pairs comprised of 205 lncRNAs and 279 genes were predicted, which were found to be mainly involved in the stress responses, transcriptional and enzymatic regulations. Moreover, the 145 DE lncRNAs were predicted as putative precursors or target mimics of miRNAs. Finally, we identified the important lncRNAs that participate in spike development by potentially targeting stress response genes, TF genes or miRNAs.

CONCLUSIONS

This study outlines an overall view of lncRNAs and their possible regulatory networks during wheat spike development, which also provides an alternative resource for genetic manipulation of wheat spike architecture and thus yield.

From "Dark Matter" to "Star": Insight Into the Regulation Mechanisms of Plant Functional Long Non-Coding RNAs

Long non-coding RNAs (lncRNAs) play a vital role in a variety of biological functions in plant growth and development. In this study, we provided an overview of the molecular mechanisms of lncRNAs in interacting with other biomolecules with an emphasis on those lncRNAs validated only by low-throughput experiments. LncRNAs function through playing multiple roles, including sponger for sequestering RNA or DNA, guider or decoy for recruiting or hijacking transcription factors or peptides, and scaffold for binding with chromatin modification complexes, as well as precursor of microRNAs or small interfering RNAs. These regulatory roles have been validated in several plant species with a comprehensive list of 73 lncRNA-molecule interaction pairs in 16 plant species found so far, suggesting their commonality in the plant kingdom. Such initial findings of a small number of functional plant lncRNAs represent the beginning of what is to come as lncRNAs with unknown functions were found in orders of magnitude more than proteins.

Interplay between miRNAs and lncRNAs: Mode of action and biological roles in plant development and stress adaptation

Plants employ sophisticated mechanisms to control developmental processes and to cope with environmental changes at transcriptional and post-transcriptional levels. MicroRNAs (miRNAs) and long noncoding RNAs (lncRNAs), two classes of endogenous noncoding RNAs, are key regulators of gene expression in plants. Recent studies have identified the interplay between miRNAs and lncRNAs as a novel regulatory layer of gene expression in plants. On one hand, miRNAs target lncRNAs for the production of phased small interfering RNAs (phasiRNAs). On the other hand, lncRNAs serve as origin of miRNAs or regulate the accumulation or activity of miRNAs at transcription and post-transcriptional levels. Theses lncRNA-miRNA interplays are crucial for plant development, physiology and responses to biotic and abiotic stresses. In this review, we summarize recent advances in the biological roles, interaction mechanisms and computational predication methods of the interplay between miRNAs and lncRNAs in plants.

Comparative Transcriptome Profiling of mRNA and lncRNA of Ovaries in High and Low Egg Production Performance in Domestic Pigeons (Columba livia)

Egg production performance is one of the most important economic traits in pigeon industry. However, little is known regarding how egg production performance is regulated by long non-coding RNAs (lncRNAs) in pigeons. To evaluate the lncRNAs and mRNAs in ovaries associated with egg production performance in domestic pigeons, high-throughput RNA sequencing of ovaries between high and low egg production performance groups were performed and analyzed in this study. A total of 34,346 mRNAs and 24,601 lncRNAs were identified, including 14,525 known lncRNAs and 10,076 novel lncRNAs, of which 811 mRNAs and 148 lncRNAs (P < 0.05) were significantly differentially expressed (DE) between the groups of high and low egg production performance. GO and KEGG annotation analysis indicated that the target genes of DE lncRNAs and DE mRNAs were related to cell differentiation, ATP binding and methylation. Moreover, we found that FOXK2, a target gene of lncRNA MSTRG.7894.4, was involved in regulating estrogen receptors. Our study provided a catalog of lncRNAs and mRNAs associated with egg production performance, and they deserve further study to deepen the understanding of biological processes in the ovaries of pigeons.

Novel targets for engineering Physostegia chlorotic mottle and tomato brown rugose fruit virus-resistant tomatoes: in silico prediction of tomato microRNA targets

Background

Physostegia chlorotic mottle virus (PhCMoV; genus: Alphanucleorhabdovirus, family: Rhabdoviridae) and tomato brown rugose fruit virus (ToBRFV; genus: Tobamovirus, family: Virgaviridae) are newly emerging plant viruses that have a dramatic effect on tomato production. Among various known virus-control strategies, RNAi-mediated defence has shown the potential to protect plants against various pathogens including viral infections. Micro(mi)RNAs play a major role in RNAi-mediated defence.

Methods

Using in silico analyses, we investigated the possibility of tomato-encoded miRNAs (TomiRNA) to target PhCMoV and ToBRFV genomes using five different algorithms, i.e., miRanda, RNAhybrid, RNA22, Tapirhybrid and psRNATarget.

Results

The results revealed that 14 loci on PhCMoV and 10 loci on ToBRFV can be targeted by the TomiRNAs based on the prediction of at least three algorithms. Interestingly, one TomiRNA, miR6026, can target open reading frames from both viruses, i.e., the phosphoprotein encoding gene of PhCMoV, and the two replicase components of ToBRFV. There are currently no commercially available PhCMoV- or ToBRFV-resistant tomato varieties, therefore the predicted data provide useful information for the development of PhCMoV- and ToBFRV-resistant tomato plants.

Noncoding RNAs: functional regulatory factors in tomato fruit ripening

Tomato has emerged as the model system for investigations into the regulation of fleshy-fruit ripening and senescence, and the ripening process involving the coordinated regulation at the gene/chromatin/epigenetic, transcriptional, post-transcriptional and protein levels. Noncoding RNAs play important roles in fruit ripening as important transcriptional and post-transcriptional regulatory factors. In this review, we systematically summarize the recent advances in the regulation of tomato fruit ripening involved in ethylene biosynthesis and signal transduction, fruit pigment accumulation, fruit flavor and aroma, fruit texture by noncoding RNAs and their coordinate regulatory network model were set up and also suggest future directions for the functional regulations of noncoding RNAs on tomato fruit ripening.

Analysis of Long Noncoding RNA and mRNA Expression Profiles of Testes with High and Low Sperm Motility in Domestic Pigeons (Columba livia)

Sperm motility is one of the most important indicators in assessing semen quality, and it is used to evaluate poultry fertility. Many long noncoding RNAs (lncRNAs) and mRNAs are involved in regulating testis development and spermatogenesis. In this study, we employed RNA sequencing to analyse the testis transcriptome (lncRNA and mRNA) of ten pigeons with high and low sperm motility. In total, 46,117 mRNAs and 17,463 lncRNAs were identified, of which 2673 mRNAs and 229 lncRNAs (P < 0.05) were significantly differentially expressed (DE) between the high and low sperm motility groups. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analysis showed that target genes of DE lncRNAs and DE mRNAs were related to calcium ion binding, ATP binding, and spermatogenesis. Moreover, we found that UBB, a target gene of lncRNA MSTRG.7787.5, was involved in germ cell development. Our study provided a catalogue of lncRNAs and mRNAs associated with sperm motility, and they deserve further study to deepen the understanding of biological processes in the pigeon testis.

Identification and characterization of mRNAs and lncRNAs of a barley shrunken endosperm mutant using RNA-seq

Barley shrunken endosperm mutants have been extensively reported. However, knowledge of the underlying molecular mechanisms of these mutants remains limited. Here, a pair of near isogenic lines (normal endosperm: Bowman and shrunken endosperm: sex1) was subjected to transcriptome analysis to identify mRNAs and lncRNAs related to endosperm development to further dissect its mechanism of molecular regulation. A total of 2123 (1140 up- and 983 down-regulated) unique differentially expressed genes (DEGs) were detected. Functional analyses showed that these DEGs were mainly involved in starch and sucrose metabolism, biosynthesis of secondary metabolites, and plant hormone signal transduction. A total of 343 unique target genes were identified for 57 differentially expressed lncRNAs (DE lncRNAs). These DE lncRNAs were mainly involved in glycerophospholipid metabolism, starch and sucrose metabolism, hormone signal transduction, and stress response. In addition, key lncRNAs were identified by constructing a co-expression network of the target genes of DE lncRNAs. Transcriptome results suggested that mRNA and lncRNA played a critical role in endosperm development. The shrunken endosperm in barley seems to be closely related to plant hormone signal transduction, starch and sucrose metabolism, and cell apoptosis. This study provides a foundation for fine mapping, elucidates the molecular mechanism of shrunken endosperm mutants, and also provides a reference for further studies of lncRNAs during the grain development of plants.

Tomato lncRNA23468 functions as a competing endogenous RNA to modulate NBS-LRR genes by decoying miR482b in the tomato-Phytophthora infestans interaction

Our previous studies indicated that tomato miR482b could negatively regulate the resistance of tomato to Phytophthora infestans and the expression of miR482b was decreased after inoculation with P. infestans. However, the mechanism by which the accumulation of miR482b is suppressed remains unclear. In this study, we wrote a program to identify 89 long noncoding RNA (lncRNA)-originated endogenous target mimics (eTMs) for 46 miRNAs from our RNA-Seq data. Three tomato lncRNAs, lncRNA23468, lncRNA01308 and lncRNA13262, contained conserved eTM sites for miR482b. When lncRNA23468 was overexpressed in tomato, miR482b expression was significantly decreased, and the expression of the target genes, NBS-LRRs, was significantly increased, resulting in enhanced resistance to P. infestans. Silencing lncRNA23468 in tomato led to the increased accumulation of miR482b and decreased accumulation of NBS-LRRs, as well as reduced resistance to P. infestans. In addition, the accumulation of both miR482b and NBS-LRRs was not significantly changed in tomato plants that overexpressed lncRNA23468 with a mutated eTM site. Based on the VIGS system, a target gene of miR482b, Solyc02g036270.2, was silenced. The disease symptoms of the VIGS-Solyc02g036270.2 tomato plants were in accordance with those of tomato plants in which lncRNA23468 was silenced after inoculation with P. infestans. More severe disease symptoms were found in the modified plants than in the control plants. Our results demonstrate that lncRNAs functioning as eTMs may modulate the effects of miRNAs in tomato and provide insight into how the lncRNA23468-miR482b-NBS-LRR module regulates tomato resistance to P. infestans.