Conjoint Analysis of Genome-Wide lncRNA and mRNA Expression of Heteromorphic Leavesin Response to Environmental Heterogeneityin Populus euphratica

Heterophylly is the phenomenon of leaf forms varying along the longitudinal axis within a single plant. Populus euphratica, a heterophyllous woody plant, develops lanceolate leaves and dentate broad-ovate leaves on the bottom and top of the canopy, respectively, which are faced with different intensities of ambient solar radiation. However, the mechanism of the heteromorphic leaf response to the microenvironment in P. euphratica remains elusive. Here, we show that the dentate broad-ovate leaves have advantages in tolerating high light intensity, while lanceolate leaves are excellent at capturing light. Compared with lanceolate leaves, more trichomes, higher stomatal density, thicker lamina, and higher specific leaf weight were observed in dentate broad-ovate leaves. Furthermore, high-throughput RNA sequencing analysis revealed that the expression patterns of genes and long noncoding RNAs (lncRNAs) are different between the two heteromorphic leaves. A total of 36,492 genes and 1725 lncRNAs were detected, among which 586 genes and 54 lncRNAs were differentially expressed. Based on targets prediction, lncRNAs and target genes involved in light adaption, protein repair, stress response, and growth and development pathways were differentially expressed in heteromorphic leaves, 10 pairs of which were confirmed by quantitative real-time PCR. Additionally, the analysis of interactions indicated that lncRNA–mRNA interactions were involved in the response to the microenvironment of heteromorphic leaves. Taken together, these results suggest that the morphological features and joint regulation of lncRNA–mRNA in heteromorphic leaves may serve as survival strategies for P. euphratica, which could lead to optimal utilization of environmental factors.

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Profiling of MicroRNAs in Midguts of Plutella xylostella Provides Novel Insights Into the Bacillus thuringiensis Resistance

Frontiers in Genetics ◽

10.3389/fgene.2021.739849 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jie Yang ◽

Xuejiao Xu ◽

Sujie Lin ◽

Shiyao Chen ◽

Guifang Lin ◽

...

Keyword(s):

Bacillus Thuringiensis ◽

Plutella Xylostella ◽

Target Genes ◽

Expression Patterns ◽

Mapk Signaling ◽

Differentially Expressed ◽

Luciferase Reporter ◽

Sequencing Analysis ◽

Bt Resistance ◽

Differentially Expressed Mirnas

The diamondback moth (DBM), Plutella xylostella, one of the most destructive lepidopteran pests worldwide, has developed field resistance to Bacillus thuringiensis (Bt) Cry toxins. Although miRNAs have been reported to be involved in insect resistance to multiple insecticides, our understanding of their roles in mediating Bt resistance is limited. In this study, we constructed small RNA libraries from midguts of the Cry1Ac-resistant (Cry1S1000) strain and the Cry1Ac-susceptible strain (G88) using a high-throughput sequencing analysis. A total of 437 (76 known and 361 novel miRNAs) were identified, among which 178 miRNAs were classified into 91 miRNA families. Transcripts per million analysis revealed 12 differentially expressed miRNAs between the Cry1S1000 and G88 strains. Specifically, nine miRNAs were down-regulated and three up-regulated in the Cry1S1000 strain compared to the G88 strain. Next, we predicted the potential target genes of these differentially expressed miRNAs and carried out GO and KEGG pathway analyses. We found that the cellular process, metabolism process, membrane and the catalytic activity were the most enriched GO terms and the Hippo, MAPK signaling pathway might be involved in Bt resistance of DBM. In addition, the expression patterns of these miRNAs and their target genes were determined by RT-qPCR, showing that partial miRNAs negatively while others positively correlate with their corresponding target genes. Subsequently, novel-miR-240, one of the differentially expressed miRNAs with inverse correlation with its target genes, was confirmed to interact with Px017590 and Px007885 using dual luciferase reporter assays. Our study highlights the characteristics of differentially expressed miRNAs in midguts of the Cry1S1000 and G88 strains, paving the way for further investigation of miRNA roles in mediating Bt resistance.

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Genome-wide analysis of changes in miRNA and target gene expression reveals key roles in heterosis for Chinese cabbage biomass

Horticulture Research ◽

10.1038/s41438-021-00474-6 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Peirong Li ◽

Tongbing Su ◽

Deshuang Zhang ◽

Weihong Wang ◽

Xiaoyun Xin ◽

...

Keyword(s):

Chinese Cabbage ◽

Leaf Development ◽

Target Genes ◽

Expression Patterns ◽

Seedling Stage ◽

Differentially Expressed ◽

Small Rna Sequencing ◽

Leaf Morphogenesis ◽

Expression Levels ◽

Parental Lines

AbstractHeterosis is a complex phenomenon in which hybrids show better phenotypic characteristics than their parents do. Chinese cabbage (Brassica rapa L. spp. pekinensis) is a popular leafy crop species, hybrids of which are widely used in commercial production; however, the molecular basis of heterosis for biomass of Chinese cabbage is poorly understood. We characterized heterosis in a Chinese cabbage F1 hybrid cultivar and its parental lines from the seedling stage to the heading stage; marked heterosis of leaf weight and biomass yield were observed. Small RNA sequencing revealed 63 and 50 differentially expressed microRNAs (DEMs) at the seedling and early-heading stages, respectively. The expression levels of the majority of miRNA clusters in the F1 hybrid were lower than the mid-parent values (MPVs). Using degradome sequencing, we identified 1,819 miRNA target genes. Gene ontology (GO) analyses demonstrated that the target genes of the MPV-DEMs and low parental expression level dominance (ELD) miRNAs were significantly enriched in leaf morphogenesis, leaf development, and leaf shaping. Transcriptome analysis revealed that the expression levels of photosynthesis and chlorophyll synthesis-related MPV-DEGs (differentially expressed genes) were significantly different in the F1 hybrid compared to the parental lines, resulting in increased photosynthesis capacity and chlorophyll content in the former. Furthermore, expression of genes known to regulate leaf development was also observed at the seedling stage. Arabidopsis plants overexpressing BrGRF4.2 and bra-miR396 presented increased and decreased leaf sizes, respectively. These results provide new insight into the regulation of target genes and miRNA expression patterns in leaf size and heterosis for biomass of B. rapa.

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Genome-Wide Identification of Long Non-coding RNA in Trifoliate Orange (Poncirus trifoliata (L.) Raf) Leaves in Response to Boron Deficiency

International Journal of Molecular Sciences ◽

10.3390/ijms20215419 ◽

2019 ◽

Vol 20 (21) ◽

pp. 5419 ◽

Cited By ~ 4

Author(s):

Gao-Feng Zhou ◽

Li-Ping Zhang ◽

Bi-Xian Li ◽

Ou Sheng ◽

Qing-Jiang Wei ◽

...

Keyword(s):

Signal Transduction ◽

Plant Hormones ◽

Target Genes ◽

Expression Patterns ◽

Poncirus Trifoliata ◽

Differentially Expressed ◽

Boron Deficiency ◽

Trifoliate Orange ◽

Genome Wide ◽

A Genome

Long non-coding RNAs (lncRNAs) play important roles in plant growth and stress responses. As a dominant abiotic stress factor in soil, boron (B) deficiency stress has impacted the growth and development of citrus in the red soil region of southern China. In the present work, we performed a genome-wide identification and characterization of lncRNAs in response to B deficiency stress in the leaves of trifoliate orange (Poncirus trifoliata), an important rootstock of citrus. A total of 2101 unique lncRNAs and 24,534 mRNAs were predicted. Quantitative real-time polymerase chain reaction (qRT-PCR) experiments were performed for a total of 16 random mRNAs and lncRNAs to validate their existence and expression patterns. Expression profiling of the leaves of trifoliate orange under B deficiency stress identified 729 up-regulated and 721 down-regulated lncRNAs, and 8419 up-regulated and 8395 down-regulated mRNAs. Further analysis showed that a total of 84 differentially expressed lncRNAs (DELs) were up-regulated and 31 were down-regulated, where the number of up-regulated DELs was 2.71-fold that of down-regulated. A similar trend was also observed in differentially expressed mRNAs (DEMs, 4.21-fold). Functional annotation of these DEMs was performed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, and the results demonstrated an enrichment of the categories of the biosynthesis of secondary metabolites (including phenylpropanoid biosynthesis/lignin biosynthesis), plant hormone signal transduction and the calcium signaling pathway. LncRNA target gene enrichment identified several target genes that were involved in plant hormones, and the expression of lncRNAs and their target genes was significantly influenced. Therefore, our results suggest that lncRNAs can regulate the metabolism and signal transduction of plant hormones, which play an important role in the responses of citrus plants to B deficiency stress. Co-expression network analysis indicated that 468 significantly differentially expressed genes may be potential targets of 90 lncRNAs, and a total of 838 matched lncRNA-mRNA pairs were identified. In summary, our data provides a rich resource of candidate lncRNAs and mRNAs, as well as their related pathways, thereby improving our understanding of the role of lncRNAs in response to B deficiency stress, and in symptom formation caused by B deficiency in the leaves of trifoliate orange.

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Identification of Differentially Expressed MicroRNAs and Their Potential Target Genes in Adipose Tissue from Pigs with Highly Divergent Backfat Thickness

Animals ◽

10.3390/ani10040624 ◽

2020 ◽

Vol 10 (4) ◽

pp. 624

Author(s):

Kai Xing ◽

Xitong Zhao ◽

Yibing Liu ◽

Fengxia Zhang ◽

Zhen Tan ◽

...

Keyword(s):

Target Genes ◽

Expression Patterns ◽

Fat Deposition ◽

Functional Enrichment ◽

Differentially Expressed ◽

Backfat Thickness ◽

P Value ◽

Sibling Pairs ◽

Differentially Expressed Mirnas

Fatty traits are very important in pig production. However, the role of microRNAs (miRNAs) in fat deposition is not clearly understood. In this study, we compared adipose miRNAs from three full-sibling pairs of female Landrace pigs, with high and low backfat thickness, to investigate the associated regulatory network. We obtained an average of 17.29 million raw reads from six libraries, 62.27% of which mapped to the pig reference genome. A total of 318 pig miRNAs were detected among the samples. Among them, 18 miRNAs were differentially expressed (p-value < 0.05, |log2fold change| ≥ 1) between the high and low backfat groups; 6 were up-regulated and 12 were down-regulated. Functional enrichment of the predicted target genes of the differentially expressed miRNAs, indicated that these miRNAs were involved mainly in lipid and carbohydrate metabolism, and glycan biosynthesis and metabolism. Comprehensive analysis of the mRNA and miRNA transcriptomes revealed possible regulatory relationships for fat deposition. Negatively correlated mRNA–miRNA pairs included miR-137–PPARGC1A, miR-141–FASN, and miR-122-5p–PKM, indicating these interactions may be key regulators of fat deposition. Our findings provide important insights into miRNA expression patterns in the backfat tissue of pig and new insights into the regulatory mechanisms of fat deposition in pig.

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RNA-Seq Analysis of Prickled and Prickle-Free Epidermis Provides Insight into the Genetics of Prickle Development in Red Raspberry (Rubus ideaus L.)

Agronomy ◽

10.3390/agronomy10121904 ◽

2020 ◽

Vol 10 (12) ◽

pp. 1904 ◽

Cited By ~ 1

Author(s):

Archana Khadgi ◽

Courtney A. Weber

Keyword(s):

Differentially Expressed Genes ◽

Expression Patterns ◽

Rubus Idaeus ◽

Differentially Expressed ◽

Pcr Analysis ◽

Sequencing Analysis ◽

Red Raspberry ◽

Specialty Crop ◽

Rubus Species ◽

R2r3 Myb

Red raspberry (Rubus idaeus L.) is a globally commercialized specialty crop with growing demand worldwide. The presence of prickles on the stems, petioles and undersides of the leaves complicates both the field management and harvesting of raspberries. An RNA sequencing analysis was used to identify differentially expressed genes in the epidermal tissue of prickled “Caroline” and prickle-free “Joan J.” and their segregating progeny. Expression patterns of differentially expressed genes (DEGs) in prickle-free plants revealed the downregulation of some vital development-related transcription factors (TFs), including a MIXTA-like R2R3-MYB family member; MADS-box; APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) and NAM, ATAF1/2 and CUC2 (NAC) in prickle-free epidermis tissue. The downregulation of these TFs was confirmed by qRT-PCR analysis, indicating a key regulatory role in prickle development. This study adds to the understanding of prickle development mechanisms in red raspberries needed for utilizing genetic engineering strategies for developing prickle-free raspberry cultivars and, possibly, other Rubus species, such as blackberry (Rubus sp.) and black raspberry (R. occidentalis L.).

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Next-generation sequencing analysis reveals segmental patterns of microRNA expression in yak epididymis

Reproduction Fertility and Development ◽

10.1071/rd20113 ◽

2020 ◽

Vol 32 (12) ◽

pp. 1067

Author(s):

Wangsheng Zhao ◽

Eugene Quansah ◽

Meng Yuan ◽

Pengcheng Li ◽

Chuanping Yi ◽

...

Keyword(s):

Gene Expression ◽

Mirna Expression ◽

Expression Patterns ◽

Differentially Expressed ◽

Sequencing Analysis ◽

Differentially Expressed Mirnas ◽

Next Generation Sequencing Analysis ◽

Cauda Epididymidis ◽

Caput Epididymidis

MicroRNAs (miRNAs) have emerged as potent regulators of gene expression and are widely expressed in biological systems. In reproduction, they have been shown to have a significant role in the acquisition and maintenance of male fertility, whereby deletion of Dicer in mouse germ cells leads to infertility. Evidence indicates that this role of miRNAs extends from the testis into the epididymis, controlling gene expression and contributing to regional variations in gene expression. In this study, RNA sequencing technology was used to investigate miRNA expression patterns in the yak epididymis. Region-specific miRNA expression was found in the yak epididymis. In all, 683 differentially expressed known miRNAs were obtained; 190, 186 and 307 differentially expressed miRNAs were identified for caput versus corpus, corpus versus cauda and caput versus cauda region pairs respectively. Kyoto Encyclopedia of Genes and Genomes results showed endocytosis as the most enriched pathway across region pairs, followed by protein processing in the endoplasmic reticulum, phagosome, spliceosome and biosynthesis of amino acids in region pair-specific hierarchical order. Gene ontology results showed varied enrichment in terms including cell, biogenesis, localisation, binding and locomotion across region pairs. In addition, significantly higher miR-34c expression was seen in the yak caput epididymidis relative to the corpus and cauda epididymidis.

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Genome-wide profiling of miRNA expression patterns in tubal endometriosis

Reproduction ◽

10.1530/rep-18-0631 ◽

2019 ◽

Vol 157 (6) ◽

pp. 525-534 ◽

Cited By ~ 4

Author(s):

Hang Qi ◽

Guiling Liang ◽

Jin Yu ◽

Xiaofeng Wang ◽

Yan Liang ◽

...

Keyword(s):

Pathway Analysis ◽

Mirna Expression ◽

Gene Networks ◽

Target Genes ◽

Expression Profiles ◽

Expression Patterns ◽

Mirna Gene ◽

Differentially Expressed ◽

Signal Pathways ◽

Differentially Expressed Mirnas

MicroRNA (miRNA) expression proﬁles in tubal endometriosis (EM) are still poorly understood. In this study, we analyzed the differential expression of miRNAs and the related gene networks and signaling pathways in tubal EM. Four tubal epithelium samples from tubal EM patients and five normal tubal epithelium samples from uterine leiomyoma patients were collected for miRNA microarray. Bioinformatics analyses, including Ingenuity Pathway Analysis (IPA), Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, were performed. Quantitative real-time polymerase chain reaction (qRT-PCR) validation of five miRNAs was performed in six tubal epithelium samples from tubal EM and six from control. A total of 17 significantly differentially expressed miRNAs and 4343 potential miRNA-target genes involved in tubal EM were identified (fold change >1.5 and FDR-adjustedPvalue <0.05). IPA indicated connections between miRNAs, target genes and other gynecological diseases like endometrial carcinoma. GO and KEGG analysis revealed that most of the identified genes were involved in the mTOR signaling pathway, SNARE interactions in vesicular transport and endocytosis. We constructed an miRNA-gene-disease network using target gene prediction. Functional analysis showed that the mTOR pathway was connected closely to tubal EM. Our results demonstrate for the first time the differentially expressed miRNAs and the related signal pathways involved in the pathogenesis of tubal EM which contribute to elucidating the pathogenic mechanism of tubal EM-related infertility.

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Transcriptome and Small RNA Combined Sequencing Analysis of Cold Tolerance in Non-heading Chinese Cabbage

Frontiers in Genetics ◽

10.3389/fgene.2021.605292 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jin Wang ◽

Qinxue Zhang ◽

Xiong You ◽

Xilin Hou

Keyword(s):

Gene Expression ◽

Brassica Rapa ◽

Small Rna ◽

Target Genes ◽

Differentially Expressed ◽

Sequencing Analysis ◽

Pak Choi ◽

Expression Levels ◽

Heading Chinese Cabbage ◽

Gene Expression Levels

BackgroundNon-heading Chinese cabbage (Brassica rapa ssp. chinensis) is an important leaf vegetable grown worldwide. However, there has currently been not enough transcriptome and small RNA combined sequencing analysis of cold tolerance, which hinders further functional genomics research.ResultsIn this study, 63.43 Gb of clean data was obtained from the transcriptome analysis. The clean data of each sample reached 6.99 Gb, and the basic percentage of Q30 was 93.68% and above. The clean reads of each sample were sequence aligned with the designated reference genome (Brassica rapa, IVFCAASv1), and the efficiency of the alignment varied from 81.54 to 87.24%. According to the comparison results, 1,860 new genes were discovered in Pak-choi, of which 1,613 were functionally annotated. Among them, 13 common differentially expressed genes were detected in all materials, including seven upregulated and six downregulated. At the same time, we used quantitative real-time PCR to confirm the changes of these gene expression levels. In addition, we sequenced miRNA of the same material. Our findings revealed a total of 34,182,333 small RNA reads, 88,604,604 kinds of small RNAs, among which the most common size was 24 nt. In all materials, the number of common differential miRNAs is eight. According to the corresponding relationship between miRNA and its target genes, we carried out Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis on the set of target genes on each group of differentially expressed miRNAs. Through the analysis, it is found that the distributions of candidate target genes in different materials are different. We not only used transcriptome sequencing and small RNA sequencing but also used experiments to prove the expression levels of differentially expressed genes that were obtained by sequencing. Sequencing combined with experiments proved the mechanism of some differential gene expression levels after low-temperature treatment.ConclusionIn all, this study provides a resource for genetic and genomic research under abiotic stress in Pak-choi.

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Chromatin run-on sequencing analysis finds that ECM remodeling plays an important role in canine hemangiosarcoma pathogenesis

10.21203/rs.2.20379/v1 ◽

2020 ◽

Author(s):

Chinatsu Mukai(New Corresponding Author) ◽

Eunju Choi ◽

Kelly L. Sams ◽

Elena Zu Klampen ◽

Lynne Anguish ◽

...

Keyword(s):

Protein Expression ◽

Differentially Expressed Genes ◽

Tumor Tissue ◽

Expression Patterns ◽

Unmet Need ◽

Splenic Tissue ◽

Differentially Expressed ◽

Sequencing Analysis ◽

Ecm Remodeling ◽

Gene And Protein Expression

Abstract Background Canine visceral hemangiosarcoma (HSA) is a highly aggressive cancer of endothelial origin that closely resembles human visceral angiosarcoma, both clinically and histopathologically. Currently there is an unmet need for new diagnostics and therapies for both forms of this disease. The goal of this study was to utilize ChRO-seq and immunohistochemistry (IHC) to identify gene and protein expression signatures that may be important drivers of HSA progression. Methods Chromatin run-on sequencing (ChRO-seq) was performed on tissue isolated from 17 HSA samples and 4 normal splenic samples. Computational analysis was then used to identify differentially expressed genes and these factors were subjected to gene ontology analysis. Next, RT-PCR was performed on a subset of candidate genes to validate the ChRO-seq data. We then performed Masson’s trichrome, H&E, and IHC staining on these tissues to investigate the morphological features of HSA tumor tissue as well as the expression patterns of several proteins identified in our ChRO-seq analysis. Results ChRO-seq analysis revealed over a thousand differentially expressed genes in HSA tissue compared with normal splenic tissue (FDR <0.005). Interestingly the majority of genes overexpressed in HSA tumor tissue were associated with extracellular matrix (ECM) remodeling. This observation correlated well with our histological analysis, which found that HSA tumors contain a rich and complex collagen network. Additionally, we characterized the protein expression patterns of two highly overexpressed molecules identified in ChRO-seq analysis, podoplanin (PDPN) and laminin alpha 4 (LAMA4). We found that the expression of these two ECM-associated factors appeared to be largely limited to transformed endothelial cells within the HSA lesions. Conclusion Outcomes from this study suggest that ECM remodeling has an important role in HSA progression. Additionally, our study identified two potential novel biomarkers of HSA, PDPN and LAMA4. Interestingly, given that function-blocking anti-PDPN have shown anti-tumor effects in mouse models of canine melanoma, our studies raise the possibility that these types of therapeutic strategies could potentially be developed for treating canine HSA.

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Genome-Wide Identification of Long Non-Coding RNAs and Their Potential Functions in Poplar Growth and Phenylalanine Biosynthesis

Frontiers in Genetics ◽

10.3389/fgene.2021.762678 ◽

2021 ◽

Vol 12 ◽

Author(s):

Lei Zhang ◽

Xiaolan Ge ◽

Jiujun Du ◽

Xingqi Cheng ◽

Xiaopeng Peng ◽

...

Keyword(s):

Target Genes ◽

Expression Patterns ◽

Wood Quality ◽

Target Prediction ◽

Wood Formation ◽

Sequencing Analysis ◽

Oxidoreductase Activity ◽

Regulatory Processes ◽

Genome Wide ◽

Phenylpropanoid Biosynthesis

Poplar is an important bioenergy tree species. lncRNAs play important roles in various biological regulatory processes, and their expression pattern is more tissue-specific than mRNAs. In this study, P. deltoides “Danhong” (Pd) and P. simonii “Tongliao1” (Ps) with different growth rates and wood quality were used as experimental materials, and the transcriptomes of their shoot apical meristem, xylem, and phloem were sequenced. Furthermore, high-throughput RNA sequencing analysis revealed that the expression patterns of genes and lncRNAs are different between the two genotypes. 6,355 lncRNAs were identified. Based on target prediction, lncRNAs and target genes were involved in ADP binding, oxidoreductase activity, phenylpropanoid biosynthesis, and cyanoamino acid metabolism. The DElncRNAs in two poplars were co-expressed with transcription factors and structural genes of lignin and flavonoid pathways. In addition, we found the potential target lncRNAs of miRNA. This result provides basic evidence for a better understanding of the regulatory role of lncRNAs in regulating phenylalanine molecular pathways and wood formation.

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