scholarly journals Genome-wide identification and functional characterization of natural antisense transcripts in Salvia miltiorrhiza

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mei Jiang ◽  
Haimei Chen ◽  
Jingting Liu ◽  
Qing Du ◽  
Shanfa Lu ◽  
...  
Keyword(s):  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Salvia Miltiorrhiza ◽  
Functional Characterization ◽  
Rna Seq ◽  
Antisense Transcripts ◽  
Natural Antisense Transcripts ◽  
Traditional Medicines ◽  
Phenylpropanoid Biosynthesis ◽  
Pathway Analyses

AbstractSalvia miltiorrhiza is one of the most widely used traditional medicines. Natural antisense transcripts (NATs) are a class of long noncoding RNAs that can regulate gene expression. Here, we identified 812 NATs, including 168 cis-NATs and 644 trans-NATs from twelve root, flower, and leaf samples of S. miltiorrhiza using RNA-seq. The expression profiles for 41 of 50 NATs and their sense transcripts (STs) obtained from RNA-Seq were validated using qRT-PCR. The expression profiles of 17 NATs positively correlated with their STs. GO and KEGG pathway analyses mapped the STs for cis-NATs to pathways for biosynthesis of secondary metabolites. We characterized four NATs in detail, including NAT0001, NAT0002, NAT0004, and NAT00023. Their STs are kaurene synthase-like 1 and the homologs of UDP-glucose flavonoid 3-O-glucosyltransferase 6, UDP-glycosyltransferase 90A1, and beta-glucosidase 40, respectively. The first gene is involved in the biosynthesis of bioactive tanshinones, the next two are involved in anthocyanin biosynthesis, whereas the last is involved in phenylpropanoid biosynthesis. Besides, we found seven STs that are potential targets of miRNAs. And we found two miRNAs including miR156a and miR7208, might originate from NATs, NAT0112 and NAT0086. The results suggest that S. miltiorrhiza NATs might interact with STs, produce miRNAs, and be regulated by miRNAs. They potentially play significant regulatory roles in the biosynthesis of bioactive compounds.

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

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Qi Wu ◽  
Yiming Luo ◽  
Xiaoyong Wu ◽  
Xue Bai ◽  
Xueling Ye ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Functional Characterization ◽  
Chenopodium Quinoa ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Rna Seq ◽  
Short Day ◽  
Homologous Genes ◽  
The Relationship ◽  
Encoding Genes

Abstract 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.

scholarly journals Combining QTL Mapping and Transcriptomics to Decipher the Genetic Architecture of Phenolic Compounds Metabolism in the Conifer White Spruce

2021 ◽  
Vol 12 ◽  
Author(s):  
Justine Laoué ◽  
Claire Depardieu ◽  
Sébastien Gérardi ◽  
Manuel Lamothe ◽  
Claude Bomal ◽  
...  
Keyword(s):  
Phenolic Compounds ◽  
Qtl Mapping ◽  
Picea Glauca ◽  
Expression Patterns ◽  
Functional Characterization ◽  
White Spruce ◽  
Transcriptional Networks ◽  
Rna Seq ◽  
Phenylpropanoid Biosynthesis ◽  
Constitutive Production

Conifer forests worldwide are becoming increasingly vulnerable to the effects of climate change. Although the production of phenolic compounds (PCs) has been shown to be modulated by biotic and abiotic stresses, the genetic basis underlying the variation in their constitutive production level remains poorly documented in conifers. We used QTL mapping and RNA-Seq to explore the complex polygenic network underlying the constitutive production of PCs in a white spruce (Picea glauca) full-sib family for 2 years. QTL detection was performed for nine PCs and differentially expressed genes (DEGs) were identified between individuals with high and low PC contents for five PCs exhibiting stable QTLs across time. A total of 17 QTLs were detected for eight metabolites, including one major QTL explaining up to 91.3% of the neolignan-2 variance. The RNA-Seq analysis highlighted 50 DEGs associated with phenylpropanoid biosynthesis, several key transcription factors, and a subset of 137 genes showing opposite expression patterns in individuals with high levels of the flavonoids gallocatechin and taxifolin glucoside. A total of 19 DEGs co-localized with QTLs. Our findings represent a significant step toward resolving the genomic architecture of PC production in spruce and facilitate the functional characterization of genes and transcriptional networks responsible for differences in constitutive production of PCs in conifers.

scholarly journals Identification of candidate genes influencing anthocyanin biosynthesis during the development and ripening of red and white strawberry fruits via comparative transcriptome analysis

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10739
Author(s):  
Fengli Zhao ◽  
Pan Song ◽  
Xiangfen Zhang ◽  
Gang Li ◽  
Panpan Hu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Transcriptome Data ◽  
Rna Seq ◽  
Qpcr Analysis ◽  
Snow White ◽  
Anthocyanin Pathway ◽  
Berry Fruits

Strawberries are one of the most economically important berry fruits worldwide and exhibit colours ranging from white to dark red, providing a rich genetic resource for strawberry quality improvement. In the present study, we conducted transcriptome analyses of three strawberry cultivars, namely, ‘Benihoppe’, ‘Xiaobai’, and ‘Snow White’, and compared their gene expression profiles. Among the high-quality sequences, 5,049 and 53,200 differentially expressed genes (DEGs) were obtained when comparing the diploid and octoploid strawberry genomes and analysed to identify anthocyanin-related candidate genes. Sixty-five DEGs in the diploid genome (transcriptome data compared to the diploid strawberry genome) and 317 DEGs in the octoploid genome (transcriptome data compared to the octoploid strawberry genome) were identified among the three cultivars. Among these DEGs, 19 and 70 anthocyanin pathway genes, six and 42 sugar pathway genes, 23 and 101 hormone pathway genes, and 17 and 104 transcription factors in the diploid and octoploid genomes, respectively, correlated positively or negatively with the anthocyanin accumulation observed among the three cultivars. Real-time qPCR analysis of nine candidate genes showed a good correlation with the transcriptome data. For example, the expression of PAL was higher in ‘Benihoppe’ and ‘Xiaobai’ than in ‘Snow White’, consistent with the RNA-seq data. Thus, the RNA-seq data and candidate DEGs identified in the present study provide a sound basis for further studies of strawberry fruit colour formation.

scholarly journals Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion

2019 ◽  
Author(s):  
Huanhuan Liu ◽  
Jikai Ma ◽  
Huogen Li
Keyword(s):  
Candidate Genes ◽  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Periodic Acid ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Nectar Secretion ◽  
Relict Species ◽  
Periodic Acid Schiff ◽  
Real Time Quantitative Pcr

Abstract Background Nectar is a major flower attractant and reward for insects for pollination. Liriodendron, a genus of the Magnoliaceae family, has only two relict species, L. chinense and L. tulipifera, that are considered “basal angiosperms” according to plant evolutionary history. The flowers of Liriodendron plants are insect pollinated and secrete nectar to attract pollinators. To date, the morphology and anatomy of the nectary, the mechanism of nectar secretion and the molecular mechanism involved in nectary development in Liriodendron remain poorly understood. Methods In this study, we examined the nectary surface cells and the change in starch in L. tulipifera by using scanning electron microscopy and periodic acid-Schiff techniques to select definitive samples for next research. Transcriptome sequencing was performed on the top and middle parts of the immature nectary and the middle parts of the mature nectary and the postsecreted nectary in L. tulipifera. We evaluated the expression profiles of 22 DEGs that were closely related to nectary development and nectar secretion for real-time quantitative PCR analysis. Results The L. tulipifera nectary is a starch-storing nectary and is located in the top and middle parts of L. tulipifera petals. After analyzing the RNA-seq data, we obtained 115.26 Gb clean data in 12 libraries and mapped the results to the L. chinense reference genome with 71.02%-79.77% efficiency. In total, 26,955 DEGs were identified by analyzing six different pairwise comparisons. The flavonoid biosynthesis, phenylpropanoid biosynthesis, anthocyanin biosynthesis and starch and sucrose metabolism pathways were enriched and related to nectar secretion and pigment change. We identified 56 transcription factor families, and members of the TCP, Trihelix, C2H2, ERF, and MADS families changed dynamically during nectary development. Moreover, to further verify the accuracy of the RNA-seq results, we validated the expression profiles of 22 candidate genes. Conclusions We evaluated the nectary development and secretion process comprehensively and identified many related candidate genes in L. tulipifera. These findings suggest that the nectary may play important roles in flavonoid synthesis and petal color presentation.

scholarly journals Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion

2019 ◽  
Author(s):  
Huanhuan Liu ◽  
Jikai Ma ◽  
Huogen Li
Keyword(s):  
Candidate Genes ◽  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Periodic Acid ◽  
Middle Part ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Nectar Secretion ◽  
Relict Species ◽  
Periodic Acid Schiff

Abstract Background: Nectar is a major floral attractant and reward for insects that ensures pollination. Liriodendron, a genus of the Magnoliaceae family, includes only two relict species, L. chinense and L. tulipifera, which are considered “basal angiosperms” according to plant evolutionary history. The flowers of Liriodendron plants are insect pollinated and secrete nectar to attract pollinators. To date, the morphology and anatomy of nectaries, the mechanism of nectar secretion and the molecular mechanism of nectary development in Liriodendron remain poorly understood. Methods: In this study, we examined the nectary surface cells and change in starch in L. tulipifera by using scanning electron microscopy and periodic acid-Schiff techniques to select appropriate samples for subsequent research. Transcriptome sequencing was of the top and middle parts of immature nectaries and the middle part of mature and postsecretory nectaries in L. tulipifera was performed. We evaluated the expression profiles of 21 DEGs that are closely related to nectary development and nectar secretion for real-time quantitative PCR analysis. Results: L. tulipifera nectaries are starch-storing nectaries and are located in the top and middle parts of L. tulipifera petals. After analyzing the RNA-seq data, we obtained 115.26 Gb of clean data in 12 libraries and mapped the results to the L. chinense reference genome with 71.02%-79.77% efficiency. In total, 26,955 DEGs were identified by performing six pairwise comparisons. The flavonoid biosynthesis, phenylpropanoid biosynthesis, anthocyanin biosynthesis and starch and sucrose metabolism pathways were enriched and related to nectar secretion and pigment change. We identified 56 transcription factor families, and members of the TCP, Trihelix, C2H2, ERF, and MADS families changed dynamically during nectary development. Moreover, to further verify the accuracy of the RNA-seq results, we validated the expression profiles of 21 candidate genes. Conclusions: We evaluated the nectary development and secretion processes comprehensively and identified many related candidate genes in L. tulipifera. These findings suggest that nectaries play important roles in flavonoid synthesis and petal color presentation.

scholarly journals Comparative RNA-Sequence Transcriptome Analysis of Phenolic Acid Metabolism in Salvia miltiorrhiza, a Traditional Chinese Medicine Model Plant

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Zhenqiao Song ◽  
Linlin Guo ◽  
Tian Liu ◽  
Caicai Lin ◽  
Jianhua Wang ◽  
...  
Keyword(s):  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Phenolic Acid ◽  
Expression Profiles ◽  
Salvia Miltiorrhiza ◽  
Lignin Biosynthesis ◽  
Biosynthesis Pathway ◽  
Acid Biosynthesis ◽  
The Core ◽  
Phenylpropanoid Biosynthesis

Salvia miltiorrhiza Bunge is an important traditional Chinese medicine (TCM). In this study, two S. miltiorrhiza genotypes (BH18 and ZH23) with different phenolic acid concentrations were used for de novo RNA sequencing (RNA-seq). A total of 170,787 transcripts and 56,216 unigenes were obtained. There were 670 differentially expressed genes (DEGs) identified between BH18 and ZH23, 250 of which were upregulated in ZH23, with genes involved in the phenylpropanoid biosynthesis pathway being the most upregulated genes. Nine genes involved in the lignin biosynthesis pathway were upregulated in BH18 and thus result in higher lignin content in BH18. However, expression profiles of most genes involved in the core common upstream phenylpropanoid biosynthesis pathway were higher in ZH23 than that in BH18. These results indicated that genes involved in the core common upstream phenylpropanoid biosynthesis pathway might play an important role in downstream secondary metabolism and demonstrated that lignin biosynthesis was a putative partially competing pathway with phenolic acid biosynthesis. The results of this study expanded our understanding of the regulation of phenolic acid biosynthesis in S. miltiorrhiza.

scholarly journals Genome-Wide Identification and Analysis of the NF-Y Gene Family in Potato (Solanum tuberosum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhen Liu ◽  
Yuanming Li ◽  
Jinyong Zhu ◽  
Wenjing Ma ◽  
Zhitao Li ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Gene Family ◽  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Solanum Tuberosum L ◽  
Abiotic Stress Tolerance ◽  
Maturation Stage ◽  
Rna Seq ◽  
Potato Genome ◽  
Potato Genome Sequencing Consortium

Nuclear factor Y (NF-Y) is a ubiquitous transcription factor in eukaryotes, which is composed of three subunits (NF-YA, NF-YB, and NF-YC). NF-Y has been identified as a key regulator of multiple pathways in plants. Although the NF-Y gene family has been identified in many plants, it has not been reported in potato (Solanum tuberosum). In the present study, a total of 41 NF-Y proteins in potato (StNF-Ys) were identified, including 10 StNF-YA, 22 StNF-YB, and nine StNF-YC subunits, and their distribution on chromosomes, gene structure, and conserved motif was analyzed. A synteny analysis indicated that 14 and 38 pairs of StNF-Y genes were orthologous to Arabidopsis and tomato (Solanum lycopersicum), respectively, and these gene pairs evolved under strong purifying selection. In addition, we analyzed the expression profiles of NF-Y genes in different tissues of double haploid (DM) potato, as well as under abiotic stresses and hormone treatments by RNA-seq downloaded from the Potato Genome Sequencing Consortium (PGSC) database. Furthermore, we performed RNA-seq on white, red, and purple tuber skin and flesh of three potato cultivars at the tuber maturation stage to identify genes that might be involved in anthocyanin biosynthesis. These results provide valuable information for improved understanding of StNF-Y gene family and further functional analysis of StNF-Y genes in fruit development, abiotic stress tolerance, and anthocyanin biosynthesis in potato.

scholarly journals Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Huanhuan Liu ◽  
Jikai Ma ◽  
Huogen Li
Keyword(s):  
Candidate Genes ◽  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Periodic Acid ◽  
Middle Part ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Nectar Secretion ◽  
Relict Species ◽  
Periodic Acid Schiff

Abstract Background Nectar is a major floral attractant and reward for insects that ensures pollination. Liriodendron, a genus of the Magnoliaceae family, includes only two relict species, L. chinense and L. tulipifera, which are considered “basal angiosperms” according to plant evolutionary history. The flowers of Liriodendron plants are insect pollinated and secrete nectar to attract pollinators. To date, the morphology and anatomy of nectaries, the mechanism of nectar secretion and the molecular mechanism of nectary development in Liriodendron remain poorly understood. Methods In this study, we examined the nectary surface cells and change in starch in L. tulipifera by using scanning electron microscopy and periodic acid-Schiff techniques to select appropriate samples for subsequent research. Transcriptome sequencing was of the top and middle parts of immature nectaries and the middle part of mature and postsecretory nectaries in L. tulipifera was performed. We evaluated the expression profiles of 21 DEGs that are closely related to nectary development and nectar secretion for real-time quantitative PCR analysis. Results L. tulipifera nectaries are starch-storing nectaries and are located in the top and middle parts of L. tulipifera petals. After analyzing the RNA-seq data, we obtained 115.26 Gb of clean data in 12 libraries and mapped the results to the L. chinense reference genome with 71.02–79.77% efficiency. In total, 26,955 DEGs were identified by performing six pairwise comparisons. The flavonoid biosynthesis, phenylpropanoid biosynthesis, anthocyanin biosynthesis and starch and sucrose metabolism pathways were enriched and related to nectar secretion and pigment change. We identified 56 transcription factor families, and members of the TCP, Trihelix, C2H2, ERF, and MADS families changed dynamically during nectary development. Moreover, to further verify the accuracy of the RNA-seq results, we validated the expression profiles of 21 candidate genes. Conclusions We evaluated the nectary development and secretion processes comprehensively and identified many related candidate genes in L. tulipifera. These findings suggest that nectaries play important roles in flavonoid synthesis and petal color presentation.

scholarly journals Long Noncoding RNA and Circular RNA Expression Profiles of Monocyte-Derived Dendritic Cells in Autoimmune Hepatitis

2021 ◽  
Vol 12 ◽  
Author(s):  
Fan Yang ◽  
Xiaoli Fan ◽  
Yifeng Liu ◽  
Yi Shen ◽  
Shenglan Zhao ◽  
...  
Keyword(s):  
Dendritic Cells ◽  
Autoimmune Hepatitis ◽  
Peripheral Blood ◽  
Noncoding Rna ◽  
Cell Function ◽  
Expression Profiles ◽  
Circular Rna ◽  
Circular Rnas ◽  
Rna Seq ◽  
Pathway Analyses

Autoimmune hepatitis (AIH) is a chronic liver disease caused by disruption of liver immune homeostasis. The effect of dendritic cells (DCs) on the pathogenesis of AIH is not fully understood. Long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) have been shown to play critical roles in the regulation of cell function. In this study, we analyzed the immunophenotypic characteristics of DCs in the peripheral blood. The percentage of mature DCs was higher in AIH patients than in healthy controls (HCs), and the proportion of mature DCs decreased after treatment. We isolated monocyte-derived DCs (moDCs) from the peripheral blood, obtained whole RNA-sequencing (RNA-seq) data for the moDCs from the two groups, and identified differentially expressed (DE) lncRNAs, circRNAs, miRNAs and mRNAs. In addition, we performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses for the DE mRNAs and constructed competing endogenous RNA (ceRNA) networks. ENST00000543334, hsa_circ_0000279, and hsa_circ_0005076 were selected and validated by RT-qPCR. These results provide a possible molecular mechanism of DCs in the pathogenesis of AIH and identify some potential therapeutic targets.

Identification of gene expression profiles in the actinomycete Gordonia neofelifaecis grown with different steroids

Genome ◽  
2014 ◽  
Vol 57 (6) ◽  
pp. 345-353 ◽  
Author(s):  
Wenjing Li ◽  
Fanglan Ge ◽  
Qingyan Zhang ◽  
Yao Ren ◽  
Jiadai Yuan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pyruvic Acid ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Differentially Expressed ◽  
Side Chain ◽  
Rna Seq ◽  
Side Chain Cleavage ◽  
Chain Cleavage ◽  
Catabolic Genes

Gordonia neofelifaecis NRRL B-59395 was initially isolated from the fresh feces of a clouded leopard based on its ability to degrade cholesterol. The transcriptome profiles of G. neofelifaecis NRRL B-59395 grown with cholesterol, androstenedione (AD), and pyruvic acid were compared by RNA-Seq. The sterol catabolic genes are highly conserved in G. neofelifaecis, Rhodococcus jostii RHA1, and Mycobacterium tuberculosis. The RNA-Seq results indicated that the genes involved in the sterol side chain cleavage were exclusively induced by cholesterol, while the genes involved in the degradation of rings A/B and C/D were up-regulated by both cholesterol and AD. It appears that the induction mechanisms for the genes responsible for side chain cleavage and those for degradation of rings are different. There are approximately 21 genes encoding transporter proteins that are differentially expressed in cholesterol or AD compared with pyruvic acid. The genes camABCD and camM encode two systems that take up cholate, and they have been shown to be cholesterol- and AD-inducible. The potential biological functions of other differentially expressed genes are also discussed. These results will promote the functional characterization of the sterol catabolic genes and also provide important clues in understanding the mechanisms of their gene expression, and they may help us understand the mechanism underlying microbial cholesterol catabolism.

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