scholarly journals Analysis of the laccase gene family and miR397-/miR408-mediated posttranscriptional regulation in Salvia miltiorrhiza

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7605
Author(s):  
Caili Li ◽  
Dongqiao Li ◽  
Hong Zhou ◽  
Jiang Li ◽  
Shanfa Lu
Keyword(s):  
Phenolic Compounds ◽  
Posttranscriptional Regulation ◽  
Salvia Miltiorrhiza ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Systematic Investigation ◽  
Whole Genome Sequence ◽  
Rna Sequences ◽  
Specific Expression ◽  
Gene Structures

Salvia miltiorrhiza is one of the most commonly used traditional Chinese medicine materials. It contains important bioactive phenolic compounds, such as salvianolic acids, flavonoids and anthocyanins. Elucidation of phenolic compound biosynthesis and its regulatory mechanism is of great significance for S. miltiorrhiza quality improvement. Laccases (LACs) are multicopper-containing enzymes potentially involved in the polymerization of phenolic compounds. So far, little has been known about LAC genes in S. miltiorrhiza. Through systematic investigation of the whole genome sequence and transcriptomes of S. miltiorrhiza, we identified 65 full-length SmLAC genes (SmLAC1–SmLAC65). Phylogenetic analysis showed that 62 of the identified SmLACs clustered with LACs from Arabidopsis and Populus trichocarpa in seven clades (C1–C7), whereas the other three fell into one S. miltiorrhiza-specific clade (C8). All of the deduced SmLAC proteins contain four conserved signature sequences and three typical Cu-oxidase domains, and gene structures of most LACs from S. miltiorrhiza, Arabidopsis and P. trichocarpa were highly conserved, however SmLACs encoding C8 proteins showed distinct intron-exon structures. It suggests the conservation and diversity of plant LACs in gene structures. The majority of SmLACs exhibited tissue-specific expression patterns, indicates manifold functions of SmLACs played in S. miltiorrhiza. Analysis of high-throughput small RNA sequences and degradome data and experimental validation using the 5′ RACE method showed that 23 SmLACs were targets of Smi-miR397. Among them, three were also targeted by Smi-miR408. It suggests the significance of miR397 and miR408 in posttranscriptional regulation of SmLAC genes. Our results provide a foundation for further demonstrating the functions of SmLACs in the production of bioactive phenolic compounds in S. miltiorrhiza.

scholarly journals Genome-Wide Identification and Characterization of SQUAMOSA—Promoter-Binding Protein (SBP) Genes Involved in the Flowering Development of Citrus Clementina

Biomolecules ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 66 ◽  
Author(s):  
Ren-Fang Zeng ◽  
Jing-Jing Zhou ◽  
Sheng-Rui Liu ◽  
Zhi-Meng Gan ◽  
Jin-Zhi Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Floral Induction ◽  
Binding Protein ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Specific Expression ◽  
Water Deficits ◽  
Citrus Clementina ◽  
Squamosa Promoter Binding Protein ◽  
Gene Structures

SQUAMOSA-promoter binding protein (SBP)-box genes encode a family of plant-specific transcription factors that play vital roles in plant growth and development. In this study, 15 SBP-box genes were identified and isolated from Citrus clementina (CclSBPs), where 10 of these genes were predicted to be putative targets of Citrus clementina microRNA156 (CclmiR156). The 15 CclSBP genes could be classified into six groups based on phylogenetic analysis, diverse intron–exon structure, and motif prediction, similar to the SQUAMOSA promoter binding protein-like (SPL) gene family of Populus trichocarpa and Arabidopsis thaliana. Furthermore, CclSBPs classified into a group/subgroup have similar gene structures and conserved motifs, implying their functional redundancy. Tissue-specific expression analysis of CclSBPs demonstrated their diversified expression patterns. To further explore the potential role of CclSBPs during floral inductive water deficits, the dynamic changes of the 15 CclSBPs were investigated during floral inductive water deficits, and the results showed that some CclSBPs were associated with floral induction. Among these genes, CclSBP6 was not homologous to the Arabidopsis SBP-box gene family, and CclSBP7 was regulated by being alternatively spliced. Therefore, CclSBP6 and CclSBP7 were genetically transformed in Arabidopsis. Overexpression of the two genes changed the flowering time of Arabidopsis.

scholarly journals Transcriptomes Analysis Reveals the Regulatory Roles of Noncoding RNA in Tanshinones Synthesis Pathway of Salvia Miltiorrhiza

2021 ◽  
Author(s):  
Caicai Lin ◽  
Changhao Zhou ◽  
Zhongqian Liu ◽  
Xingfeng Li ◽  
Zhenqiao Song
Keyword(s):  
Noncoding Rna ◽  
Target Genes ◽  
Salvia Miltiorrhiza ◽  
Expression Patterns ◽  
Noncoding Rnas ◽  
Synthesis Process ◽  
Circular Rnas ◽  
Regulation Mechanism ◽  
Pentatricopeptide Repeat ◽  
Specific Expression

Abstract Background: Long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) have been shown to play fundamental roles in plant development. However, the information of these noncoding RNAs (ncRNAs) in Salvia miltiorrhiza remains largely unexplored. In this study, the expression pattern of ncRNAs in six tissues from the same strain of S. miltiorrhiza was analyzed to study the biological function of ncRNAs on active ingredients synthesis.Methods: Analysis of tanshinone content differences of two root simples was carried out on high-performance liquid chromatography (HPLC). RNA sequencing, GO and KEGG enrichment analysis were applied to analyzing the targets of diferentially expressed ncRNAs in different organs.Results: A total of 6,929 lncRNAs, 6,239 circRNAs, and 360 miRNAs were identified. Forty-eight lncRNAs, 70 miRNAs, and 26 circRNAs expressed differentially between red and white root tissues with significantly different tanshinone content. GO and KEGG pathway analysis of target genes of differently expressed ncRNAs indicated that some target genes are involved in the synthesis pathway of terpene, including diterpene and sesquiterpene. We also found many target genes related to secondary metabolites, including 2-C-Methyl-d-erythritol 2,4-cyclodiphosphate Synthase (SmMCS) and several CYP450s. Furthermore, most target genes may be related to the resistance of pathogens, such as receptor kinases, disease-resistant proteins, and pentatricopeptide repeat-containing proteins. Conclusions: The present study exhibited the tissue-specific expression patterns of ncRNAs preliminarily in S. miltiorrhiza, which may reflect that the formation of white root or red root is related to regulation by ncRNAs. It would provide a basis for further research about the regulation mechanism in the tanshinone synthesis process.

Expression and localization of SWEETs in Populus and the effect of SWEET7 overexpression in secondary growth

2020 ◽  
Author(s):  
Li Zhang ◽  
Lijuan Wang ◽  
Jin Zhang ◽  
Cai Song ◽  
Yu Li ◽  
...  
Keyword(s):  
Populus Trichocarpa ◽  
Sugar Content ◽  
Expression Patterns ◽  
Secondary Growth ◽  
Wood Formation ◽  
Pcr Analysis ◽  
Sugar Transporters ◽  
Real Time Quantitative Pcr ◽  
Physiological Processes ◽  
Gene Structures

Abstract In trees, wood formation needs carbon import from the photosynthetic source tissues. Sugar transporters play important roles in carbohydrate transport into wood-forming cells. SWEETs (Sugars Will Eventually be Exported Transporters) play essential roles in many physiological processes. However, the roles of this family in the growth and development of woody plants have not been systematically investigated. In this study, 27 SWEET genes were identified in the Populus trichocarpa genome. These SWEET genes were classified into four clades based on their phylogenetic relationships, gene structures, conserved motifs, and chromosomal locations. Representative SWEET members from each clade were selected for further studies. The PagSWEETs were localized to plasma membrane, vacuolar, endoplasmic reticulum (ER) or Golgi. Real-time quantitative PCR analysis showed that PagSWEETs have distinct expression patterns in various tissues, and PagSWEET5, 7, 10b, 10c, 15b, 17a, and 17c exhibited high expression levels in stems. PagSWEET7 is localized to the cytoplasmic membrane and specifically expressed in the phloem as detected by histochemical GUS assays. Xylem production and xylem sugar content were greater in developing wood of SWEET7 overexpression (OX) than Wild-type (WT) lines. Collectively, these results provide valuable information for further investigating functions of PagSWEET genes, and identify PagSWEET7 as a candidate gene for using biotechnology to modify the wood formation in poplar.

scholarly journals Conservation and Divergence of the CONSTANS-Like (COL) Genes Related to Flowering and Circadian Rhythm in Brassica napus

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuxi Chen ◽  
Rijin Zhou ◽  
Qiong Hu ◽  
Wenliang Wei ◽  
Jia Liu
Keyword(s):  
Brassica Napus ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Protein Structures ◽  
Three Dimensional ◽  
Evolutionary Relationship ◽  
Specific Expression ◽  
Circadian Expression ◽  
Photoperiod Pathway ◽  
Gene Structures

The CONSTANS-LIKE (COL) genes are important signaling component in the photoperiod pathway and flowering regulation pathway. However, people still know little about their role in Brassica napus. To achieve a better understanding of the members of the BnaCOL gene family, reveal their evolutionary relationship and related functions involved in photoperiod regulation, we systematically analyzed the BnaCOL family members in B. napus genome. A total of 33 BnaCOL genes distributed unevenly on 16 chromosomes were identified in B. napus and could be classified into three subfamilies. The same subfamilies have relatively conservative gene structures, three-dimensional protein structures and promoter motifs such as light-responsive cis-elements. The collinearity analysis detected 37 pairs of repetitive genes in B. napus genome. A 67.7% of the BnaCOL genes were lost after B. napus genome polyploidization. In addition, the BnaCOL genes showed different tissue-specific expression patterns. A 81.8% of the BnaCOL genes were mainly expressed in leaves, indicating that they may play a conservative role in leaves. Subsequently, we tested the circadian expression profiles of nine homologous genes that regulate flowering in Arabidopsis. Most BnaCOL genes exhibit several types of circadian rhythms, indicating that these BnaCOL genes are involved in the photoperiod pathway. As such, our research has laid the foundation for understanding the exact role of the BnaCOL family in the growth and development of rapeseed, especially in flowering.

scholarly journals Genome-wide analysis of fatty acid desaturase genes in rice (Oryza sativa L.)

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Zhiguo E ◽  
Chen Chen ◽  
Jinyu Yang ◽  
Hanhua Tong ◽  
Tingting Li ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
Unsaturated Fatty Acids ◽  
Oryza Sativa L ◽  
Expression Patterns ◽  
Rice Genome ◽  
Regulatory Elements ◽  
Segmental Duplications ◽  
Specific Expression ◽  
Gene Structures

AbstractFatty acid desaturases can catalyze saturated or unsaturated fatty acids to form a double bond at various locations in the hydrocarbon chain. In the present study, a total of 20 full-length desaturase genes were identified from rice genome. An exhaustive analysis was performed to describe their chromosomal locations, gene structures, phylogeny, cis-regulatory elements, sub-cellular localizations and expression patterns. The rice desaturase genes were distributed on ten of 12 chromosomes and phylogenetically classified into six subfamilies with the Arabidopsis counterparts, FAB2, FAD2, FAD3/7/8, FAD6, DES1 and SLD1. Among of them, 9 members were expanded via chromosomal tandem or segmental duplications. The gene structures and motif constituents were evolutionarily conserved in the same subfamilies. The majority of desaturase genes showed tissue-specific expression patterns and response to abiotic stresses and hormones based on microarray data and qRT-PCR analyses. This study will provide useful clues for functional validation of desaturase genes and contribute to produce nutritionally important fatty acids by genetic modification in rice.

scholarly journals Identification and Characterization of the APX Gene Family and Its Expression Pattern under Phytohormone Treatment and Abiotic Stress in Populus trichocarpa

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 334
Author(s):  
Xue Leng ◽  
Hanzeng Wang ◽  
Shuang Zhang ◽  
Chunpu Qu ◽  
Chuanping Yang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Stress Responses ◽  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Ammonium Concentration ◽  
Cis Elements ◽  
Specific Expression ◽  
Real Time Quantitative Pcr ◽  
Gene Structures

Ascorbate peroxidase (APX) is a member of class I of the heme-containing peroxidase family. The enzyme plays important roles in scavenging reactive oxygen species for protection against oxidative damage and maintaining normal plant growth and development, as well as in biotic stress responses. In this study, we identified 11 APX genes in the Populus trichocarpa genome using bioinformatic methods. Phylogenetic analysis revealed that the PtrAPX proteins were classifiable into three clades and the members of each clade shared similar gene structures and motifs. The PtrAPX genes were distributed on six chromosomes and four segmental-duplicated gene pairs were identified. Promoter cis-elements analysis showed that the majority of PtrAPX genes contained a variety of phytohormone- and abiotic stress-related cis-elements. Tissue-specific expression profiles indicated that the PtrAPX genes primarily function in roots and leaves. Real-time quantitative PCR (RT-qPCR) analysis indicated that PtrAPX transcription was induced in response to drought, salinity, high ammonium concentration, and exogenous abscisic acid treatment. These results provide important information on the phylogenetic relationships and functions of the APX gene family in P. trichocarpa.

scholarly journals Genome-Wide Investigation of the NF-X1 Gene Family in Populus trichocarpa Expression Profiles during Development and Stress

2021 ◽  
Vol 22 (9) ◽  
pp. 4664
Author(s):  
Fang He ◽  
Yu-Jie Shi ◽  
Jia-Xuan Mi ◽  
Kuang-Ji Zhao ◽  
Xing-Lei Cui ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Molecular Genetic ◽  
Mechanical Damage ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genetic Progress ◽  
Whole Genome Analysis ◽  
Element Analysis

Poplar are planted extensively in reforestation and afforestation. However, their successful establishment largely depends on the environmental conditions of the newly established plantation and their resistance to abiotic as well as biotic stresses. NF-X1, a widespread transcription factor in plants, plays an irreplaceable role in plant growth, development, and stress tolerance. Although the whole genome sequence of Populus trichocarpa has been published for a long time, little is known about the NF-X1 genes in poplar, especially those related to drought stress, mechanical damage, insect feeding, and hormone response at the whole genome level. In this study, whole genome analysis of the poplar NF-X1 family was performed, and 4 PtrNF-X1 genes were identified. Then, bioinformatics analysis and qRT-PCR were applied to analyze the gene structure, phylogeny, chromosomal localization, gene replication, Cis-elements, and expression patterns of PtrNF-X1genes. Sequence analysis revealed that one-quarter of the PtrNF-X1 genes did not contain introns. Phylogenetic analysis revealed that all NF-X1 genes were split into three subfamilies. The number of two pairs of segmented replication genes were detected in poplars. Cis-acting element analysis identified a large number of elements of growth and development and stress-related elements on the promoters of different NF-X1 members. In addition, some PtrNF-X1 could be significantly induced by polyethylene glycol (PEG) and abscisic acid (ABA), thus revealing their potential role in regulating stress response. Comprehensive analysis is helpful in selecting candidate NF-X1 genes for the follow-up study of the biological function, and molecular genetic progress of stress resistance in forest trees provides genetic resources.

scholarly journals Genome-wide investigation and expression profiling of polyphenol oxidase (PPO) family genes uncover likely functions in organ development and stress responses in Populus trichocarpa

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Fang He ◽  
Yu-Jie Shi ◽  
Qian Zhao ◽  
Kuang-Ji Zhao ◽  
Xing-Lei Cui ◽  
...  
Keyword(s):  
Polyphenol Oxidase ◽  
Stress Responses ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Mechanical Damage ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Element Analysis ◽  
Genome Wide ◽  
A Genome

Abstract Background Trees such as Populus are planted extensively for reforestation and afforestation. However, their successful establishment greatly depends upon ambient environmental conditions and their relative resistance to abiotic and biotic stresses. Polyphenol oxidase (PPO) is a ubiquitous metalloproteinase in plants, which plays crucial roles in mediating plant resistance against biotic and abiotic stresses. Although the whole genome sequence of Populus trichocarpa has long been published, little is known about the PPO genes in Populus, especially those related to drought stress, mechanical damage, and insect feeding. Additionally, there is a paucity of information regarding hormonal responses at the whole genome level. Results A genome-wide analysis of the poplar PPO family was performed in the present study, and 18 PtrPPO genes were identified. Bioinformatics and qRT-PCR were then used to analyze the gene structure, phylogeny, chromosomal localization, gene replication, cis-elements, and expression patterns of PtrPPOs. Sequence analysis revealed that two-thirds of the PtrPPO genes lacked intronic sequences. Phylogenetic analysis showed that all PPO genes were categorized into 11 groups, and woody plants harbored many PPO genes. Eighteen PtrPPO genes were disproportionally localized on 19 chromosomes, and 3 pairs of segmented replication genes and 4 tandem repeat genomes were detected in poplars. Cis-acting element analysis identified numerous growth and developmental elements, secondary metabolism processes, and stress-related elements in the promoters of different PPO members. Furthermore, PtrPPO genes were expressed preferentially in the tissues and fruits of young plants. In addition, the expression of some PtrPPOs could be significantly induced by polyethylene glycol, abscisic acid, and methyl jasmonate, thereby revealing their potential role in regulating the stress response. Currently, we identified potential upstream TFs of PtrPPOs using bioinformatics. Conclusions Comprehensive analysis is helpful for selecting candidate PPO genes for follow-up studies on biological function, and progress in understanding the molecular genetic basis of stress resistance in forest trees might lead to the development of genetic resources.

scholarly journals Genome-wide investigation and expression profiling of polyphenol oxidase (PPO) family genes uncover likely functions in organ development and stress responses in populus trichocarpa

2021 ◽  
Author(s):  
Fang He ◽  
Yu-Jie Shi ◽  
Qian Zhao ◽  
Kuang-Ji Zhao ◽  
Xing-Lei Cui ◽  
...  
Keyword(s):  
Polyphenol Oxidase ◽  
Stress Responses ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genetic Progress ◽  
Element Analysis ◽  
Genome Wide ◽  
A Genome

Abstract Background: Trees such as Populus are planted extensively for reforestation and afforestation. However, their successful establishment greatly depends upon ambient environmental conditions and their relative resistance to abiotic as well as biotic stress. Polyphenol oxidase (PPO) is a ubiquitous metalloproteinase in plants, which plays crucial roles in plant resistance against biotic and abiotic stresses. Although the whole genome sequence of populus trichocarpa has long been published, little is known about the PPO genes in Populus, especially those related to drought stress, mechanical damage, insect feeding and hormone response at the whole genome level. Results: In the recent research, a genome-wide analysis of the Poplar PPOs family was finished and 18 PtrPPOs gene were identified. Then, bioinformatics and qRT-PCR were applied to analyze the gene structure, phylogeny, chromosomal localization, gene replication, Cis-elements, expression patterns of PtrPPOs. Sequence analysis revealed that 2/3 of the PtrPPO genes not contained introns. Phylogenetic analysis revealed that all PPOs gene were split into 11 subfamilies, and woody plants differentiated a large number of PPO genes. 18 PtrPPOs gene were disproportionally apportioned on 19 chromosomes, and the number of three pairs of segmented replication genes and four tandem repeat genomes were detected in poplars. Cis-acting element analysis identified a large number elements of growth and development, secondary metabolism process, and stress-related elements on the promoters of different PPO members. Furthermore, PtrPPO genes were expressed preferably in young plant tissues and fruits. In addition, some PtrPPOs could be significantly induced by PEG, ABA and JA, thus revealing their potential role in regulating stress response. Conclusions: Comprehensive analysis is helpful to select candidate PPO genes for the follow-up study of the biological function, and molecular genetic progress of stress resistance in forest trees provides genetic resources.

scholarly journals Genome-wide investigation of malate dehydrogenase gene family in poplar (Populus trichocarpa) and their expression analysis under salt stress

2019 ◽  
Author(s):  
Xinghao Chen ◽  
Jun Zhang ◽  
Chao Zhang ◽  
Shijie Wang ◽  
Minsheng Yang
Keyword(s):  
Salt Stress ◽  
Gene Family ◽  
Malate Dehydrogenase ◽  
Molecular Mechanisms ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Subcellular Location ◽  
Genome Wide ◽  
Duplication Events ◽  
Gene Structures

Malate dehydrogenase (MDH) is widely distributed in plants and animals, and plays an important role in many metabolic processes. However, there have been few studies on MDH genes in poplar. In this study, 16 MDH gene sequences were identified from the Populus trichocarpa genome and renamed according to their chromosomal locations. Based on phylogenetic analysis, the PtMDH genes were divided into five groups, and genes that grouped together all shared the same subcellular location and had similar sequence lengths, gene structures, and conserved motifs. Two pairs of tandem duplication events and three segmental duplication events involving five genes were identified from the 15 PtMDH genes located on the chromosomes. Each pair of genes had a Ka/Ks ratios <1, indicating that the MDH gene family of P. trichocarpa was purified during evolution. Based on the transcriptome data of P. trichocarpa under salt stress and qRT-PCR verification, the expression patterns of PtMDH genes under salt stress were analyzed. The results showed that most of the genes were upregulated under salt stress, indicating that they play a role in the response of poplar to salt stress. The PtmMDH1 gene can be used as an important salt-tolerant candidate gene for further investigations of molecular mechanisms. This study lays the foundation for functional analysis of MDH genes and genetic improvement in poplar.

Sign in / Sign up

Export Citation Format

Share Document