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Song Y, Du X, Li A, Fan A, He L, Sun Z, Niu Y, Qiao Y. Assembly and analysis of the complete mitochondrial genome of Forsythia suspensa (Thunb.) Vahl. BMC Genomics 2023; 24:708. [PMID: 37996801 PMCID: PMC10666317 DOI: 10.1186/s12864-023-09821-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Forsythia suspensa (Thunb.) Vahl is a valuable ornamental and medicinal plant. Although the nuclear and chloroplast genomes of F. suspensa have been published, its complete mitochondrial genome sequence has yet to be reported. In this study, the genomic DNA of F. suspensa yellowish leaf material was extracted, sequenced by using a mixture of Illumina Novaseq6000 short reads and Oxford Nanopore PromethION long reads, and the sequencing data were assembled and annotated. RESULT The F. suspensa mitochondrial genome was obtained in the length of 535,692 bp with a circular structure, and the GC content was 44.90%. The genome contains 60 genes, including 36 protein-coding genes, 21 tRNA genes, and three rRNA genes. We further analyzed RNA editing of the protein-coding genes, relative synonymous codon usage, and sequence repeats based on the genomic data. There were 25 homologous sequences between F. suspensa mitochondria and chloroplast genome, which involved the transfer of 8 mitochondrial genes, and 9473 homologous sequences between mitochondrial and nuclear genomes. Analysis of the nucleic acid substitution rate, nucleic acid diversity, and collinearity of protein-coding genes of the F. suspensa mitochondrial genome revealed that the majority of genes may have undergone purifying selection, exhibiting a slower rate of evolution and a relatively conserved structure. Analysis of the phylogenetic relationships among different species revealed that F. suspensa was most closely related to Olea europaea subsp. Europaea. CONCLUSION In this study, we sequenced, assembled, and annotated a high-quality F. suspensa mitochondrial genome. The results of this study will enrich the mitochondrial genome data of Forsythia, lay a foundation for the phylogenetic development of Forsythia, and promote the evolutionary analysis of Oleaceae species.
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Affiliation(s)
- Yun Song
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.
| | - Xiaorong Du
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Aoxuan Li
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Amei Fan
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Longjiao He
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Zhe Sun
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Yanbing Niu
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Yonggang Qiao
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.
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Xia HX, Li Q, Cushman SA, Yuan WJ, Li Y. Expression dosage effects of a small number of genes after the artificial doubling of weeping forsythia. Plant Physiol Biochem 2023; 202:107945. [PMID: 37562202 DOI: 10.1016/j.plaphy.2023.107945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/04/2023] [Accepted: 08/04/2023] [Indexed: 08/12/2023]
Abstract
Whole genome doubling (WGD) plays a critical role in plant evolution, yet the mechanisms underlying the maintenance of overall equilibrium following an artificial doubling event, as well as its impact on phenotype and adaptability, remain unclear. By comparing the gene expression of naturally occurring weeping forsythia diploids and colchicine-induced autotetraploids under normal growth conditions and cold stress, we identified gene expression dosage responses resulting from ploidy change. Only a small proportion of effectively expressed genes showed dosage effect, and most genes did not exhibit significant expression differences. However, the genes that showed expression dosage effect were largely random. The autotetraploids had slower overall growth rates, possibly resulting from negative gene dosage effects on zeatin synthesis and multiple metabolic delays caused by other negative dosage genes. Our comparative analysis of cold response genes in diploids and autotetraploids revealed that genes related to "response to abscisic acid" and "cold acclimation" were key factors contributing to greater cold tolerance in the autotetraploids. In particular, gene expression related to "cold acclimation" might mitigate the effects of cold stress. Taken together, our findings suggested that overall gene expression equilibrium following WGD of weeping forsythia autotetraploids was achieved through the inactivation of the majority of duplicated genes. Our research provides new insights into the mechanisms regulating expression dosage balance following polyploidization events.
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Affiliation(s)
- He-Xiao Xia
- College of Life Science and Technology, Inner Mongolia Normal University, Huhehaote, China; College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, China
| | - Qian Li
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Samuel A Cushman
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA
| | - Wang-Jun Yuan
- School of Pharmacy, Henan University, Kaifeng, China
| | - Yong Li
- College of Life Science and Technology, Inner Mongolia Normal University, Huhehaote, China; State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.
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Li Y, Shi LC, Pei NC, Cushman SA, Si YT. Transcriptomic responses to drought stress among natural populations provide insights into local adaptation of weeping forsythia. BMC Plant Biol 2021; 21:273. [PMID: 34130656 PMCID: PMC8204298 DOI: 10.1186/s12870-021-03075-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/26/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Understanding the genetic mechanisms of local adaptation is an important emerging topic in molecular ecology and evolutionary biology. RESULTS Here, we identify the physiological changes and differential expression of genes among different weeping forsythia populations under drought stress in common garden experiments. Physiological results showed that HBWZ might have higher drought tolerance among four populations. RNA-seq results showed that significant differential expression in the genes responding to the synthesis of flavonoids, aromatic substances, aromatic amino acids, oxidation-reduction process, and transmembrane transport occured among four populations. By further reanalysis of results of previous studies, sequence differentiation was found in the genes related to the synthesis of aromatic substances among different weeping forsythia populations. CONCLUSIONS Overall, our study supports the hypothesis that the dual differentiation in gene efficiency and expression increases among populations in response to heterogeneous environments and is an important evolutionary process of local adaptation. Here, we proposed a new working model of local adaptation of weeping forsythia populations under different intensities of drought stress, which provides new insights for understanding the genetic mechanisms of local adaptation for non-model species.
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Affiliation(s)
- Yong Li
- Innovation Platform of Molecular Biology, College of Landscape and Art, Henan Agricultural University, Zhengzhou, China
| | - Long-Chen Shi
- Innovation Platform of Molecular Biology, College of Landscape and Art, Henan Agricultural University, Zhengzhou, China
| | - Nan-Cai Pei
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Samuel A. Cushman
- U.S. Forest Service, Rocky Mountain Research Station, 2500 S. Pine Knoll Dr., Flagstaff, AZ USA
| | - Yu-Tao Si
- Innovation Platform of Molecular Biology, College of Landscape and Art, Henan Agricultural University, Zhengzhou, China
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Cheng-Dong N, Xin-Jia Y, Jing W, Wen-Lan LI, Yu F, Yuan-Yuan J, Xin Z, Chang L. [Study on molecular of anti-tumor mechanism of Forsythia suspensa based on molecular docking and network pharmacology]. Zhongguo Zhong Yao Za Zhi 2020; 45:4455-4465. [PMID: 33164376 DOI: 10.19540/j.cnki.cjcmm.20200428.601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this paper, the possible molecular mechanism of Forsythia suspensa for the anti-tumor effect was investigated through the network pharmacology and molecular docking. The main components of F. suspensa were obtained by literature mining and TCMSP database. Cancer-related genes were collected with use of GAD and OMIM databases. The interaction network of Compounds-Targets-Pathways was constructed through Cytoscpe software. The targets were analyzed by GO and KEGG means in DAVID database, and the KEGG signal pathways were visualized. Component-Target network analysis results were verified by PyRx molecular docking. The results showed that a total of 26 main components of F. suspensa may act on key targets such as AKT1, IL6, ESR1, EGFR, EGF and CCND1, and were involved in 20 signal pathways. Molecular docking analysis showed that hydrogen bonding, hydrophobic action and Pi-cation bonding maybe the main forms of interaction. In this study, we revealed the anti-tumor effect of F. suspensa through the network of Compounds-Targets-Pathways and molecular docking verification, providing reference and guidance for systematically elucidating the anti-tumor molecular mechanism of the main components of F. suspensa.
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Affiliation(s)
- Nie Cheng-Dong
- College of Pharmacy, Harbin University of Commerce Harbin 150076, China Heilongjiang Provincial Key Laboratory of Drug Prevention and Treatment for Senile Diseases Harbin 150076, China
| | - Yan Xin-Jia
- College of Pharmacy, Harbin University of Commerce Harbin 150076, China Heilongjiang Provincial Key Laboratory of Drug Prevention and Treatment for Senile Diseases Harbin 150076, China
| | - Wen Jing
- College of Pharmacy, Harbin University of Commerce Harbin 150076, China Heilongjiang Provincial Key Laboratory of Drug Prevention and Treatment for Senile Diseases Harbin 150076, China
| | - L I Wen-Lan
- College of Pharmacy, Harbin University of Commerce Harbin 150076, China Heilongjiang Provincial Key Laboratory of Drug Prevention and Treatment for Senile Diseases Harbin 150076, China
| | - Fan Yu
- College of Pharmacy, Harbin University of Commerce Harbin 150076, China Heilongjiang Provincial Key Laboratory of Drug Prevention and Treatment for Senile Diseases Harbin 150076, China
| | - Jiang Yuan-Yuan
- College of Pharmacy, Harbin University of Commerce Harbin 150076, China Heilongjiang Provincial Key Laboratory of Drug Prevention and Treatment for Senile Diseases Harbin 150076, China
| | - Zheng Xin
- College of Pharmacy, Harbin University of Commerce Harbin 150076, China Heilongjiang Provincial Key Laboratory of Drug Prevention and Treatment for Senile Diseases Harbin 150076, China
| | - Liu Chang
- College of Pharmacy, Harbin University of Commerce Harbin 150076, China Heilongjiang Provincial Key Laboratory of Drug Prevention and Treatment for Senile Diseases Harbin 150076, China
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Wang W, Yu H, Wang J, Lei W, Gao J, Qiu X, Wang J. The Complete Chloroplast Genome Sequences of the Medicinal Plant Forsythia suspensa (Oleaceae). Int J Mol Sci 2017; 18:E2288. [PMID: 29088105 PMCID: PMC5713258 DOI: 10.3390/ijms18112288] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/24/2017] [Accepted: 10/25/2017] [Indexed: 11/16/2022] Open
Abstract
Forsythia suspensa is an important medicinal plant and traditionally applied for the treatment of inflammation, pyrexia, gonorrhea, diabetes, and so on. However, there is limited sequence and genomic information available for F. suspensa. Here, we produced the complete chloroplast genomes of F. suspensa using Illumina sequencing technology. F. suspensa is the first sequenced member within the genus Forsythia (Oleaceae). The gene order and organization of the chloroplast genome of F. suspensa are similar to other Oleaceae chloroplast genomes. The F. suspensa chloroplast genome is 156,404 bp in length, exhibits a conserved quadripartite structure with a large single-copy (LSC; 87,159 bp) region, and a small single-copy (SSC; 17,811 bp) region interspersed between inverted repeat (IRa/b; 25,717 bp) regions. A total of 114 unique genes were annotated, including 80 protein-coding genes, 30 tRNA, and four rRNA. The low GC content (37.8%) and codon usage bias for A- or T-ending codons may largely affect gene codon usage. Sequence analysis identified a total of 26 forward repeats, 23 palindrome repeats with lengths >30 bp (identity > 90%), and 54 simple sequence repeats (SSRs) with an average rate of 0.35 SSRs/kb. We predicted 52 RNA editing sites in the chloroplast of F. suspensa, all for C-to-U transitions. IR expansion or contraction and the divergent regions were analyzed among several species including the reported F. suspensa in this study. Phylogenetic analysis based on whole-plastome revealed that F. suspensa, as a member of the Oleaceae family, diverged relatively early from Lamiales. This study will contribute to strengthening medicinal resource conservation, molecular phylogenetic, and genetic engineering research investigations of this species.
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Affiliation(s)
- Wenbin Wang
- College of Life Science, Shanxi Agricultural University, Taigu 030801, China.
| | - Huan Yu
- College of Life Science, Shanxi Agricultural University, Taigu 030801, China.
| | - Jiahui Wang
- College of Plant Protection, Northwest Agriculture & Forestry University, Yangling 712100, China.
| | - Wanjun Lei
- College of Life Science, Shanxi Agricultural University, Taigu 030801, China.
| | - Jianhua Gao
- College of Life Science, Shanxi Agricultural University, Taigu 030801, China.
| | - Xiangpo Qiu
- College of Life Science, Shanxi Agricultural University, Taigu 030801, China.
| | - Jinsheng Wang
- College of Life Science, Shanxi Agricultural University, Taigu 030801, China.
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Cui ZH, Jiang C, Li MH, Chen M, Zhou LS, Yuan Y. [Molecular identification of raw materials from lian qiao bai du wan]. Yao Xue Xue Bao 2013; 48:590-596. [PMID: 23833950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Lian Qiao Bai Du Wan was used to study the identification of Chinese patent medicine by molecular marker technique. DNA was extracted through modified CTAB method. The psbA-trnH and rbcL sequences were gradient amplified, and PCR products were ligated with the pEASY-T5 vector and then transformed into Trans1-T1 cells, respectively. Clones were selected randomly and sequenced. All sequences were analyzed by BlastN and the neighbor-joining (NJ) phylogenetic tree was constructed by MEGA 4.0. The results showed that nine kinds of medicinal materials can be identified by psbA-trnH sequences, and six kinds of medicinal materials by rbcL sequences from Lian Qiao Bai Du Wan. Molecular marker technique can stably and accurately distinguish multi-origin medicinal materials in Chinese patent medicine.
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Affiliation(s)
- Zhan-Hu Cui
- Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou 014060, China
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Kim DK, Kim JH. Molecular phylogeny of tribe Forsythieae (Oleaceae) based on nuclear ribosomal DNA internal transcribed spacers and plastid DNA trnL-F and matK gene sequences. J Plant Res 2011; 124:339-347. [PMID: 21042926 DOI: 10.1007/s10265-010-0383-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Accepted: 08/24/2010] [Indexed: 05/30/2023]
Abstract
The tribe Forsythieae comprises 2 genera (Forsythia and Abeliophyllum) and 14 species distributed mostly in the Far East. Although Forsythieae is considered monophyletic, with many symplesiomorphic characters, the phylogenetic status of Abeliophyllum remains controversial. We assessed the phylogenetic relationships of Forsythieae, based on a 3.3-kb plastid fragment (trnL-F region and matK gene) and nuclear internal transcribed spacer (ITS) region DNA sequences. We obtained a highly resolved and strongly supported topology with possible outgroups. The topology of the combined tree was congruent with those of the ITS region and matK gene. Maximum parsimony, maximum likelihood, and Bayesian inference tree analyses for the combined data also yielded identical relationships. Combined sequence data strongly supported the monophyly of Forsythieae and the close relationship between Fontanesia and Jasminum. Oleaceae, not Fontanesia, was found to be a sister group to Forsythieae. Moreover, the genus Abeliophyllum was distinctly independent of Forsythia. Three Forsythia lineages were suggested: (a) ONJ (ovata-nakaii-japonica clade), (b) VGE (viridissima-giraldiana-europaea), and (c) KISS (koreana-intermedia-saxatilis-suspensa). Our results indicated that F. × intermedia is not a hybrid between F. suspensa and F. viridissima, but further studies are needed to determine its taxonomic identity. Furthermore, the diverse fruit shapes in Oleaceae are assumed to be the result of parallelism or convergence.
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Affiliation(s)
- Dong-Kap Kim
- Department of Life Science, Kyungwon University, Gyeonggi-do, 461-701, Korea
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Kim HJ, Ono E, Morimoto K, Yamagaki T, Okazawa A, Kobayashi A, Satake H. Metabolic engineering of lignan biosynthesis in Forsythia cell culture. Plant Cell Physiol 2009; 50:2200-9. [PMID: 19887541 DOI: 10.1093/pcp/pcp156] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Lignans are a large class of secondary metabolites in plants, with numerous biological effects in mammals, including antitumor and antioxidant activities. Sesamin, the most abundant furofuran-class lignan in sesame seeds (Sesamum plants), is produced by the cytochrome P450 enzyme CYP81Q1 from the precursor lignan, pinoresinol. In contrast, Forsythia plants produce dibenzylbutyrolactone-class lignans, such as matairesinol, from pinoresinol via the catalysis of pinoresinol/lariciresinol reductase (PLR) and secoisolariciresinol dehydrogenase. Here we present the engineering of lignan biosynthesis in Forsythia cell suspension cultures for the development of an efficient production method of beneficial lignans. A suspension cell culture prepared from leaves of Forsythia koreana produced lignans, mainly pinoresinol and matairesinol glucosides, at levels comparable with that obtained from the leaves. In an attempt to increase the pinoresinol content in Forsythia, we generated a transgenic cell line overexpressing an RNA interference (RNAi) construct of PLR (PLR-RNAi). Down-regulation of PLR expression led to a complete loss of matairesinol and an accumulation of approximately 20-fold pinoresinol in its glucoside form in comparison with the non-transformant. Moreover, the Forsythia transgenic cells co-expressing CYP81Q1 and PLR-RNAi exhibited production of sesamin as well as accumulation of pinoresinol glucoside. These data suggest Forsythia cell suspension to be a promising tool for the engineering of lignan production. To the best of our knowledge, this is the first report on transgenic production of an exogenous lignan in a plant species.
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Affiliation(s)
- Hyun Jung Kim
- Suntory Institute for Bioorganic Research, 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka, 618-8503, Japan
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Yuan WJ, Xu SM, Zhang WR. [Identify the original plant of Forsythia suspensa by nucleotide sequence]. Zhong Yao Cai 2009; 32:1524-1526. [PMID: 20112711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
OBJECTIVE To investigate the means of distinguishing the original plant of Forsythia suspensa from confusion. METHODS To amplify the chloroplast matK gene by PCR using a consensus primer set and determine their nucleotide sequence by PCR direct sequencing. The ITS sequences were gained from NCBI. The characteristic analysis of matK and ITS sequences were generated using Clustal aligned. RESULTS There were 30 bp and 8 bp unique nucleotide in ITS and matK sequence in Forsythia suspensa. The matK gene and ITS sequences might be good molecular marker to be used to identify the original plant of Forsythia suspensa. CONCLUSION The sequence analysis of matK gene ITS sequences might become the mean to identify the original plant of Forsythia suspensa.
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Affiliation(s)
- Wang-Jun Yuan
- Institute of Natural Products, Henan University, Kaifeng 475004, China.
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