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Transcriptome analysis of Akebia quinata (Thunb.) Decne. and discovery of key enzyme genes in the phenylpropanoid biosynthesis pathway

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Abstract

Akebia quinata is a dry vine stem of Akebia quinata (Thunb.) Decne. in the Lardizabalaceae Akebia Decne, which has antibacterial, anti-tumor, and diuretic properties. Calceolarioside B is a known effective component of Akebia quinata. Moreover, calceolarioside B is a phenylpropanoid, the current understanding of the molecular mechanisms of phenylpropanoid biosynthetic pathway is not clear. In this study, we performed RNA-Seq analysis of the flowers, leaves, roots, and stems of Akebia quinata using the BGISEQ-500 platform. The assembly of transcripts from all four types of tissues generated 123,576 unigenes, of which 90,273 were mapped to several public databases for functional annotation. We identified 182 genes encoding 13 key enzymes involved in phenylpropanoid biosynthesis through their KEGG annotation. DEGs were identified via the comparison of gene expression levels between stems and other tissues (flowers, leaves, and roots). We also verified the expression levels of some unigenes encoding key enzymes using qRT-PCR. This analysis of the phenylpropanoid biosynthesis pathway and its crucial enzymes in Akebia quinata lays a foundation for uncovering the regulatory mechanism of phenylpropanoid biosynthesis. The expression patterns of genes involved in the phenylpropanoid biosynthesis pathway were verified using qRT-PCR. We suggest that transcripts of 4CL may be key regulators in the phenylpropanoid biosynthetic pathway. Our results greatly extend the public transcriptome data set of Akebia quinata and provide valuable information for the identification of candidate genes involved in phenylpropanoid biosynthesis.

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Data availability

In this study, the RNA-Seq raw data reads have been deposited in NCBI Sequence Read Archive (SRA) database. Reviewer link: https://dataview.ncbi.nlm.nih.gov/object/PRJNA860796?reviewer=2gocus2ljundflnokhdusp9s6u.

Abbreviations

RNA-Seq:

RNA sequencing

KEGG:

Kyoto Encyclopedia of Genes and Genomes

DEGs:

Differentially expressed genes

qRT-PCR:

Quantitative real-time polymerase chain reaction

NR:

NCBI non-redundant protein sequence

NT:

NCBI nucleotide sequence

KOG:

Clusters of euKaryotic Orthologous Groups

PFAM:

Protein families database

GO:

Gene ontology

PAL:

Phenylalanine ammonia-lyase

C4H:

Cinnamate 4-hydroxylase

4CL:

4-Coumarate–CoA ligase

HCT:

Shikimate O-hydroxycinnamoyltransferase

C3′H:

5-O-(4-coumaroyl)-D-quinate 3′-monooxygenase

CCoAOMT:

Caffeoyl-CoA O-methyltransferase

CCR:

Cinnamoyl-CoA reductase

F5H:

Ferulate-5-hydroxylase

COMT:

Caffeic acid 3-O-methyltransferase

CAD:

Cinnamyl-alcohol dehydrogenase

CHS:

Chalcone synthase

CHI:

Chalcone isomerase

F3H:

Naringenin 3-dioxygenase 

ORF:

Open reading frame

TFs:

Transcription factors

References

  • Ablise M, Cartier A, Siest G, Visvikis S, Loppinet V (2002) Molecular pharmacophore determination of lipid lowering drugs with the receptor mapping method. Mini Rev Med Chem 2(2):97–102

    Article  CAS  PubMed  Google Scholar 

  • Chen CH, Song TY, Liang YC, Hu ML (2009) Acteoside and 6-O-acetylacteoside downregulate cell adhesion molecules induced by IL-1beta through inhibition of ERK and JNK in human vascular endothelial cells. J Agric Food Chem 57(19):8852–8859

    Article  CAS  PubMed  Google Scholar 

  • Chen GL, Zhu MZ, Guo MQ (2019) Research advances in traditional and modern use of Nelumbo nucifera: phytochemicals, health promoting activities and beyond. Crit Rev Food Sci Nutr 59(sup1):S189–S209

    Article  CAS  PubMed  Google Scholar 

  • Chu HB, Tan NH, Peng CS (2009) Progress in research on Pedicularis plants. China J Chin Mater Med 34(19):2536–2546

    CAS  Google Scholar 

  • Fu LG (2000) Chinese higher plants. Qingdao Publishing House, Qingdao, p 586

    Google Scholar 

  • Gao W, Xin WN, Ao WC, Xu LC, Gong C, Peng YY (2015) Phenylethanoid glycosides B content of Akebia plants determined by HPLC. South China for Sci 43(05):48–51

    CAS  Google Scholar 

  • Gao RG, Li H, Xiang QZ, Li M (2020) Cloning and protein expression analysis of 4-coumarate coenzyme A ligase gene Cs4CL1 in tea tree. Shandong Agric Sci 52(03):8–12

    Google Scholar 

  • Gu XW, Chen Y, Wang M, Dong YF, Feng X, Liang JY (2012) Progress in the research on the phenylpropanoids and its related chemical constituents of Malvaceae. Chin Wild Plant Resour 31(01):17–21

    Google Scholar 

  • Jiang X, Lu LM, Zhang CL, Wang XY, Sun Q, Wang JT, Yuan GJ (2017) Antibacterial phenylethanoid glycosides from fruits of Forsythia suspensa. Mod Chin Med 19(05):642–647

    Google Scholar 

  • Julião Lde S, Piccinelli AL, Marzocco S, Leitão SG, Lotti C, Autore G, Rastrelli L (2009) Phenylethanoid glycosides from Lantana fucata with in vitro anti-inflammatory activity. J Nat Prod 72(08):1424–1428

    Article  PubMed  Google Scholar 

  • Kim CS, Winn MD, Sachdeva V, Jordan KE (2017) K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of trinity. BMC Bioinform 18(01):467

    Article  Google Scholar 

  • Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(04):357–359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li L (2018) Study on the resource and quality evaluation of Akebia quinata in Anhui province. Anhui University of Chinese Medicine, Hefei

    Google Scholar 

  • Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform 12:323

    Article  CAS  Google Scholar 

  • Li L, Chen XZ, Yao XH, Tian H, Huang HW (2010) Geographic distribution and resource status of three important Akebia species. J Wuhan Bot Res 28(04):497–506

    Google Scholar 

  • Li LX, Chen DL, Zhou XJ (2020) Research progress on chemical constituents, pharmacological activity and Q-marker analysis and prediction of Scrophularia ningpoensis Hemsl. Chin Tradit Patent Med 42(09):2417–2426

    Google Scholar 

  • Lin L, Liu YC, Huang JL, Liu XB, Qing ZX, Zeng JG, Liu ZY (2018) Medicinal plants of the genus Macleaya (Macleaya cordata, Macleaya microcarpa): a review of their phytochemistry, pharmacology, and toxicology. Phytother Res 32(01):19–48

    Article  CAS  PubMed  Google Scholar 

  • Liu H, Wang DQ (2011) Research the medicinal plant resources of Akebia plants in Anhui Province. Mod Chin Med 13(09):9–11

    CAS  Google Scholar 

  • Liu YT, Hou XJ, Xie Y, Feng YL, Ou YS, Yang SL (2012) Overview of research on chemical constituents and pharmacological activities of Akebia Dence. J Jiangxi Univ Chin Med 24(04):87–93

    CAS  Google Scholar 

  • Liu YC, Li HL, Zeng XH, Wang XB (2020) Research progress on chemical components and pharmacological effects of Akebia trifoliata (Thunb.) koidz. stem. Acad J Shanghai Univ Tradit Chin Med 34(03):99–106

    Google Scholar 

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25(04):402–408

    Article  CAS  PubMed  Google Scholar 

  • Mistry J, Finn RD, Eddy SR, Bateman A, Punta M (2013) Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions. Nucleic Acids Res 41(12):e121

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mu HN, Sun TZ, Xu C, Li HG, Yang XL, Wang LG (2016) Gene clone and expression analysis of 4-coumarate-CoA ligase in sweet Osmanthus (Osmanthus fragrans Lour.). Mol Plant Breed 14(03):536–541

    CAS  Google Scholar 

  • Nassiri-Asl M, Hosseinzadeh H (2016) Review of the pharmacological effects of Vitis vinifera (grape) and its bioactive constituents: an update. Phytother Res 30(09):1392–1403

    Article  CAS  PubMed  Google Scholar 

  • Ou JM, Chu XQ, Zhang H (2015) Determination of three active components of Akebia from Anhui Province, China, by high-performance liquid chromatography. J Anhui Univ Chin Med 34(01):70–73

    Google Scholar 

  • Ou JM, Yang X, Shan CM, Zhang SX, Shi YY, Wu JW, Huang LQ, Wang R (2020) Transcriptome analysis of “Langmei” fruits and key enzyme genes structure and function prediction involved in citric acid biosynthesis. China J Chin Mater Med 45(19):4606–4616

    Google Scholar 

  • Peng SP, Dong CM, Zhu YH (2021) Screening and identification of R2R3-MYB transcription factor related to lignan synthesis in Forsythia suspensa. J Chin Med Mater 44(07):1590–1596

    Google Scholar 

  • Pertea G, Huang XQ, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19(05):651

    Article  CAS  PubMed  Google Scholar 

  • Pirooznia M, Perkins EJ, Deng Y (2008) Batch Blast Extractor: an automated blastx parser application. BMC Genom 9(Suppl 2):S10

    Article  Google Scholar 

  • Qian CC, Zhao LQ, Yang YT, Han BX, Wu JW, Ou JM (2022) Analysis of the transcriptome and discovery of key enzyme genes of the triterpenoid saponin biosynthesis pathway in Akebia trifoliata (Thunb.) Koidz. Plant Sci J 40(03):378–389

    Google Scholar 

  • Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16(06):276–277

    Article  CAS  PubMed  Google Scholar 

  • Shan CM, Wang CK, Shi YY, Zhang SX, Zhao LQ, Wu JW (2020a) Identification of key enzyme genes involved in biosynthesis of steroidal saponins and analysis of biosynthesis pathway in Polygonatum cyrtonema. China J Chin Mater Med 45(12):2847–2857

    Google Scholar 

  • Shan CM, Wang CK, Zhang SX, Shi YY, Ma KL, Yang QS, Wu JW (2020b) Transcriptome analysis of Clinopodium gracile (Benth.) Matsum and identification of genes related to Triterpenoid Saponin biosynthesis. BMC Genom 21(01):49

    Article  Google Scholar 

  • Shi YY, Zhang SX, Peng DY, Wang CK, Zhao DR, Ma KL, Wu JW, Huang LQ (2019) Transcriptome analysis of Clinopodium chinense (Benth.) O. Kuntze and identification of genes involved in triterpenoid saponin biosynthesis. Int J Mol Sci 20(11):2643

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Singh S, Bhatt V, Kumar V, Kumawat S, Khatri P, Singla P, Shivaraj SM, Nadaf A, Deshmukh R, Sharma TR, Sonah H (2020) Evolutionary understanding of aquaporin transport system in the basal eudicot model species Aquilegia coerulea. Plants (Basel) 9(06):799

    CAS  PubMed  Google Scholar 

  • Stuible HP, Kombrink E (2001) Identification of the substrate specificity-conferring amino acid residues of 4-coumarate: coenzyme A ligase allows the rational design of mutant enzymes with new catalytic properties. J Biol Chem 276(29):26893–26897

    Article  CAS  PubMed  Google Scholar 

  • Tian XM, Yan LH, Xiang GF, Jiang LY (2017) Research progress on 4-coumarate: coenzyme A ligase (4CL) in plants. Biotechnol Bull 33(04):19–26

    Google Scholar 

  • Wang J, Zhou ZY, Xu QL, Tan JW (2014) Phenylpropanoids from the stems of Akebia trifoliata. J Trop Subtrop Bot 22(05):511–515

    CAS  Google Scholar 

  • Wang FQ, Yang X, Zuo X, Miao CY, Zhang ZY (2022) Full-length transcriptome sequence and identification of genes involved in phenylethanol glycoside biosynthesis in Rehmannia glutinosa. Acta Pharm Sin 57(03):831–838

    Google Scholar 

  • Yang ZY, Ji YH (2017) Comparative and phylogenetic analyses of the complete chloroplast genomes of three Arcto-Tertiary relicts: Camptotheca acuminata, Davidia involucrata, and Nyssa sinensis. Front Plant Sci 8:1536

    Article  PubMed  PubMed Central  Google Scholar 

  • Yang YN, Liu HC, Gao EG, Li YY, Chen SS, Xin XH (2022) Phenological investigation and variation analysis of yield and quality of Akebia Decne. germplasm resources. J South Agric 53(01):134–145

    CAS  Google Scholar 

  • Zhai Y, Liu QS, Shi DW, Wu YK, Zhang NQ, Qi QS (2017) cloning and sequence analysis of a 4-coumaryl: CoA ligase gene from Arabidopsis thaliana. Biol Chem Eng 3(03):1–8

  • Zhang KM, Geng GG, Qiao F (2022) 4CL Activity and gene expression during fruit development of Lycium chinense. Mol Plant Breed. http://kns.cnki.net/kcms/detail/46.1068.S.20220328.1531.014.html

  • Zhao LQ, Shan CM, Zhang SX, Shi YY, Ma KL, Wu JW (2020) Identification of key enzyme genes involved in anthocyanin synthesis pathway in Clinopodium gracile by transcriptome analysis. Bull Bot Res 40(06):886–896

    Google Scholar 

  • Zheng Y, Jin XF (2021) The research progress on development and utilization of family Lardizabalaceae plant resources. Chin Wild Plant Resour 40(10):83–108

  • Zhu F, Cai YZ, Sun M, Ke J, Lu D, Corke H (2009) Comparison of major phenolic constituents and in vitro antioxidant activity of diverse Kudingcha genotypes from Ilex kudingcha, Ilex cornuta, and Ligustrum robustum. J Agric Food Chem 57(14):6082–6089

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This research was supported by the Research Project on pharmacodynamic material basis of Anhui genuine main medicinal materials (RZ2100000757), the Natural Science Foundation of Education Department of Anhui Province, China (KJ2019A0479), the Demonstration Funds for the Promotion of Forestry Science and Technology from the Central Finance (Z175070050002), and the Talent Project of Anhui University of Chinese Medicine (2021RCYB011).

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Authors and Affiliations

  1. College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China

    Chengcheng Qian, Yatian Yang, Rui Wu, Deling Wu & Jinmei Ou

  2. College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, 237012, China

    Bangxing Han

  3. Anhui Key Laboratory of New Technology of Chinese Herbs Pieces Manufacturing, Hefei, 230012, China

    Jinmei Ou

  4. Institute of Conservation and Development of Traditional Chinese Medicine Resources, Anhui Academy of Chinese Medicine, Hefei, 230012, China

    Jinmei Ou

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  1. Chengcheng Qian
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Qian, C., Yang, Y., Wu, R. et al. Transcriptome analysis of Akebia quinata (Thunb.) Decne. and discovery of key enzyme genes in the phenylpropanoid biosynthesis pathway. Acta Physiol Plant 45, 117 (2023). https://doi.org/10.1007/s11738-023-03603-x

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