Full-length transcriptome combined with RNA sequence analysis of Fraxinus chinensis.
DEGs
Fraxinus chinensis
Phenylpropane metabolism pathway
Transcriptome
Journal
Genes & genomics
ISSN: 2092-9293
Titre abrégé: Genes Genomics
Pays: Korea (South)
ID NLM: 101481027
Informations de publication
Date de publication:
05 2023
05 2023
Historique:
received:
31
10
2022
accepted:
25
02
2023
medline:
20
4
2023
pubmed:
12
3
2023
entrez:
11
3
2023
Statut:
ppublish
Résumé
The dry root or stem bark of Fraxinus chinensis is a famous herb Qin Pi which is known for its anti-inflammatory, analgesic, anti-tumor, liver protective and diuretic pharmacological effects, the fundamental chemical components are coumarin, phenylethanol glycosides and flavonoids. However, it is difficult to clarify the secondary metabolite synthesis pathway and key genes involved in the pathway because of lack genome information of Fraxinus chinensis. To generate a complete transcriptome of Fraxinus chinensis and to clarify the differentially expressed genes (DEGs) in leaves and stem barks. In this study, full-length transcriptome analysis and RNA-Seq were combined to characterize Fraxinus chinensis transcriptome. A total of 69,145 transcripts were acquired and regarded as reference transcriptome, 67,441 transcripts (97.47%) were annotated to NCBI non-redundant protein (Nr), SwissProt, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and eukaryotic orthologous groups (KOG) databases. A total of 18,917 isoforms were annotated to KEGG database and classified to 138 biological pathways. In total, 10,822 simple sequence repeat (SSRs) and 11,319 resistance (R) gene were classified to 18 types, and 3947 transcription factors (TFs) were identified in full-length transcriptome analysis. Additionally, 15,095 DEGs were detected by RNA-seq in leaves and barks, including 4696 significantly up-regulated and 10,399 significantly down-regulated genes. And 254 transcripts were annotated into phenylpropane metabolism pathway containing 86 DEGs and ten of these enzyme genes were verified by qRT-PCR. It laid the foundation for further exploration of the biosynthetic pathway of phenylpropanoids and related key enzyme genes.
Sections du résumé
BACKGROUND
The dry root or stem bark of Fraxinus chinensis is a famous herb Qin Pi which is known for its anti-inflammatory, analgesic, anti-tumor, liver protective and diuretic pharmacological effects, the fundamental chemical components are coumarin, phenylethanol glycosides and flavonoids. However, it is difficult to clarify the secondary metabolite synthesis pathway and key genes involved in the pathway because of lack genome information of Fraxinus chinensis.
OBJECTIVE
To generate a complete transcriptome of Fraxinus chinensis and to clarify the differentially expressed genes (DEGs) in leaves and stem barks.
METHODS
In this study, full-length transcriptome analysis and RNA-Seq were combined to characterize Fraxinus chinensis transcriptome.
RESULTS
A total of 69,145 transcripts were acquired and regarded as reference transcriptome, 67,441 transcripts (97.47%) were annotated to NCBI non-redundant protein (Nr), SwissProt, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and eukaryotic orthologous groups (KOG) databases. A total of 18,917 isoforms were annotated to KEGG database and classified to 138 biological pathways. In total, 10,822 simple sequence repeat (SSRs) and 11,319 resistance (R) gene were classified to 18 types, and 3947 transcription factors (TFs) were identified in full-length transcriptome analysis. Additionally, 15,095 DEGs were detected by RNA-seq in leaves and barks, including 4696 significantly up-regulated and 10,399 significantly down-regulated genes. And 254 transcripts were annotated into phenylpropane metabolism pathway containing 86 DEGs and ten of these enzyme genes were verified by qRT-PCR.
CONCLUSION
It laid the foundation for further exploration of the biosynthetic pathway of phenylpropanoids and related key enzyme genes.
Identifiants
pubmed: 36905551
doi: 10.1007/s13258-023-01374-w
pii: 10.1007/s13258-023-01374-w
doi:
Substances chimiques
Flavonoids
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
553-567Informations de copyright
© 2023. The Author(s) under exclusive licence to The Genetics Society of Korea.
Références
Alamancos GP, Pagès A, Trincado JL, Bellora N, Eyras E (2015) Leveraging transcript quantification for fast computation of alternative splicing profiles. RNA 21:1521–1531
pubmed: 26179515
pmcid: 4536314
doi: 10.1261/rna.051557.115
Amato A, Cavallini E, Zenoni S, Finezzo L, Begheldo M, Ruperti B, Tornielli GB (2017) A grapevine TTG2-Like WRKY transcription factor is involved in regulating vacuolar transport and flavonoid biosynthesis. Front Plant Sci 7:1979
pubmed: 28105033
pmcid: 5214514
doi: 10.3389/fpls.2016.01979
Byrne A, Cole C, Volden R, Vollmers C (2019) Realizing the potential of full-length transcriptome sequencing. Philos Trans R Soc Lond B Biol Sci 374:20190097
pubmed: 31587638
pmcid: 6792442
doi: 10.1098/rstb.2019.0097
Chang HC, Wang SW, Chen CY, Hwang TL, Cheng MJ, Sung PJ, Liao KW, Chen JJ (2020) Secoiridoid glucosides and anti-inflammatory constituents from the stem bark of Fraxinus chinensis. Molecules 25:5911
pubmed: 33327368
pmcid: 7764309
doi: 10.3390/molecules25245911
Cochrane FC, Davin LB, Lewis NG (2004) The Arabidopsis phenylalanine ammonia lyase gene family: kinetic characterization of the four PAL isoforms. Phytochemistry 11:1557–1564
doi: 10.1016/j.phytochem.2004.05.006
Conesa A, Gotz　S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18):3674–3676
pubmed: 16081474
doi: 10.1093/bioinformatics/bti610
Deng A, Li J, Yao Z, Afriyie G, Chen Z, Guo Y, Luo J, Wang Z (2021) SMRT sequencing of the full-length transcriptome of the coelomactra antiquata. Front Genet 12:741243
pubmed: 34721529
pmcid: 8552913
doi: 10.3389/fgene.2021.741243
Di P, Wang P, Yan M, Han P, Huang X, Yin L, Yan Y, Xu Y, Wang Y (2021) Genome-wide characterization and analysis of WRKY transcription factors in Panax ginseng. BMC Genom 22:834
doi: 10.1186/s12864-021-08145-5
Dong NQ, Lin HX (2021) Contribution of phenylpropanoid metabolism to plant development and plant-environment interactions. J Integr Plant Biol 63(1):180–209
pubmed: 33325112
doi: 10.1111/jipb.13054
Du YT, Zhao MJ, Wang CT, Gao Y, Wang YX, Liu YW, Chen M, Chen J, Zhou YB, Xu ZS, Ma YZ (2018) Identification and characterization of GmMYB118 responses to drought and salt stress. BMC Plant Biol 18:320
pubmed: 30509166
pmcid: 6276260
doi: 10.1186/s12870-018-1551-7
Duan Z, Yan Q, Wu F, Wang Y, Wang S, Zong X, Zhou P, Zhang J (2021) Genome-wide analysis of the udp-glycosyltransferase family reveals its roles in coumarin biosynthesis and abiotic stress in Melilotus albus. Int J Mol Sci 22:10826
pubmed: 34639166
pmcid: 8509628
doi: 10.3390/ijms221910826
Feng Y, Zhao Y, Zhang J, Wang B, Yang C, Zhou H, Qiao J (2021) Full-length SMRT transcriptome sequencing and microsatellite characterization in Paulownia catalpifolia. Sci Rep 11(1):8734
pubmed: 33888729
pmcid: 8062547
doi: 10.1038/s41598-021-87538-8
Franco-Zorrilla JM, Solano R (2017) Identification of plant transcription factor target sequences. Biochim Biophys Acta Gene Regul Mech 1860(1):21–30
pubmed: 27155066
doi: 10.1016/j.bbagrm.2016.05.001
Franke R, Humphreys JM, Hemm MR, Denault JW, Ruegger MO, Cusumano JC, Chapple C (2002) The Arabidopsis REF8 gene encodes the 3-hydroxylase of phenylpropanoid metabolism. Plant J 30(1):33–45
pubmed: 11967091
doi: 10.1046/j.1365-313X.2002.01266.x
Gallegos J (2018) Alternative splicing plays a major role in plant response to cold temperatures. Plant Cell 30(7):1378–1379
pubmed: 29871987
pmcid: 6096596
doi: 10.1105/tpc.18.00430
Ha YJ, Sa KJ, Lee JK (2021) Identifying SSR markers associated with seed characteristics in Perilla (Perilla frutescens L.). Physiol Mol Biol Plants 27(1):93–105
pubmed: 33627965
pmcid: 7873175
doi: 10.1007/s12298-021-00933-3
He Z, Su Y, Wang T (2021) Full-length transcriptome analysis of four different tissues of Cephalotaxus oliveri. Int J Mol Sci 22:787
pubmed: 33466772
pmcid: 7830723
doi: 10.3390/ijms22020787
Hestand MS, Ameur A (2019) The versatility of SMRT sequencing. Genes 10(1):24
pubmed: 30621217
pmcid: 6357146
doi: 10.3390/genes10010024
Karlson CKS, Mohd Noor SN, Khalid N, Tan BC (2022) CRISPRi-Mediated down-regulation of the cinnamate-4-hydroxylase (C4H) gene enhances the flavonoid biosynthesis in Nicotiana tabacum. Biology 11:1127
pubmed: 36009753
pmcid: 9404795
doi: 10.3390/biology11081127
Knut M, Joanne C, Cusumano CSV, Clint CSChapple (1996) Ferulate-5-hydroxylase from arabidopsis thaliana defines a new family of cytochrome P450-dependent monooxygenases. Proc Natl Acad Sci 93:6869–6874
doi: 10.1073/pnas.93.14.6869
Lam PY, Wang L, Lo C, Zhu FY (2022) Alternative splicing and its roles in plant metabolism. Int J Mol Sci 23:7355
pubmed: 35806361
pmcid: 9266299
doi: 10.3390/ijms23137355
Lavhale SG, Kalunke RM, Giri AP (2018) Structural, functional and evolutionary diversity of 4-coumarate-CoA ligase in plants. Planta 248(5):1063–1078
pubmed: 30078075
doi: 10.1007/s00425-018-2965-z
Li X, Qiao L, Chen B, Zheng Y, Zhi C, Zhang S, Pan Y, Cheng Z (2022) SSR markers development and their application in genetic diversity evaluation of garlic (Allium sativum) germplasm. Plant Divers 44(5):481–491
pubmed: 36187554
doi: 10.1016/j.pld.2021.08.001
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15(12):550
pubmed: 25516281
pmcid: 4302049
doi: 10.1186/s13059-014-0550-8
Ma D, Constabel CP (2019a) MYB Repressors as regulators of phenylpropanoid metabolism in plants. Trends Plant Sci 24(3):275–289
pubmed: 30704824
doi: 10.1016/j.tplants.2018.12.003
Ma Q, Xia Z, Cai Z, Li L, Cheng Y, Liu J, Nian H (2019b) GmWRKY16 enhances drought and salt tolerance through an aba-mediated pathway in Arabidopsis thaliana. Front Plant Sci 9:1979
pubmed: 30740122
pmcid: 6357947
doi: 10.3389/fpls.2018.01979
Oh JE, Kwon Y, Kim JH, Noh H, Hong SW, Lee H (2011) A dual role for MYB60 in stomatal regulation and root growth of Arabidopsis thaliana under drought stress. Plant Mol Biol 77:91–103
pubmed: 21637967
doi: 10.1007/s11103-011-9796-7
Park HL, Bhoo SH, Kwon M, Lee SW, Cho MH (2017) Biochemical and expression analyses of the rice cinnamoyl-coa reductase gene family. Front Plant Sci 8:2099
pubmed: 29312373
pmcid: 5732984
doi: 10.3389/fpls.2017.02099
Phukan UJ, Jeena GS, Shukla RK (2016) WRKY transcription factors: molecular regulation and stress responses in plants. Front Plant Sci 7:760
pubmed: 27375634
pmcid: 4891567
doi: 10.3389/fpls.2016.00760
Schilmiller AL, Stout J, Weng JK, Humphreys J, Ruegger MO, Chapple C (2009) Mutations in the cinnamate 4-hydroxylase gene impact metabolism, growth and development in Arabidopsis. Plant J 60(5):771–782
pubmed: 19682296
doi: 10.1111/j.1365-313X.2009.03996.x
Seo MS, Kim JS (2017) Understanding of MYB transcription factors involved in glucosinolate biosynthesis in brassicaceae. Molecules 22:1549
pubmed: 28906468
pmcid: 6151624
doi: 10.3390/molecules22091549
Sharma A, Shahzad B, Rehman A, Bhardwaj R, Landi M, Zheng B (2019) Response of phenylpropanoid pathway and the role of polyphenols in plants under abiotic stress. Molecules 24:2452
pubmed: 31277395
pmcid: 6651195
doi: 10.3390/molecules24132452
Shi Y, Zhang S, Peng D, Shan C, Zhao L, Wang B, Wu J (2020) De novo transcriptome analysis of Cnidium monnieri (L.) Cuss and detection of genes related to coumarin biosynthesis. PeerJ 8:e10157
pubmed: 33194397
pmcid: 7651471
doi: 10.7717/peerj.10157
Siwinska J, Siatkowska K, Olry A, Grosjean J, Hehn A, Bourgaud F, Meharg AA, Carey M, Lojkowska E, Ihnatowicz A (2018) Scopoletin 8-hydroxylase: a novel enzyme involved in coumarin biosynthesis and iron-deficiency responses in Arabidopsis. J Exp Bot 69(7):1735–1748
pubmed: 29361149
pmcid: 5888981
doi: 10.1093/jxb/ery005
Song H, Wang P, Nan Z, Wang X (2014) The WRKY transcription factor genes in Lotus japonicus. Int J Genom 2014:420128
Sui Z, Luo J, Yao R, Huang C, Zhao Y, Kong L (2019) Functional characterization and correlation analysis of phenylalanine ammonia-lyase (PAL) in coumarin biosynthesis from Peucedanum praeruptorum Dunn. Phytochemistry 158:35–45
pubmed: 30448740
doi: 10.1016/j.phytochem.2018.11.006
Szakonyi D, Duque P (2018) Alternative splicing as a regulator of early plant development. Front Plant Sci 9:1174
pubmed: 30158945
pmcid: 6104592
doi: 10.3389/fpls.2018.01174
Vogt T (2010) Phenylpropanoid biosynthesis. Mol Plant 3(1):2–20
pubmed: 20035037
doi: 10.1093/mp/ssp106
Wang D, Chen Q, Chen W, Liu X, Xia Y, Guo Q, Jing D, Liang G (2021a) A WRKY transcription factor, EjWRKY17, from Eriobotrya japonica enhances drought tolerance in transgenic Arabidopsis. Int J Mol Sci 22(11):5593
pubmed: 34070474
pmcid: 8197471
doi: 10.3390/ijms22115593
Wang L, Lu W, Ran L, Dou L, Yao S, Hu J, Fan D, Li C, Luo K (2019) R2R3-MYB transcription factor MYB6 promotes anthocyanin and proanthocyanidin biosynthesis but inhibits secondary cell wall formation in Populus tomentosa. Plant J 99(4):733–751
pubmed: 31021017
doi: 10.1111/tpj.14364
Wang Y, Zhang Y, Fan C, Wei Y, Meng J, Li Z, Zhong C (2021b) Genome-wide analysis of MYB transcription factors and their responses to salt stress in Casuarina equisetifolia. BMC Plant Biol 21(1):328
pubmed: 34238224
pmcid: 8265015
doi: 10.1186/s12870-021-03083-6
Wu J, Jiang Y, Liang Y, Chen L, Chen W, Cheng B (2019) Expression of the maize MYB transcription factor ZmMYB3R enhances drought and salt stress tolerance in transgenic plants. Plant Physiol Bioch 137:179–188
doi: 10.1016/j.plaphy.2019.02.010
Xiao K, Song QH, Zhang SW, Xuan LJ (2008) Water-soluble constituents of the root barks of Fraxinus rhynchophylla (Chinese drug Qinpi). J Asian Nat Prod Res 10:205–210
pubmed: 18253890
doi: 10.1080/10286020701394514
Yan H, Pei X, Zhang H, Li X, Zhang X, Zhao M, Chiang VL, Sederoff RR, Zhao X (2021) MYB-mediated regulation of anthocyanin biosynthesis. Int J Mol Sci 22:3103
pubmed: 33803587
pmcid: 8002911
doi: 10.3390/ijms22063103
Yang S, Tang F, Zhu H (2014) Alternative splicing in plant immunity. Int J Mol Sci 15(6):10424–10445
pubmed: 24918296
pmcid: 4100160
doi: 10.3390/ijms150610424
Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. 34:293–297
doi: 10.1093/nar/gkl031
Zhang R, Chen Z, Zhang L, Yao W, Xu Z, Liao B, Mi Y, Gao H, Jiang C, Duan L, Ji A (2020) Genomic characterization of WRKY transcription factors related to Andrographolide biosynthesis in Andrographis paniculata. Front Genet 11:601689
pubmed: 33537059
doi: 10.3389/fgene.2020.601689
Zhao L, Zhang S, Shan C, Shi Y, Wu H, Wu J, Peng D (2021) De novo transcriptome assembly of Angelica dahurica and characterization of coumarin biosynthesis pathway genes. Gene 791:145713
pubmed: 33979682
doi: 10.1016/j.gene.2021.145713
Zhong F, Huang L, Qi L, Ma Y, Yan Z (2020) Full-length transcriptome analysis of Coptis deltoidea and identification of putative genes involved in benzylisoquinoline alkaloids biosynthesis based on combined sequencing platforms. Plant Mol Biol 102:477–499
pubmed: 31902069
doi: 10.1007/s11103-019-00959-y