[1]

Xiao Q, Li Z, Qu M, Xu W, Su Z, et al. 2021. LjaFGD: Lonicera japonica functional genomics database. Journal of Integrative Plant Biology 63(8):1422−36

doi: 10.1111/jipb.13112
[2]

Shang X, Pan H, Li M, Miao X, Ding H. 2011. Lonicera japonica Thunb.: ethnopharmacology, phytochemistry and pharmacology of an important traditional Chinese medicine. Journal of Ethnopharmacology 138(1):1−21

doi: 10.1016/j.jep.2011.08.016
[3]

Ge L, Xie Q, Jiang Y, Xiao L, Wan H, et al. 2022. Genus Lonicera: New drug discovery from traditional usage to modern chemical and pharmacological research. Phytomedicine 96:153889

doi: 10.1016/j.phymed.2021.153889
[4]

Yuan Y, Wang Z, Jiang C, Wang X, Huang L. 2014. Exploiting genes and functional diversity of chlorogenic acid and luteolin biosyntheses in Lonicera japonica and their substitutes. Gene 534(2):408−16

doi: 10.1016/j.gene.2012.09.051
[5]

Zha L, Liu S, Liu J, Jiang C, Yu S, et al. 2017. DNA methylation influences chlorogenic acid biosynthesis in Lonicera japonica by mediating LjbZIP8 to regulate phenylalanine ammonia-lyase 2 expression. Frontiers in Plant Science 8:1178

doi: 10.3389/fpls.2017.01178
[6]

Kwon SH, Ma SX, Hong SI, Lee SY, Jang CG. 2015. Lonicera japonica THUNB. extract inhibits lipopolysaccharide-stimulated inflammatory responses by suppressing NF-κB signaling in BV-2 microglial cells. Journal of Medicinal Food 18(7):762−75

doi: 10.1089/jmf.2014.3341
[7]

Li RJ, Kuang XP, Wang WJ, Wan CP, Li WX. 2020. Comparison of chemical constitution and bioactivity among different parts of Lonicera japonica Thunb. Journal of the Science of Food and Agriculture 100(2):614−22

doi: 10.1002/jsfa.10056
[8]

Yang B, Guan Q, Tian J, Komatsu S. 2017. Transcriptomic and proteomic analyses of leaves from Clematis terniflora DC. under high level of ultraviolet-B irradiation followed by dark treatment. Journal of Proteomics 150:323−40

doi: 10.1016/j.jprot.2016.10.001
[9]

Wang T, Yang B, Guan Q, Chen X, Zhong Z, et al. 2019. Transcriptional regulation of Lonicera japonica Thunb. during flower development as revealed by comprehensive analysis of transcription factors. BMC Plant Biology 19(1):198

doi: 10.1186/s12870-019-1803-1
[10]

Geng JL, Li HB, Liu WJ, Wang ZZ, Ge W, et al. 2022. Two new chemical constituents from Lonicera japonica. Natural Product Research 36(20):5174−80

doi: 10.1080/14786419.2021.1921769
[11]

Wang X, Chen J, Ni H, Mustafa G, Yang Y, et al. 2021. Use Chou's 5-steps rule to identify protein post-translational modification and its linkage to secondary metabolism during the floral development of Lonicera japonica Thunb. Plant Physiology and Biochemistry 167:1035−48

doi: 10.1016/j.plaphy.2021.09.009
[12]

Guan R, Guo F, Guo R, Wang S, Sun X, et al. 2023. Integrated metabolic profiling and transcriptome analysis of Lonicera japonica flowers for chlorogenic acid, luteolin and endogenous hormone syntheses. Gene 888:147739

doi: 10.1016/j.gene.2023.147739
[13]

Xia H, Zhang L, Wu G, Fu C, Long Y, et al. 2016. Genome-wide identification and characterization of MicroRNAs and target genes in Lonicera japonica. PLoS One 11(10):e0164140

doi: 10.1371/journal.pone.0164140
[14]

Li M, Tian X, Mustafa G, Chen Y, Shan L, et al. 2024. Involvement of miRNAs regulation on both flower development and secondary metabolism in Lonicera japonica Thunb. Environmental and Experimental Botany 218:105569

doi: 10.1016/j.envexpbot.2023.105569
[15]

Ner-Gaon H, Halachmi R, Savaldi-Goldstein S, Rubin E, Ophir R, et al. 2004. Intron retention is a major phenomenon in alternative splicing in Arabidopsis. The Plant Journal 39(6):877−85

doi: 10.1111/j.1365-313X.2004.02172.x
[16]

Wright CJ, Smith CWJ, Jiggins CD. 2022. Alternative splicing as a source of phenotypic diversity. Nature Reviews Genetics 23(11):697−710

doi: 10.1038/s41576-022-00514-4
[17]

Muhammad S, Xu X, Zhou W, Wu L. 2023. Alternative splicing: an efficient regulatory approach towards plant developmental plasticity. Wiley Interdisciplinary Reviews: RNA 14(3):e1758

doi: 10.1002/wrna.1758
[18]

Wang H, You C, Chang F, Wang Y, Wang L, et al. 2014. Alternative splicing during Arabidopsis flower development results in constitutive and stage-regulated isoforms. Frontiers in Genetics 5:25

doi: 10.3389/fgene.2014.00025
[19]

Zhang J, Liu G, Guo C, He Y, Li Z, et al. 2011. The FLOWERING LOCUS T orthologous gene of Platanus acerifolia is expressed as alternatively spliced forms with distinct spatial and temporal patterns. Plant Biology 13(5):809−20

doi: 10.1111/j.1438-8677.2010.00432.x
[20]

Qin Z, Wu J, Geng S, Feng N, Chen F, et al. 2017. Regulation of FT splicing by an endogenous cue in temperate grasses. Nature Communications 8:14320

doi: 10.1038/ncomms14320
[21]

Qi HD, Lin Y, Ren QP, Wang YY, Xiong F, et al. 2019. RNA splicing of FLC modulates the transition to flowering. Frontiers in Plant Science 10:1625

doi: 10.3389/fpls.2019.01625
[22]

Zhang JZ, Li ZM, Mei L, Yao JL, Hu CG. 2009. PtFLC homolog from trifoliate orange (Poncirus trifoliata) is regulated by alternative splicing and experiences seasonal fluctuation in expression level. Planta 229(4):847−59

doi: 10.1007/s00425-008-0885-z
[23]

Lam PY, Wang L, Lo C, Zhu FY. 2022. Alternative splicing and its roles in plant metabolism. International Journal Of Molecular Sciences 23(13):7355

doi: 10.3390/ijms23137355
[24]

Carqueijeiro I, Koudounas K, de Bernonville TD, Sepúlveda LJ, Mosquera A, et al. 2021. Alternative splicing creates a pseudo-strictosidine β-d-glucosidase modulating alkaloid synthesis in Catharanthus roseus. Plant Physiology 185(3):836−56

doi: 10.1093/plphys/kiaa075
[25]

Lamberto I, Percudani R, Gatti R, Folli C, Petrucco S. 2010. Conserved alternative splicing of Arabidopsis transthyretin-like determines protein localization and S-allantoin synthesis in peroxisomes. The Plant Cell 22(5):1564−74

doi: 10.1105/tpc.109.070102
[26]

Qi T, Song S, Ren Q, Wu D, Huang H, et al. 2011. The Jasmonate-ZIM-domain proteins interact with the WD-Repeat/bHLH/MYB complexes to regulate Jasmonate-mediated anthocyanin accumulation and trichome initiation in Arabidopsis thaliana. The Plant Cell 23(5):1795−814

doi: 10.1105/tpc.111.083261
[27]

Zhu J, Yan X, Liu S, Xia X, An Y, et al. 2022. Alternative splicing of CsJAZ1 negatively regulates flavan-3-ol biosynthesis in tea plants. The Plant Journal 110(1):243−61

doi: 10.1111/tpj.15670
[28]

Dombrecht B, Xue GP, Sprague SJ, Kirkegaard JA, Ross JJ, et al. 2007. MYC2 differentially modulates diverse jasmonate-dependent functions in Arabidopsis. The Plant Cell 19(7):2225−45

doi: 10.1105/tpc.106.048017
[29]

Chen D, Liu Y, Yin S, Qiu J, Jin Q, et al. 2020. Alternatively spliced BnaPAP2. A7 isoforms play opposing roles in anthocyanin biosynthesis of Brassica napus L. Frontiers in Plant Science 11:983

doi: 10.3389/fpls.2020.00983
[30]

Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. 2019. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature Biotechnology 37(8):907−15

doi: 10.1038/s41587-019-0201-4
[31]

Stewart MJ, Stewart P, Rivera-Posada J. 2015. De novo assembly of the transcriptome of Acanthaster planci testes. Molecular Ecology Resources 15(4):953−66

doi: 10.1111/1755-0998.12360
[32]

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, et al. 2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols 7:562−78

doi: 10.1038/nprot.2012.016
[33]

Usadel B, Nagel A, Thimm O, Redestig H, Blaesing OE, et al. 2005. Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses. Plant Physiology 138(3):1195−204

doi: 10.1104/pp.105.060459
[34]

Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K, et al. 2017. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Research 45(D1):D353−D361

doi: 10.1093/nar/gkw1092
[35]

Zhang M, Li M, Fu H, Wang K, Tian X, et al. 2022. Transcriptomic analysis unravels the molecular response of Lonicera japonica leaves to chilling stress. Frontiers in Plant Science 13:1092857

doi: 10.3389/fpls.2022.1092857
[36]

Cai Z, Wang C, Chen C, Zou L, Yin S, et al. 2022. Comparative transcriptome analysis reveals variations of bioactive constituents in Lonicera japonica flowers under salt stress. Plant Physiology and Biochemistry 173:87−96

doi: 10.1016/j.plaphy.2022.01.022
[37]

Melzer R. 2017. Regulation of flowering time: a splicy business. Journal of Experimental Botany 68(18):5017−20

doi: 10.1093/jxb/erx353
[38]

Xing YQ, He ZX, Liu GQ, Lu C. 2019. Differential analysis of gene expression and alternative splicing in different tissues of Arabidopsis thaliana. Progress in Biochemistry and Biophysics 46(11):1118−29

doi: 10.16476/j.pibb.2019.0139
[39]

Barbazuk WB, Fu Y, McGinnis KM. 2008. Genome-wide analyses of alternative splicing in plants: opportunities and challenges. Genome Research 18(9):1381−92

doi: 10.1101/gr.053678.106
[40]

Marquez Y, Brown JWS, Simpson C, Barta A, Kalyna M. 2012. Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Research 22(6):1184−95

doi: 10.1101/gr.134106.111
[41]

Yang H, Li P, Jin G, Gui D, Liu L, et al. 2022. Temporal regulation of alternative splicing events in rice memory under drought stress. Plant Diversity 44(1):116−25

doi: 10.1016/j.pld.2020.11.004
[42]

Xu T, Zhang J, Liu Y, Zhang Q, Li W, Zhang Y, et al. 2022. Exon skipping in IspE gene is associated with abnormal chloroplast development in rice albino leaf 4 mutant. Front. Frontiers in Plant Science 13:986678

doi: 10.3389/fpls.2022.986678
[43]

Chaudhary S, Jabre I, Syed NH. 2021. Epigenetic differences in an identical genetic background modulate alternative splicing in A. thaliana. Genomics 113(6):3476−86

doi: 10.1016/j.ygeno.2021.08.006
[44]

Jabre I, Chaudhary S, Guo W, Kalyna M, Reddy ASN, et al. 2021. Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana. New Phytologist 229(4):1937−45

doi: 10.1111/nph.17062
[45]

Tang Y, Abdelrahman M, Li J, Wang F, Ji Z, et al. 2021. CRISPR/Cas9 induces exon skipping that facilitates development of fragrant rice. Plant Biotechnology Journal 19(4):642−44

doi: 10.1111/pbi.13514
[46]

Kesari R, Lasky JR, Villamor JG, Des Marais DL, Chen YC, et al. 2012. Intron-mediated alternative splicing of Arabidopsis P5CS1 and its association with natural variation in proline and climate adaptation. Proceedings of the National Academy of Sciences of the United States of America 109(23):9197−202

doi: 10.1073/pnas.1203433109
[47]

Tang W, Zheng Y, Dong J, Yu J, Yue J, et al. 2016. Comprehensive transcriptome profiling reveals long noncoding RNA expression and alternative splicing regulation during fruit development and ripening in Kiwifruit (Actinidia chinensis). Frontiers in Plant Science 7:335

doi: 10.3389/fpls.2016.00335
[48]

Ye J, Cheng S, Zhou X, Chen Z, Kim SU, et al. 2019. A global survey of full-length transcriptome of Ginkgo biloba reveals transcript variants involved in flavonoid biosynthesis. Industrial Crops and Products 139:111547

doi: 10.1016/j.indcrop.2019.111547
[49]

Wu YQ, Zhu MY, Jiang Y, Zhao DQ, Tao J. 2018. Molecular characterization of chalcone isomerase (CHI) regulating flower color in herbaceous peony (Paeonia lactiflora Pall.). Journal of Integrative Agriculture 17(1):122−29

doi: 10.1016/S2095-3119(16)61628-3
[50]

Luo XP, Bai YC, Fei G, Chenglei Li, Hui C, et al. 2013. Gene cloning and expression level of chalcone isomerase during florescence and content of flavonoids in Fagopyrum dibotrys. Chinese Traditional and Herbal Drugs 44(11):1481−85

doi: 10.7501/j.issn.0253-2670.2013.11.023
[51]

McKhann HI, Paiva NL, Dixon RA, Hirsch AM. 1998. Expression of genes for enzymes of the flavonoid biosynthetic pathway in the early stages of the Rhizobium-legume symbiosis. Advances in Experimental Medicine and Biology 439:45−54

doi: 10.1007/978-1-4615-5335-9_4
[52]

Gui Y, Fu G, Li X, Dai Y. 2023. Identification and analysis of isoflavone reductase gene family in Gossypium hirsutum L. Scientific Reports 13(1):5703

doi: 10.1038/s41598-023-32213-3
[53]

Jiao C, Gu Z. 2019. iTRAQ-based analysis of proteins involved in secondary metabolism in response to ABA in soybean sprouts. Food Research International 116:878−82

doi: 10.1016/j.foodres.2018.09.023
[54]

Khatoon A, Rehman S, Hiraga S, Makino T, Komatsu S. 2012. Organ-specific proteomics analysis for identification of response mechanism in soybean seedlings under flooding stress. Journal of Proteomics 75(18):5706−23

doi: 10.1016/j.jprot.2012.07.031
[55]

Yang B, Zhong Z, Wang T, Ou Y, Tian J, et al. 2019. Integrative omics of Lonicera japonica Thunb. flower development unravels molecular changes regulating secondary metabolites. Journal of Proteomics 208:103470

doi: 10.1016/j.jprot.2019.103470