AI Chat Paper
Discover the SciOpen Platform and Achieve Your Research Goals with Ease.
Search articles, authors, keywords, DOl and etc.
{{expandStatus?'Exit ':''}}Advanced Search
Plants of the Caprifoliaceae family are widely cultivated worldwide as ornamental plants owing to their numerous, sweet-smelling, beautiful flowers and fruits. Heptacodium miconioides Rehd., a member of the family, is endemic to eastern China and is cultivated as a popular ornamental plant in North America and European countries. It has a rather novel and beautiful trait of high horticultural value, that is, its sepals persist and enlarge, turning purplish red. Here, we report the chromosome-level genome assembly of H. miconioides to understand its evolution and floral characteristics. The 622.28 Mb assembled genome harbored a shared whole-genome duplication with a related species, Lonicera japonica. Comparative genomic analysis suggested that chromosome fission events following genome duplication underlie the unusual chromosome number of these two species, as well as chromosome fission of another five chromosomes in H. miconioides, giving rise to a haploid chromosome number of 14 (versus 9 in L. japonica). In addition, based on transcriptome and chloroplast genome analysis of 17 representative species in the Caprifoliaceae, we assumed that large structural variations in the chromosomes of H. miconioides were not caused by hybridization. Changes in the candidate genes of the MADS-box family were detected in the H. miconioides genome, including AP1-, AP3-, and SEP- expanded, which might underlie the sepal elongation and development in this species. The current findings provided a critical resource for genome evolution studies in Caprifoliaceae and it was an example of how multi-omics data can elucidate the regulation of important ornamental traits.
Adey, A., Kitzman, J.O., Burton, J.N., Daza, R., Kumar, A., Christiansen, L., Steemers, F.J., 2014. In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Res, 24: 2041-2049.
Anders, S., Huber, W., 2010. Differential expression analysis for sequence count data. Genome Biol, 11: 1344-1349.
APG, I.V., 2016. An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG IV. Bot J Linn Soc, 181: 1-20.
Baurens, F.C., Martin, G., Hervouet, C., Salmon, F., Yohomé, D., 2018. Recombination and large structural variations shape interspecific edible bananas genomes. Mol Biol Evol, 36: 97-111.
Bian, C.M., Jin, Z.X., Li, J.M., 2002. A study on the reproductive biology of Heptacodium miconioides. Acta Bot Yunanica, 24: 613-618. (in Chinese)
Burton, J.N., Adey, A., Patwardhan, R.P., Qiu, R., Kitzman, J.O., Shendure, J., 2013. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat Biotechnol, 31: 1119-1125.
Castresana, J., 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol, 17: 540-552.
Chen, S.F., Zhou, Y.Q., Chen, Y.R., Gu, J., 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34: 884-890.
Chen, Y., Ma, T., Zhang, L.S., Kang, M.H., Zhang, Z.Y., Zeng, Z.Y., Sun, P.C., Shrestha, N., Liu, J.Q., Yang, Y.Z., 2020. Genomic analyses of a “living fossil”: the endangered dove-tree. Mol Ecol Resour, 20: 1-14.
Chin, C.S., Peluso, P., Sedlazeck, F.J., Nattestad, M., Concepcion, G.T., Clum, A., Dunn, C., O'Malley, R., Figueroa-Balderas, R., Morales-Cruz, A., Cramer, G.R., Delledonne, M., Luo, C., Ecker, J.R., Cantu, D., Rank, D.R., Schatz, M.C., 2016. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods, 13: 1050-1054.
Chung, K.S., Hipp, A.L., Roalson, E.H., 2012. Chromosome number evolves independently of genome size in a clade with nonlocalized centromeres (Carex: Cyperaceae). Evolution, 66: 2708-2722.
Coombe, L., Zhang, J., Vandervalk, B.P., Chu, J., Jackman, S.D., Birol, I., Warren, R.L., 2018. ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers. BMC Bioinf, 19: 234.
Coombes, A.J., 1990. Heptacodium jasminoides the Chinese seven-son flower in Britain. Curtis’s Bot Mag, 7: 133-138.
Cox, A.V., Abdelnour, G.J., Bennett, M.D., Leitch, I.J., 1998. Genome size and karyotype evolution in the slipper orchids (Cypripedioideae: Orchidaceae). Am J Bot, 85: 681-687.
De Storme, N., Mason, A., 2014. Plant speciation through chromosome instability and ploidy change: cellular mechanisms, molecular factors and evolutionary relevance. Curr Opin Plant Biol, 1: 10-33.
Ditta, C., Pinyopich, A., Robles, P., Pelaz, S., Yanofsky, M.F., 2004. The SEP4 gene of Arabidopsis thaliana functions in floral organ and meristem identity. Curr Biol, 14: 1935-1940.
Donoghue, M.J., Eriksson, T., Reeves, P.A., Olmstesd, R.G., 2001. Phylogeny and phylogenetic taxonomy of Dipsacales, with special reference to Sinadoxa and Tetradoxa (Adoxaceae). Harv Pap Bot, 6: 459-479.
Edgar, R.C., 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinf, 5: 113.
Fishman, L., Willis, J.H., Wu, C.A., Lee, Y.W., 2014. Comparative linkage maps suggest that fission, not polyploidy, underlies near-doubling of chromosome number within monkeyflowers (Mimulus; Phrymaceae). Heredity, 112: 562-568.
Fu, L.G., Jin, J.M., 1992. Red List of Endangered Plants in China. Science Press, Beijing. (in Chinese)
Gao, W.L., Zhang, L.M., Xue, C.L., Zhang, Y., Liu, M.J., Zhao, J., 2022. Expression of E-type MADS-box genes in flower and fruits and protein interaction analysis in Chinese jujube. Acta Hortic Sin, 49: 739-748. (in Chinese)
Giménez, E., Pineda, B., Capel, J., Antón, M.T., Atarés, A., Pérez-Martín, F., García-Sogo, B., Angosto, T., Moreno, V., Lozano, R., 2010. Functional analysis of the Arlequin mutant corroborates the essential role of the ARLEQUIN/TAGL1 gene during reproductive development of tomato. PLoS One, 5: e14427.
Haas, B.J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P.D., Bowden, J., Couger, M.B., Eccles, D., Li, B., Lieber, M., MacManes, M.D., Ott, M., Orvis, J., Pochet, N., Strozzi, F., Weeks, N., Westerman, R., William, T., Dewey, C.N., Henschel, R., LeDuc, R.D., Friedman, N., Regev, A., 2013. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc, 8: 1494-1512.
Hao, C.Y., Guo, W.D., Liu, P., 2005. RAPD analysis of the population genetic diversity and genetic variatio of Heptacodium miconioides. Acta Hortic Sin, 32: 463-467. (in Chinese)
Hasegawa, M., Kishino, H., Yano, T., 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol, 22: 160-174.
He, L., Qian, J., Li, X., Sun, Z.Y., Xu, X.L., Chen, S.L., 2017. Complete chloroplast genome of medicinal plant Lonicera japonica: genome rearrangement, intron gain and loss, and implications for phylogenetic studies. Molecules, 22: 249.
Jacobs, B., Geuten, K., Pyck, N., Huysmans, S., Jansen, S., Smets, E., 2011. Unraveling the phylogeny of Heptacodium and Zabelia (Caprifoliaceae): an interdisciplinary approach. Syst Bot, 36: 231-252.
Jacobs, B., Huysmans, S., Smets, E., 2010. Evolution and systematic value of fruit and seed characters in Adoxaceae (Dipsacales). Taxon, 59: 850-866.
Jacobs, B., Lens, F., Smets, E., 2009. Evolution of fruit and seed characters in the Diervilla and Lonicera clades (Caprifoliaceae, Dipsacales). Ann Bot, 104: 253-276.
Jin, J.J., Yu, W.B., Yang, J.B., Song, Y., Yi, T.S., Li, D.Z., 2020. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol, 21: 241.
Jin, Z.X., Li, J.M., Ding, L.Y., 2013. Fine scale spatial genetic structure of the endangered Heptacodium miconioides endemic to China. Biochem Systemat Ecol, 48: 228-234.
Jones, K., 1998. Robertsonian fusion and centric fission in karyotype evolution of higher plants. Bot Rev, 64: 273-289.
Katoh, K., Standley, D.M., 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol, 30: 772-780.
Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxtion, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Meintjes, P., Drummond, A., 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics, 28: 1647-1649.
Kim, D., Langmead, B., Salzberg, S.L., 2015. HISAT: a fast spliced aligner with low memory requirements. Nat Methods, 12: 357.
Levin, D., 2002. The Role of Chromosomal Change in Plant Evolution. Oxford University Press, New York.
Li, C.R., Dong, N., Li, X.P., Wu, S.S., Liu, Z.J., Zhai, J.W., 2020. A review of MADS-box genes, the molecular regulatory genes for floral organ development in Orchidaceae. Acta Hortic Sin, 47: 2047-2062. (in Chinese)
Li, H., Durbin, R., 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25: 1754-1760.
Li, L., Stoeckert, C.J., Roos, D.S., 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res, 13: 2178-2189.
Li, N., Huang, B., Tang, N., Jian, W., Zou, J., Chen, J., Cao, H., Habib, S., Dong, X., Wei, W., Gao, Y., Li, Z., 2017. The MADS-box gene SlMBP21 regulates sepal size mediated by ethylene and auxin in tomato. Plant Cell Physiol, 58: 2241-2256.
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., Li, S., Yang, H., Wang, J., Wang, J., 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res, 20: 265-272.
Li, Y.L., Zhang, Y.F., Li, D.D., Shi, Q.S., Lou, Y., Yang, Z.N., Zhu, J., 2019. Acyl-CoA synthetases from Physcomitrella, rice and Arabidopsis: different substrate preferences but common regulation by MS188 in sporopollenin synthesis. Planta, 250: 535-548.
Liu, P., Yang, Y.S., Xu, G.D., Hao, C.Y., 2006. Physiological response of rare and endangered seven-son-flower (Heptacodium miconioides) to light stress under habitat fragmentation. Environ Exp Bot, 57: 32-40.
Lu, H., Liu, Z., Lan, S., 2019. Genome sequencing reveals the role of MADS-box gene families in the floral morphology evolution of Orchids. Hortic Plant J, 5: 247-254.
Luo, C., Wang, S.L., Ning, K., Chen, Z.J., Yang, J.J., Wang, Y.X., Qi, M.X., Wang, Q., 2022. Time-course transcriptome landscape of achene development in lettuce. Hortic Plant J, 8: 99-109.
Miao, Y.H., Luo, D.D., Zhao, T.T., Du, H.Z., Liu, Z.H., Xu, Z.P., Guo, L.P., Chen, C.J., Peng, S.N., Li, J.X., Ma, L., Ning, G.G., Liu, D.H., Huang, L.Q., 2022. Genome sequencing reveals chromosome fusion and extensive expansion of genes related to secondary metabolism in Artemisia argyi. Plant Biotechnol J, 20: 1902-1915.
Mitoma, M., Kajino, Y., Hayashi, R., Endo, M., Kubota, S., Kanno, A., 2019. Molecular mechanism underlying pseudopeloria in Habenaria radiata (Orchidaceae). Plant J, 99: 439-451.
Nicolson, D., Hara, H., 1983. A revision of the Caprifoliaceae of Japan with reference to allied plants in other districts and the Adoxaceae. Brittonia, 35: 184-188.
Olson, K., Gorelick, R., 2011. Chromosomal fission accounts for small-scale radiations in Zamia (Zamiaceae; Cycadales). Bot J Linn Soc, 165: 168-185.
Pei, Q.Y., Yu, T., Wu, T., Yang, Q.H., Gong, K., Zhou, R., Cui, C.L., Yu, Y., Zhao, W., Kang, X., Cao, R., Song, X.M., 2021. Comprehensive identification and analyses of the Hsf gene family in the whole-genome of three Apiaceae species. Hortic Plant J, 7: 457-468.
Pelaz, S., Ditta, G.S., Baumann, E., Wisman, E., Yanofsky, M.F., 2000. B and C floral organ identity functions require SEPALLATA MADS-box genes. Nature, 405: 200-203.
Pu, X., Li, Z., Tian, Y., Gao, R., Hao, L., Hu, Y., He, C., Sun, W., Xu, M., Peters, R.J., Van de Peer, Y., Xu, Z., Song, J., 2020. The honeysuckle genome provides insight into the molecular mechanism of carotenoid metabolism underlying dynamic flower coloration. New Phytol, 227: 930-943.
Pyck, N., Smets, E., 2000. A search for the phylogenetic position of the seven-son flower (Heptacodium, Dipsacales): combining molecular and morphological evidence. Plant Systemat Evol, 225: 185-199.
Schilling, S., Pan, S.R., Kennedy, A., Melzer, R., 2018. MADS-box genes and crop domestication: the jack of all traits. J Exp Bot, 69: 1447-1469.
Shi, Y., Song, B.Q., Liang, Q., Su, D.D., Lu, W., Liu, Y.D., Li, Z.G., 2023. Molecular regulatory events of flower and fruit abscission in horticultural plants. Hortic Plant J, 9: 867-883.
Simao, F.A., Waterhouse, R.M., Ioannidis, P., Kriventseva, E.V., Zdobnov, E.M., 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31: 3210-3212.
Song, C., Liu, Y., Song, A., Dong, G., Zhao, H., Sun, W., Ramakrishnan, S., Wang, Y., Wang, S., Li, T., Niu, Y., Jiang, J., Dong, B., Xia, Y., Chen, S., Hu, Z., Chen, F., Chen, S., 2018. The Chrysanthemum nankingense genome provides insights into the evolution and diversification of chrysanthemum flowers and medicinal traits. Mol Plant, 11: 1482-1491.
Stamatakis, A., 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30: 1312-1313.
Theißen, G., Melzer, R., Rümpler, F., 2016. MADS-domain transcription factors and the floral quartet model of flower development: linking plant development and evolution. Development, 143: 3259-3271.
Walker, B.J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C.A., Zeng, Q., Wortman, J., Young, S.K., Earl, A.M., 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One, 9: e112963.
Wang, H.X., Liu, H., Moore, M.J., Landrein, S., Liu, B., Zhu, Z.X., Wang, H.F., 2020. Plastid phylogenomic insights into the evolution of the Caprifoliaceae s.l. (Dipsacales). Mol Phylogenet Evol, 142: 106641.
Wang, Y., Tang, H., Debarry, J.D., Tan, X., Li, J., Wang, X., Lee, T.H., Jin, H., Marler, B., Guo, H., Kissinger, J.C., Paterson, A.H., 2012. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res, 40: e49.
Wang, Z., Miao, H., Liu, J., Xu, B., Yao, X., Xu, C., Zhao, S., Fang, X., Jia, C., Wang, J., Ma, W., Wu, Z., Yu, L., Yang, Y., Liu, C., Guo, Y., Sun, S., Baurens, F.C., Martin, G., Salmon, F., Garsmeur, O., Yahiaoui, N., Hervouet, C., Rouard, M., Laboureau, N., Habas, R., Ricci, S., Peng, M., Guo, A., Xie, J., Li, Y., Ding, Z., Yan, Y., Tie, W., D'Hont, A., Hu, W., Jin, Z., 2019. Musa balbisiana genome reveals subgenome evolution and functional divergence. Nat Plants, 5: 810-821.
Winkworth, R.C., Bell, C.D., Donoghue, M.J., 2008. Mitochondrial sequence data and Dipsacales phylogeny: mixed models, partitioned Bayesian analyses, and model selection. Mol Phylogenet Evol, 46: 830-843.
Wood, T.E., Takebayashi, N., Barker, M.S., Mayrose, I., Greenspoon, P.B., Rieseberg, L.H., 2009. The frequency of polyploid speciation in vascular plants. Proc Natl Acad Sci, 106: 13875-13879.
Wyman, S.K., Jansen, R.K., Boore, J.L., 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics, 20: 3252-3255.
Xiang, C.L., Dong, H.J., Landrein, S., Zhao, F., Yu, W.B., Esoltis, D., Ssoltis, P., Backlund, A., Wang, H.F., Li, D.Z., 2020a. Revisiting the phylogeny of Dipsacales: new insights from phylogenomic analyses of complete chloroplast genome sequences. J Syst Evol, 58: 103-117.
Xiang, Y.P., Wang, Y.D., He, H.J., Xu, Q.J., 2020b. Plant transposable elements and the effects of insertion mutations on flower development in horticultural plants. Acta Hortic Sin, 47: 2247-2266. (in Chinese)
Xie, Q., Hu, Z., Zhu, Z., Dong, T., Zhao, Z., Cui, B., Chen, G., 2014. Overexpression of a novel MADS-box gene SlFYFL delays senescence, fruit ripening and abscission in tomato. Sci Rep, 4: 4367.
Xin, H.B., Ji, F.F., Wu, J., Zhang, S.Y., Yi, C.J., Zhao, S.W., Cong, R.C., Zhao, L.J., Zhang, H., Zhang, Z., 2023. Chromosome-scale genome assembly of marigold (Tagetes erecta L.): an ornamental plant and feedstock for industrial lutein production. Hortic Plant J, 9: 1119-1130.
Yamaguchi, S., 2008. Gibberellin metabolism and its regulation. Annu Rev Plant Biol, 59: 225-251.
Yang, Y., Huang, L., Xu, C., Qi, L., Wu, Z., Li, J., Chen, H., Wu, Y., Fu, T., Zhu, H., Saand, M.A., Li, J., Liu, L., Fan, H., Zhou, H., Qin, W., 2021. Chromosome-scale genome assembly of areca palm (Areca catechu). Mol Ecol Resour, 21: 2504-2519.
Yang, Y., Ma, T., Wang, Z., Lu, Z., Li, Y., Fu, C., Chen, X., Zhao, M., Olson, M.S., Liu, J., 2018. Genomic effects of population collapse in a critically endangered ironwood tree Ostrya rehderiana. Nat Commun, 9: 5449.
Yang, Z., 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol, 24: 1586-1591.
Zahn, L.M., Kong, H., Leebens-Mack, J.H., Kim, S., Soltis, P.S., Landherr, L.L., Soltis, D.E., Depamphilis, C.W., Ma, H., 2005. The evolution of the SEPALLATA subfamily of MADS-box genes: a preangiosperm origin with multiple duplications throughout angiosperm history. Genetics, 169: 2209-2223.
Zhang, J., Hu, Z., Wang, Y., Yu, X., Liao, C., Zhu, M., Chen, G., 2018. Suppression of a tomato SEPALLATA MADS-box gene, SlCMB1, generates altered inflorescence architecture and enlarged sepals. Plant Sci, 272: 75-87.
Zhang, W., Liu, J., Zhang, Y., Qiu, J., Li, Y., Zheng, B., Hu, F., Dai, S., Huang, X., 2020. A high-quality genome sequence of alkaligrass provides insights into halophyte stress tolerance. Sci China Life Sci, 63: 1269-1282.
Zhang, Y., Zhang, Y.C., Li, B., Tan, X., Zhu, C.P., Wu, T., Feng, S.Y., Yang, Q.H., Shen, S.Q., Yu, T., Liu, Z., Song, X.M., 2022. Polyploidy events shaped the expansion of transcription factors in Cucurbitaceae and exploitation of genes for tendril development. Hortic Plant J, 8: 562-574.
Zhang, Z.Y., Zhou, Z.K., Gu, Z.J., 2002. Karyomorphology of Heptacodium (Caprifoliaceae s. str.) and its phylogenetic implications. Taxon, 51: 499-505.
Zhao, D., Hamilton, J.P., Pham, G.M., Crisovan, E., Wiegert-Rininger, K., Vaillancourt, B., DellaPenna, D., Buell, C.R., 2017. De novo genome assembly of Camptotheca acuminata, a natural source of the anti-cancer compound camptothecin. GigaScience, 6: 1-7.
Zhao, J., Tian, Y., Zhang, J.S., Zhao, M., Gong, P., Riss, S., Saedler, R., He, C., 2013. The euAP1 protein MPF3 represses MPF2 to specify floral calyx identity and displays crucial roles in Chinese lantern development in Physalis. Plant Cell, 25: 2002-2021.
This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
京公网安备11010802044758号