Hamidpour, R., Hamidpour, S., Hamidpour, M. & Shahlari, M. Camphor (Cinnamomum camphora), a conventional treatment with the historical past of treating a number of ailments. Int. J. Case Rep. Imag. 4, 86–89 (2013).
Google Scholar
Christenhusz, M. J. M. & Byng, J. W. The variety of recognized vegetation species on the planet and its annual enhance. Phytotaxa 261, 201–217 (2016).
Google Scholar
Palmer, J. D., Soltis, D. E. & Chase, M. W. The plant tree of life: an summary and a few factors of view. Am. J. Bot. 91, 1437–1445 (2004).
Google Scholar
Moore, M. J., Bell, C. D., Soltis, P. S. & Soltis, D. E. Utilizing plastid genome-scale information to resolve enigmatic relationships amongst basal angiosperms. Proc. Natl Acad. Sci. USA 104, 19363–19368 (2007).
Google Scholar
Endress, P. Ok. & Doyle, J. A. Reconstructing the ancestral angiosperm flower and its preliminary specializations. Am. J. Bot. 96, 22–66 (2009).
Google Scholar
Qiu, Y.-L. et al. Angiosperm phylogeny inferred from sequences of 4 mitochondrial genes. J. Syst. Evol. 48, 391–425 (2010).
Google Scholar
Zhang, N., Zeng, L. P., Shan, H. Y. & Ma, H. Extremely conserved low-copy nuclear genes as efficient markers for phylogenetic analyses in angiosperms. New Phytol. 195, 923–937 (2012).
Google Scholar
Zeng, L. et al. Decision of deep angiosperm phylogeny utilizing conserved nuclear genes and estimates of early divergence occasions. Nat. Commun. 5, 4956 (2014).
Google Scholar
Byng, J. W. et al. An replace of the Angiosperm Phylogeny Group classification for the orders and households of flowering vegetation: APG IV. Bot. J. Linn. Soc. 181, 1–20 (2016).
Google Scholar
Cui, L. et al. Widespread genome duplications all through the historical past of flowering vegetation. Genome Res. 16, 738–749 (2006).
Google Scholar
Liu, Y. C., Lu, F. Y. & Ou, C. H. Bushes of Taiwan. Monograph. Pub. 7, 105–131 (1988).
Fujita, Y. Classification and phylogeny of the genus Cinnamomum seen from the constituents of important oils. Bot. Magazine. Tokyo 80, 261–271 (1967).
Google Scholar
Chang, T. T. & Chou, W. N. Antrodia cinnamomea sp. nov. on Cinnamomum kanehirai in Taiwan. Mycol. Res. 99, 756–758 (1995).
Google Scholar
Wu, S. H., Ryvarden, L. & Chang, T. T. Antrodia camphorata (“niu-chang-chih”), new mixture of a medicinal fungus in Taiwan. Bot. Bull. Acad. Sinica 38, 273–275 (1997).
Hseu, Y. C., Chen, S. C., Yech, Y. J., Wang, L. & Yang, H. L. Antioxidant exercise of Antrodia camphorata on free radical-induced endothelial cell injury. J. Ethnopharmacol. 118, 237–245 (2008).
Google Scholar
Liao, P. C. et al. Historic spatial vary enlargement and a really current bottleneck of Cinnamomum kanehirae Hay. (Lauraceae) in Taiwan inferred from nuclear genes. BMC Evol. Biol. 10, 124 (2010).
Google Scholar
Zerbe, P. & Bohlmann, J. Plant diterpene synthases: exploring modularity and metabolic range for bioengineering. Tendencies Biotechnol. 33, 419–428 (2015).
Google Scholar
Holt, C. & Yandell, M. MAKER2: an annotation pipeline and genome-database administration instrument for second-generation genome tasks. BMC Bioinformatics 12, 491 (2011).
Google Scholar
Huerta-Cepas, J. et al. Quick genome-wide practical annotation by orthology task by eggNOG-Mapper. Mol. Biol. Evol. 34, 2115–2122 (2017).
Google Scholar
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome meeting and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015).
Emms, D. M. & Kelly, S. OrthoFinder: fixing basic biases in entire genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 16, 157 (2015).
Google Scholar
Azuma, J.-I. & Tetsuo, Ok. Lignin–carbohydrate complexes from numerous sources. Strategies Enzymol. 161, 12–18 (1988).
Google Scholar
Li, H. & Durbin, R. Inference of human inhabitants historical past from particular person whole-genome sequences. Nature 475, 493–496 (2011).
Google Scholar
Sibuet, J.-C. & Hsu, S.-Ok. How was Taiwan created? Tectonophysics 379, 159–181 (2004).
Google Scholar
Dong, P. F. et al. 3D chromatin structure of enormous plant genomes decided by native A/B compartments. Mol. Plant 10, 1497–1509 (2017).
Google Scholar
Watson, J. M. & Riha, Ok. Comparative biology of telomeres: the place vegetation stand. FEBS Lett. 584, 3752–3759 (2010).
Google Scholar
Stamatakis, A. RAxML-VI-HPC: most likelihood-based phylogenetic analyses with 1000’s of taxa and blended fashions. Bioinformatics 22, 2688–2690 (2006).
Google Scholar
Mirarab, S. & Warnow, T. ASTRAL-II: coalescent-based species tree estimation with many lots of of taxa and 1000’s of genes. Bioinformatics 31, i44–i52 (2015).
Google Scholar
Matasci, N. et al. Knowledge entry for the 1,000 Vegetation (1KP) challenge. Gigascience 3, 17 (2014).
Google Scholar
Yang, Z. PAML 4: phylogenetic evaluation by most probability. Mol. Biol. Evol. 24, 1586–1591 (2007).
Google Scholar
Massoni, J., Couvreur, T. L. & Sauquet, H. 5 main shifts of diversification by the lengthy evolutionary historical past of Magnoliidae (angiosperms). BMC Evol. Biol. 15, 49 (2015).
Google Scholar
Morris, J. L. et al. The timescale of early land plant evolution. Proc. Natl Acad. Sci. USA 115, E2274–E2283 (2018).
Google Scholar
Zhong, B. J. & Betancur-R, R. Expanded taxonomic sampling coupled with gene family tree interrogation offers unambiguous decision for the evolutionary root of angiosperms. Genome Biol. Evol. 9, 3154–3161 (2017).
Google Scholar
Lang, T. G. et al. Protein area evaluation of genomic sequence information reveals regulation of LRR associated domains in plant transpiration in Ficus. PLoS ONE 9, e108719 (2014).
Google Scholar
Jourda, C. et al. Growth of banana (Musa acuminata) gene households concerned in ethylene biosynthesis and signalling after lineage-specific whole-genome duplications. New Phytol. 202, 986–1000 (2014).
Google Scholar
Gu, C. et al. A number of regulatory roles of AP2/ERF transcription consider angiosperm. Bot. Stud. 58, 6 (2017).
Google Scholar
Seyfferth, C. et al. Ethylene-related gene expression networks in wooden formation. Entrance. Plant Sci. 9, 272 (2018).
Google Scholar
Chen, T. et al. Expression of an alfalfa (Medicago sativa L.) ethylene response issue gene MsERF8 in tobacco vegetation enhances resistance to salinity. Mol. Biol. Rep. 39, 6067–6075 (2012).
Google Scholar
Wu, L., Zhang, Z., Zhang, H., Wang, X. C. & Huang, R. Transcriptional modulation of ethylene response issue protein JERF3 within the oxidative stress response enhances tolerance of tobacco seedlings to salt, drought, and freezing. Plant Physiol. 148, 1953–1963 (2008).
Google Scholar
Dodds, P. N. et al. Direct protein interplay underlies gene-for-gene specificity and coevolution of the flax resistance genes and flax rust avirulence genes. Proc. Natl Acad. Sci. USA 103, 8888–8893 (2006).
Google Scholar
Chen, F., Tholl, D., Bohlmann, J. & Pichersky, E. The household of terpene synthases in vegetation: a mid-size household of genes for specialised metabolism that’s extremely diversified all through the dominion. Plant J. 66, 212–229 (2011).
Google Scholar
Martin, D. M., Faldt, J. & Bohlmann, J. Purposeful characterization of 9 Norway spruce TPS genes and evolution of gymnosperm terpene synthases of the TPS-d subfamily. Plant Physiol. 135, 1908–1927 (2004).
Google Scholar
Cheng, S. S. et al. Chemical polymorphism and composition of leaf important oils of Cinnamomum kanehirae utilizing fuel chromatography/mass spectrometry, cluster evaluation, and principal element evaluation. J. Wooden Chem. Technol. 35, 207–219 (2015).
Google Scholar
Peripolli, E. et al. Runs of homozygosity: present data and functions in livestock. Anim. Genet. 48, 255–271 (2017).
Google Scholar
Soltis, D. E. & Soltis, P. S. Isozyme proof for historical polyploidy in primitive angiosperms. Syst. Bot. 15, 328–337 (1990).
Google Scholar
Jiao, Y. et al. A genome triplication related to early diversification of the core eudicots. Genome Biol. 13, R3 (2012).
Google Scholar
Chanderbali, A. S., Berger, B. A., Howarth, D. G., Soltis, D. E. & Soltis, P. S. Evolution of floral range: genomics, genes and gamma. Phil. Trans. R. Soc. 372, 20150509 (2017).
Google Scholar
Geethangili, M. & Tzeng, Y. M. Evaluation of pharmacological results of Antrodia camphorata and its bioactive compounds. Evid. Primarily based Complement. Alternat. Med. 2011, 1–17 (2011).
Google Scholar
Lu, M. Y. J. et al. Genomic and transcriptomic analyses of the medicinal fungus Antrodia cinnamomea for its metabolite biosynthesis and sexual improvement. Proc. Natl Acad. Sci. USA 111, E4743–E4752 (2014).
Google Scholar
Loehlin, D. W. & Carroll, S. B. Expression of tandem gene duplicates is usually better than twofold. Proc. Natl Acad. Sci. USA 113, 5988–5992 (2016).
Google Scholar
Sandbrink, J. M., Vellekoop, P., Vanham, R. & Vanbrederode, J. A way for evolutionary research on RFLP of chloroplast DNA, relevant to a spread of plant-species. Biochem. Syst. Ecol. 17, 45–49 (1989).
Google Scholar
Doyle, J. J. & Doyle, J. L. A speedy DNA isolation process for small portions of recent leaf tissue. Phytochem. Bull. 19, 11–15 (1987).
Kolosova, N., Gorenstein, N., Kish, C. M. & Dudareva, N. Regulation of circadian methyl benzoate emission in diurnally and nocturnally emitting vegetation. Plant Cell 13, 2333–2347 (2001).
Google Scholar
Suen, D. F. et al. Project of DNA markers to Nicotiana sylvestris chromosomes utilizing monosomic alien addition strains. Theor. Appl. Genet. 94, 331–337 (1997).
Google Scholar
Dolezel, J., Greilhuber, J. & Suda, J. Estimation of nuclear DNA content material in vegetation utilizing circulation cytometry. Nat. Protoc. 2, 2233–2244 (2007).
Google Scholar
Vurture, G. W. et al. GenomeScope: quick reference-free genome profiling from quick reads. Bioinformatics 33, 2202–2204 (2017).
Google Scholar
Chin, C. S. et al. Phased diploid genome meeting with single-molecule real-time sequencing. Nat. Strategies 13, 1050–1054 (2016).
Google Scholar
Chin, C. S. et al. Nonhybrid, completed microbial genome assemblies from long-read SMRT sequencing information. Nat. Strategies 10, 563–569 (2013).
Google Scholar
Walker, B. J. et al. Pilon: an built-in instrument for complete microbial variant detection and genome meeting enchancment. PLoS ONE 9, e112963 (2014).
Google Scholar
Putnam, N. H. et al. Chromosome-scale shotgun meeting utilizing an in vitro methodology for long-range linkage. Genome Res. 26, 342–350 (2016).
Google Scholar
Benson, G. Tandem repeats finder: a program to research DNA sequences. Nucleic Acids Res. 27, 573–580 (1999).
Google Scholar
Dobin, A., Davis, C. & Schlesinger, F. STAR: ultrafast common RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Google Scholar
Haas, B. J. et al. De novo transcript sequence reconstruction from RNA-seq utilizing the Trinity platform for reference technology and evaluation. Nat. Protoc. 8, 1494–1512 (2013).
Google Scholar
Pertea, M. et al. StringTie allows improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290–295 (2015).
Google Scholar
Music, L., Sabunciyan, S. & Florea, L. CLASS2: correct and environment friendly splice variant annotation from RNA-seq reads. Nucleic Acids Res. 44, e98 (2016).
Google Scholar
Wu, T. D. & Watanabe, C. Ok. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21, 1859–1875 (2005).
Google Scholar
Venturini, L., Caim, S., Kaithakottil, G. G., Mapleson, D. L. & Swarbreck, D. Leveraging a number of transcriptome meeting strategies for improved gene construction annotation. Gigascience 7, giy093 (2018).
Google Scholar
Stanke, M., Tzvetkova, A. & Morgenstern, B. AUGUSTUS at EGASP: utilizing EST, protein and genomic alignments for improved gene prediction within the human genome. Genome Biol. 7, S11 (2006).
Google Scholar
Korf, I. Gene discovering in novel genomes. BMC Bioinformatics 5, 59 (2004).
Google Scholar
Hoff, Ok. J., Lange, S., Lomsadze, A., Borodovsky, M. & Stanke, M. BRAKER1: unsupervised RNA-seq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics 32, 767–769 (2016).
Google Scholar
Conesa, A. et al. Blast2GO: a common instrument for annotation, visualization and evaluation in practical genomics analysis. Bioinformatics 21, 3674–3676 (2005).
Google Scholar
Wu, C. C., Ho, C. Ok. & Chang, S. H. The whole chloroplast genome of Cinnamomum kanehirae Hayata (Lauraceae). Mitochondrial DNA A DNA Mapp. Seq. Anal. 27, 2681–2682 (2016).
Google Scholar
Smith, D. R., Crosby, Ok. & Lee, R. W. Correlation between nuclear plastid DNA abundance and plastid quantity helps the restricted switch window speculation. Genome Biol. Evol. 3, 365–371 (2011).
Google Scholar
Li, H. & Durbin, R. Quick and correct quick learn alignment with Burrows–Wheeler rework. Bioinformatics 25, 1754–1760 (2009).
Google Scholar
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Google Scholar
Danecek, P. et al. The variant name format and VCFtools. Bioinformatics 27, 2156–2158 (2011).
Google Scholar
Buschiazzo, E., Ritland, C., Bohlmann, J. & Ritland, Ok. Sluggish however not low: genomic comparisons reveal slower evolutionary charge and better dN/dS in conifers in comparison with angiosperms. BMC Evol. Biol. 12, 8 (2012).
Google Scholar
Cao, Y. N. et al. Inferring spatial patterns and drivers of inhabitants divergence of Neolitsea sericea (Lauraceae), based mostly on molecular phylogeography and panorama genomics. Mol. Phylogenet. Evol. 126, 162–172 (2018).
Google Scholar
Smit, A. & Hubley, R. RepeatModeler Open-1.0 (Institute for Techniques Biology, 2015).
Smit, A., Hubley, R. & Inexperienced, P. RepeatMasker Open-4.0 (Institute for Techniques Biology, 2015).
Abrusan, G., Grundmann, N., DeMester, L. & Makalowski, W. TEclass—a instrument for automated classification of unknown eukaryotic transposable components. Bioinformatics 25, 1329–1330 (2009).
Google Scholar
Guan, R. et al. Draft genome of the residing fossil Ginkgo biloba. Gigascience 5, 49 (2016).
Google Scholar
Katoh, Ok. & Standley, D. M. MAFFT a number of sequence alignment software program model 7: enhancements in efficiency and value. Mol. Biol. Evol. 30, 772–780 (2013).
Google Scholar
Value, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—roughly maximum-likelihood timber for big alignments. PLoS ONE 5, e9490 (2010).
Google Scholar
Paradis, E., Claude, J. & Strimmer, Ok. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289–290 (2004).
Google Scholar
Sundell, D. et al. The plant genome integrative explorer useful resource: PlantGenIE.org. New Phytol. 208, 1149–1156 (2015).
Google Scholar
Sneddon, T. P., Li, P. & Edmunds, S. C. GigaDB: asserting the GigaScience database. Gigascience 1, 11 (2012).
Google Scholar
Bolser, D., Staines, D. M., Pritchard, E. & Kersey, P. in Plant Bioinformatics: Strategies and Protocols (ed. Edwards, D.) 115–140 (Springer, New York, 2016).
De Bie, T., Cristianini, N., Demuth, J. P. & Hahn, M. W. CAFE: a computational instrument for the examine of gene household evolution. Bioinformatics 22, 1269–1271 (2006).
Google Scholar
Kumar, S., Stecher, G., Suleski, M. & Hedges, S. B. TimeTree: a useful resource for timelines, timetrees, and divergence occasions. Mol. Biol. Evol. 34, 1812–1819 (2017).
Google Scholar
Pryer, Ok. M. et al. Horsetails and ferns are a monophyletic group and the closest residing kin to seed vegetation. Nature 409, 618–622 (2001).
Google Scholar
Lyons, E. et al. Discovering and evaluating syntenic areas amongst Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with Rosids. Plant Physiol. 148, 1772–1781 (2008).
Google Scholar
Haas, B. J., Delcher, A. L., Wortman, J. R. & Salzberg, S. L. DAGchainer: a instrument for mining segmental genome duplications and synteny. Bioinformatics 20, 3643–3646 (2004).
Google Scholar
Wright, E. S. Utilizing DECIPHER v2.Zero to research huge organic sequence information in R. R J. 8, 352–359 (2016).
Google Scholar
Quinlan, A. R. & Corridor, I. M. Bedtools: a versatile suite of utilities for evaluating genomic options. Bioinformatics 26, 841–842 (2010).
Google Scholar
Ming, R. et al. The pineapple genome and the evolution of CAM photosynthesis. Nat. Genet. 47, 1435–1442 (2015).
Google Scholar
Lozano, R., Hamblin, M. T., Prochnik, S. & Jannink, J. L. Identification and distribution of the NBS-LRR gene household within the Cassava genome. BMC Genomics 16, 360 (2015).
Google Scholar
Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).
Google Scholar
Finn, R. D. et al. InterPro in 2017—past protein household and area annotations. Nucleic Acids Res. 45, D190–D199 (2017).
Google Scholar
He, Z. et al. Evolviewv2: a web-based visualization and administration instrument for personalized and annotated phylogenetic timber. Nucleic Acids Res. 44, W236–W241 (2016).
Google Scholar
Aubourg, S., Lecharny, A. & Bohlmann, J. Genomic evaluation of the terpenoid synthase (AtTPS) gene household of Arabidopsis thaliana. Mol. Genet. Genomics 267, 730–745 (2002).
Google Scholar
Irmisch, S., Jiang, Y. F., Chen, F., Gershenzon, J. & Kollner, T. G. Terpene synthases and their contribution to herbivore-induced unstable emission in western balsam poplar (Populus trichocarpa). BMC Plant Biol. 14, 270 (2014).
Google Scholar
Martin, D. M. et al. Purposeful annotation, genome group and phylogeny of the grapevine (Vitis vinifera) terpene synthase gene household based mostly on genome meeting, FLcDNA cloning, and enzyme assays. BMC Plant Biol. 10, 226 (2010).
Google Scholar
Wheeler, T. J. & Eddy, S. R. nhmmer: DNA homology search with profile HMMs. Bioinformatics 29, 2487–2489 (2013).
Google Scholar
Kumar, S., Stecher, G. & Tamura, Ok. MEGA7: molecular evolutionary genetics evaluation model 7.Zero for greater datasets. Mol. Biol. Evol. 33, 1870–1874 (2016).
Google Scholar