{"id":1035972,"date":"2021-10-17T17:20:35","date_gmt":"2021-10-17T21:20:35","guid":{"rendered":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/uncategorized\/three-chromosome-scale-papaver-genomes-reveal-punctuated-patchwork-evolution-of-the-morphinan-and-noscapine-biosynthesis-pathway-nature-com\/"},"modified":"2021-10-17T17:20:35","modified_gmt":"2021-10-17T21:20:35","slug":"three-chromosome-scale-papaver-genomes-reveal-punctuated-patchwork-evolution-of-the-morphinan-and-noscapine-biosynthesis-pathway-nature-com","status":"publish","type":"post","link":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/transhuman-news-blog\/genome\/three-chromosome-scale-papaver-genomes-reveal-punctuated-patchwork-evolution-of-the-morphinan-and-noscapine-biosynthesis-pathway-nature-com\/","title":{"rendered":"Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway &#8211; Nature.com"},"content":{"rendered":"<p><p>Field, B. & Osbourn, A. E. Metabolic diversification-independent assembly of operon-like gene clusters in different plants. Science 320, 543547 (2008).<\/p>\n<p>ADS    CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Winzer, T. et al. A Papaver somniferum 10-gene cluster for synthesis of the anticancer alkaloid noscapine. Science 336, 17041708 (2012).<\/p>\n<p>ADS    CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Itkin, M. et al. Biosynthesis of antinutritional alkaloids in solanaceous crops is mediated by clustered genes. Science 341, 175179 (2013).<\/p>\n<p>ADS    CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Wilderman, P. R., Xu, M., Jin, Y., Coates, R. M. & Peters, R. J. Identification of syn-pimara-7,15-diene synthase reveals functional clustering of terpene synthases involved in rice phytoalexin\/allelochemical biosynthesis. Plant Physiol. 135, 20982105 (2004).<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Jonczyk, R. et al. Elucidation of the final reactions of DIMBOA-glucoside biosynthesis in maize: characterization of Bx6 and Bx7. Plant Physiol. 146, 10531063 (2008).<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Xiong, X. et al. The Taxus genome provides insights into paclitaxel biosynthesis. Nat. Plants <a href=\"https:\/\/doi.org\/10.1038\/s41477-021-00963-5\" rel=\"nofollow\">https:\/\/doi.org\/10.1038\/s41477-021-00963-5<\/a> (2021).<\/p>\n<p>Kautsar, S. A., Suarez Duran, H. G., Blin, K., Osbourn, A. & Medema, M. H. plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters. Nucleic Acids Res. 45, W55W63 (2017).<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Topfer, N., Fuchs, L. M. & Aharoni, A. The PhytoClust tool for metabolic gene clusters discovery in plant genomes. Nucleic Acids Res. 45, 70497063 (2017).<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Nutzmann, H. W., Scazzocchio, C. & Osbourn, A. Metabolic gene clusters in eukaryotes. Annu Rev. Genet. 52, 159183 (2018).<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Takos, A. M. & Rook, F. Why biosynthetic genes for chemical defense compounds cluster. Trends Plant Sci. 17, 383388 (2012).<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Hurst, L. D., Pal, C. & Lercher, M. J. The evolutionary dynamics of eukaryotic gene order. Nat. Rev. Genet. 5, 299310 (2004).<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Wong, S. & Wolfe, K. H. Birth of a metabolic gene cluster in yeast by adaptive gene relocation. Nat. Genet. 37, 777782 (2005).<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Slot, J. C. & Rokas, A. Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi. Proc. Natl Acad. Sci. USA 107, 1013610141 (2010).<\/p>\n<p>ADS    CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Rosewich, U. L. & Kistler, H. C. Role of horizontal gene transfer in the evolution of fungi. Annu. Rev. Phytopathol. 38, 325363 (2000).<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Rokas, A., Wisecaver, J. H. & Lind, A. L. The birth, evolution and death of metabolic gene clusters in fungi. Nat. Rev. Microbiol. 16, 731744 (2018).<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Norn, S., Kruse, P. R. & Kruse, E. History of opium poppy and morphine. Dan. Med. Arbog. 33, 171184 (2005).<\/p>\n<p>                    Google Scholar                <\/p>\n<p>Zhu, L. & Chen, L. Progress in research on paclitaxel and tumor immunotherapy. Cell Mol. Biol. Lett. 24, 40 (2019).<\/p>\n<p>PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Mao, L. et al. Genomic evidence for convergent evolution of gene clusters for momilactone biosynthesis in land plants. Proc. Natl Acad. Sci. USA 117, 1247212480 (2020).<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Chen, S., Krinsky, B. H. & Long, M. New genes as drivers of phenotypic evolution. Nat. Rev. Genet. 14, 645660 (2013).<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Long, M., Betran, E., Thornton, K. & Wang, W. The origin of new genes: glimpses from the young and old. Nat. Rev. Genet. 4, 865875 (2003).<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Kaessmann, H. Origins, evolution, and phenotypic impact of new genes. Genome Res. 20, 13131326 (2010).<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Qi, X. et al. A gene cluster for secondary metabolism in oat: implications for the evolution of metabolic diversity in plants. Proc. Natl Acad. Sci. USA 101, 82338238 (2004).<\/p>\n<p>ADS    CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Leong, B. J. & Last, R. L. Promiscuity, impersonation and accommodation: evolution of plant specialized metabolism. Curr. Opin. Struct. Biol. 47, 105112 (2017).<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Guo, L. et al. The opium poppy genome and morphinan production. Science 362, 343347 (2018).<\/p>\n<p>ADS    CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Liu, Z. et al. Formation and diversification of a paradigm biosynthetic gene cluster in plants. Nat. Commun. 11, 5354 (2020).<\/p>\n<p>ADS    CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Boutanaev, A. M. & Osbourn, A. E. Multigenome analysis implicates miniature inverted-repeat transposable elements (MITEs) in metabolic diversification in eudicots. Proc. Natl Acad. Sci. USA 115, E6650E6658 (2018).<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Granick, S. The structural and functional relationships between heme and chlorophyll. Harvey Lect. Ser. 44, 220245 (1948).<\/p>\n<p>                    Google Scholar                <\/p>\n<p>Granick, S. Speculations on the origins and evolution of photosynthesis. Ann. N. Y. Acad. Sci. 69, 292308 (1957).<\/p>\n<p>ADS    CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Horowitz, N. H. On the evolution of biochemical syntheses. Proc. Natl Acad. Sci. USA 31, 153157 (1945).<\/p>\n<p>ADS    CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Jensen, R. A. Enzyme recruitment in evolution of new function. Annu. Rev. Microbiol. 30, 409425 (1976).<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Ycas, M. On earlier states of the biochemical system. J. Theor. Biol. 44, 145160 (1974).<\/p>\n<p>ADS    CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Beaudoin, G. A. & Facchini, P. J. Benzylisoquinoline alkaloid biosynthesis in opium poppy. Planta 240, 1932 (2014).<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Hagel, J. M. & Facchini, P. J. Benzylisoquinoline alkaloid metabolism: a century of discovery and a brave new world. Plant Cell Physiol. 54, 647672 (2013).<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Menendez-Perdomo, I. M. & Facchini, P. J. Isolation and characterization of two O-methyltransferases involved in benzylisoquinoline alkaloid biosynthesis in sacred lotus (Nelumbo nucifera). J. Biol. Chem. 295, 15981612 (2020).<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Galanie, S., Thodey, K., Trenchard, I. J., Filsinger Interrante, M. & Smolke, C. D. Complete biosynthesis of opioids in yeast. Science 349, 10951100 (2015).<\/p>\n<p>ADS    CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Farrow, S. C., Hagel, J. M., Beaudoin, G. A., Burns, D. C. & Facchini, P. J. Stereochemical inversion of (S)-reticuline by a cytochrome P450 fusion in opium poppy. Nat. Chem. Biol. 11, 728732 (2015).<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Winzer, T. et al. Morphinan biosynthesis in opium poppy requires a P450-oxidoreductase fusion protein. Science 349, 309312 (2015).<\/p>\n<p>ADS    CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Singh, A., Menndez-Perdomo, I. M. & Facchini, P. J. Benzylisoquinoline alkaloid biosynthesis in opium poppy: an update. Phytochem. Rev. 18, 14571482 (2019).<\/p>\n<p>Article    CAS                        Google Scholar                <\/p>\n<p>Ziegler, J. et al. Evolution of morphine biosynthesis in opium poppy. Phytochemistry 70, 16961707 (2009).<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Chen, X. et al. A pathogenesis-related 10 protein catalyzes the final step in thebaine biosynthesis. Nat. Chem. Biol. 14, 738743 (2018).<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Hrishi, N. J. Cytogenetical studies on Papaver somniferum L. and Papaver setigerum DC their hybrid. Genetica 31, 1130 (1960).<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Choe, S. et al. Species identification of Papaver by metabolite profiling. Forensic Sci. Int. 211, 5160 (2011).<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Asghari-Zakaria, R., Razmi, S., Madadi, R. & Fathi, M. Karyological study of the medicinal plant Papaver rhoeas from northwest of Iran. Afr. J. Biotechnol. 10, 1117311177 (2011).<\/p>\n<p>Article                        Google Scholar                <\/p>\n<p>Claudia, V., Mdlina, V. & Ion, B. I. The study of mitotic chromosomes at Papaver rhoeas l. (2n=14) species. Analele tiin ifice ale Universit. Cuza din Ia (serie nou), Sec iunea I, Genetic Biologie Molecular 188190 (2004).<\/p>\n<p>Simao, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 32103212 (2015).<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Jaillon, O. et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449, 463467 (2007).<\/p>\n<p>ADS    CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Murat, F., Armero, A., Pont, C., Klopp, C. & Salse, J. Reconstructing the genome of the most recent common ancestor of flowering plants. Nat. Genet. 49, 490496 (2017).<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Kumar, S., Stecher, G., Suleski, M. & Hedges, S. B. TimeTree: a resource for timelines, timetrees, and divergence times. Mol. Biol. Evol. 34, 18121819 (2017).<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 238 (2019).<\/p>\n<p>PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Sankoff, D. & Blanchette, M. International Computing and Combinatorics Conference 251263 (Springer, 1997).<\/p>\n<p>Zheng, C., Zhu, Q. & Sankoff, D. Genome halving with an outgroup. Evol. Bioinformatics Online 2, 295302 (2007).<\/p>\n<p>                    Google Scholar                <\/p>\n<p>Gaynor, M. L., Lim-Hing, S. & Mason, C. M. Impact of genome duplication on secondary metabolite composition in non-cultivated species: a systematic meta-analysis. Ann. Bot. 126, 363376 (2020).<\/p>\n<p><!-- Auto Generated --><\/p>\n<p>Go here to read the rest:<br \/>\n<a target=\"_blank\" href=\"https:\/\/www.nature.com\/articles\/s41467-021-26330-8\" title=\"Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway - Nature.com\" rel=\"noopener\">Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway - Nature.com<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p> Field, B. &#038; Osbourn, A. E <a href=\"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/transhuman-news-blog\/genome\/three-chromosome-scale-papaver-genomes-reveal-punctuated-patchwork-evolution-of-the-morphinan-and-noscapine-biosynthesis-pathway-nature-com\/\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":9,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[25],"tags":[],"class_list":["post-1035972","post","type-post","status-publish","format-standard","hentry","category-genome"],"_links":{"self":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/posts\/1035972"}],"collection":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/users\/9"}],"replies":[{"embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/comments?post=1035972"}],"version-history":[{"count":0,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/posts\/1035972\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/media?parent=1035972"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/categories?post=1035972"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/tags?post=1035972"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}