Gene and genome duplications in the evolution of chemodiversity: perspectives from studies of Lamiaceae
Tài liệu tham khảo
Kim, 2015, A revolution in plant metabolism: genome-enabled pathway discovery, Plant Physiol, 169, 1532
Kyriakidou, 2018, Current strategies of polyploid plant genome sequence assembly, Front Plant Sci, 871, 1
Li, 2018, A guide to sequence your favorite plant genomes, Appl Plant Sci, 6, 1, 10.1002/aps3.1030
Michael, 2018, High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell, Nat Commun, 9, 10.1038/s41467-018-03016-2
Schmidt, 2017, Next-generation sequencing: big data meets high performance computing, Drug Discov Today, 22, 712, 10.1016/j.drudis.2017.01.014
Mint Evolutionary Genomics Consortium, 2018, Phylogenomic mining of the mints reveals multiple mechanisms contributing to the evolution of chemical diversity in Lamiaceae, Mol Plant, 11, 1084, 10.1016/j.molp.2018.06.002
One Thousand Plant Transcriptomes Initiative, 2019, One thousand plant transcriptomes and the phylogenomics of green plants, Nature, 574, 679, 10.1038/s41586-019-1693-2
Boutanaev, 2015, Investigation of terpene diversification across multiple sequenced plant genomes, Proc Natl Acad Sci U S A, 112, E81, 10.1073/pnas.1419547112
Kautsar, 2017, PlantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters, Nucleic Acids Res, 45, W55, 10.1093/nar/gkx305
Nützmann, 2016, Plant metabolic clusters – from genetics to genomics, New Phytol, 211, 771, 10.1111/nph.13981
Chae, 2014, Genomic signatures of specialized metabolism in plants, Science, 344, 510, 10.1126/science.1252076
Edger, 2015, The butterfly plant arms-race escalated by gene and genome duplications, Proc Natl Acad Sci U S A, 112, 8362, 10.1073/pnas.1503926112
Miyamoto, 2016, Evolutionary trajectory of phytoalexin biosynthetic gene clusters in rice, Plant J, 87, 293, 10.1111/tpj.13200
Sheehan, 2019, Evolution of L‐DOPA 4,5-dioxygenase activity allows for recurrent specialisation to betalain pigmentation in Caryophyllales, New Phytol
Panchy, 2016, Evolution of gene duplication in plants, Plant Phys, 171, 2294, 10.1104/pp.16.00523
Denoeud, 2014, The coffee genome provides insight into the convergent evolution of caffeine biosynthesis, Science, 345, 1181, 10.1126/science.1255274
Yang, 2018, Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events, New Phytol, 217, 855, 10.1111/nph.14812
Hodgson, 2019, Identification of key enzymes responsible for protolimonoid biosynthesis in plants: opening the door to azadirachtin production, Proc Natl Aca Sci U S A, 116, 17096, 10.1073/pnas.1906083116
Sherden, 2018, Identification of iridoid synthases from Nepeta species: iridoid cyclization does not determine nepetalactone stereochemistry, Phytochemistry, 145, 48, 10.1016/j.phytochem.2017.10.004
Johnson, 2019, A database-driven approach identifies additional diterpene synthase activities in the mint family (Lamiaceae), J Biol Chem, 294, 1349, 10.1074/jbc.RA118.006025
Cai, 2019, Widespread ancient whole-genome duplications in Malpighiales coincide with eocene global climatic upheaval, New Phytol, 221, 565, 10.1111/nph.15357
Smith, 2018, Disparity, diversity, and duplications in the Caryophyllales, New Phytol, 217, 836, 10.1111/nph.14772
Unruh, 2018, Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae), Am J Bot, 105, 631, 10.1002/ajb2.1047
Soltis, 2016, Ancient WGD events as drivers of key innovations in angiosperms, Curr Opin Plant Biol, 30, 159, 10.1016/j.pbi.2016.03.015
Brockington, 2015, Lineage-specific gene radiations underlie the evolution of novel betalain pigmentation in Caryophyllales, New Phytol, 207, 1170, 10.1111/nph.13441
Kersey, 2019, Plant genome sequences: past, present, future, Curr Opin Plant Biol, 48, 1, 10.1016/j.pbi.2018.11.001
Belser, 2018, Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps, Nat Plants, 4, 879, 10.1038/s41477-018-0289-4
Deschamps, 2018, A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping, Nat Commun, 9, 10.1038/s41467-018-07271-1
Schmidt, 2017, De novo assembly of a new Solanum pennellii accession using nanopore sequencing, Plant Cell, 29, 2336, 10.1105/tpc.17.00521
Hoang, 2018, Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and oxford nanopore technologies, Plant J, 96, 670, 10.1111/tpj.14049
Shafin, 2019, Efficient de novo assembly of eleven human genomes using PromethION sequencing and a novel nanopore toolkit, bioRxiv
Kolmogorov, 2019, Assembly of long, error-prone reads using repeat graphs, Nat Biotechnol, 37, 540, 10.1038/s41587-019-0072-8
Guan, 2020, Identifying and removing haplotypic duplication in primary genome assemblies, Bioinformatics, 10.1093/bioinformatics/btaa025
Ghurye, 2019, Integrating Hi-C links with assembly graphs for chromosome-scale assembly, PLoS Comput Biol, 15, 10.1371/journal.pcbi.1007273
Dudchenko, 2018, The juicebox assembly tools module facilitates de novoassembly of mammalian genomes with chromosome-length scaffolds for under $1000, bioRxiv
Kovaka, 2019, Transcriptome assembly from long-read RNA-seq alignments with StringTie2, Genome Biol, 20, 278, 10.1186/s13059-019-1910-1
Tang, 2020, Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns, Nat Commun, 11, 1438, 10.1038/s41467-020-15171-6
Grassa, 2018, A complete Cannabis chromosome assembly and adaptive admixture for elevated cannabidiol (CBD) content, bioRxiv
Guo, 2018, The opium poppy genome and morphinan production, Science, 362, 343, 10.1126/science.aat4096
Liu, 2019, Drivers of metabolic diversification: how dynamic genomic neighbourhoods generate new biosynthetic pathways in the Brassicaceae, New Phytol
Fang, 2019, Metabolic GWAS-based dissection of genetic bases underlying the diversity of plant metabolism, Plant J, 97, 91, 10.1111/tpj.14097
Wu, 2018, Mapping the Arabidopsis metabolic landscape by untargeted metabolomics at different environmental conditions, Mol Plant, 11, 118, 10.1016/j.molp.2017.08.012
Zhou, 2019, Metabolome-scale genome-wide association studies reveal chemical diversity and genetic control of maize specialized metabolites, Plant Cell, 31, 937, 10.1105/tpc.18.00772
Hardigan, 2016, Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum, Plant Cell, 28, 388, 10.1105/tpc.15.00538
Winzer, 2012, A Papaver somniferum 10-gene cluster for synthesis of the anticancer alkaloid noscapine, Science, 336, 1704, 10.1126/science.1220757
Zhang, 2016, Multiple functions of volatiles in flowers and leaves of Elsholtzia rugulosa (Lamiaceae) from southwestern China, Sci Rep, 6, 27616, 10.1038/srep27616
Ahmad, 2020, Antifungal effect of Lamiaceae herb water extracts against fusarium root rot in Asparagus, J Plant Dis Prot, 127, 229, 10.1007/s41348-019-00293-x
Linhart, 2015, Variable phytotoxic effects of Thymus vulgaris (Lamiaceae) terpenes on associated species, Int J Plant Sci, 176, 20, 10.1086/678772
Sakai, 2012, Monoterpenes of Salvia leucophylla, Curr Bioact Compd, 8, 90, 10.2174/157340712799828205
Mishra, 2019, Human health-relevant bioactives and associated functionalities of herbs in the Lamiaceae family
Dong, 2018, High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant, GigaScience, 7, 1, 10.1093/gigascience/giy068
He, 2018, Data descriptor: building an octaploid genome and transcriptome of the medicinal plant pogostemon cablin from lamiales, Sci Data, 5, 1, 10.1038/sdata.2018.274
He, 2016, Survey of the genome of Pogostemon cablin provides insights into its evolutionary history and sesquiterpenoid biosynthesis, Sci Rep, 6, 1
Malli, 2019, De novo sequencing of the Lavandula angustifolia genome reveals highly duplicated and optimized features for essential oil production, Planta, 249, 251, 10.1007/s00425-018-3012-9
Rastogi, 2015, Unravelling the genome of Holy basil: an "incomparable" "elixir of life" of traditional Indian medicine, BMC Genomics, 16, 413, 10.1186/s12864-015-1640-z
Upadhyay, 2015, Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties, BMC Plant Biol, 15, 1, 10.1186/s12870-015-0562-x
Vining, 2017, Draft genome sequence of Mentha longifolia and development of resources for mint cultivar improvement, Mol Plant, 10, 323, 10.1016/j.molp.2016.10.018
Xu, 2016, Analysis of the genome sequence of the medicinal plant Salvia miltiorrhiza, Mol Plant, 9, 949, 10.1016/j.molp.2016.03.010
Yasodha, 2018, Draft genome of a high value tropical timber tree, teak (Tectona grandis L. f): insights into SSR diversity, phylogeny and conservation, DNA Res, 25, 409, 10.1093/dnares/dsy013
Zhang, 2015, Hybrid de novo genome assembly of the Chinese herbal plant danshen (Salvia miltiorrhiza Bunge), GigaScience, 4, 62, 10.1186/s13742-015-0104-3
Zhao, 2019, A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways, GigaScience, 8, 1, 10.1093/gigascience/giz005
Zhao, 2019, The reference genome sequence of Scutellaria baicalensis provides insights into the evolution of wogonin biosynthesis, Mol Plant, 12, 935, 10.1016/j.molp.2019.04.002
Godden, 2019, Phylotranscriptomic analyses reveal asymmetrical gene duplication dynamics and signatures of ancient polyploidy in mints, Genome Biol Evol, 11, 3393
Huang, 2017, Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution, Proc Natl Acad Sci U S A, 114, E6005, 10.1073/pnas.1705567114
Franke, 2019, Gene discovery in gelsemium highlights conserved gene clusters in monoterpene indole alkaloid biosynthesis, ChemBioChem, 20, 83, 10.1002/cbic.201800592
Cui, 2015, Functional divergence of diterpene syntheses in the medicinal plant Salvia miltiorrhiza, Plant Physiol, 169, 1607
Guo, 2013, CYP76AH1 catalyzes turnover of miltiradiene in tanshinones biosynthesis and enables heterologous production of ferruginol in yeasts, Proc Natl Acad Sci U S A, 110, 12108, 10.1073/pnas.1218061110
Matsuba, 2013, Evolution of a complex locus for terpene biosynthesis in Solanum, Plant Cell, 25, 2022, 10.1105/tpc.113.111013
Sikosek, 2012, Escape from adaptive conflict follows from weak functional trade-offs and mutational robustness, Proc Natl Acad Sci U S A, 109, 14888, 10.1073/pnas.1115620109
Guo, 2016, Cytochrome P450 promiscuity leads to a bifurcating biosynthetic pathway for tanshinones, New Phytol, 210, 525, 10.1111/nph.13790
Heskes, 2018, Biosynthesis of bioactive diterpenoids in the medicinal plant Vitex agnus-castus, Plant J, 93, 943, 10.1111/tpj.13822
Pateraki, 2017, Total biosynthesis of the cyclic AMP booster forskolin from Coleus forskohlii, eLife, 6, 10.7554/eLife.23001
Du, 2018, SmbHLH37 functions antagonistically with smMYC2 in regulating jasmonate-mediated biosynthesis of phenolic acids in Salvia miltiorrhiza, Front Plant Sci, 871, 1
Zhang, 2015, Genome-wide characterisation and analysis of bHLH transcription factors related to tanshinone biosynthesis in Salvia miltiorrhiza, Sci Rep, 5, 1
Zhang, 2018, Genomic survey of bZIP transcription factor genes related to tanshinone biosynthesis in Salvia miltiorrhiza, Acta Pharm Sin B, 8, 295, 10.1016/j.apsb.2017.09.002
Ding, 2017, SmMYB36, a novel R2R3-MYB transcription factor, enhances tanshinone accumulation and decreases phenolic acid content in Salvia miltiorrhiza hairy roots, Sci Rep, 7, 1
Lichman, 2019, Uncoupled activation and cyclisation in catmint reductive terpenoid biosynthesis, Nat Chem Biol, 15, 71, 10.1038/s41589-018-0185-2
Zhou, 2016, Evolution of herbivore-induced early defense signaling was shaped by genome-wide duplications in Nicotiana, eLife, 5, 10.7554/eLife.19531
Shoji, 2019, The recruitment model of metabolic evolution: jasmonate-responsive transcription factors and a conceptual model for the evolution of metabolic pathways, Front Plant Sci, 10, 1, 10.3389/fpls.2019.00560
Qiao, 2019, Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants, Genome Biol, 20, 1, 10.1186/s13059-019-1650-2
Gao, 2019, The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor, Nat Genet, 51, 1044, 10.1038/s41588-019-0410-2
Moore, 2019, Robust predictions of specialized metabolism genes through machine learning, Proc Natl Acad Sci U S A, 116, 2344, 10.1073/pnas.1817074116
Chen, 2018, The sequenced angiosperm genomes and genome databases, Front Plant Sci, 9, 1
Pluskal, 2019, The biosynthetic origin of psychoactive kavalactones in kava, Nat Plants, 5, 867, 10.1038/s41477-019-0474-0
Kellner, 2015, Genome-guided investigation of plant natural product biosynthesis, Plant J, 82, 680, 10.1111/tpj.12827
Xu, 2017, Wild tobacco genomes reveal the evolution of nicotine biosynthesis, Proc Natl Acad Sci U S A, 114, 6133, 10.1073/pnas.1700073114