The opium poppy genome and morphinan production

Guo, Li; Winzer, Thilo; Yang, Xiaofei; Li, Yang; Ning, Zemin; He, Zhesi; Teodor, Roxana; Lu, Ying; Bowser, Tim; Graham, Ian A.; Ye, Kai

doi:10.1126/science.aat4096

Cited by 222 publications

(256 citation statements)

References 74 publications

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“…Within-genome synteny (Fig. 1) shows that columbine is an example of the latter, confirming the conclusions from other studies [23,24,51]. Here we show that this columbine tetraploidy is a remnant of a WGD at the base of all eudicots and is thus far more ancient than previously thought [23,51].…”

Section: Discussionsupporting

confidence: 92%

“…1) shows that columbine is an example of the latter, confirming the conclusions from other studies [23,24,51]. Here we show that this columbine tetraploidy is a remnant of a WGD at the base of all eudicots and is thus far more ancient than previously thought [23,51]. Furthermore, we use this observation to argue that the hexaploidy shared by the core eudicots must have involved allopolyploidy, i.e., presumably hybridization between the ancestral tetraploid and a diploid species.…”

Section: Discussionsupporting

confidence: 89%

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The Aquilegia genome reveals a hybrid origin of core eudicots

Aköz

Nordborg

2018

Preprint

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9Background: Whole-genome duplications (WGD) have dominated the evolutionary 10 history of plants. One consequence of WGD is a dramatic restructuring of the genome as 11 it undergoes diploidization, a process under which deletions and rearrangements of 12 various sizes scramble the genetic material, leading to a repacking of the genome and 13 eventual return to diploidy. Here, we investigate the history of WGD in the columbine 14 genus Aquilegia, a basal eudicot, and use it to illuminate the origins of the core eudicots. 15Results: Within-genome synteny confirms that columbines are ancient tetraploids, and 16 comparison with the grape genome reveals that this tetraploidy appears to be shared 17 with the core eudicots. Thus, the ancient gamma hexaploidy found in all core eudicots 18 must have involved a two-step process: first tetraploidy in the ancestry of all eudicots, 19 then hexaploidy in the ancestry of core eudicots. Furthermore, the precise pattern of 20 synteny sharing suggests that the latter involved allopolyploidization, and that core 21 eudicots thus have a hybrid origin. 22Conclusions: Novel analyses of synteny sharing together with the well-preserved 23 structure of the columbine genome reveal that the gamma hexaploidy at the root of core 24 eudicots is likely a result of hybridization between a tetraploid and a diploid species. 25 26 Background 27 Whole-genome duplication (WGD) is common in the evolutionary history of plants 28 [reviewed in 1,2]. All flowering plants are descended from a polyploid ancestor, which in 29 turn shows evidence of an even older WGD shared by all seed plants [3]. These repeated 30 cycles of polyploidy dramatically restructure plant genomes. Presumably driven by the 31 "diploidization" process, whereby genomes are returned to an effectively diploid state, 32 chromosomes are scrambled via fusions and fissions, lose both repetitive and genic 33sequences, or are lost entirely [4][5][6][7][8][9][10][11]. Intriguingly, gene loss after WGD is non-random: 34 not only is there a bias against the retention of certain genes [12,13], but also against the 35 retention of one of the WGD-derived paralog chromosomes [6,9,[14][15][16]. 37We investigated the history of WGDs in the columbine genus Aquilegia for two reasons. 38The first is related to its phylogenetic position: columbines are "basal" eudicots, having 39 diverged early from the remaining "core" eudicots [17,18]. This matters because our 40 understanding of eudicot karyotype evolution is limited to the heavily sampled core 41 eudicots. Using the recently published Aquilegia coerulea genome [19], we were able to 42 address key questions about the history of polyploidization in all eudicots. Second, we 43 traced the origins of the columbine chromosomes with a particular focus on the strange 44 chromosome 4, which differs from the rest of the genome many ways. In particular, it 45 harbors more genetic polymorphism and transposable elements, has lower gene density 46 and reduced gene expression, and appears to migrate more,...

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Section: Discussionsupporting

confidence: 92%

Section: Discussionsupporting

confidence: 89%

The Aquilegia genome reveals a hybrid origin of core eudicots

Aköz

Nordborg

2018

Preprint

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“…Grossly, we obtained a high‐quality assembled genome. Among 33 representative plant species recently sequenced, this value was second only to Papaver somniferum (Guo et al, ; Table S11).…”

Section: Resultsmentioning

confidence: 99%

Deciphering the high‐quality genome sequence of coriander that causes controversial feelings

Song

Wang

et al. 2020

Plant Biotechnology Journal

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Coriander (Coriandrum sativum L. 2n = 2x = 22), a plant from the Apiaceae family, also called cilantro or Chinese parsley, is a globally important crop used as vegetable, spice, fragrance and traditional medicine. Here, we report a high-quality assembly and analysis of its genome sequence, anchored to 11 chromosomes, with total length of 2118.68 Mb and N50 scaffold length of 160.99 Mb. We found that two whole-genome duplication events, respectively, dated to~45-52 and~54-61 million years ago, were shared by the Apiaceae family after their split from lettuce. Unbalanced gene loss and expression are observed between duplicated copies produced by these two events. Gene retention, expression, metabolomics and comparative genomic analyses of terpene synthase (TPS) gene family, involved in terpenoid biosynthesis pathway contributing to coriander's special flavour, revealed that tandem duplication contributed to coriander TPS gene family expansion, especially compared to their carrot counterparts. Notably, a TPS gene highly expressed in all 4 tissues and 3 development stages studied is likely a major-effect gene encoding linalool synthase and myrcene synthase. The present genome sequencing, transcriptome, metabolome and comparative genomic efforts provide valuable insights into the genome evolution and spice trait biology of Apiaceae and other related plants, and facilitated further research into important gene functions and crop improvement.1444

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“…The genome survey of S. barbata showed a 404.6 Mb genome size and 0.28% heterozygosity via the 21 k -mer distribution analysis (Figure 1A, Figure S1). Third-generation sequencing platforms, including PacBio and Oxford Nanopore technologies, have been confirmed to have a significant advantage in de novo assembly and in processing data with complex structural variation due to high heterozygosity and repeat content [25−27]. Thus, 52.1 Gb Oxford Nanopore technology (ONT) reads (∼120 ×) with an N50 of 16.3 kb from S. baicalensis and 51.7 Gb single molecule, real-time sequencing (SMRT) reads from the PacBio platform (∼130 ×) with an N50 of 9.8 kb from S. barbata were produced to assemble highly contiguous genomes (Table S1).…”

Section: Resultsmentioning

confidence: 99%

Comparative Genome Analysis of Scutellaria baicalensis and Scutellaria barbata Reveals the Evolution of Active Flavonoid Biosynthesis

Gao

et al. 2020

Preprint

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39 Scutellaria baicalensis and Scutellaria barbata, common medicinal plants of the 40 Lamiaceae family, produce specific flavonoid compounds with antioxidant and 41 antitumor activities, including baicalein, scutellarein, norwogonin, wogonin, and their 42 glycosides. Here, we reported two chromosome-level genome assemblies of S. 43 baicalensis and S. barbata with significant quantitative chromosomal variation (2n = 44 18 and 2n = 26, respectively). The divergence of S. baicalensis and S. barbata occurred 45 far earlier than previously reported, and a whole-genome duplication event was 46 identified. The insertion of long terminal repeat elements after speciation might be 47 responsible for the observed chromosomal expansion and rearrangement. The 48 comparative genome analysis of congeneric species elucidated the species-specific 49 evolution of chrysin and apigenin biosynthetic genes, such as the S. baicalensis-specific 50 tandem duplication of the phenylalanine ammonia lyase (PAL) and chalcone synthase 51 (CHS) genes, and the S. barbata-specific duplication of 4-CoA ligase (4CL) genes. In 52 addition, the paralogous duplication, collinearity, and expression diversity of CYP82D 53 subfamily members revealed the functional divergence of flavone hydroxylase genes 54 between S. baicalensis and S. barbata. These Scutellaria genomes highlight the 55 common and species-specific evolution of flavone biosynthetic genes, promoting the 56 development of molecular breeding and the study of the biosynthesis and regulation of 57 bioactive compounds.58 59 KEYWORDS: Scutellaria; comparative genome; flavonoid biosynthesis; tandem 60 duplication; species-specific evolution 61 62 63 65 proanthocyanidins, and isoflavones, play important functions in plants, such as flower 66 pigmentation, UV protection, and symbiotic nitrogen fixation [1−3]. Flavonoid 67 metabolites also have biological and pharmacological activities in human health, 68 including antibacterial and antioxidant functions, and the treatment of cancer, 69 inflammatory, and cardiovascular diseases [3]. The genus Scutellaria, belong to the 70 Lamiaceae family, comprises common herbal plants enriched by bioactive flavonoids, 71 and approximately 300 to 360 Scutellaria species have been documented as having the 72 characteristic flower form of upper and lower lips [4,5]. Only two Scutellaria species, 73 Scutellaria baicalensis and Scutellaria barbata, are recorded in the Chinese 74 pharmacopoeia, and the roots of S. baicalensis and dried herbs of S. barbata are the 75 basis of the Chinese medicines Huang Qin and Ban Zhi Lian, respectively, which have 76 been well known heat-clearing and detoxifying herbs for thousands of years [6]. The 77 main biologically active compounds in Scutellaria are derivatives of chrysin and 78 apigenin, such as baicalein, scutellarein, wogonin, and their glycosides (baicalin, 79 scutellarin, and wogonoside) [7−10]. Baicalin has been confirmed to activate carnitine 80 palmitoyltransferase 1 in the treatment of diet-induced obesity and hepatic st...

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The opium poppy genome and morphinan production

Cited by 222 publications

References 74 publications

The Aquilegia genome reveals a hybrid origin of core eudicots

The Aquilegia genome reveals a hybrid origin of core eudicots

Deciphering the high‐quality genome sequence of coriander that causes controversial feelings

Comparative Genome Analysis of Scutellaria baicalensis and Scutellaria barbata Reveals the Evolution of Active Flavonoid Biosynthesis

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