Genome evolution and diversity of wild and cultivated potatoes

Nature, Journal Year: 2022, Volume and Issue: 606(7914), P. 535 - 541

Published: June 8, 2022

Potato (Solanum tuberosum L.) is the world's most important non-cereal food crop, and vast majority of commercially grown cultivars are highly heterozygous tetraploids. Advances in diploid hybrid breeding based on true seeds have potential to revolutionize future potato production1-4. So far, relatively few studies examined genome evolution diversity wild cultivated landrace potatoes, which limits application their breeding. Here we assemble 44 high-quality genomes from 24 20 accessions that representative Solanum section Petota, tuber-bearing clade, as well 2 neighbouring section, Etuberosum. Extensive discordance phylogenomic relationships suggests complexity evolution. We find substantially expanded its repertoire disease-resistance genes when compared with closely related seed-propagated solanaceous crops, indicative effect tuber-based propagation strategies genome. discover a transcription factor determines tuber identity interacts mobile tuberization inductive signal SP6A. also identify 561,433 high-confidence structural variants construct map large inversions, provides insights for improving inbred lines precluding linkage drag, exemplified by 5.8-Mb inversion associated carotenoid content tubers. This study will accelerate enrich our understanding biology global staple crop.

Language: Английский

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Current status of structural variation studies in plants

Plant Biotechnology Journal, Journal Year: 2021, Volume and Issue: 19(11), P. 2153 - 2163

Published: June 8, 2021

Structural variations (SVs) including gene presence/absence and copy number are a common feature of genomes in plants and, together with single nucleotide polymorphisms epigenetic differences, responsible for the heritable phenotypic diversity observed within between species. Understanding contribution SVs to plant variation is important breeders assist producing improved varieties. The low resolution early genetic technologies inefficient methods have previously limited our understanding plants. However, rapid expansion genomic technologies, it possible assess an ever-greater accuracy. Here, we review current status SV studies plants, examine roles that play traits, compare future challenges studies.

Language: Английский

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Improved genome assembly and pan‐genome provide key insights into eggplant domestication and breeding

The Plant Journal, Journal Year: 2021, Volume and Issue: 107(2), P. 579 - 596

Published: May 9, 2021

Eggplant (Solanum melongena L.) is an important horticultural crop and one of the most widely grown vegetables from Solanaceae family. It was domesticated a wild, prickly progenitor carrying small, round, non-anthocyanic fruits. We obtained novel, highly contiguous genome assembly eggplant '67/3' reference line, by Hi-C retrofitting previously released short read- optical mapping-based assembly. The sizes 12 chromosomes fraction anchored genes in improved were comparable to those chromosome-level resequenced 23 accessions S. representative worldwide phenotypic, geographic, genetic diversity species, each closely related species Solanum insanum incanum. pan-genome contained approximately 51.5 additional megabases 816 compared with genome, while pan-plastome showed little variation. identified 53 selective sweeps fruit color, prickliness, shape nuclear highlighting selection leading emergence present-day cultivars its wild ancestors. Candidate underlying included MYBL1 repressor CHALCONE ISOMERASE (for color), homologs Arabidopsis GLABRA1 GLABROUS INFLORESCENCE STEMS2 prickliness), orthologs tomato FW2.2, OVATE, LOCULE NUMBER/WUSCHEL, SUPPRESSOR OF CELL SIZE REGULATOR size/shape), further suggesting that for latter trait relied on common set orthologous eggplant.

Language: Английский

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The 3D architecture of the pepper genome and its relationship to function and evolution

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: June 16, 2022

Abstract The organization of chromatin into self-interacting domains is universal among eukaryotic genomes, though how and why they form varies considerably. Here we report a chromosome-scale reference genome assembly pepper ( Capsicum annuum ) explore its 3D through integrating high-resolution Hi-C maps with epigenomic, transcriptomic, genetic variation data. Chromatin folding in are as prominent TADs mammals but exhibit unique characteristics. They tend to coincide heterochromatic regions enriched retrotransposons frequently embedded loops, which may correlate transcription factories. Their boundaries hotspots for chromosome rearrangements otherwise depleted variation. While conformation broadly affects variance, it does not predict differential gene expression between tissues. Our results suggest that explained by model heterochromatin-driven promoted factories such spatial architecture under structural functional constraints.

Language: Английский

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Revealing evolution of tropane alkaloid biosynthesis by analyzing two genomes in the Solanaceae family

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: March 15, 2023

Tropane alkaloids (TAs) are widely distributed in the Solanaceae, while some important medicinal tropane (mTAs), such as hyoscyamine and scopolamine, restricted to certain species/tribes this family. Little is known about genomic basis evolution of TAs biosynthesis specialization Solanaceae. Here, we present chromosome-level genomes two representative mTAs-producing species: Atropa belladonna Datura stramonium. Our results reveal that species employ a conserved biosynthetic pathway produce mTAs despite being distantly related within nightshade A gene cluster combined with duplication underlies wide distribution We also provide evidence branching genes leading likely have evolved early ancestral Solanaceae but been lost most lineages, A. D. stramonium exceptions. Furthermore, identify cytochrome P450 modifies into norhyoscyamine. for evolutionary insights will be useful biotechnological production via synthetic biology approaches. synthesized by authors assemble producing species, show loss shapes uneven catalyzing N-demethylation generate

Language: Английский

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Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors

Nature Genetics, Journal Year: 2023, Volume and Issue: 55(9), P. 1579 - 1588

Published: Aug. 28, 2023

Abstract Potato ( Solanum tuberosum ) and tomato lycopersicon crops suffer severe losses to late blight caused by the oomycete pathogen Phytophthora infestans . americanum , a relative of potato tomato, is globally distributed most accessions are highly resistant. We generated high-quality reference genomes four S. accessions, resequenced 52 defined pan-NLRome immune receptor genes. further screened for variation in recognition 315 P. RXLR effectors accessions. Using these genomic phenotypic data, we cloned three NLR-encoding genes, Rpi-amr4 R02860 R04373 that recognize cognate PITG_22825 AVRamr4 ), PITG_02860 PITG_04373 These resources methodologies will support efforts engineer potatoes with durable resistance can be applied diseases other crops.

Language: Английский

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Eggplant transcription factor SmMYB5 integrates jasmonate and light signaling during anthocyanin biosynthesis

PLANT PHYSIOLOGY, Journal Year: 2023, Volume and Issue: 194(2), P. 1139 - 1165

Published: Oct. 10, 2023

Abstract Low light conditions severely suppress anthocyanin synthesis in fruit skins, leading to compromised quality eggplant (Solanum melongena L.) production. In this study, we found that exogenous methyl-jasmonate (MeJA) application can effectively rescue the poor coloration of pericarp under low conditions. However, regulatory relationship between jasmonate and signaling for regulating remains unclear. Here, identified a JA response factor, SmMYB5, as an positive regulator by applying RNA-sequencing characterization transgenic plants. Firstly, resolved SmMYB5 interact with TRANSPARENT TESTA8 (SmTT8), anthocyanin-promoted BASIC HELIX-LOOP-HELIX (bHLH) transcription form SmMYB5–SmTT8 complex activate CHALCONE SYNTHASE (SmCHS), FLAVANONE-3-HYDROXYLASE (SmF3H), ANTHOCYANIN (SmANS) promoters direct binding. Secondly, revealed repressors JASMONATE ZIM DOMAIN5 (SmJAZ5) SmJAZ10 interfere stability transcriptional activity interacting SmMYB5. partially activation SmF3H SmANS inducing SmJAZ5/10 degradation. Thirdly, demonstrated protein abundance is regulated light. CONSTITUTIVELY PHOTOMORPHOGENIC1 (SmCOP1) interacts trigger degradation via 26S proteasome pathway. Finally, delineated light-dependent JA-SmMYB5 pathway promotes skins. These results provide insights into mechanism integration signals secondary metabolite

Language: Английский

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Genome-Wide Comparative Analysis of the R2R3-MYB Gene Family in Five Solanaceae Species and Identification of Members Regulating Carotenoid Biosynthesis in Wolfberry

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(4), P. 2259 - 2259

Published: Feb. 18, 2022

The R2R3-MYB is a large gene family involved in various plant functions, including carotenoid biosynthesis. However, this lacks comprehensive analysis wolfberry (Lycium barbarum L.) and other Solanaceae species. recent sequencing of the genome provides an opportunity for investigating organization evolutionary characteristics genes A total 610 were identified five species, 137 wolfberry. LbaR2R3-MYB grouped into 31 subgroups based on phylogenetic analysis, conserved structures, motif composition. Five groups only functionally divergent during evolution. Dispersed whole duplication events are critical expanding family. There 287 orthologous pairs between four selected RNA-seq expression level differential (DEGs) biosynthesis (CBGs) fruit development stages. highly expressed co-expressed with CBGs development. quantitative Real-Time (qRT)-PCR verified seven candidate genes. Thus, Lba11g0183 Lba02g01219 regulating This study elucidates evolution function

Language: Английский

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Genetics and breeding of phenolic content in tomato, eggplant and pepper fruits

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: March 21, 2023

Phenolic acids and flavonoids are large groups of secondary metabolites ubiquitous in the plant kingdom. They currently spotlight due to numerous health benefits associated with their consumption, as well for vital roles biological processes plant-environment interaction. Tomato, eggplant pepper top ten most consumed vegetables world, fruit accumulation profiles have been extensively characterized, showing substantial differences. A broad array genetic genomic tools has helped identify QTLs candidate genes biosynthesis phenolic flavonoids. The aim this review was synthesize available information making it easily researchers breeders. phenylpropanoid pathway is tightly regulated by structural genes, which conserved across species, along a complex network regulatory elements like transcription factors, especially MYB family, cellular transporters. Moreover, compounds accumulate tissue-specific developmental-dependent ways, different paths metabolic activated/deactivated development. We retrieved 104 annotated putative orthologues encoding key enzymes tomato (37), (29) (38) compiled 267 (217 tomato, 16 34 pepper) linked acids, total phenolics content. Combining molecular variability, through both conventional engineering strategies, feasible approach improve content pepper. Finally, although biosynthetic well-studied Solanaceae, more research needed on identification behind many QTLs, interactions other genes.

Language: Английский

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Genome-wide characterization and expression analysis of AP2/ERF genes in eggplant (Solanum melongena L.)

Plant Physiology and Biochemistry, Journal Year: 2021, Volume and Issue: 167, P. 492 - 503

Published: Aug. 14, 2021

Language: Английский

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