Haplotype-resolved genome assembly for tetraploid Chinese cherry (Prunus pseudocerasus) offers insights into fruit firmness

Horticulture Research, Journal Year: 2024, Volume and Issue: 11(7)

Published: June 21, 2024

Chinese cherry (

Language: Английский

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Chromosome-level genome assembly provides insights into the genetic diversity, evolution, and flower development of Prunus conradinae

Molecular Horticulture, Journal Year: 2024, Volume and Issue: 4(1)

Published: June 19, 2024

Abstract Prunus conradinae , a valuable flowering cherry belonging to the Rosaceae family subgenus Cerasus and endemic China, has high economic ornamental value. However, high-quality P. genome is unavailable, which hinders our understanding of its genetic relationships phylogenesis, ultimately, possibility mining key genes for important traits. Herein, we have successfully assembled chromosome-scale genome, identifying 31,134 protein-coding genes, with 98.22% them functionally annotated. Furthermore, determined that repetitive sequences constitute 46.23% genome. Structural variation detection revealed some syntenic regions, inversions, translocations, duplications, highlighting diversity complexity . Phylogenetic analysis demonstrated most closely related campanulata from it diverged ~ 19.1 million years ago (Mya). avium earlier than cerasus Similar other species, underwent common whole-genome duplication event at 138.60 Mya. 79 MADS -box members were identified in accompanied by expansion SHORT VEGETATIVE PHASE subfamily. Our findings shed light on complex relationships, evolution will facilitate research molecular breeding functions horticultural characteristics

Language: Английский

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Haplotype-resolved genome assembly of poplar line NL895 provides a valuable tree genomic resource

Forestry Research, Journal Year: 2024, Volume and Issue: 4(1), P. 0 - 0

Published: Jan. 1, 2024

Poplar line NL895 can potentially become a model plant for poplar study as it is widely cultivated elite line. However, the lack of genome resources hindered use major material in poplar. In this study, we provided high-quality assembly with PacBio single molecule real-time (SMRT) sequencing and High-throughput chromosome conformation capture (Hi-C) technology. The raw diploid included 606 contigs total size ~815 Mb, monoploid 246 ~412 Mb. haplotype-resolved chromosomes genomes were also generated. All monoploid, diploid, showed more than 97% completeness they largely improve mapping efficiency RNA-Seq analysis. By comprehensively comparing two haplotype found heterozygosity much higher other lines. We that harbors genomic variants gene diversity. haplotype-specific genes variable expression patterns. These characters would be attributed to high heterosis NL895. allele-specific (ASE) was investigated lots alleles biased expressions different tissues or environmental conditions. Taken together, sequence valuable tree resource greatly facilitate studies

Language: Английский

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Novel insight of the SVP gene involved in pedicel length based on genomics analysis in cherry

Plant Cell Reports, Journal Year: 2025, Volume and Issue: 44(2)

Published: Feb. 1, 2025

Language: Английский

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New insights into genome assembly at the chromosome‐level of Prunus tomentosa in evolution and cold tolerance

iMeta, Journal Year: 2025, Volume and Issue: unknown

Published: March 20, 2025

This study assembled a high-quality chromosome-level genome of Prunus tomentosa, offering vital resource for elucidating its genetic architecture, evolutionary relationships, and facilitating genome-assisted breeding efforts. Multi-omics integration revealed PtIMP3 PtMIOX1L as key factors in cold tolerance P. tomentosa. drives the conversion glucose-6-phosphate to myo-inositol, while catalyzes myo-inositol d-glucuronic acid. Specifically, high expression abundance low resulted endogenous inositol levels The application enhanced cherry rootstocks by modulating reactive oxygen species concentrations maintaining stable relative water content. finding supports superior performance tomentosa adapting extreme low-temperatures environmental conditions. These insights advance strategies improving horticultural crops, bridging fundamental research with practical applications developing climate-resilient crops. To Editor, family Rosaceae, comprising over 100 genera approximately 3000 species, plays crucial role horticulture agricultural production globally [1]. L., encompassing 200 shrubs trees, is significant component Northern Hemisphere forests desert ecosystems [2]. classification genus previously subdivided into six subgenera (Amygdalus, Cerasus, Laurocerasus, Microcerasus, Padus, Prunophora) [3, 4], has been controversial, partly owing ease interspecific hybridization [5]. Thunb., commonly known Nanking cherry, long classified within subgenus Microcerasus [6]. However, studies on chromosome-scale genomes phylogenetic analyses are lacking, rendering background relatively unknown. Chinese diet 2000 years, noted rich content vitamins (B1, B2, C, D, E) other antioxidant compounds, such carotene niacin [7, 8]. It features dark green oval leaves, 2–7 cm long, hairy topside subglobular fruits 0.5–1.2 diameter (Figure 1A, Figure S1, Table S1). ripen between June September, sweet, slightly tart flavor ideal fresh consumption or processing pies jams exhibits tolerance, withstanding temperatures −40°C [8], is, therefore, promising candidate ornamental fruit regions. Despite this, mechanisms governing potential molecular markers remain largely unexplored. We 211.55 Mb, 25,991 protein-coding genes, 99.09% which were functionally annotated. Repetitive sequences constituted 41.53% genome. showed close affinity humilis (Phum), from it diverged 19.63 million years ago (Mya). Several syntenic regions, translocations, inversions, duplications highlighting their diversity complexity. underwent whole triploidization event 115–130 Mya (Ks = 1.22), shared core eudicots. Combined analysis transcriptome metabolome identified monophosphatase 3 myoinositol oxygenase 1-like tolerance. findings enhance our understanding complex genetics, evolution, adaptation environments, support further breeding. obtained 85.94 55.26 Gb Illumina short-read Oxford Nanopore Technology (ONT) long-read data, respectively (Table S2). Before de novo assembly was estimated be 232.19 Mb using k-mer survey (k 23) short reads, closely matched testing value (210.46 Mb) determined via flow cytometry S2 S3). at chromosomal level 109.94 Hi-C reads 172 scaffolds covering scaffold N50 25.22 contig 3.40 1B S4). Notably, size smaller than those serrulata (Pser) (265.4 [9], campanulata (Pcam) (280.2 [10], conradinae (Pcon) (289.62 [11], pusilliflora (Ppus) (309.62 [5], avium (Pavi) (341.62 [12] genomes. Benchmarking Universal Single-Copy Orthologs (BUSCO) 98.5% completeness, only 0.9% missing BUSCOs S5). Moreover, we anchored 201.58 95.29% genome, eight pseudochromosomes S6). heatmap that good, demonstrating well-connected along diagonal somatic cells contained 16 chromosomes cytological observation method 1C). 83.72 repetitive (~39.58% genome), included tandem repeats transposable elements (TEs; S7). most abundant terminal repeat (LTR) retrotransposons LTR/Gypsy LTR/Copia, 10.51% 7.59% total retrotransposons, sequence rate (~39.58%) lower Pser (49.02%) Pcam (50.33%) Pcon (~46.23%) Ppus (49.08%) Pavi (~59.29%) [12]. may explain compared species. genes BUSCO completeness metrics demonstrated concordance, displaying annotated gene set indicating 97.7% based annotation S8). Furthermore, 25,754 (~99.09%) across various databases S9). LTR index 12.50 S10), quality assembly. analyzed dynamics 15 comparing unique paralogs, multiple- single-copy orthologs, unclustered S4 S11). In observed 629 families expanding 978 contracting during speciation Phum 1D). exhibited more expanded contracted persica (Pper), mume (Pmum), (Pcam). Expanded, unique, significantly enriched (p < 0.05) 2464, 174, 2014 GO terms, (Figures S5–S7 Tables S12–S14). Expanded notably (MI) transport (GO:0015798) MI transmembrane transporter activity (GO:0005365) S5 S12). Using TimeTree database (http://www.timetree.org/) fossil calibration common ancestor (95% highest posterior density [HPD] 3.96–25.14 Mya; divergence two (P. Phum) Prunophora (Parm Pmum) about 32.43 HPD 28.14–38.38 Mya). plant explore evolution Vitis vinifera Arabidopsis thaliana outgroups. Phylogenetic related humilis, both belonging Microcerasus. (Pmum Parm) located branches clustered (Pper Pdul) Amygdalus, followed seven Cerasus Their makeup aligned consistent previous [13-15]. Consequently, proposed have reclassified Prunophora, challenging earlier morphology-based classifications [6, 16]. four 14,321 families, (519) (459) Pper (107) 1E). compare structural variations multiple duplications, unaligned genomic segments. Our blocks each species—140.71 Pavi, 129.14 Pper, 123.49 Pser—indicating conservation (Tables S15–S17). Additionally, rearrangements, including inversions (21.66 18.69 16.28 Pser), translocations (4.65 2.60 8.56 (0.52 1.03 1.25 Pser) comparison 1F). A notable aspect considerable portion (37.49, 50.76, 58.35 Mb), complexity among these contribute architecture relationships importance rearrangements adaptation. there exist greater number variations, One possible explanation experienced intense artificial selection Pser, leading variations. needed substantiate observations. explored polyploidization events plants homologous dot plots Initially, grapes three grape corresponded chromosomes, showing 1:1 ratio red fragments 1G). results indicated single whole-genome triplication gamma (γ) event, duplication one according report [17]. Further likely comparable Extended homology dulcis, Ppus, reference (Rosa chinensis V. vinifera) confirmed 1H). synonymous nucleotide substitution then calculated data 12 2 plants, 1 peak affirming lineage just γ eudicots 1I, Figures S8, S9, S18). Variations rates different could potentially skew estimates time. address used benchmark correction, aiming deduce accurate timeline evolution. By employing Ks reference, values adjusted all fitted S19). occurred 115 130 Mya, 1.22. intergenomic collinearity assessed following S20). Analysis collinear regions ratio, occurrence ancient events. comparisons performed 1J). retention S21). overall ranged 28% 36%, associated event. stability throughout strongly linked reduced loss 1K,L). After undergoing polyploidization, fusion, translocation events, reconstruction ancestral provides processes impacts chromosome rearrangements. enhances structure function clarifies Rosaceae (R. chinensis), (V. vinifera), reconstructed genes. Through S10–S12), clear relationship evident. enabled us infer consisted 1M). no fusion transition state current Instead, involving cross-exchanges occurred. change Cold stress often exerts adverse impact growth development resulting decreased chlorophyll synthesis elevated (ROS), cellular membrane lipid peroxidation an excessive malondialdehyde (MDA) [18]. tolerating necessitates specific transcriptional metabolic regulatory networks response stress. this study, generated profiles species: pseudocerasus (Ppse), serrula (Psea), identifying 2482 differentially expressed (DEGs) primarily pathways, biosynthesis secondary metabolites, cofactors, 381 differential metabolites metabolite biosynthesis, ABC transporters 2A–D S22–S27). KEGG enrichment differentials functions co-enriched phosphate, ascorbate, aldarate metabolism pathways 2E,F). 1D-myo-inositol-1P/1D-myo-inositol-3P displays higher cold-sensitive namely Ppse, Psea 2G). d-glucuronate, notion tomentosa's conditions, contributing better comprehension functional roles lack supporting evidence emphasizes necessity additional validate extend discoveries. subcellular localization cytoplasm, predictions CELLO v.2.5 2H S28). addition, investigated physiological against cherries 2I–T). Phenotypic exogenous 2I–L). Exogenous led reduction MDA hydrogen peroxide (H2O2) contents, catalase (CAT), peroxidase (POD), superoxide dismutase (SOD) activities 2N–R). Relative (RWC) increased treatment groups 2S). Finally, fluorescence (Fv/Fm), marker photosynthetic efficiency, improved 2T). suggest compatible solute, protection regulating ROS RWC. indicate effective cell turgor binding molecules, aligning [19]. Comprehensive detailed procedures provided Supplementary Information. Songtao Jiu: Project administration; conceptualization; investigation; formal analysis; writing—review editing. Muhammad Aamir Manzoor: Investigation; Zhengxin Lv: analysis. Baozheng Chen: methodology; Shaoqin Shen: Yan Xu: Validation; visualization. Moyang Liu: Methodology. Chengwei Li: Investigation. Xunju Yanhong Fu: Formal Qijing Zhang: Resources. Ruie Xinyu Visualization. Shiping Wang: administration. Xiaoming Song: Methodology; Conceptualization; project supervision. Yang Dong: Caixi funding acquisition; resources; funded Natural Science Foundation Shanghai (Grant No. 23ZR1430600), Agriculture Applied Development Program China 2022-02-08-00-12-F01111), Research System CARS-30), National 32102347). thank Dr. Meng Li Nanjing Forestry University, Zongyi Sun Wuhan Grandomics Bioscience Co., Ltd., Xiao Dong Max Planck Institute Plant Breeding providing valuable advice. authors declare conflicts interest. No animals humans involved study. available supplementary material article. raw sequencing Genomics Data Center (https://ngdc.cncb.ac.cn/gsa/browse/CRA015735). uploaded NCBI Sequence Read Archive (SRA) accession PRJNA1230348 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1230348). scripts saved GitHub https://github.com/ericchenbz/The-genome-of-the-Prunus-tomentosa. materials (methods, figures, tables, graphical abstract, slides, videos, translated version, update materials) found online DOI iMeta http://www.imeta.science/. S1. parameters, (A) weight, (B) hardness, (C) titratable acid, (D) soluble solids, (E) longitudinal transverse diameters fruits. S2. Estimation size. S3. High-resolution contact matrix S4. Gene distribution single- copies paralogs (Atha), (Vvin), Rosa (Rchi), dulcis (Pdul), armeniaca (Parm), (Pavi), cerasus (Pcer), fruticosa (Pfru), (Pcam), (Ppus), (Pser), yedoensis (Pyed), (Ptom). S5. S6. S7. S8. curve before correction. S9. Distribution map S10. Homologous dotplots S11. S12. ancestors characteristics flower organs statistics estimation cytometry. Statistics Completeness measured (BUSCO). ordering orienting 8 pseudomolecules. Long-terminal-repeat (LAI) N50s assemblies Comparison families' ontology (GO) S13. S14. S15. Structural-variant detection S16. S17. S18. Kernel (before correction). S19. (after S20. list S21. percentage retained vinifera. S22. vs. Ptom. S23. S24. Ppse S25. Ptom S26. S27. S28. Primer Please note: publisher not responsible functionality any information supplied authors. Any queries (other content) should directed corresponding author

Language: Английский

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Advances in the omics research of Rosaceae

Ornamental Plant Research, Journal Year: 2024, Volume and Issue: 4(1), P. 0 - 0

Published: Jan. 1, 2024

Rosaceae plants are widely distributed worldwide. These plants, including well-known ornamental and those producing temperate fruits, have significant economic value. The utilization of omics technologies has significantly advanced the research progress on in various areas germplasm resources, molecular breeding, evolutionary domestication. Here, we provide an overview applications Rosaceae. It includes whole-genome sequencing assembly as well genome-wide association studies, transcriptome, proteomics, metabolomics, comparative genomics. techniques used to understand genetic regulatory mechanisms underlying important traits such flower color, fragrance, stress tolerance, fruit quality. We outline prospects genomics aiming establish a foundation for comprehending breeding traits. This could potentially theoretical support rapidly cultivating new varieties.

Language: Английский

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Characterization of Key Odorants in Lushan Yunwu Tea in Response to Intercropping with Flowering Cherry

Foods, Journal Year: 2024, Volume and Issue: 13(8), P. 1252 - 1252

Published: April 19, 2024

Lushan Yunwu tea (LSYWT) is a famous green in China. However, the effects of intercropping with flowering cherry on overall aroma have not been well understood. In this study, headspace solid-phase microextraction (HS-SPME) coupled gas chromatography-mass spectrometry (GC-MS) was used for analysis. A total 54 volatile compounds from eight chemical classes were identified samples both and pure-tea-plantation groups. Principal component analysis (PCA), orthogonal partial least-squares discriminant (OPLS-DA), odor activity value (OAV) methods combined sensory evaluation cis-jasmone, nonanal, linalool as key group. Benzaldehyde, α-farnesene, methyl benzene main using microextraction/gas (HS-SPME/GC-MS). These findings will enrich research chemistry offer new insights into product development quality improvement LSYWT.

Language: Английский

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In vitro regeneration, photomorphogenesis and light signaling gene expression in Hydrangea quercifolia cv. 'Harmony' under different LED environments

Planta, Journal Year: 2024, Volume and Issue: 259(3)

Published: Feb. 14, 2024

Language: Английский

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Genome-Wide Identified MADS-Box Genes in Prunus campanulata ‘Plena’ and Theirs Roles in Double-Flower Development

Plants, Journal Year: 2023, Volume and Issue: 12(17), P. 3171 - 3171

Published: Sept. 4, 2023

The MADS-box gene family plays key roles in flower induction, floral initiation, and morphogenesis flowering plants. To understand their functions the double-flower formation of Prunus campanulata ‘Plena’ (hereafter referred to as PCP), which is an excellent cherry cultivar, we performed genome-wide identification family. In this study, 71 genes were identified grouped into Mα, Mβ, Mγ MIKC subfamilies according structures phylogenetic relationships. All located on eight chromosomes PCP. Analysis cis-acting elements promoter region indicated that they associated mainly with auxin, abscisic acid, gibberellin, MeJA (methyl jasmonate), salicylic acid responsiveness, may be involved development differentiation. By observing organ phenotype, found phenotype PCP originated from petaloid stamens. analysis MIKC-type vegetative organs by qRT–PCR revealed six upregulated petal three downregulated participating stamen identity. Comparative stamens normal also expression level AG (PcMADS40) was significantly reduced. Thus, speculated these genes, especially PcMADS40, lead thus double flowers. This study lays a theoretical foundation for classification studying molecular mechanism underlying flowers other ornamental

Language: Английский

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Functional Analysis of the PoSERK-Interacting Protein PorbcL in the Embryogenic Callus Formation of Tree Peony (Paeonia ostii T. Hong et J. X. Zhang)

Plants, Journal Year: 2024, Volume and Issue: 13(19), P. 2697 - 2697

Published: Sept. 26, 2024

SERK is a marker gene for early somatic embryogenesis. We screened and functionally verified SERK-interacting protein to gain insights into tree-peony Using PoSERK as bait, we identified PorbcL (i.e., the large subunit of Rubisco) from yeast two-hybrid (Y2H) library cDNA developing embryos. The interaction between was by Y2H bimolecular fluorescence complementation analyses. encodes 586-amino-acid acidic non-secreted hydrophobic non-transmembrane that mainly localized in chloroplast plasma membrane. highly expressed roots flowers up-regulated during zygotic embryo development. overexpression caused up-regulation (encoding embryogenesis receptor-like kinase), PoAGL15 agamous-like 15), PoGPT1 glucose-6-phosphate translocator), while it down-regulation PoLEC1 leafy cotyledon 1) callus. led increased indole-3-acetic acid (IAA) content but decreasing contents abscisic (ABA) 6-benzyladenosine (BAPR). changes expression, high IAA levels, ratio ABA, BAPR, 1-Aminocyclopropanecarboxylic (ACC), 5-Deoxystrigol (5DS), brassinolide (BL) promoted These results provide foundation establishing embryogenic callus system.

Language: Английский

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