ae041c1a7c01f2d34e28f9479b6ed0a7 pmc_10599238.pdf acc8af5518505260b8085e9a7ddcc3f9c9afffaf pmc_10599238.pdf 6a0878f17a73c402e124be1ce97e8a3cef964c97dd6251a317fc9904b882fa02 pmc_10599238.pdf Title: The haplotype-resolved T2T reference genome highlights structural variation underlying agronomic traits of melon Subject: DOI: 10.1093/hr/uhad182, Horticulture Research, 10, 00, 1 10 2023. Abstract: Melon (Cucumis melo L.) is an important vegetable crop that has an extensive history of cultivation. However, the genome of wild and semi-wild melon types that can be used for the analysis of agronomic traits is not yet available. Here we report a chromosome-level T2T genome assembly for 821 (C. melo ssp. agrestis var. acidulus), a semi-wild melon with two haplotypes of ~373 Mb and ~364 Mb, respectively. Comparative genome analysis discovered a significant number of structural variants (SVs) between melo (C. melo ssp. melo) and agrestis (C. melo ssp. agrestis) genomes, including a copy number variation located in the ToLCNDV resistance locus on chromosome 11. Genome-wide association studies detected a significant signal associated with climacteric ripening and identified one candidate gene CM_ac12g14720.1 (CmABA2), encoding a cytoplasmic short chain dehydrogenase/reductase, which controls the biosynthesis of abscisic acid. This study provides valuable genetic resources for future research on melon breeding. Keywords: Author: Creator: LaTeX with hyperref package Producer: Acrobat Distiller 23.0 (Windows) CreationDate: Fri Dec 15 14:30:29 2023 CET ModDate: Fri Dec 15 14:30:29 2023 CET Custom Metadata: yes Metadata Stream: yes Tagged: yes UserProperties: no Suspects: no Form: none JavaScript: no Pages: 13 Encrypted: no Page size: 595.26 x 782.337 pts Page rot: 0 File size: 2145985 bytes Optimized: yes PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- PPFLKC+CaeciliaLTStd-Bold Type 1C Custom yes yes yes 2924 0 PPFLKD+CaeciliaLTStd-Roman Type 1C Custom yes yes yes 2843 0 PPFMAC+CaeciliaLTStd-Italic Type 1C Custom yes yes yes 2844 0 PPFMGB+CaeciliaLTStd-Light Type 1C Custom yes yes yes 2925 0 PPFNKK+CaeciliaLTStd-Heavy Type 1C Custom yes yes yes 2926 0 PPFNKL+MTSYN Type 1C Custom yes yes yes 2927 0 PPFNNL+CaeciliaLTStd-LightItalic Type 1C Custom yes yes yes 2928 0 PPHDPE+CaeciliaLTStd-BoldItalic Type 1C Custom yes yes yes 52 0 PPHECE+MTMI Type 1C Custom yes yes yes 53 0 Jhove (Rel. 1.28.0, 2023-05-18) Date: 2025-03-12 02:10:12 CET RepresentationInformation: pmc_10599238.pdf ReportingModule: PDF-hul, Rel. 1.12.4 (2023-03-16) LastModified: 2025-03-12 02:03:50 CET Size: 2145985 Format: PDF Version: 1.7 Status: Well-Formed, but not valid SignatureMatches: PDF-hul ErrorMessage: Invalid indirect destination - referenced object 'reciaff2' cannot be found ID: PDF-HUL-149 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'reciaff2' cannot be found ID: PDF-HUL-122 Offset: 1851370 MIMEtype: application/pdf Profile: Linearized PDF, Tagged PDF PDFMetadata: Objects: 2960 FreeObjects: 1 IncrementalUpdates: 1 DocumentCatalog: ViewerPreferences: HideToolbar: false HideMenubar: false HideWindowUI: false FitWindow: true CenterWindow: false DisplayDocTitle: true NonFullScreenPageMode: UseNone Direction: L2R ViewArea: CropBox ViewClip: CropBox PrintArea: CropBox PageClip: CropBox PageLayout: SinglePage PageMode: UseOutlines Language: en Outlines: Item: Title: The haplotype-resolved T2T reference genome highlights structural variation underlying agronomic traits of melon Destination: toc.chapter Children: Item: Title: Introduction Destination: section.20.1.1 Item: Title: Results Destination: section.27.1.2 Item: Title: Discussion Destination: section.36.1.3 Item: Title: Materials and methods Destination: section.37.1.4 Item: Title: Acknowledgements Destination: section.47.1.5 Item: Title: Author contributions Destination: section.48.1.6 Item: Title: Data availability Destination: section.49.1.7 Item: Title: Conflict of interest statement Destination: section.50.1.8 Item: Title: Supplementary data Destination: section.51.1.9 Info: Title: The haplotype-resolved T2T reference genome highlights structural variation underlying agronomic traits of melon Author: Subject: DOI: 10.1093/hr/uhad182, Horticulture Research, 10, 00, 1 10 2023. Abstract: Melon (Cucumis melo L.) is an important vegetable crop that has an extensive history of cultivation. However, the genome of wild and semi-wild melon types that can be used for the analysis of agronomic traits is not yet available. Here we report a chromosome-level T2T genome assembly for 821 (C. melo ssp. agrestis var. acidulus), a semi-wild melon with two haplotypes of ~373 Mb and ~364 Mb, respectively. Comparative genome analysis discovered a significant number of structural variants (SVs) between melo (C. melo ssp. melo) and agrestis (C. melo ssp. agrestis) genomes, including a copy number variation located in the ToLCNDV resistance locus on chromosome 11. Genome-wide association studies detected a significant signal associated with climacteric ripening and identified one candidate gene CM_ac12g14720.1 (CmABA2), encoding a cytoplasmic short chain dehydrogenase/reductase, which controls the biosynthesis of abscisic acid. This study provides valuable genetic resources for future research on melon breeding. Keywords: Creator: LaTeX with hyperref package Producer: Acrobat Distiller 23.0 (Windows) CreationDate: Fri Dec 15 14:30:29 CET 2023 ModDate: Fri Dec 15 14:30:29 CET 2023 ID: 0xe6c9213334c83e1fc66cb885879825bc, 0x822997e15a7a6d2f7f68c72fa5e4d84c Filters: FilterPipeline: FlateDecode FilterPipeline: DCTDecode Images: Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 1750 ImageHeight: 2199 ColorSpace: RGB BitsPerSample: 8 BitsPerSampleUnit: integer Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 2000 ImageHeight: 2237 ColorSpace: RGB BitsPerSample: 8 BitsPerSampleUnit: integer Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 2000 ImageHeight: 1943 ColorSpace: RGB BitsPerSample: 8 BitsPerSampleUnit: integer Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 2000 ImageHeight: 1827 ColorSpace: RGB BitsPerSample: 8 BitsPerSampleUnit: integer Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 2000 ImageHeight: 1913 ColorSpace: RGB BitsPerSample: 8 BitsPerSampleUnit: integer Fonts: Type1: Font: BaseFont: PPFNNL+CaeciliaLTStd-LightItalic FontSubset: true FirstChar: 40 LastChar: 121 FontDescriptor: FontName: PPFNNL+CaeciliaLTStd-LightItalic Flags: Serif, Symbolic, Italic FontBBox: -166, -267, 1033, 909 FontFile3: true EncodingDictionary: Differences: true ToUnicode: true Font: BaseFont: PPHDPE+CaeciliaLTStd-BoldItalic FontSubset: true FirstChar: 46 LastChar: 117 FontDescriptor: FontName: PPHDPE+CaeciliaLTStd-BoldItalic Flags: Serif, Symbolic, Italic, ForceBold FontBBox: -169, -273, 1082, 932 FontFile3: true EncodingDictionary: Differences: true ToUnicode: true Font: BaseFont: PPHECE+MTMI FontSubset: true FirstChar: 2 LastChar: 62 FontDescriptor: FontName: PPHECE+MTMI Flags: Serif, Symbolic, Italic FontBBox: 0, -213, 987, 680 FontFile3: true EncodingDictionary: Differences: true ToUnicode: true Font: BaseFont: PPFLKD+CaeciliaLTStd-Roman FontSubset: true FirstChar: 40 LastChar: 169 FontDescriptor: FontName: PPFLKD+CaeciliaLTStd-Roman Flags: Serif, Symbolic FontBBox: -167, -270, 1136, 926 FontFile3: true EncodingDictionary: Differences: true ToUnicode: true Font: BaseFont: PPFLKC+CaeciliaLTStd-Bold FontSubset: true FirstChar: 44 LastChar: 122 FontDescriptor: FontName: PPFLKC+CaeciliaLTStd-Bold Flags: Serif, Symbolic, ForceBold FontBBox: -166, -273, 1141, 938 FontFile3: true EncodingDictionary: Differences: true ToUnicode: true Font: BaseFont: PPFMAC+CaeciliaLTStd-Italic FontSubset: true FirstChar: 46 LastChar: 117 FontDescriptor: FontName: PPFMAC+CaeciliaLTStd-Italic Flags: Serif, Symbolic, Italic FontBBox: -166, -270, 1053, 915 FontFile3: true EncodingDictionary: Differences: true ToUnicode: true Font: BaseFont: PPFMGB+CaeciliaLTStd-Light FontSubset: true FirstChar: 37 LastChar: 243 FontDescriptor: FontName: PPFMGB+CaeciliaLTStd-Light Flags: Serif, Symbolic FontBBox: -164, -266, 1130, 908 FontFile3: true EncodingDictionary: Differences: true ToUnicode: true Font: BaseFont: PPFNKK+CaeciliaLTStd-Heavy FontSubset: true FirstChar: 46 LastChar: 124 FontDescriptor: FontName: PPFNKK+CaeciliaLTStd-Heavy Flags: Serif, Symbolic, ForceBold FontBBox: -170, -277, 1146, 970 FontFile3: true EncodingDictionary: Differences: true ToUnicode: true Font: BaseFont: PPFNKL+MTSYN FontSubset: true FirstChar: 2 LastChar: 215 FontDescriptor: FontName: PPFNKL+MTSYN Flags: Symbolic FontBBox: 0, -954, 1043, 900 FontFile3: true EncodingDictionary: Differences: true ToUnicode: true XMP: application/pdf The haplotype-resolved T2T reference genome highlights structural variation underlying agronomic traits of melon Li GuoliTang LingliHe YuhuaXu YongyangBendahmane AbdelhafidGarcia-Mas JordiLin TaoZhao Guangwei DOI: 10.1093/hr/uhad182, Horticulture Research, 10, 00, 1 10 2023. Abstract: Melon (Cucumis melo L.) is an important vegetable crop that has an extensive history of cultivation. However, the genome of wild and semi-wild melon types that can be used for the analysis of agronomic traits is not yet available. Here we report a chromosome-level T2T genome assembly for 821 (C. melo ssp. agrestis var. acidulus), a semi-wild melon with two haplotypes of ~373 Mb and ~364 Mb, respectively. Comparative genome analysis discovered a significant number of structural variants (SVs) between melo (C. melo ssp. melo) and agrestis (C. melo ssp. agrestis) genomes, including a copy number variation located in the ToLCNDV resistance locus on chromosome 11. Genome-wide association studies detected a significant signal associated with climacteric ripening and identified one candidate gene CM_ac12g14720.1 (CmABA2), encoding a cytoplasmic short chain dehydrogenase/reductase, which controls the biosynthesis of abscisic acid. This study provides valuable genetic resources for future research on melon breeding. © The Author(s) 2023. Published by Oxford University Press on behalf of Nanjing Agricultural University. 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