4ad52e7ee9ee14c600869f83c816adb6 Gen_a2022v13n1p52iENG.pdf 3842460631955c073320abbaf120b0b02be8923e Gen_a2022v13n1p52iENG.pdf 6513632b2e92104d89a1d2876a209e738010b50e3e0e56376788f283d93a334c Gen_a2022v13n1p52iENG.pdf Title: Improved High-Quality Genome Assembly and Annotation of Pineapple (Ananas comosus) Cultivar MD2 Revealed Extensive Haplotype Diversity and Diversified FRS/FRF Gene Family Subject: Pineapple (Ananas comosus (L.) Merr.) is the second most important tropical fruit crop globally, and ‘MD2’ is the most important cultivated variety. A high-quality genome is important for molecular-based breeding, but available pineapple genomes still have some quality limitations. Here, PacBio and Hi-C data were used to develop a new high-quality MD2 assembly and gene prediction. Compared to the previous MD2 assembly, major improvements included a 26.6-fold increase in contig N50 length, phased chromosomes, and >6000 new genes. The new MD2 assembly also included 161.6 Mb additional sequences and >3000 extra genes compared to the F153 genome. Over 48% of the predicted genes harbored potential deleterious mutations, indicating that the high level of heterozygosity in this species contributes to maintaining functional alleles. The genome was used to characterize the FAR1-RELATED SEQUENCE (FRS) genes that were expanded in pineapple and rice. Transposed and dispersed duplications contributed to expanding the numbers of these genes in the pineapple lineage. Several AcFRS genes were differentially expressed among tissue-types and stages of flower development, suggesting that their expansion contributed to evolving specialized functions in reproductive tissues. The new MD2 assembly will serve as a new reference for genetic and genomic studies in pineapple. Keywords: pineapple MD2; Ananas comosus; improved assembly; haplotype diversity; FHY3/FAR1 genes; FRS/FRF genes Author: Ashley G. Yow, Hamed Bostan, Raúl Castanera, Valentino Ruggieri, Molla F. Mengist, Julien Curaba, Roberto Young, Nicholas Gillitt and Massimo Iorizzo Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Fri Dec 24 14:38:00 2021 CET ModDate: Fri Dec 24 15:22:56 2021 CET Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 20 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 3762019 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- CYOTZE+VnURWPalladioL Type 1 Custom yes yes no 10 0 LUJFPF+URWPalladioL-Bold Type 1 Custom yes yes no 15 0 GDDMON+URWPalladioL-Roma Type 1 Custom yes yes no 20 0 DGWYUA+URWPalladioL-Ital Type 1 Custom yes yes no 24 0 SAQRPE+URWPalladioL-BoldItal Type 1 Custom yes yes no 28 0 ENLEMO+VnURWPalladioL-Bold Type 1 Custom yes yes no 32 0 MCBCCI+SourceSansRoman-Regular Type 1C Custom yes yes no 40 0 MCBCCM+SourceSansRoman.613wght Type 1C Custom yes yes no 44 0 MCBCCO+SourceSansRoman-Bold Type 1C Custom yes yes no 48 0 KONDUX+EuphemiaUCAS-Bold Type 1C WinAnsi yes yes no 60 0 HIZBRM+TimesNewRomanPS-BoldItalicMT Type 1C WinAnsi yes yes no 63 0 YZIJXT+CMSY10 Type 1 Builtin yes yes no 85 0 Jhove (Rel. 1.22.1, 2019-04-17) Date: 2023-05-12 02:29:52 CEST RepresentationInformation: Gen_a2022v13n1p52iENG.pdf ReportingModule: PDF-hul, Rel. 1.12.1 (2019-04-17) LastModified: 2023-05-11 11:57:10 CEST Size: 3762019 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 420 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@44c8afef Item: Title: Materials and Methods Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7b69c6ba Children: Item: Title: Plant Material Collection, DNA and RNA Extraction, and Sequencing Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@46daef40 Item: Title: Genome Assembly, Phasing, and Scaffolding Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@12f41634 Item: Title: Assembly Error Correction and Gap-Filling Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@13c27452 Item: Title: Genome Quality Analysis Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@262b2c86 Item: Title: Genome Annotation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@371a67ec Item: Title: Haplotype Comparison Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5ed828d Item: Title: Identification and Characterization of FRS/FRF Transcription Factors Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@50d0686 Item: Title: Results and Discussion Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7a3d45bd Children: Item: Title: Genome Assembly and Quality Assessment Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1e7c7811 Item: Title: Genome Assembly Comparisons Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77ec78b9 Item: Title: Repetitive Sequence Annotation and Analysis Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1a3869f4 Item: Title: Gene Prediction and Annotation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@a38d7a3 Item: Title: Haplotype Comparison Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77f99a05 Item: Title: Characterization of FRS/FRF Family Transcription Factors Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@63440df3 Item: Title: Conclusions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@3aeaafa6 Item: Title: References Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@76a3e297 Info: Title: Improved High-Quality Genome Assembly and Annotation of Pineapple (Ananas comosus) Cultivar MD2 Revealed Extensive Haplotype Diversity and Diversified FRS/FRF Gene Family Author: Ashley G. Yow, Hamed Bostan, Raúl Castanera, Valentino Ruggieri, Molla F. Mengist, Julien Curaba, Roberto Young, Nicholas Gillitt and Massimo Iorizzo Subject: Pineapple (Ananas comosus (L.) Merr.) is the second most important tropical fruit crop globally, and ‘MD2’ is the most important cultivated variety. A high-quality genome is important for molecular-based breeding, but available pineapple genomes still have some quality limitations. Here, PacBio and Hi-C data were used to develop a new high-quality MD2 assembly and gene prediction. Compared to the previous MD2 assembly, major improvements included a 26.6-fold increase in contig N50 length, phased chromosomes, and >6000 new genes. The new MD2 assembly also included 161.6 Mb additional sequences and >3000 extra genes compared to the F153 genome. Over 48% of the predicted genes harbored potential deleterious mutations, indicating that the high level of heterozygosity in this species contributes to maintaining functional alleles. The genome was used to characterize the FAR1-RELATED SEQUENCE (FRS) genes that were expanded in pineapple and rice. Transposed and dispersed duplications contributed to expanding the numbers of these genes in the pineapple lineage. Several AcFRS genes were differentially expressed among tissue-types and stages of flower development, suggesting that their expansion contributed to evolving specialized functions in reproductive tissues. The new MD2 assembly will serve as a new reference for genetic and genomic studies in pineapple. Keywords: pineapple MD2; Ananas comosus; improved assembly; haplotype diversity; FHY3/FAR1 genes; FRS/FRF genes Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Fri Dec 24 14:38:00 CET 2021 ModDate: Fri Dec 24 15:22:56 CET 2021 ID: 0x90a038957edda1dec405bf1a186eddd8, 0x90a038957edda1dec405bf1a186eddd8 Filters: FilterPipeline: FlateDecode Fonts: Type1: Font: BaseFont: ENLEMO+VnURWPalladioL-Bold FontSubset: true FirstChar: 243 LastChar: 243 FontDescriptor: FontName: ENLEMO+VnURWPalladioL-Bold Flags: Symbolic FontBBox: -152, -301, 1000, 935 FontFile: true EncodingDictionary: Differences: true Font: BaseFont: GDDMON+URWPalladioL-Roma FontSubset: true FirstChar: 2 LastChar: 241 FontDescriptor: FontName: GDDMON+URWPalladioL-Roma Flags: Symbolic FontBBox: -166, -283, 1021, 943 FontFile: true EncodingDictionary: Differences: true Font: BaseFont: YZIJXT+CMSY10 FontSubset: true FirstChar: 0 LastChar: 48 FontDescriptor: FontName: YZIJXT+CMSY10 Flags: Symbolic FontBBox: -29, 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