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| 1 | Haplotype-resolved genome assembly and allele- specific gene expression in cultivated ginger显示文摘Ginger(Zingiber officinale)is one of the most valued spice plants worldwide;it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance.Here,we present a haplotype-resolved,chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb.Remarkable structural variation was identified between haplotypes,and two inversions larger than 15Mb on chromosome 4 may be associated with ginger infertility.We performed a comprehensive,spatiotemporal,genome-wide analysis of allelic expression patterns,revealing that most alleles are coordinately expressed.The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements,greater coding sequence divergence,more relaxed selection pressure,and more transcription factor binding site differences.We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis.Our allele-aware assembly provides a powerful platform for future functional genomics,molecular breeding,and genome editing in ginger. | Shi-Ping Cheng Kai-Hua Jia Hui Liu Ren-Gang Zhang Zhi-Chao Li Shan-Shan Zhou Tian-Le Shi Ai-Chu Ma Cong-Wen Yu Chan Gao Guang-Lei Cao Wei Zhao Shuai Nie Jing-Fang Guo Si-Qian Jiao Xue-Chan Tian Xue-Mei Yan Yu-Tao Bao Quan-Zheng Yun Xin-Zhu Wang Ilga Porth Yousry AEl-Kassaby Xiao-Ru Wang Zhen Li Yves Van de Peer Jian-Feng Mao | 2021 | Horticulture Research2021，8，1： | 3 |
| 2 | Compilation of small ribosomal subunit RNA sequences显示文摘 | DAMS E HENDRIKS L VAN DE PEER Y | 1988 | Nucleic Acids Res1988，16，： | 1 |
| 3 | Choose your partners: dimerization in eukaryotic transcription factors显示文摘 | Grigoris D. Amoutzias David L. Robertson Yves Van de Peer Stephen G. Oliver | 2008 | Trends in Biochemical Sciences2008，，5： | 1 |
| 4 | Compilation of small ribosomal subunit RNA sequences显示文摘 | NEEFS J-M VAN DE PEER Y DE RIJK P | 1991 | Nucleic Acids Res1991，19，： | 1 |
| 5 | Compilation of small ribosomal subunit RNA structures显示文摘 | NEEFS J-M VAN DE PEER Y DE RIJK P | 1993 | Nucleic Acids Res1993，21，： | 1 |
| 6 | The indent reflow sealing(IRS) technique-A method for the Fabrication of sealed cavities for MEMS devices 显示文摘 | Harrie A C Tilmans Myriam D J Van de Peer Eric Beyne | 2000 | J Microelectromechan Systems2000，9，2： | 1 |
| 7 | Database on the structure of small ribosomal subunit RNA显示文摘 | VAN DE PEER Y VAN DEN BROECK DE RIJK P | 1994 | Nucleic Acids Res1994，22，： | 1 |
| 8 | Database on the structure of small ribosomal subunit RNA显示文摘 | VAN DE PEER Y NICOLAI S DE WACHTER R | 1996 | Nucleic Acids Res1996，24，： | 1 |
| 9 | Database on the structure of small ribosomal subunit RNA显示文摘 | VAN DE PEER Y CAERS A DE RIJK P | 1998 | Nucleic Acids Res1998，26，： | 1 |
| 10 | Database on the structure of small ribosomal subunit RNA显示文摘 | VAN DE PEER Y JANSEN J DE RIJK P | 1997 | Nucleic Acids Res1997，25，： | 1 |
| 11 | Database on the structure of small subunit ribosomal RNA显示文摘 | VAN DE PEER Y ROBBRECHT E DE HOOG S | 1999 | Nucleic Acids Res1999，27，： | 1 |
| 12 | The European ribosomal RNA database显示文摘 | WUYTS J PERRIERE G VAN DE PEER Y | 2004 | Nucleic Acids Res2004，32，： | 1 |
| 13 | Robust biomarker identification for cancer diagnosis with ensemble feature selection methods 显示文摘 | Abeel T Helleputte T Van De Peer Y | 2009 | Bioinformatics2009，26，3： | 1 |
| 14 | Characterization of root surface and endorhizosphere Pseudomonads in relation to their colonization of roots显示文摘 | van Peer R Punte H L de Weger L A | 1990 | Applied and Environmental Microbiology1990，56，8： | 1 |
| 15 | A quantitative map of nucleotide substitution rates in bacterial rRNA显示文摘 | Van de Peer Y Chapelle S De Wachter R | 1996 | Nucleic Acids Res1996，24，17： | 1 |
| 16 | Compilation of small ribosomal subunit RNA sequences显示文摘 | Neefs J M Van de Peer Y De Rijik P | 1991 | Nucleic Acids Res1991，19，： | 1 |
| 17 | Genome-wide structural annotation andevolutionary analysis of the type Ⅰ MADS-box genes in plants显示文摘 | DE BODT S RAES J FLORQUIN K ROMBAUTS S ROUZE P THESSEN G VAN DE PEER Y | 2003 | J Mol Evol2003，56，： | 1 |
| 18 | The small RNA world of plants显示文摘 | Bonnet E Van de Peer Y Rouz: P | 2006 | New Phytol2006，171，3： | 1 |
| 19 | TREECON for windows: a software package for construction and drawing of evolutionary trees for the microsoft windows environment 显示文摘 | PEER van der Y WACHTER de R | 1994 | Comput Appl Biosci1994，10，： | 1 |
| 20 | Redundancy and rewiring of genetic networks following genome-wide duplication e vents显示文摘 | DE SMET R VAN DE PEER Y | 2012 | Current Opinion in Plant Biology2012，15，2： | 1 |
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