A High-Quality Melon Genome Assembly Provides Insights into Genetic Basis of Fruit Trait Improvement
Accurate reference genomes have become indispensable tools for characterization of genetic and functional variations. Here we generated a high-quality assembly of the melon Payzawat using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic m...
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| Published in | iScience Vol. 22; pp. 16 - 27 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
20.12.2019
Elsevier |
| Subjects | |
| Online Access | Get full text |
| ISSN | 2589-0042 2589-0042 |
| DOI | 10.1016/j.isci.2019.10.049 |
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| Abstract | Accurate reference genomes have become indispensable tools for characterization of genetic and functional variations. Here we generated a high-quality assembly of the melon Payzawat using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. The final 12 chromosome-level scaffolds cover ∼94.13% of the estimated genome (398.57 Mb). Compared with the published DHL92 genome, our assembly exhibits a 157-fold increase in contig length and remarkable improvements in the assembly of centromeres and telomeres. Six genes within STHQF12.4 on pseudochromosome 12, identified from whole-genome comparison between Payzawat and DHL92, may explain a considerable proportion of the skin thickness. In addition, our population study showed that melon domesticated at multiple times from whole-genome perspective and melons in China are introduced from different routes. Selective sweeps underlying the genes related to desirable traits, haplotypes of alleles associated with agronomic traits, and the variants from resequencing data enable efficient breeding.
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•Provides a high-quality assembly for melon genome•Explains a considerable proportion of epidermis thickness•Melons in China are introduced from different routes•Haplotypes of alleles associated with agronomic traits enable efficient breeding
Biological Sciences; Genetics; Plant Genetics; Plant Evolution |
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| AbstractList | Accurate reference genomes have become indispensable tools for characterization of genetic and functional variations. Here we generated a high-quality assembly of the melon Payzawat using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. The final 12 chromosome-level scaffolds cover ∼94.13% of the estimated genome (398.57 Mb). Compared with the published DHL92 genome, our assembly exhibits a 157-fold increase in contig length and remarkable improvements in the assembly of centromeres and telomeres. Six genes within STHQF12.4 on pseudochromosome 12, identified from whole-genome comparison between Payzawat and DHL92, may explain a considerable proportion of the skin thickness. In addition, our population study showed that melon domesticated at multiple times from whole-genome perspective and melons in China are introduced from different routes. Selective sweeps underlying the genes related to desirable traits, haplotypes of alleles associated with agronomic traits, and the variants from resequencing data enable efficient breeding.
[Display omitted]
•Provides a high-quality assembly for melon genome•Explains a considerable proportion of epidermis thickness•Melons in China are introduced from different routes•Haplotypes of alleles associated with agronomic traits enable efficient breeding
Biological Sciences; Genetics; Plant Genetics; Plant Evolution Accurate reference genomes have become indispensable tools for characterization of genetic and functional variations. Here we generated a high-quality assembly of the melon Payzawat using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. The final 12 chromosome-level scaffolds cover ∼94.13% of the estimated genome (398.57 Mb). Compared with the published DHL92 genome, our assembly exhibits a 157-fold increase in contig length and remarkable improvements in the assembly of centromeres and telomeres. Six genes within STHQF12.4 on pseudochromosome 12, identified from whole-genome comparison between Payzawat and DHL92, may explain a considerable proportion of the skin thickness. In addition, our population study showed that melon domesticated at multiple times from whole-genome perspective and melons in China are introduced from different routes. Selective sweeps underlying the genes related to desirable traits, haplotypes of alleles associated with agronomic traits, and the variants from resequencing data enable efficient breeding.Accurate reference genomes have become indispensable tools for characterization of genetic and functional variations. Here we generated a high-quality assembly of the melon Payzawat using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. The final 12 chromosome-level scaffolds cover ∼94.13% of the estimated genome (398.57 Mb). Compared with the published DHL92 genome, our assembly exhibits a 157-fold increase in contig length and remarkable improvements in the assembly of centromeres and telomeres. Six genes within STHQF12.4 on pseudochromosome 12, identified from whole-genome comparison between Payzawat and DHL92, may explain a considerable proportion of the skin thickness. In addition, our population study showed that melon domesticated at multiple times from whole-genome perspective and melons in China are introduced from different routes. Selective sweeps underlying the genes related to desirable traits, haplotypes of alleles associated with agronomic traits, and the variants from resequencing data enable efficient breeding. Accurate reference genomes have become indispensable tools for characterization of genetic and functional variations. Here we generated a high-quality assembly of the melon Payzawat using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. The final 12 chromosome-level scaffolds cover ∼94.13% of the estimated genome (398.57 Mb). Compared with the published DHL92 genome, our assembly exhibits a 157-fold increase in contig length and remarkable improvements in the assembly of centromeres and telomeres. Six genes within STHQF12.4 on pseudochromosome 12, identified from whole-genome comparison between Payzawat and DHL92, may explain a considerable proportion of the skin thickness. In addition, our population study showed that melon domesticated at multiple times from whole-genome perspective and melons in China are introduced from different routes. Selective sweeps underlying the genes related to desirable traits, haplotypes of alleles associated with agronomic traits, and the variants from resequencing data enable efficient breeding. : Biological Sciences; Genetics; Plant Genetics; Plant Evolution Subject Areas: Biological Sciences, Genetics, Plant Genetics, Plant Evolution Accurate reference genomes have become indispensable tools for characterization of genetic and functional variations. Here we generated a high-quality assembly of the melon Payzawat using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. The final 12 chromosome-level scaffolds cover ∼94.13% of the estimated genome (398.57 Mb). Compared with the published DHL92 genome, our assembly exhibits a 157-fold increase in contig length and remarkable improvements in the assembly of centromeres and telomeres. Six genes within STHQF12.4 on pseudochromosome 12, identified from whole-genome comparison between Payzawat and DHL92, may explain a considerable proportion of the skin thickness. In addition, our population study showed that melon domesticated at multiple times from whole-genome perspective and melons in China are introduced from different routes. Selective sweeps underlying the genes related to desirable traits, haplotypes of alleles associated with agronomic traits, and the variants from resequencing data enable efficient breeding. Accurate reference genomes have become indispensable tools for characterization of genetic and functional variations. Here we generated a high-quality assembly of the melon Payzawat using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. The final 12 chromosome-level scaffolds cover ∼94.13% of the estimated genome (398.57 Mb). Compared with the published DHL92 genome, our assembly exhibits a 157-fold increase in contig length and remarkable improvements in the assembly of centromeres and telomeres. Six genes within STHQF12.4 on pseudochromosome 12, identified from whole-genome comparison between Payzawat and DHL92, may explain a considerable proportion of the skin thickness. In addition, our population study showed that melon domesticated at multiple times from whole-genome perspective and melons in China are introduced from different routes. Selective sweeps underlying the genes related to desirable traits, haplotypes of alleles associated with agronomic traits, and the variants from resequencing data enable efficient breeding. • Provides a high-quality assembly for melon genome • Explains a considerable proportion of epidermis thickness • Melons in China are introduced from different routes • Haplotypes of alleles associated with agronomic traits enable efficient breeding Biological Sciences; Genetics; Plant Genetics; Plant Evolution |
| Author | Li, Song Wang, Dengming Wang, Haojie Ji, Changmian Zhang, Hong Yu, Haiyan Li, Xuming Li, Meihua Liu, Min Zheng, Hongkun Yi, Hongping Ma, Liming Miao, Jianshun Fu, Qiushi Tang, Juan Zhang, Yongbing Wang, Huaisong |
| AuthorAffiliation | 3 Biomarker Technologies Corporation, Beijing 101200, China 2 The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China 1 Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China |
| AuthorAffiliation_xml | – name: 3 Biomarker Technologies Corporation, Beijing 101200, China – name: 2 The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China – name: 1 Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China |
| Author_xml | – sequence: 1 givenname: Hong surname: Zhang fullname: Zhang, Hong organization: Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China – sequence: 2 givenname: Xuming surname: Li fullname: Li, Xuming organization: Biomarker Technologies Corporation, Beijing 101200, China – sequence: 3 givenname: Haiyan surname: Yu fullname: Yu, Haiyan organization: Biomarker Technologies Corporation, Beijing 101200, China – sequence: 4 givenname: Yongbing surname: Zhang fullname: Zhang, Yongbing organization: Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China – sequence: 5 givenname: Meihua surname: Li fullname: Li, Meihua organization: Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China – sequence: 6 givenname: Haojie surname: Wang fullname: Wang, Haojie organization: Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China – sequence: 7 givenname: Dengming surname: Wang fullname: Wang, Dengming organization: Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China – sequence: 8 givenname: Huaisong surname: Wang fullname: Wang, Huaisong organization: The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China – sequence: 9 givenname: Qiushi surname: Fu fullname: Fu, Qiushi organization: The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China – sequence: 10 givenname: Min surname: Liu fullname: Liu, Min organization: Biomarker Technologies Corporation, Beijing 101200, China – sequence: 11 givenname: Changmian surname: Ji fullname: Ji, Changmian organization: Biomarker Technologies Corporation, Beijing 101200, China – sequence: 12 givenname: Liming surname: Ma fullname: Ma, Liming organization: Biomarker Technologies Corporation, Beijing 101200, China – sequence: 13 givenname: Juan surname: Tang fullname: Tang, Juan organization: Biomarker Technologies Corporation, Beijing 101200, China – sequence: 14 givenname: Song surname: Li fullname: Li, Song organization: Biomarker Technologies Corporation, Beijing 101200, China – sequence: 15 givenname: Jianshun surname: Miao fullname: Miao, Jianshun organization: Biomarker Technologies Corporation, Beijing 101200, China – sequence: 16 givenname: Hongkun surname: Zheng fullname: Zheng, Hongkun email: zhenghk@biomarker.com.cn organization: Biomarker Technologies Corporation, Beijing 101200, China – sequence: 17 givenname: Hongping surname: Yi fullname: Yi, Hongping email: hpyi1223@163.com organization: Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China |
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| Cites_doi | 10.1023/A:1016086206423 10.1111/tpj.13838 10.1038/srep31900 10.1093/mp/sss121 10.1126/science.1159023 10.1038/ncomms5026 10.1111/pbi.12484 10.1126/science.aac8370 10.3389/fpls.2017.01679 10.1007/s00122-017-2928-y 10.1038/nature21370 10.1038/ng.3839 10.1038/s41467-019-09142-9 10.5511/plantbiotechnology.13.0813a 10.1002/ajb2.1172 10.1016/S1360-1385(01)02045-3 10.1186/1471-2229-11-111 10.1186/s13059-015-0767-1 10.1111/pbi.12737 10.1126/science.aae0344 10.1038/s41467-019-09518-x 10.1093/bioinformatics/btv351 10.1270/jsbbs.55.197 10.1038/s41598-018-26416-2 10.1371/journal.pone.0096537 10.1101/gr.215087.116 10.1111/tpj.12814 10.1038/s41588-018-0182-0 10.1038/ng.3802 10.1007/s00425-004-1246-1 10.1111/tpj.13596 10.1073/pnas.1205415109 10.1186/s12864-014-1196-3 |
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| Keywords | Plant Evolution Biological Sciences Genetics Plant Genetics |
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| References | Jeon, Cho, Park, Han, Choi, Ko (bib20) 2016; 14 Akdemir, Chin (bib2) 2015; 16 Garcia-Mas, Benjak, Sanseverino, Bourgeois, Mir, González, Hénaff, Câmara, Cozzuto, Lowy (bib17) 2012; 109 Kitamura (bib21) 1951; 14 Koren, Walenz, Berlin, Miller, Bergman, Phillippy (bib22) 2017; 27 Tzuri, Zhou, Chayut, Yuan, Portnoy, Meir, Sa'ar, Baumkoler, Mazourek, Lewinsohn (bib29) 2015; 82 Galpaz, Gonda, Shem-Tov, Barad, Tzuri, Lev, Fei, Xu, Mao, Jiao, Harel-Beja (bib16) 2018; 94 Akashi, Fukuda, Wako, Masuda, Kato (bib1) 2002; 125 Boualem, Fergany, Fernandez, Troadec, Martin, Morin, Sari, Collin, Flowers, Pitrat (bib9) 2008; 321 Feder, Burger, Gao, Lewinsohn, Katzir, Schaffer, Meir, Davidovich-Rikanati, Portnoy, Gal-On (bib15) 2015; 169 Diaz, Fergany, Formisano, Ziarsolo, Blanca, Fei, Staub, Zalapa, Cuevas, Dace (bib6) 2011; 11 Xie, Chung, Li, Wong, Wang, Liu, Wang, Leung, Wong, Tong (bib31) 2019; 10 Gordon, Huddleston, Chaisson, Hill, Kronenberg, Munson, Malig, Raja, Fiddes, Hillier (bib18) 2016; 352 Wang, Xu, Zhang, Cao, Huang, Cheng, Wu, Tian, Chen, Liu (bib30) 2017; 49 Argyris, Díaz, Ruggieri, Fernández, Jahrmann, Gibon, Picó, Martín-Hernández, Monforte, Garcia-Mas (bib5) 2017; 8 Bai, Xiao, Zhao, Song, Hu, Zeng, Li, Hou, Luo, Li, Pei (bib7) 2014; 9 Endl, Achigandako, Pandey, Monforte, Pico, Schaefer (bib14) 2018; 105 Zhang, Hu, Han, Gao, Richards, Zhang, Tian, Liu, Gul (bib35) 2019; 10 Micheli (bib23) 2001; 6 Alqsous, Carpentier, Kleineude, Burel, Mareck, Dauchel, Gomord, Balangé (bib3) 2004; 219 Bickhart, Rosen, Koren, Sayre, Hastie, Chan, Lee, Lam, Liachko, Sullivan (bib8) 2017; 49 Pitrat (bib24) 2013; 30 Yang, Huang, Xiong, Xian, Su, Ren, Li (bib32) 2017; 15 Yashiro, Iwata, Akashi, Tomita, Kuzuya, Tsumura, Kato (bib33) 2005; 55 Jarvis, Ho, Lightfoot, Schmockel, Li, Borm, Ohyanagi, Mineta, Michell, Saber (bib19) 2017; 542 Ríos, Argyris, Vegas, Leida, Kenigswald, Tzuri, Troadec, Bendahmane, Katzir, Picó (bib25) 2017; 91 Cohen, Itkin, Yeselson, Tzuri, Portnoy, Harel-Baja, Lev, Sa'ar, Davidovitz-Rikanati, Baranes (bib12) 2014; 5 Simao, Waterhouse, Ioannidis, Kriventseva, Zdobnov (bib27) 2015; 31 Argyris, Ruiz-Herrera, Madriz-Masis, Sanseverino, Morata, Pujol, Ramos-Onsins, Garcia-Mas (bib4) 2015; 16 Ye, Hill, Wu, Ruan, Ma (bib34) 2016; 6 Ruggieri, Alexiou, Morata, Argyris, Pujol, Yano, Nonaka, Ezura, Latrasse, Boualem (bib26) 2018; 8 Brotman, Normantovich, Goldenberg, Zvirin, Kovalski, Stovbun, Doniger, Bolger, Troadec, Bendahmane (bib11) 2013; 6 Boualem, Troadec, Céline, Lemhemdi, Morin, Sari, Fraenkel-Zagouri, Kovalski, Dogimont, Perl-Treves, Bendahmane (bib10) 2015; 350 Diaz, Martinhernandez, Dolcetsanjuan, Garcesclaver, Alvarez, Garciamas, Monforte (bib13) 2017; 130 Sun, Zhou, Chen, Shi, Zhao, Zhao, Song, Zhang, Cui, Dong (bib28) 2018; 50 Xie (10.1016/j.isci.2019.10.049_bib31) 2019; 10 Sun (10.1016/j.isci.2019.10.049_bib28) 2018; 50 Boualem (10.1016/j.isci.2019.10.049_bib9) 2008; 321 Boualem (10.1016/j.isci.2019.10.049_bib10) 2015; 350 Koren (10.1016/j.isci.2019.10.049_bib22) 2017; 27 Ríos (10.1016/j.isci.2019.10.049_bib25) 2017; 91 Zhang (10.1016/j.isci.2019.10.049_bib35) 2019; 10 Diaz (10.1016/j.isci.2019.10.049_bib13) 2017; 130 Galpaz (10.1016/j.isci.2019.10.049_bib16) 2018; 94 Feder (10.1016/j.isci.2019.10.049_bib15) 2015; 169 Kitamura (10.1016/j.isci.2019.10.049_bib21) 1951; 14 Simao (10.1016/j.isci.2019.10.049_bib27) 2015; 31 Yang (10.1016/j.isci.2019.10.049_bib32) 2017; 15 Akashi (10.1016/j.isci.2019.10.049_bib1) 2002; 125 Wang (10.1016/j.isci.2019.10.049_bib30) 2017; 49 Tzuri (10.1016/j.isci.2019.10.049_bib29) 2015; 82 Argyris (10.1016/j.isci.2019.10.049_bib5) 2017; 8 Bickhart (10.1016/j.isci.2019.10.049_bib8) 2017; 49 Akdemir (10.1016/j.isci.2019.10.049_bib2) 2015; 16 Argyris (10.1016/j.isci.2019.10.049_bib4) 2015; 16 Cohen (10.1016/j.isci.2019.10.049_bib12) 2014; 5 Ruggieri (10.1016/j.isci.2019.10.049_bib26) 2018; 8 Jeon (10.1016/j.isci.2019.10.049_bib20) 2016; 14 Micheli (10.1016/j.isci.2019.10.049_bib23) 2001; 6 Diaz (10.1016/j.isci.2019.10.049_bib6) 2011; 11 Jarvis (10.1016/j.isci.2019.10.049_bib19) 2017; 542 Alqsous (10.1016/j.isci.2019.10.049_bib3) 2004; 219 Pitrat (10.1016/j.isci.2019.10.049_bib24) 2013; 30 Gordon (10.1016/j.isci.2019.10.049_bib18) 2016; 352 Endl (10.1016/j.isci.2019.10.049_bib14) 2018; 105 Garcia-Mas (10.1016/j.isci.2019.10.049_bib17) 2012; 109 Bai (10.1016/j.isci.2019.10.049_bib7) 2014; 9 Brotman (10.1016/j.isci.2019.10.049_bib11) 2013; 6 Yashiro (10.1016/j.isci.2019.10.049_bib33) 2005; 55 Ye (10.1016/j.isci.2019.10.049_bib34) 2016; 6 |
| References_xml | – volume: 219 start-page: 369 year: 2004 end-page: 378 ident: bib3 article-title: Identification and isolation of a pectin methylesterase isoform that could be involved in flax cell wall stiffening publication-title: Planta – volume: 321 start-page: 836 year: 2008 end-page: 838 ident: bib9 article-title: A conserved mutation in an ethylene biosynthesis enzyme leads to andromonoecy in melons publication-title: Science – volume: 6 start-page: 414 year: 2001 end-page: 419 ident: bib23 article-title: Pectin methylesterases: cell wall enzymes with important roles in plant physiology publication-title: Trends Plant Sci. – volume: 16 start-page: 198 year: 2015 ident: bib2 article-title: HiCPlotter integrates genomic data with interaction matrices publication-title: Genome Biol. – volume: 130 start-page: 1837 year: 2017 end-page: 1856 ident: bib13 article-title: Quantitative trait loci analysis of melon ( publication-title: Theor. Appl. Genet. – volume: 8 start-page: 8088 year: 2018 ident: bib26 article-title: An improved assembly and annotation of the melon ( publication-title: Sci. Rep. – volume: 94 start-page: 169 year: 2018 end-page: 191 ident: bib16 article-title: Deciphering genetic factors that determine melon fruit-quality traits using RNA-seq-based high-resolution QTL and eQTL mapping publication-title: Plant J. – volume: 169 start-page: 1714 year: 2015 end-page: 1726 ident: bib15 article-title: A Kelch domain-containing F-box coding gene negatively regulates flavonoid accumulation in publication-title: Plant Physiol. – volume: 10 start-page: 1494 year: 2019 ident: bib35 article-title: A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour publication-title: Nat. Commun. – volume: 15 start-page: 1544 year: 2017 end-page: 1555 ident: bib32 article-title: Silencing of SlPL, which encodes a pectate lyase in tomato, confers enhanced fruit firmness, prolonged shelf-life and reduced susceptibility to grey mould publication-title: Plant Biotechnol. J. – volume: 9 start-page: e96537 year: 2014 ident: bib7 article-title: Gibberellin overproduction promotes sucrose synthase expression and secondary cell wall deposition in cotton fibers publication-title: PLoS One – volume: 109 start-page: 11872 year: 2012 ident: bib17 article-title: The genome of melon ( publication-title: Proc. Natl. Acad. Sci. U S A – volume: 82 start-page: 267 year: 2015 end-page: 279 ident: bib29 article-title: A 'golden' SNP in CmOr governs the fruit flesh color of melon ( publication-title: Plant J. Cell Mol. Biol. – volume: 49 start-page: 643 year: 2017 end-page: 650 ident: bib8 article-title: Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome publication-title: Nat. Genet. – volume: 50 start-page: 1289 year: 2018 end-page: 1295 ident: bib28 article-title: Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes publication-title: Nat. Genet. – volume: 16 start-page: 4 year: 2015 ident: bib4 article-title: Use of targeted SNP selection for an improved anchoring of the melon ( publication-title: BMC Genomics – volume: 352 start-page: aae0344 year: 2016 ident: bib18 article-title: Long-read sequence assembly of the gorilla genome publication-title: Science – volume: 350 start-page: 688 year: 2015 end-page: 691 ident: bib10 article-title: A cucurbit androecy gene reveals how unisexual flowers develop and dioecy emerges publication-title: Science – volume: 27 start-page: 722 year: 2017 end-page: 736 ident: bib22 article-title: Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation publication-title: Genome Res. – volume: 49 start-page: 765 year: 2017 end-page: 772 ident: bib30 article-title: Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction publication-title: Nat. Genet. – volume: 10 start-page: 1 year: 2019 end-page: 12 ident: bib31 article-title: A reference-grade wild soybean genome publication-title: Nat. Commun. – volume: 8 start-page: 1679 year: 2017 ident: bib5 article-title: QTL analyses in multiple populations employed for the fine mapping and identification of candidate genes at a locus affecting sugar accumulation in melon ( publication-title: Front. Plant Sci. – volume: 105 start-page: 1662 year: 2018 end-page: 1671 ident: bib14 article-title: Repeated domestication of melon ( publication-title: Am. J. Bot. – volume: 5 start-page: 4026 year: 2014 ident: bib12 article-title: The PH gene determines fruit acidity and contributes to the evolution of sweet melons publication-title: Nat. Commun. – volume: 91 start-page: 671 year: 2017 end-page: 683 ident: bib25 article-title: ETHQV6.3 is involved in melon climacteric fruit ripening and is encoded by a NAC domain transcription factor publication-title: Plant J. – volume: 31 start-page: 3210 year: 2015 end-page: 3212 ident: bib27 article-title: 1,440 BUSCO embryophyta subset of genes: assessing genome assembly and annotation completeness with single-copy orthologs publication-title: Bioinformatics – volume: 6 start-page: 31900 year: 2016 ident: bib34 article-title: DBG2OLC: efficient assembly of large genomes using long erroneous reads of the third generation sequencing technologies publication-title: Sci. Rep. – volume: 125 start-page: 385 year: 2002 end-page: 396 ident: bib1 article-title: Genetic variation and phylogenetic relationships in East and South Asian melons, publication-title: Euphytica – volume: 30 start-page: 273 year: 2013 end-page: 278 ident: bib24 article-title: Phenotypic diversity in wild and cultivated melons ( publication-title: Plant Biotechnol. – volume: 55 start-page: 197 year: 2005 end-page: 206 ident: bib33 article-title: Genetic relationship among East and South Asian melon ( publication-title: Breed. Sci. – volume: 542 start-page: 307 year: 2017 end-page: 312 ident: bib19 article-title: The genome of publication-title: Nature – volume: 14 start-page: 1161 year: 2016 end-page: 1170 ident: bib20 article-title: Developing xylem-preferential expression of PdGA20ox1, a gibberellin 20-oxidase 1 from publication-title: Plant Biotechnol. J. – volume: 14 start-page: 81 year: 1951 end-page: 86 ident: bib21 article-title: The origin of cultivated plants of China publication-title: Acta Phyotaxon. Geobot. – volume: 6 start-page: 235 year: 2013 end-page: 238 ident: bib11 article-title: Dual resistance of melon to publication-title: Mol. Plant – volume: 11 start-page: 111 year: 2011 ident: bib6 article-title: A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon ( publication-title: BMC Plant Biol. – volume: 125 start-page: 385 year: 2002 ident: 10.1016/j.isci.2019.10.049_bib1 article-title: Genetic variation and phylogenetic relationships in East and South Asian melons, Cucumis melo L. based on the analysis of five isozymes publication-title: Euphytica doi: 10.1023/A:1016086206423 – volume: 94 start-page: 169 year: 2018 ident: 10.1016/j.isci.2019.10.049_bib16 article-title: Deciphering genetic factors that determine melon fruit-quality traits using RNA-seq-based high-resolution QTL and eQTL mapping publication-title: Plant J. doi: 10.1111/tpj.13838 – volume: 6 start-page: 31900 year: 2016 ident: 10.1016/j.isci.2019.10.049_bib34 article-title: DBG2OLC: efficient assembly of large genomes using long erroneous reads of the third generation sequencing technologies publication-title: Sci. Rep. doi: 10.1038/srep31900 – volume: 6 start-page: 235 year: 2013 ident: 10.1016/j.isci.2019.10.049_bib11 article-title: Dual resistance of melon to Fusarium oxysporum races 0 and 2 and to papaya ring-spot virus is controlled by a pair of head-to-head-oriented NB-LRR genes of unusual architecture publication-title: Mol. Plant doi: 10.1093/mp/sss121 – volume: 321 start-page: 836 year: 2008 ident: 10.1016/j.isci.2019.10.049_bib9 article-title: A conserved mutation in an ethylene biosynthesis enzyme leads to andromonoecy in melons publication-title: Science doi: 10.1126/science.1159023 – volume: 5 start-page: 4026 year: 2014 ident: 10.1016/j.isci.2019.10.049_bib12 article-title: The PH gene determines fruit acidity and contributes to the evolution of sweet melons publication-title: Nat. Commun. doi: 10.1038/ncomms5026 – volume: 14 start-page: 1161 year: 2016 ident: 10.1016/j.isci.2019.10.049_bib20 article-title: Developing xylem-preferential expression of PdGA20ox1, a gibberellin 20-oxidase 1 from Pinus densiflora, improves woody biomass production in a hybrid poplar publication-title: Plant Biotechnol. J. doi: 10.1111/pbi.12484 – volume: 169 start-page: 1714 year: 2015 ident: 10.1016/j.isci.2019.10.049_bib15 article-title: A Kelch domain-containing F-box coding gene negatively regulates flavonoid accumulation in Cucumis melo L publication-title: Plant Physiol. – volume: 350 start-page: 688 year: 2015 ident: 10.1016/j.isci.2019.10.049_bib10 article-title: A cucurbit androecy gene reveals how unisexual flowers develop and dioecy emerges publication-title: Science doi: 10.1126/science.aac8370 – volume: 8 start-page: 1679 year: 2017 ident: 10.1016/j.isci.2019.10.049_bib5 article-title: QTL analyses in multiple populations employed for the fine mapping and identification of candidate genes at a locus affecting sugar accumulation in melon (Cucumis melo L.) publication-title: Front. Plant Sci. doi: 10.3389/fpls.2017.01679 – volume: 130 start-page: 1837 year: 2017 ident: 10.1016/j.isci.2019.10.049_bib13 article-title: Quantitative trait loci analysis of melon (Cucumis melo L.) domestication-related traits publication-title: Theor. Appl. Genet. doi: 10.1007/s00122-017-2928-y – volume: 542 start-page: 307 year: 2017 ident: 10.1016/j.isci.2019.10.049_bib19 article-title: The genome of Chenopodium quinoa publication-title: Nature doi: 10.1038/nature21370 – volume: 49 start-page: 765 year: 2017 ident: 10.1016/j.isci.2019.10.049_bib30 article-title: Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction publication-title: Nat. Genet. doi: 10.1038/ng.3839 – volume: 10 start-page: 1 year: 2019 ident: 10.1016/j.isci.2019.10.049_bib31 article-title: A reference-grade wild soybean genome publication-title: Nat. Commun. doi: 10.1038/s41467-019-09142-9 – volume: 30 start-page: 273 year: 2013 ident: 10.1016/j.isci.2019.10.049_bib24 article-title: Phenotypic diversity in wild and cultivated melons (Cucumis melo) publication-title: Plant Biotechnol. doi: 10.5511/plantbiotechnology.13.0813a – volume: 105 start-page: 1662 year: 2018 ident: 10.1016/j.isci.2019.10.049_bib14 article-title: Repeated domestication of melon (Cucumis melo) in Africa and Asia and a new close relative from India publication-title: Am. J. Bot. doi: 10.1002/ajb2.1172 – volume: 14 start-page: 81 year: 1951 ident: 10.1016/j.isci.2019.10.049_bib21 article-title: The origin of cultivated plants of China publication-title: Acta Phyotaxon. Geobot. – volume: 6 start-page: 414 year: 2001 ident: 10.1016/j.isci.2019.10.049_bib23 article-title: Pectin methylesterases: cell wall enzymes with important roles in plant physiology publication-title: Trends Plant Sci. doi: 10.1016/S1360-1385(01)02045-3 – volume: 11 start-page: 111 year: 2011 ident: 10.1016/j.isci.2019.10.049_bib6 article-title: A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.) publication-title: BMC Plant Biol. doi: 10.1186/1471-2229-11-111 – volume: 16 start-page: 198 year: 2015 ident: 10.1016/j.isci.2019.10.049_bib2 article-title: HiCPlotter integrates genomic data with interaction matrices publication-title: Genome Biol. doi: 10.1186/s13059-015-0767-1 – volume: 15 start-page: 1544 year: 2017 ident: 10.1016/j.isci.2019.10.049_bib32 article-title: Silencing of SlPL, which encodes a pectate lyase in tomato, confers enhanced fruit firmness, prolonged shelf-life and reduced susceptibility to grey mould publication-title: Plant Biotechnol. J. doi: 10.1111/pbi.12737 – volume: 352 start-page: aae0344 year: 2016 ident: 10.1016/j.isci.2019.10.049_bib18 article-title: Long-read sequence assembly of the gorilla genome publication-title: Science doi: 10.1126/science.aae0344 – volume: 10 start-page: 1494 year: 2019 ident: 10.1016/j.isci.2019.10.049_bib35 article-title: A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour publication-title: Nat. Commun. doi: 10.1038/s41467-019-09518-x – volume: 31 start-page: 3210 year: 2015 ident: 10.1016/j.isci.2019.10.049_bib27 article-title: 1,440 BUSCO embryophyta subset of genes: assessing genome assembly and annotation completeness with single-copy orthologs publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv351 – volume: 55 start-page: 197 year: 2005 ident: 10.1016/j.isci.2019.10.049_bib33 article-title: Genetic relationship among East and South Asian melon (Cucumis melo L.) revealed by AFLP analysis publication-title: Breed. Sci. doi: 10.1270/jsbbs.55.197 – volume: 8 start-page: 8088 year: 2018 ident: 10.1016/j.isci.2019.10.049_bib26 article-title: An improved assembly and annotation of the melon (Cucumis melo L.) reference genome publication-title: Sci. Rep. doi: 10.1038/s41598-018-26416-2 – volume: 9 start-page: e96537 year: 2014 ident: 10.1016/j.isci.2019.10.049_bib7 article-title: Gibberellin overproduction promotes sucrose synthase expression and secondary cell wall deposition in cotton fibers publication-title: PLoS One doi: 10.1371/journal.pone.0096537 – volume: 27 start-page: 722 year: 2017 ident: 10.1016/j.isci.2019.10.049_bib22 article-title: Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation publication-title: Genome Res. doi: 10.1101/gr.215087.116 – volume: 82 start-page: 267 year: 2015 ident: 10.1016/j.isci.2019.10.049_bib29 article-title: A 'golden' SNP in CmOr governs the fruit flesh color of melon (Cucumis melo) publication-title: Plant J. Cell Mol. Biol. doi: 10.1111/tpj.12814 – volume: 50 start-page: 1289 year: 2018 ident: 10.1016/j.isci.2019.10.049_bib28 article-title: Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes publication-title: Nat. Genet. doi: 10.1038/s41588-018-0182-0 – volume: 49 start-page: 643 year: 2017 ident: 10.1016/j.isci.2019.10.049_bib8 article-title: Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome publication-title: Nat. Genet. doi: 10.1038/ng.3802 – volume: 219 start-page: 369 year: 2004 ident: 10.1016/j.isci.2019.10.049_bib3 article-title: Identification and isolation of a pectin methylesterase isoform that could be involved in flax cell wall stiffening publication-title: Planta doi: 10.1007/s00425-004-1246-1 – volume: 91 start-page: 671 year: 2017 ident: 10.1016/j.isci.2019.10.049_bib25 article-title: ETHQV6.3 is involved in melon climacteric fruit ripening and is encoded by a NAC domain transcription factor publication-title: Plant J. doi: 10.1111/tpj.13596 – volume: 109 start-page: 11872 year: 2012 ident: 10.1016/j.isci.2019.10.049_bib17 article-title: The genome of melon (Cucumis melo L.) publication-title: Proc. Natl. Acad. Sci. U S A doi: 10.1073/pnas.1205415109 – volume: 16 start-page: 4 year: 2015 ident: 10.1016/j.isci.2019.10.049_bib4 article-title: Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly publication-title: BMC Genomics doi: 10.1186/s12864-014-1196-3 |
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| Title | A High-Quality Melon Genome Assembly Provides Insights into Genetic Basis of Fruit Trait Improvement |
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