The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

Zhangjun Fei and colleagues report the draft genome of a Chinese elite watermelon inbred line 97103 and resequencing of 20 diverse accessions that represent the three subspecies of Citrullus lunatus . Comparative genome-wide analyses identify the extent of genetic diversity and population structure...

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Published inNature genetics Vol. 45; no. 1; pp. 51 - 58
Main Authors Guo, Shaogui, Zhang, Jianguo, Sun, Honghe, Salse, Jerome, Lucas, William J, Zhang, Haiying, Zheng, Yi, Mao, Linyong, Ren, Yi, Wang, Zhiwen, Min, Jiumeng, Guo, Xiaosen, Murat, Florent, Ham, Byung-Kook, Zhang, Zhaoliang, Gao, Shan, Huang, Mingyun, Xu, Yimin, Zhong, Silin, Bombarely, Aureliano, Mueller, Lukas A, Zhao, Hong, He, Hongju, Zhang, Yan, Zhang, Zhonghua, Huang, Sanwen, Tan, Tao, Pang, Erli, Lin, Kui, Hu, Qun, Kuang, Hanhui, Ni, Peixiang, Wang, Bo, Liu, Jingan, Kou, Qinghe, Hou, Wenju, Zou, Xiaohua, Jiang, Jiao, Gong, Guoyi, Klee, Kathrin, Schoof, Heiko, Huang, Ying, Hu, Xuesong, Dong, Shanshan, Liang, Dequan, Wang, Juan, Wu, Kui, Xia, Yang, Zhao, Xiang, Zheng, Zequn, Xing, Miao, Liang, Xinming, Huang, Bangqing, Lv, Tian, Wang, Junyi, Yin, Ye, Yi, Hongping, Li, Ruiqiang, Wu, Mingzhu, Levi, Amnon, Zhang, Xingping, Giovannoni, James J, Wang, Jun, Li, Yunfu, Fei, Zhangjun, Xu, Yong
Format Journal Article
LanguageEnglish
Published New York Nature Publishing Group US 01.01.2013
Nature Publishing Group
Subjects
631/181/757
631/208/212
631/208/2491
Agriculture
Animal Genetics and Genomics
Biomedicine
Cancer Research
Chromosome Mapping
Chromosomes
Chromosomes, Plant
Citrullus - classification
Citrullus - genetics
Citrullus lanatus
Computational Biology - methods
Cultivars
DNA sequencing
Domestication
Evolution, Molecular
Food quality
Fruits
Gene Expression Profiling
Gene Expression Regulation, Plant
Gene Function
Genes
Genetic aspects
Genetic diversity
Genetic Variation
Genome, Plant
Genomes
Genomics
Haplotypes
High-Throughput Nucleotide Sequencing
Human Genetics
Life Sciences
Molecular Sequence Annotation
Molecular Sequence Data
Nucleotide sequencing
Phylogeny
Physiological aspects
Population structure
Quality
R&D
Repetitive Sequences, Nucleic Acid
Research & development
Ribosomal DNA
Transcriptome
Transfer RNA
Watermelons
France
United States
China
PLANT
DNA-SEQUENCES
DISTANCE
EVOLUTION
FRUIT
RNA-SEQ
MADS-BOX GENE
IDENTIFICATION
EXPRESSION
TOMATO
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Abstract Zhangjun Fei and colleagues report the draft genome of a Chinese elite watermelon inbred line 97103 and resequencing of 20 diverse accessions that represent the three subspecies of Citrullus lunatus . Comparative genome-wide analyses identify the extent of genetic diversity and population structure of watermelon germplasm. Watermelon, Citrullus lanatus , is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia watermelon cultivar 97103 (2 n = 2× = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an evolutionary scenario for the origin of the 11 watermelon chromosomes derived from a 7-chromosome paleohexaploid eudicot ancestor. Resequencing of 20 watermelon accessions representing three different C. lanatus subspecies produced numerous haplotypes and identified the extent of genetic diversity and population structure of watermelon germplasm. Genomic regions that were preferentially selected during domestication were identified. Many disease-resistance genes were also found to be lost during domestication. In addition, integrative genomic and transcriptomic analyses yielded important insights into aspects of phloem-based vascular signaling in common between watermelon and cucumber and identified genes crucial to valuable fruit-quality traits, including sugar accumulation and citrulline metabolism.
AbstractList Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia watermelon cultivar 97103 (2n = 2× = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an evolutionary scenario for the origin of the 11 watermelon chromosomes derived from a 7-chromosome paleohexaploid eudicot ancestor. Resequencing of 20 watermelon accessions representing three different C. lanatus subspecies produced numerous haplotypes and identified the extent of genetic diversity and population structure of watermelon germplasm. Genomic regions that were preferentially selected during domestication were identified. Many disease-resistance genes were also found to be lost during domestication. In addition, integrative genomic and transcriptomic analyses yielded important insights into aspects of phloem-based vascular signaling in common between watermelon and cucumber and identified genes crucial to valuable fruit-quality traits, including sugar accumulation and citrulline metabolism.
Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia watermelon cultivar 97103 (2n = 2x = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an evolutionary scenario for the origin of the 11 watermelon chromosomes derived from a 7-chromosome paleohexaploid eudicot ancestor. Resequencing of 20 watermelon accessions representing three different C. lanatus subspecies produced numerous haplotypes and identified the extent of genetic diversity and population structure of watermelon germplasm. Genomic regions that were preferentially selected during domestication were identified. Many disease-resistance genes were also found to be lost during domestication. In addition, integrative genomic and transcriptomic analyses yielded important insights into aspects of phloem-based vascular signaling in common between watermelon and cucumber and identified genes crucial to valuable fruit-quality traits, including sugar accumulation and citrulline metabolism.
Zhangjun Fei and colleagues report the draft genome of a Chinese elite watermelon inbred line 97103 and resequencing of 20 diverse accessions that represent the three subspecies of Citrullus lunatus . Comparative genome-wide analyses identify the extent of genetic diversity and population structure of watermelon germplasm. Watermelon, Citrullus lanatus , is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia watermelon cultivar 97103 (2 n = 2× = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an evolutionary scenario for the origin of the 11 watermelon chromosomes derived from a 7-chromosome paleohexaploid eudicot ancestor. Resequencing of 20 watermelon accessions representing three different C. lanatus subspecies produced numerous haplotypes and identified the extent of genetic diversity and population structure of watermelon germplasm. Genomic regions that were preferentially selected during domestication were identified. Many disease-resistance genes were also found to be lost during domestication. In addition, integrative genomic and transcriptomic analyses yielded important insights into aspects of phloem-based vascular signaling in common between watermelon and cucumber and identified genes crucial to valuable fruit-quality traits, including sugar accumulation and citrulline metabolism.
Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia watermelon cultivar 97103 (2n = 2x = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an evolutionary scenario for the origin of the 11 watermelon chromosomes derived from a 7-chromosome paleohexaploid eudicot ancestor. Resequencing of 20 watermelon accessions representing three different C. lanatus subspecies produced numerous haplotypes and identified the extent of genetic diversity and population structure of watermelon germplasm. Genomic regions that were preferentially selected during domestication were identified. Many diseaseresistance genes were also found to be lost during domestication. In addition, integrative genomic and transcriptomic analyses yielded important insights into aspects of phloem-based vascular signaling in common between watermelon and cucumber and identified genes crucial to valuable fruit-quality traits, including sugar accumulation and citrulline metabolism.
Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia watermelon cultivar 97103 (2n = 2× = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an evolutionary scenario for the origin of the 11 watermelon chromosomes derived from a 7-chromosome paleohexaploid eudicot ancestor. Resequencing of 20 watermelon accessions representing three different C. lanatus subspecies produced numerous haplotypes and identified the extent of genetic diversity and population structure of watermelon germplasm. Genomic regions that were preferentially selected during domestication were identified. Many disease-resistance genes were also found to be lost during domestication. In addition, integrative genomic and transcriptomic analyses yielded important insights into aspects of phloem-based vascular signaling in common between watermelon and cucumber and identified genes crucial to valuable fruit-quality traits, including sugar accumulation and citrulline metabolism.Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia watermelon cultivar 97103 (2n = 2× = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an evolutionary scenario for the origin of the 11 watermelon chromosomes derived from a 7-chromosome paleohexaploid eudicot ancestor. Resequencing of 20 watermelon accessions representing three different C. lanatus subspecies produced numerous haplotypes and identified the extent of genetic diversity and population structure of watermelon germplasm. Genomic regions that were preferentially selected during domestication were identified. Many disease-resistance genes were also found to be lost during domestication. In addition, integrative genomic and transcriptomic analyses yielded important insights into aspects of phloem-based vascular signaling in common between watermelon and cucumber and identified genes crucial to valuable fruit-quality traits, including sugar accumulation and citrulline metabolism.
Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia watermelon cultivar 97103 (2n = 2 = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an evolutionary scenario for the origin of the 11 watermelon chromosomes derived from a 7-chromosome paleohexaploid eudicot ancestor. Resequencing of 20 watermelon accessions representing three different C. lanatus subspecies produced numerous haplotypes and identified the extent of genetic diversity and population structure of watermelon germplasm. Genomic regions that were preferentially selected during domestication were identified. Many disease-resistance genes were also found to be lost during domestication. In addition, integrative genomic and transcriptomic analyses yielded important insights into aspects of phloem-based vascular signaling in common between watermelon and cucumber and identified genes crucial to valuable fruit-quality traits, including sugar accumulation and citrulline metabolism.
Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draftgenome sequence of the east Asia watermelon cultivar 97103 (2n = 2× = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an evolutionary scenario for the origin of the 11 watermelon chromosomes derived from a 7-chromosome paleohexaploid eudicot ancestor. Resequencing of 20 watermelon accessions representing three different C. lanatus subspecies produced numerous haplotypes and identified the extent of genetic diversity and population structure of watermelon germplasm. Genomic regions that were preferentially selected during domestication were identified. Many disease-resistance genes were also found to be lost during domestication. In addition, integrative genomic and transcriptomic analyses yielded important insights into aspects of phloem-based vascular signaling in common between watermelon and cucumber and identified genes crucial to valuable fruit-quality traits, including sugar accumulation and citrulline metabolism. [PUBLICATION ABSTRACT]
Audience Academic
Author Yin, Ye
Zhang, Zhaoliang
Wu, Kui
Gong, Guoyi
Zou, Xiaohua
Ham, Byung-Kook
Zhang, Yan
Jiang, Jiao
Huang, Ying
Wu, Mingzhu
Hu, Xuesong
Lin, Kui
Ni, Peixiang
Ren, Yi
Wang, Zhiwen
Li, Yunfu
Zheng, Yi
Schoof, Heiko
Huang, Mingyun
Bombarely, Aureliano
Zhao, Hong
Dong, Shanshan
Guo, Shaogui
He, Hongju
Wang, Bo
Zhang, Jianguo
Pang, Erli
Wang, Junyi
Levi, Amnon
Zhao, Xiang
Salse, Jerome
Lucas, William J
Xu, Yimin
Giovannoni, James J
Klee, Kathrin
Liang, Dequan
Hu, Qun
Li, Ruiqiang
Yi, Hongping
Murat, Florent
Hou, Wenju
Fei, Zhangjun
Huang, Sanwen
Liang, Xinming
Gao, Shan
Mao, Linyong
Xing, Miao
Lv, Tian
Zhang, Zhonghua
Kou, Qinghe
Kuang, Hanhui
Xu, Yong
Xia, Yang
Zhong, Silin
Wang, Jun
Wang, Juan
Guo, Xiaosen
Zhang, Xingping
Min, Jiumeng
Zheng, Zequn
Huang, Bangqing
Liu, Jingan
Sun, Honghe
Zhang, Haiying
Mueller, Lukas A
Tan, Tao
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DNA-SEQUENCES
DISTANCE
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FRUIT
RNA-SEQ
MADS-BOX GENE
IDENTIFICATION
EXPRESSION
TOMATO
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Snippet Zhangjun Fei and colleagues report the draft genome of a Chinese elite watermelon inbred line 97103 and resequencing of 20 diverse accessions that represent...
Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia...
Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draftgenome sequence of the east Asia...
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StartPage 51
SubjectTerms 631/181/757
631/208/212
631/208/2491
Agriculture
Animal Genetics and Genomics
Biomedicine
Cancer Research
Chromosome Mapping
Chromosomes
Chromosomes, Plant
Citrullus - classification
Citrullus - genetics
Citrullus lanatus
Computational Biology - methods
Cultivars
DNA sequencing
Domestication
Evolution, Molecular
Food quality
Fruits
Gene Expression Profiling
Gene Expression Regulation, Plant
Gene Function
Genes
Genetic aspects
Genetic diversity
Genetic Variation
Genome, Plant
Genomes
Genomics
Haplotypes
High-Throughput Nucleotide Sequencing
Human Genetics
Life Sciences
Molecular Sequence Annotation
Molecular Sequence Data
Nucleotide sequencing
Phylogeny
Physiological aspects
Population structure
Quality
R&D
Repetitive Sequences, Nucleic Acid
Research & development
Ribosomal DNA
Transcriptome
Transfer RNA
Watermelons
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Title The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions
URI https://link.springer.com/article/10.1038/ng.2470
https://www.ncbi.nlm.nih.gov/pubmed/23179023
https://www.proquest.com/docview/1282099907
https://www.proquest.com/docview/1273604783
https://www.proquest.com/docview/1291614240
https://hal.science/hal-01190670
Volume 45
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