Genome sequence of the date palm Phoenix dactylifera L

Ibrahim S. Al-Mssallem; Songnian Hu; Xiaowei Zhang; Qiang Lin; Wanfei Liu; Jun Tan; Xiaoguang Yu; Jiucheng Liu; Linlin Pan; Tongwu Zhang; Yuxin Yin; Chengqi Xin; Hao Wu; Guangyu Zhang; Mohammed M. Ba Abdullah; Dawei Huang; Yongjun Fang; Yasser O. Alnakhli; Shangang Jia; An Yin; Eman M. Alhuzimi; Burair A. Alsaihati; Saad A. Al-Owayyed; Duojun Zhao; Sun Zhang; Noha A. Al-Otaibi; Gaoyuan Sun; Majed A. Majrashi; Fusen Li; Jixiang Wang; Quanzheng Yun; Nafla A. Alnassar; Lei Wang; Meng Yang; Rasha F. Al-Jelaify; Kan Liu; Shenghan Gao; Kaifu Chen; Samiyah R. Alkhaldi; Guiming Liu; Meng Zhang; Haiyan Guo; Jun Yu

doi:10.1038/ncomms3274

Genome sequence of the date palm Phoenix dactylifera L

Ibrahim S. Al-Mssallem, Songnian Hu, Xiaowei Zhang, Qiang Lin, Wanfei Liu, Jun Tan, Xiaoguang Yu, Jiucheng Liu, Linlin Pan, Tongwu Zhang, Yuxin Yin, Chengqi Xin, Hao Wu, Guangyu Zhang, Mohammed M. Ba Abdullah, Dawei Huang, Yongjun Fang, Yasser O. Alnakhli, Shangang Jia, An YinEman M. Alhuzimi, Burair A. Alsaihati, Saad A. Al-Owayyed, Duojun Zhao, Sun Zhang, Noha A. Al-Otaibi, Gaoyuan Sun, Majed A. Majrashi, Fusen Li, Jixiang Wang, Quanzheng Yun, Nafla A. Alnassar, Lei Wang, Meng Yang, Rasha F. Al-Jelaify, Kan Liu, Shenghan Gao, Kaifu Chen, Samiyah R. Alkhaldi, Guiming Liu, Meng Zhang, Haiyan Guo, Jun Yu

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228 Scopus citations

Abstract

Date palm (Phoenix dactylifera L.) is a cultivated woody plant species with agricultural and economic importance. Here we report a genome assembly for an elite variety (Khalas), which is 605.4 Mb in size and covers >90% of the genome (∼671 Mb) and >96% of its genes (∼41,660 genes). Genomic sequence analysis demonstrates that P. dactylifera experienced a clear genome-wide duplication after either ancient whole genome duplications or massive segmental duplications. Genetic diversity analysis indicates that its stress resistance and sugar metabolism-related genes tend to be enriched in the chromosomal regions where the density of single-nucleotide polymorphisms is relatively low. Using transcriptomic data, we also illustrate the date palm's unique sugar metabolism that underlies fruit development and ripening. Our large-scale genomic and transcriptomic data pave the way for further genomic studies not only on P. dactylifera but also other Arecaceae plants.

Original language	English (US)
Article number	2274
Journal	Nature Communications
Volume	4
DOIs	https://doi.org/10.1038/ncomms3274
State	Published - 2013

ASJC Scopus subject areas

Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)
Physics and Astronomy(all)

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Al-Mssallem, IS, Hu, S, Zhang, X, Lin, Q, Liu, W, Tan, J, Yu, X, Liu, J, Pan, L, Zhang, T, Yin, Y, Xin, C, Wu, H, Zhang, G, Ba Abdullah, MM, Huang, D, Fang, Y, Alnakhli, YO, Jia, S, Yin, A, Alhuzimi, EM, Alsaihati, BA, Al-Owayyed, SA, Zhao, D, Zhang, S, Al-Otaibi, NA, Sun, G, Majrashi, MA, Li, F, Wang, J, Yun, Q, Alnassar, NA, Wang, L, Yang, M, Al-Jelaify, RF, Liu, K, Gao, S, Chen, K, Alkhaldi, SR, Liu, G, Zhang, M, Guo, H & Yu, J 2013, 'Genome sequence of the date palm Phoenix dactylifera L', Nature Communications, vol. 4, 2274. https://doi.org/10.1038/ncomms3274

@article{ffe62d43973b46198f3e7cebfbd77111,

title = "Genome sequence of the date palm Phoenix dactylifera L",

abstract = "Date palm (Phoenix dactylifera L.) is a cultivated woody plant species with agricultural and economic importance. Here we report a genome assembly for an elite variety (Khalas), which is 605.4 Mb in size and covers >90% of the genome (∼671 Mb) and >96% of its genes (∼41,660 genes). Genomic sequence analysis demonstrates that P. dactylifera experienced a clear genome-wide duplication after either ancient whole genome duplications or massive segmental duplications. Genetic diversity analysis indicates that its stress resistance and sugar metabolism-related genes tend to be enriched in the chromosomal regions where the density of single-nucleotide polymorphisms is relatively low. Using transcriptomic data, we also illustrate the date palm's unique sugar metabolism that underlies fruit development and ripening. Our large-scale genomic and transcriptomic data pave the way for further genomic studies not only on P. dactylifera but also other Arecaceae plants.",

author = "Al-Mssallem, {Ibrahim S.} and Songnian Hu and Xiaowei Zhang and Qiang Lin and Wanfei Liu and Jun Tan and Xiaoguang Yu and Jiucheng Liu and Linlin Pan and Tongwu Zhang and Yuxin Yin and Chengqi Xin and Hao Wu and Guangyu Zhang and {Ba Abdullah}, {Mohammed M.} and Dawei Huang and Yongjun Fang and Alnakhli, {Yasser O.} and Shangang Jia and An Yin and Alhuzimi, {Eman M.} and Alsaihati, {Burair A.} and Al-Owayyed, {Saad A.} and Duojun Zhao and Sun Zhang and Al-Otaibi, {Noha A.} and Gaoyuan Sun and Majrashi, {Majed A.} and Fusen Li and Jixiang Wang and Quanzheng Yun and Alnassar, {Nafla A.} and Lei Wang and Meng Yang and Al-Jelaify, {Rasha F.} and Kan Liu and Shenghan Gao and Kaifu Chen and Alkhaldi, {Samiyah R.} and Guiming Liu and Meng Zhang and Haiyan Guo and Jun Yu",

note = "Funding Information: The project was supported by KACST grant AT428-29, Saudi Arabia. We thank Sheikh Mohammed S. Alnowairan (Alshuqiq, Al-Hssa) and Mr Abdulaziz N. Al-Jelaify (Al-Kharj, Riyadh) for providing some of the plant samples. We also acknowledge Drs Hongshan Jiang and Max Ingman for providing the HAPS scaffolding tool for sequence assembling. Genome sequencing and analyses were both performed in JCGR, KACST, SA.",

year = "2013",

doi = "10.1038/ncomms3274",

language = "English (US)",

volume = "4",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Publishing Group",

}

TY - JOUR

T1 - Genome sequence of the date palm Phoenix dactylifera L

AU - Al-Mssallem, Ibrahim S.

AU - Hu, Songnian

AU - Zhang, Xiaowei

AU - Lin, Qiang

AU - Liu, Wanfei

AU - Tan, Jun

AU - Yu, Xiaoguang

AU - Liu, Jiucheng

AU - Pan, Linlin

AU - Zhang, Tongwu

AU - Yin, Yuxin

AU - Xin, Chengqi

AU - Wu, Hao

AU - Zhang, Guangyu

AU - Ba Abdullah, Mohammed M.

AU - Huang, Dawei

AU - Fang, Yongjun

AU - Alnakhli, Yasser O.

AU - Jia, Shangang

AU - Yin, An

AU - Alhuzimi, Eman M.

AU - Alsaihati, Burair A.

AU - Al-Owayyed, Saad A.

AU - Zhao, Duojun

AU - Zhang, Sun

AU - Al-Otaibi, Noha A.

AU - Sun, Gaoyuan

AU - Majrashi, Majed A.

AU - Li, Fusen

AU - Wang, Jixiang

AU - Yun, Quanzheng

AU - Alnassar, Nafla A.

AU - Wang, Lei

AU - Yang, Meng

AU - Al-Jelaify, Rasha F.

AU - Liu, Kan

AU - Gao, Shenghan

AU - Chen, Kaifu

AU - Alkhaldi, Samiyah R.

AU - Liu, Guiming

AU - Zhang, Meng

AU - Guo, Haiyan

AU - Yu, Jun

N1 - Funding Information: The project was supported by KACST grant AT428-29, Saudi Arabia. We thank Sheikh Mohammed S. Alnowairan (Alshuqiq, Al-Hssa) and Mr Abdulaziz N. Al-Jelaify (Al-Kharj, Riyadh) for providing some of the plant samples. We also acknowledge Drs Hongshan Jiang and Max Ingman for providing the HAPS scaffolding tool for sequence assembling. Genome sequencing and analyses were both performed in JCGR, KACST, SA.

PY - 2013

Y1 - 2013

N2 - Date palm (Phoenix dactylifera L.) is a cultivated woody plant species with agricultural and economic importance. Here we report a genome assembly for an elite variety (Khalas), which is 605.4 Mb in size and covers >90% of the genome (∼671 Mb) and >96% of its genes (∼41,660 genes). Genomic sequence analysis demonstrates that P. dactylifera experienced a clear genome-wide duplication after either ancient whole genome duplications or massive segmental duplications. Genetic diversity analysis indicates that its stress resistance and sugar metabolism-related genes tend to be enriched in the chromosomal regions where the density of single-nucleotide polymorphisms is relatively low. Using transcriptomic data, we also illustrate the date palm's unique sugar metabolism that underlies fruit development and ripening. Our large-scale genomic and transcriptomic data pave the way for further genomic studies not only on P. dactylifera but also other Arecaceae plants.

AB - Date palm (Phoenix dactylifera L.) is a cultivated woody plant species with agricultural and economic importance. Here we report a genome assembly for an elite variety (Khalas), which is 605.4 Mb in size and covers >90% of the genome (∼671 Mb) and >96% of its genes (∼41,660 genes). Genomic sequence analysis demonstrates that P. dactylifera experienced a clear genome-wide duplication after either ancient whole genome duplications or massive segmental duplications. Genetic diversity analysis indicates that its stress resistance and sugar metabolism-related genes tend to be enriched in the chromosomal regions where the density of single-nucleotide polymorphisms is relatively low. Using transcriptomic data, we also illustrate the date palm's unique sugar metabolism that underlies fruit development and ripening. Our large-scale genomic and transcriptomic data pave the way for further genomic studies not only on P. dactylifera but also other Arecaceae plants.

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U2 - 10.1038/ncomms3274

DO - 10.1038/ncomms3274

M3 - Article

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AN - SCOPUS:84882301829

SN - 2041-1723

VL - 4

JO - Nature Communications

JF - Nature Communications

M1 - 2274

ER -

Genome sequence of the date palm Phoenix dactylifera L

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