High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height

Abstract Background Coconut is an important tropical oil and fruit crop whose evolutionary position renders it a fantastic species for the investigation of the evolution of monocot chromosomes and the subsequent differentiation of ancient plants. Results Here, we report the assembly and annotation o...

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Autores principales:	Shouchuang Wang, Yong Xiao, Zhi-Wei Zhou, Jiaqing Yuan, Hao Guo, Zhuang Yang, Jun Yang, Pengchuan Sun, Lisong Sun, Yuan Deng, Wen-Zhao Xie, Jia-Ming Song, Muhammad Tahir ul Qamar, Wei Xia, Rui Liu, Shufang Gong, Yong Wang, Fuyou Wang, Xianqing Liu, Alisdair R. Fernie, Xiyin Wang, Haikuo Fan, Ling-Ling Chen, Jie Luo
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Biology (General) QH301-705.5 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/2207a8ec37ba482bad341e460a74d924
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spelling	oai:doaj.org-article:2207a8ec37ba482bad341e460a74d9242021-11-08T11:17:16ZHigh-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height10.1186/s13059-021-02522-91474-760Xhttps://doaj.org/article/2207a8ec37ba482bad341e460a74d9242021-11-01T00:00:00Zhttps://doi.org/10.1186/s13059-021-02522-9https://doaj.org/toc/1474-760XAbstract Background Coconut is an important tropical oil and fruit crop whose evolutionary position renders it a fantastic species for the investigation of the evolution of monocot chromosomes and the subsequent differentiation of ancient plants. Results Here, we report the assembly and annotation of reference-grade genomes of Cn. tall and Cn. dwarf, whose genome sizes are 2.40 Gb and 2.39 Gb, respectively. The comparative analysis reveals that the two coconut subspecies diverge about 2–8 Mya while the conserved Arecaceae-specific whole-genome duplication (ω WGD) occurs approximately 47–53 Mya. It additionally allows us to reconstruct the ancestral karyotypes of the ten ancient monocot chromosomes and the evolutionary trajectories of the 16 modern coconut chromosomes. Fiber synthesis genes in Cn. tall, related to lignin and cellulose synthesis, are found at a higher copy number and expression level than dwarf coconuts. Integrated multi-omics analysis reveals that the difference in coconut plant height is the result of altered gibberellin metabolism, with both the GA20ox copy number and a single-nucleotide change in the promoter together leading to the difference in plant height between Cn. tall and Cn. dwarf. Conclusion We provide high-quality coconut genomes and reveal the genetic basis of trait differences between two coconuts through multi-omics analysis. We also reveal that the selection of plant height has been targeted for the same gene for millions of years, not only in natural selection of ancient plant as illustrated in coconut, but also for artificial selection in cultivated crops such as rice and maize.Shouchuang WangYong XiaoZhi-Wei ZhouJiaqing YuanHao GuoZhuang YangJun YangPengchuan SunLisong SunYuan DengWen-Zhao XieJia-Ming SongMuhammad Tahir ul QamarWei XiaRui LiuShufang GongYong WangFuyou WangXianqing LiuAlisdair R. FernieXiyin WangHaikuo FanLing-Ling ChenJie LuoBMCarticleBiology (General)QH301-705.5GeneticsQH426-470ENGenome Biology, Vol 22, Iss 1, Pp 1-25 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5 Genetics QH426-470
spellingShingle	Biology (General) QH301-705.5 Genetics QH426-470 Shouchuang Wang Yong Xiao Zhi-Wei Zhou Jiaqing Yuan Hao Guo Zhuang Yang Jun Yang Pengchuan Sun Lisong Sun Yuan Deng Wen-Zhao Xie Jia-Ming Song Muhammad Tahir ul Qamar Wei Xia Rui Liu Shufang Gong Yong Wang Fuyou Wang Xianqing Liu Alisdair R. Fernie Xiyin Wang Haikuo Fan Ling-Ling Chen Jie Luo High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height
description	Abstract Background Coconut is an important tropical oil and fruit crop whose evolutionary position renders it a fantastic species for the investigation of the evolution of monocot chromosomes and the subsequent differentiation of ancient plants. Results Here, we report the assembly and annotation of reference-grade genomes of Cn. tall and Cn. dwarf, whose genome sizes are 2.40 Gb and 2.39 Gb, respectively. The comparative analysis reveals that the two coconut subspecies diverge about 2–8 Mya while the conserved Arecaceae-specific whole-genome duplication (ω WGD) occurs approximately 47–53 Mya. It additionally allows us to reconstruct the ancestral karyotypes of the ten ancient monocot chromosomes and the evolutionary trajectories of the 16 modern coconut chromosomes. Fiber synthesis genes in Cn. tall, related to lignin and cellulose synthesis, are found at a higher copy number and expression level than dwarf coconuts. Integrated multi-omics analysis reveals that the difference in coconut plant height is the result of altered gibberellin metabolism, with both the GA20ox copy number and a single-nucleotide change in the promoter together leading to the difference in plant height between Cn. tall and Cn. dwarf. Conclusion We provide high-quality coconut genomes and reveal the genetic basis of trait differences between two coconuts through multi-omics analysis. We also reveal that the selection of plant height has been targeted for the same gene for millions of years, not only in natural selection of ancient plant as illustrated in coconut, but also for artificial selection in cultivated crops such as rice and maize.
format	article
author	Shouchuang Wang Yong Xiao Zhi-Wei Zhou Jiaqing Yuan Hao Guo Zhuang Yang Jun Yang Pengchuan Sun Lisong Sun Yuan Deng Wen-Zhao Xie Jia-Ming Song Muhammad Tahir ul Qamar Wei Xia Rui Liu Shufang Gong Yong Wang Fuyou Wang Xianqing Liu Alisdair R. Fernie Xiyin Wang Haikuo Fan Ling-Ling Chen Jie Luo
author_facet	Shouchuang Wang Yong Xiao Zhi-Wei Zhou Jiaqing Yuan Hao Guo Zhuang Yang Jun Yang Pengchuan Sun Lisong Sun Yuan Deng Wen-Zhao Xie Jia-Ming Song Muhammad Tahir ul Qamar Wei Xia Rui Liu Shufang Gong Yong Wang Fuyou Wang Xianqing Liu Alisdair R. Fernie Xiyin Wang Haikuo Fan Ling-Ling Chen Jie Luo
author_sort	Shouchuang Wang
title	High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height
title_short	High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height
title_full	High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height
title_fullStr	High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height
title_full_unstemmed	High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height
title_sort	high-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height
publisher	BMC
publishDate	2021
url	https://doaj.org/article/2207a8ec37ba482bad341e460a74d924
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High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height

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