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The Phoebe genome sheds light on the evolution of magnoliids

Lauraceae includes the genus Phoebe, and the family is linked to the evolution of magnoliids. We sequenced the genome of Phoebe bournei Nanmu. The assembled genome size was 989.19 Mb, with a contig N50 value of 2.05 Mb. A total of 28,198 protein-coding genes were annotated in P. bournei. Whole-genom...

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Autores principales: Chen, Shi-Pin, Sun, Wei-Hong, Xiong, Yuan-Fang, Jiang, Yu-Ting, Liu, Xue-Die, Liao, Xing-Yu, Zhang, Di-Yang, Jiang, Shu-Zhen, Li, Yu, Liu, Bin, Ma, Liang, Yu, Xia, He, Li, Liu, Bao, Feng, Jin-Lin, Feng, Li-Zhen, Wang, Zhi-Wen, Zou, Shuang-Quan, Lan, Si-Ren, Liu, Zhong-Jian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7459323/
https://www.ncbi.nlm.nih.gov/pubmed/32922818
http://dx.doi.org/10.1038/s41438-020-00368-z
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author Chen, Shi-Pin
Sun, Wei-Hong
Xiong, Yuan-Fang
Jiang, Yu-Ting
Liu, Xue-Die
Liao, Xing-Yu
Zhang, Di-Yang
Jiang, Shu-Zhen
Li, Yu
Liu, Bin
Ma, Liang
Yu, Xia
He, Li
Liu, Bao
Feng, Jin-Lin
Feng, Li-Zhen
Wang, Zhi-Wen
Zou, Shuang-Quan
Lan, Si-Ren
Liu, Zhong-Jian
author_facet Chen, Shi-Pin
Sun, Wei-Hong
Xiong, Yuan-Fang
Jiang, Yu-Ting
Liu, Xue-Die
Liao, Xing-Yu
Zhang, Di-Yang
Jiang, Shu-Zhen
Li, Yu
Liu, Bin
Ma, Liang
Yu, Xia
He, Li
Liu, Bao
Feng, Jin-Lin
Feng, Li-Zhen
Wang, Zhi-Wen
Zou, Shuang-Quan
Lan, Si-Ren
Liu, Zhong-Jian
author_sort Chen, Shi-Pin
collection PubMed
description Lauraceae includes the genus Phoebe, and the family is linked to the evolution of magnoliids. We sequenced the genome of Phoebe bournei Nanmu. The assembled genome size was 989.19 Mb, with a contig N50 value of 2.05 Mb. A total of 28,198 protein-coding genes were annotated in P. bournei. Whole-genome duplication (WGD) analysis showed that Lauraceae has experienced two WGD events; the older WGD event occurred just before the divergence of Lauraceae and Magnoliales, and the more recent WGD was shared by all lineages of Lauraceae. The phylogenetic tree showed that magnoliids form a sister clade to monocots and eudicots. We also identified 63 MADS-box genes, including AGL12-like genes that may be related to the regulation of P. bournei roots and FIN219-like genes encoding GH3 proteins, which are involved in photomorphogenesis. SAUR50-like genes involved in light signal-mediated pedicel or stem development were also identified. Four ATMYB46- and three PtrEPSP-homologous genes related to lignin biosynthesis were identified. These genes may be associated with the formation of straight trunks in P. bournei. Overall, the P. bournei reference genome provides insight into the origin, evolution, and diversification of Phoebe and other magnoliids.
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spelling pubmed-74593232020-09-11 The Phoebe genome sheds light on the evolution of magnoliids Chen, Shi-Pin Sun, Wei-Hong Xiong, Yuan-Fang Jiang, Yu-Ting Liu, Xue-Die Liao, Xing-Yu Zhang, Di-Yang Jiang, Shu-Zhen Li, Yu Liu, Bin Ma, Liang Yu, Xia He, Li Liu, Bao Feng, Jin-Lin Feng, Li-Zhen Wang, Zhi-Wen Zou, Shuang-Quan Lan, Si-Ren Liu, Zhong-Jian Hortic Res Article Lauraceae includes the genus Phoebe, and the family is linked to the evolution of magnoliids. We sequenced the genome of Phoebe bournei Nanmu. The assembled genome size was 989.19 Mb, with a contig N50 value of 2.05 Mb. A total of 28,198 protein-coding genes were annotated in P. bournei. Whole-genome duplication (WGD) analysis showed that Lauraceae has experienced two WGD events; the older WGD event occurred just before the divergence of Lauraceae and Magnoliales, and the more recent WGD was shared by all lineages of Lauraceae. The phylogenetic tree showed that magnoliids form a sister clade to monocots and eudicots. We also identified 63 MADS-box genes, including AGL12-like genes that may be related to the regulation of P. bournei roots and FIN219-like genes encoding GH3 proteins, which are involved in photomorphogenesis. SAUR50-like genes involved in light signal-mediated pedicel or stem development were also identified. Four ATMYB46- and three PtrEPSP-homologous genes related to lignin biosynthesis were identified. These genes may be associated with the formation of straight trunks in P. bournei. Overall, the P. bournei reference genome provides insight into the origin, evolution, and diversification of Phoebe and other magnoliids. Nature Publishing Group UK 2020-09-01 /pmc/articles/PMC7459323/ /pubmed/32922818 http://dx.doi.org/10.1038/s41438-020-00368-z Text en © The Author(s) 2020 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Chen, Shi-Pin
Sun, Wei-Hong
Xiong, Yuan-Fang
Jiang, Yu-Ting
Liu, Xue-Die
Liao, Xing-Yu
Zhang, Di-Yang
Jiang, Shu-Zhen
Li, Yu
Liu, Bin
Ma, Liang
Yu, Xia
He, Li
Liu, Bao
Feng, Jin-Lin
Feng, Li-Zhen
Wang, Zhi-Wen
Zou, Shuang-Quan
Lan, Si-Ren
Liu, Zhong-Jian
The Phoebe genome sheds light on the evolution of magnoliids
title The Phoebe genome sheds light on the evolution of magnoliids
title_full The Phoebe genome sheds light on the evolution of magnoliids
title_fullStr The Phoebe genome sheds light on the evolution of magnoliids
title_full_unstemmed The Phoebe genome sheds light on the evolution of magnoliids
title_short The Phoebe genome sheds light on the evolution of magnoliids
title_sort phoebe genome sheds light on the evolution of magnoliids
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7459323/
https://www.ncbi.nlm.nih.gov/pubmed/32922818
http://dx.doi.org/10.1038/s41438-020-00368-z
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