Fern genomes elucidate land plant evolution and cyanobacterial symbioses

Fay Wei Li; Paul Brouwer; Lorenzo Carretero-Paulet; Shifeng Cheng; Jan De Vries; Pierre Marc Delaux; Ariana Eily; Nils Koppers; Li Yaung Kuo; Zheng Li; Mathew Simenc; Ian Small; Eric Wafula; Stephany Angarita; Michael S. Barker; Andrea Bräutigam; Claude Depamphilis; Sven Gould; Prashant S. Hosmani; Yao Moan Huang; Bruno Huettel; Yoichiro Kato; Xin Liu; Steven Maere; Rose McDowell; Lukas A. Mueller; Klaas G.J. Nierop; Stefan A. Rensing; Tanner Robison; Carl J. Rothfels; Erin M. Sigel; Yue Song; Prakash R. Timilsena; Yves Van De Peer; Hongli Wang; Per K.I. Wilhelmsson; Paul G. Wolf; Xun Xu; Joshua P. Der; Henriette Schluepmann; Gane K.S. Wong; Kathleen M. Pryer

doi:10.1038/s41477-018-0188-8

Fern genomes elucidate land plant evolution and cyanobacterial symbioses

Fay Wei Li, Paul Brouwer, Lorenzo Carretero-Paulet, Shifeng Cheng, Jan De Vries, Pierre Marc Delaux, Ariana Eily, Nils Koppers, Li Yaung Kuo, Zheng Li, Mathew Simenc, Ian Small, Eric Wafula, Stephany Angarita, Michael S. Barker, Andrea Bräutigam, Claude Depamphilis, Sven Gould, Prashant S. Hosmani, Yao Moan HuangBruno Huettel, Yoichiro Kato, Xin Liu, Steven Maere, Rose McDowell, Lukas A. Mueller, Klaas G.J. Nierop, Stefan A. Rensing, Tanner Robison, Carl J. Rothfels, Erin M. Sigel, Yue Song, Prakash R. Timilsena, Yves Van De Peer, Hongli Wang, Per K.I. Wilhelmsson, Paul G. Wolf, Xun Xu, Joshua P. Der, Henriette Schluepmann, Gane K.S. Wong, Kathleen M. Pryer

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Abstract

Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns - one at the base of 'core leptosporangiates' and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N₂-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla-cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.

Original language	English (US)
Pages (from-to)	460-472
Number of pages	13
Journal	Nature plants
Volume	4
Issue number	7
DOIs	https://doi.org/10.1038/s41477-018-0188-8
State	Published - Jul 1 2018

ASJC Scopus subject areas

Plant Science

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Li, F. W., Brouwer, P., Carretero-Paulet, L., Cheng, S., De Vries, J., Delaux, P. M., Eily, A., Koppers, N., Kuo, L. Y., Li, Z., Simenc, M., Small, I., Wafula, E., Angarita, S., Barker, M. S., Bräutigam, A., Depamphilis, C., Gould, S., Hosmani, P. S., ... Pryer, K. M. (2018). Fern genomes elucidate land plant evolution and cyanobacterial symbioses. Nature plants, 4(7), 460-472. https://doi.org/10.1038/s41477-018-0188-8

Li, FW, Brouwer, P, Carretero-Paulet, L, Cheng, S, De Vries, J, Delaux, PM, Eily, A, Koppers, N, Kuo, LY, Li, Z, Simenc, M, Small, I, Wafula, E, Angarita, S, Barker, MS, Bräutigam, A, Depamphilis, C, Gould, S, Hosmani, PS, Huang, YM, Huettel, B, Kato, Y, Liu, X, Maere, S, McDowell, R, Mueller, LA, Nierop, KGJ, Rensing, SA, Robison, T, Rothfels, CJ, Sigel, EM, Song, Y, Timilsena, PR, Van De Peer, Y, Wang, H, Wilhelmsson, PKI, Wolf, PG, Xu, X, Der, JP, Schluepmann, H, Wong, GKS & Pryer, KM 2018, 'Fern genomes elucidate land plant evolution and cyanobacterial symbioses', Nature plants, vol. 4, no. 7, pp. 460-472. https://doi.org/10.1038/s41477-018-0188-8

@article{9151fb558357445d82f829b72e22bab3,

title = "Fern genomes elucidate land plant evolution and cyanobacterial symbioses",

abstract = "Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns - one at the base of 'core leptosporangiates' and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N2-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla-cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.",

author = "Li, {Fay Wei} and Paul Brouwer and Lorenzo Carretero-Paulet and Shifeng Cheng and {De Vries}, Jan and Delaux, {Pierre Marc} and Ariana Eily and Nils Koppers and Kuo, {Li Yaung} and Zheng Li and Mathew Simenc and Ian Small and Eric Wafula and Stephany Angarita and Barker, {Michael S.} and Andrea Br{\"a}utigam and Claude Depamphilis and Sven Gould and Hosmani, {Prashant S.} and Huang, {Yao Moan} and Bruno Huettel and Yoichiro Kato and Xin Liu and Steven Maere and Rose McDowell and Mueller, {Lukas A.} and Nierop, {Klaas G.J.} and Rensing, {Stefan A.} and Tanner Robison and Rothfels, {Carl J.} and Sigel, {Erin M.} and Yue Song and Timilsena, {Prakash R.} and {Van De Peer}, Yves and Hongli Wang and Wilhelmsson, {Per K.I.} and Wolf, {Paul G.} and Xun Xu and Der, {Joshua P.} and Henriette Schluepmann and Wong, {Gane K.S.} and Pryer, {Kathleen M.}",

note = "Publisher Copyright: {\textcopyright} 2018 The Author(s).",

year = "2018",

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doi = "10.1038/s41477-018-0188-8",

language = "English (US)",

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T1 - Fern genomes elucidate land plant evolution and cyanobacterial symbioses

AU - Li, Fay Wei

AU - Brouwer, Paul

AU - Carretero-Paulet, Lorenzo

AU - Cheng, Shifeng

AU - De Vries, Jan

AU - Delaux, Pierre Marc

AU - Eily, Ariana

AU - Koppers, Nils

AU - Kuo, Li Yaung

AU - Li, Zheng

AU - Simenc, Mathew

AU - Small, Ian

AU - Wafula, Eric

AU - Angarita, Stephany

AU - Barker, Michael S.

AU - Bräutigam, Andrea

AU - Depamphilis, Claude

AU - Gould, Sven

AU - Hosmani, Prashant S.

AU - Huang, Yao Moan

AU - Huettel, Bruno

AU - Kato, Yoichiro

AU - Liu, Xin

AU - Maere, Steven

AU - McDowell, Rose

AU - Mueller, Lukas A.

AU - Nierop, Klaas G.J.

AU - Rensing, Stefan A.

AU - Robison, Tanner

AU - Rothfels, Carl J.

AU - Sigel, Erin M.

AU - Song, Yue

AU - Timilsena, Prakash R.

AU - Van De Peer, Yves

AU - Wang, Hongli

AU - Wilhelmsson, Per K.I.

AU - Wolf, Paul G.

AU - Xu, Xun

AU - Der, Joshua P.

AU - Schluepmann, Henriette

AU - Wong, Gane K.S.

AU - Pryer, Kathleen M.

PY - 2018/7/1

Y1 - 2018/7/1

N2 - Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns - one at the base of 'core leptosporangiates' and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N2-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla-cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.

AB - Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns - one at the base of 'core leptosporangiates' and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N2-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla-cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.

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U2 - 10.1038/s41477-018-0188-8

DO - 10.1038/s41477-018-0188-8

M3 - Article

C2 - 29967517

AN - SCOPUS:85049597352

SN - 2055-026X

VL - 4

SP - 460

EP - 472

JO - Nature plants

JF - Nature plants

IS - 7

ER -

Fern genomes elucidate land plant evolution and cyanobacterial symbioses

Abstract

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