The Cardamine hirsuta genome offers insight into the evolution of morphological diversity

Xiangchao Gan; Angela Hay; Michiel Kwantes; Georg Haberer; Asis Hallab; Raffaele Dello Ioio; Hugo Hofhuis; Bjorn Pieper; Maria Cartolano; Ulla Neumann; Lachezar A. Nikolov; Baoxing Song; Mohsen Hajheidari; Roman Briskine; Evangelia Kougioumoutzi; Daniela Vlad; Suvi Broholm; Jotun Hein; Khalid Meksem; David Lightfoot; Kentaro K. Shimizu; Rie Shimizu-Inatsugi; Martha Imprialou; David Kudrna; Rod Wing; Shusei Sato; Peter Huijser; Dmitry Filatov; Klaus F.X. Mayer; Richard Mott; Miltos Tsiantis

doi:10.1038/nplants.2016.167

The Cardamine hirsuta genome offers insight into the evolution of morphological diversity

Xiangchao Gan, Angela Hay, Michiel Kwantes, Georg Haberer, Asis Hallab, Raffaele Dello Ioio, Hugo Hofhuis, Bjorn Pieper, Maria Cartolano, Ulla Neumann, Lachezar A. Nikolov, Baoxing Song, Mohsen Hajheidari, Roman Briskine, Evangelia Kougioumoutzi, Daniela Vlad, Suvi Broholm, Jotun Hein, Khalid Meksem, David LightfootKentaro K. Shimizu, Rie Shimizu-Inatsugi, Martha Imprialou, David Kudrna, Rod Wing, Shusei Sato, Peter Huijser, Dmitry Filatov, Klaus F.X. Mayer, Richard Mott, Miltos Tsiantis

LIF - Ecological Developmental Adaptability Life Sciences

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69 Citations (Scopus)

Abstract

Finding causal relationships between genotypic and phenotypic variation is a key focus of evolutionary biology, human genetics and plant breeding. To identify genome-wide patterns underlying trait diversity, we assembled a high-quality reference genome of Cardamine hirsuta, a close relative of the model plant Arabidopsis thaliana. We combined comparative genome and transcriptome analyses with the experimental tools available in C. hirsuta to investigate gene function and phenotypic diversification. Our findings highlight the prevalent role of transcription factors and tandem gene duplications in morphological evolution. We identified a specific role for the transcriptional regulators PLETHORA5/7 in shaping leaf diversity and link tandem gene duplication with differential gene expression in the explosive seed pod of C. hirsuta. Our work highlights the value of comparative approaches in genetically tractable species to understand the genetic basis for evolutionary change.

Original language	English
Article number	16167
Journal	Nature Plants
Volume	2
DOIs	https://doi.org/10.1038/nplants.2016.167
Publication status	Published - 2016 Oct 31

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Gan, X., Hay, A., Kwantes, M., Haberer, G., Hallab, A., Ioio, R. D., Hofhuis, H., Pieper, B., Cartolano, M., Neumann, U., Nikolov, L. A., Song, B., Hajheidari, M., Briskine, R., Kougioumoutzi, E., Vlad, D., Broholm, S., Hein, J., Meksem, K., ... Tsiantis, M. (2016). The Cardamine hirsuta genome offers insight into the evolution of morphological diversity. Nature Plants, 2, Article 16167. https://doi.org/10.1038/nplants.2016.167

@article{cc62bb2df6f343d2ba63a8b43d484a81,

title = "The Cardamine hirsuta genome offers insight into the evolution of morphological diversity",

abstract = "Finding causal relationships between genotypic and phenotypic variation is a key focus of evolutionary biology, human genetics and plant breeding. To identify genome-wide patterns underlying trait diversity, we assembled a high-quality reference genome of Cardamine hirsuta, a close relative of the model plant Arabidopsis thaliana. We combined comparative genome and transcriptome analyses with the experimental tools available in C. hirsuta to investigate gene function and phenotypic diversification. Our findings highlight the prevalent role of transcription factors and tandem gene duplications in morphological evolution. We identified a specific role for the transcriptional regulators PLETHORA5/7 in shaping leaf diversity and link tandem gene duplication with differential gene expression in the explosive seed pod of C. hirsuta. Our work highlights the value of comparative approaches in genetically tractable species to understand the genetic basis for evolutionary change.",

author = "Xiangchao Gan and Angela Hay and Michiel Kwantes and Georg Haberer and Asis Hallab and Ioio, {Raffaele Dello} and Hugo Hofhuis and Bjorn Pieper and Maria Cartolano and Ulla Neumann and Nikolov, {Lachezar A.} and Baoxing Song and Mohsen Hajheidari and Roman Briskine and Evangelia Kougioumoutzi and Daniela Vlad and Suvi Broholm and Jotun Hein and Khalid Meksem and David Lightfoot and Shimizu, {Kentaro K.} and Rie Shimizu-Inatsugi and Martha Imprialou and David Kudrna and Rod Wing and Shusei Sato and Peter Huijser and Dmitry Filatov and Mayer, {Klaus F.X.} and Richard Mott and Miltos Tsiantis",

note = "Funding Information: We thank J. Martinez-Garcia for critical reading, the Wellcome Trust Centre for Human Genetics, University of Oxford, for sequencing, R. Berndtgen, W. Faigl, S. Tabata and the Centre for Genomic Research, University of Liverpool for assistance, H. North for seeds, S. Theologis for DNA isolation and helpful discussions, and B. Scheres and S. Grigg for discussions on PLT genes. This work was supported by Biotechnology and Biological Sciences Research Council grants BB/H011455/1 (M.T.) and BB/H01313X/1 (An.H.), a Gatsby Charitable foundation grant (M.T.), a Deutsche Forschungsgemeinschaft priority programme 'Adaptomics' grant TS 229/1-1 and HA 6316/1-3 (M.T. and An.H.), a University of Oxford pump-priming grant (M.T.), a Human Frontiers Science Programme Young Investigators grant RGY0087/2011 (An.H. and K.S.S.), EU Cofund Plant Fellow to R.B., URPP Evolution in Action to K.S.S. and R.S.-I., MEXT KAKENHI 16H06469 and Swiss National Science Foundation to K.S.S. An.H. was supported by the Max Planck Society W2 Minerva programme and M.T. by the Cluster of Excellence on Plant Sciences and a core grant of the Max Planck Society. Publisher Copyright: {\textcopyright} 2016 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.",

year = "2016",

month = oct,

day = "31",

doi = "10.1038/nplants.2016.167",

language = "English",

volume = "2",

journal = "Nature Plants",

issn = "2055-026X",

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Gan, X, Hay, A, Kwantes, M, Haberer, G, Hallab, A, Ioio, RD, Hofhuis, H, Pieper, B, Cartolano, M, Neumann, U, Nikolov, LA, Song, B, Hajheidari, M, Briskine, R, Kougioumoutzi, E, Vlad, D, Broholm, S, Hein, J, Meksem, K, Lightfoot, D, Shimizu, KK, Shimizu-Inatsugi, R, Imprialou, M, Kudrna, D, Wing, R, Sato, S, Huijser, P, Filatov, D, Mayer, KFX, Mott, R & Tsiantis, M 2016, 'The Cardamine hirsuta genome offers insight into the evolution of morphological diversity', Nature Plants, vol. 2, 16167. https://doi.org/10.1038/nplants.2016.167

TY - JOUR

T1 - The Cardamine hirsuta genome offers insight into the evolution of morphological diversity

AU - Gan, Xiangchao

AU - Hay, Angela

AU - Kwantes, Michiel

AU - Haberer, Georg

AU - Hallab, Asis

AU - Ioio, Raffaele Dello

AU - Hofhuis, Hugo

AU - Pieper, Bjorn

AU - Cartolano, Maria

AU - Neumann, Ulla

AU - Nikolov, Lachezar A.

AU - Song, Baoxing

AU - Hajheidari, Mohsen

AU - Briskine, Roman

AU - Kougioumoutzi, Evangelia

AU - Vlad, Daniela

AU - Broholm, Suvi

AU - Hein, Jotun

AU - Meksem, Khalid

AU - Lightfoot, David

AU - Shimizu, Kentaro K.

AU - Shimizu-Inatsugi, Rie

AU - Imprialou, Martha

AU - Kudrna, David

AU - Wing, Rod

AU - Sato, Shusei

AU - Huijser, Peter

AU - Filatov, Dmitry

AU - Mayer, Klaus F.X.

AU - Mott, Richard

AU - Tsiantis, Miltos

N1 - Funding Information: We thank J. Martinez-Garcia for critical reading, the Wellcome Trust Centre for Human Genetics, University of Oxford, for sequencing, R. Berndtgen, W. Faigl, S. Tabata and the Centre for Genomic Research, University of Liverpool for assistance, H. North for seeds, S. Theologis for DNA isolation and helpful discussions, and B. Scheres and S. Grigg for discussions on PLT genes. This work was supported by Biotechnology and Biological Sciences Research Council grants BB/H011455/1 (M.T.) and BB/H01313X/1 (An.H.), a Gatsby Charitable foundation grant (M.T.), a Deutsche Forschungsgemeinschaft priority programme 'Adaptomics' grant TS 229/1-1 and HA 6316/1-3 (M.T. and An.H.), a University of Oxford pump-priming grant (M.T.), a Human Frontiers Science Programme Young Investigators grant RGY0087/2011 (An.H. and K.S.S.), EU Cofund Plant Fellow to R.B., URPP Evolution in Action to K.S.S. and R.S.-I., MEXT KAKENHI 16H06469 and Swiss National Science Foundation to K.S.S. An.H. was supported by the Max Planck Society W2 Minerva programme and M.T. by the Cluster of Excellence on Plant Sciences and a core grant of the Max Planck Society. Publisher Copyright: © 2016 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

PY - 2016/10/31

Y1 - 2016/10/31

N2 - Finding causal relationships between genotypic and phenotypic variation is a key focus of evolutionary biology, human genetics and plant breeding. To identify genome-wide patterns underlying trait diversity, we assembled a high-quality reference genome of Cardamine hirsuta, a close relative of the model plant Arabidopsis thaliana. We combined comparative genome and transcriptome analyses with the experimental tools available in C. hirsuta to investigate gene function and phenotypic diversification. Our findings highlight the prevalent role of transcription factors and tandem gene duplications in morphological evolution. We identified a specific role for the transcriptional regulators PLETHORA5/7 in shaping leaf diversity and link tandem gene duplication with differential gene expression in the explosive seed pod of C. hirsuta. Our work highlights the value of comparative approaches in genetically tractable species to understand the genetic basis for evolutionary change.

AB - Finding causal relationships between genotypic and phenotypic variation is a key focus of evolutionary biology, human genetics and plant breeding. To identify genome-wide patterns underlying trait diversity, we assembled a high-quality reference genome of Cardamine hirsuta, a close relative of the model plant Arabidopsis thaliana. We combined comparative genome and transcriptome analyses with the experimental tools available in C. hirsuta to investigate gene function and phenotypic diversification. Our findings highlight the prevalent role of transcription factors and tandem gene duplications in morphological evolution. We identified a specific role for the transcriptional regulators PLETHORA5/7 in shaping leaf diversity and link tandem gene duplication with differential gene expression in the explosive seed pod of C. hirsuta. Our work highlights the value of comparative approaches in genetically tractable species to understand the genetic basis for evolutionary change.

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DO - 10.1038/nplants.2016.167

M3 - Article

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AN - SCOPUS:84994047680

SN - 2055-026X

VL - 2

JO - Nature Plants

JF - Nature Plants

M1 - 16167

ER -

The Cardamine hirsuta genome offers insight into the evolution of morphological diversity

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