From genes to networks

From genes to networks editorial Sixty years ago, Francis Crick articulated the central dogma of molecular biology to explain the sequential information flow between genes and proteins. Nowadays our understanding of genes and the information they convey is no longer limited to the single-molecule level. he Cold Spring Harbor Laboratory the seed collection in the Arabidopsis Such newly developed technologies (CSHL), recently hosted their 11th Biological Resource Center (ABRC) or liberate researchers from conventional TPlant Genomes meeting while also access to the Arabidopsis Information research scenarios and open a new dimension celebrating the 20th anniversary of their Resource (TAIR). of network thinking. But translating biennial Plant meeting series. This year also Rice (Oryza sativa) was the second information from genes to proteins is not an marks the 20th anniversary of the National plant species to have its whole genome easy road. Simply analysing the sequences 3,4 Plant Genome Initiative (NPGI), which has sequenced . The release of the reference of genes will never tell the true stories of been dedicated to accelerating the basic and genome of rice and other important gene regulation. Using high-throughput translational research of plant genomics. crops has provided great opportunities chromosome confirmation capture (Hi-C) With the support of the NPGI and various to understand the history of crop and chromatin interaction analysis through global collaborations, Arabidopsis thaliana domestication and identify landmarks paired-end tag sequencing (ChIA-PET), 1 11 became the first sequenced plant . for crop improvement. Combining the Wang et al. present the 3D genome The publication of its genome in 2000 knowledge gained from functional genomics architecture of cotton and show how its was three years ahead of the completion of and modern plant breeding, scientists have evolutionary dynamics altered the networks the Human Genome Project, marking the successfully designed and developed new of gene regulation, again in this issue. dawn of the genome era in plant research. rice varieties with high-yield and superior- If there were a time machine, it would Now there are at least 264 plant species with quality grains . Similar improvements in be fascinating to shuttle back to 1997, to their reference genomes sequenced and other crops are also ongoing. fact-check the memories of the scientists published (http://www.plabipd.de), from These achievements and foundations who attended the first CSHL Plant meeting: superficially simple algae and bryophytes to have pushed plant research into the fast The Arabidopsis Genome: From Sequence complex gymnosperms and angiosperms. lane. The sequencing and assembly of to Function. Whether you regard the 6–8 Opening the abstract book of the first high-quality ‘platinum’ genomes further intervening 20 years as long or short, they CSHL Plant Genomes meeting (1997), we empowers plant scientists to pursue the have seen a remarkable accumulation of can still feel the beat of the Arabidopsis details of genetic regulation and deepen knowledge and technologies in plant science. genome project. The sequencing updates our understanding of plant evolution. For The scope of the recent CSHL Plant meeting of Chromosome 1-5 were made by at least example, in this issue, Wan and colleagues Plant Genomes & Biotechnology: From Genes eight international research groups from report a high-quality draft genome of to Networks reflected those changes. With our regions including the United States, the Gnetum montanum, a gymnosperm and current ability to do incredible research in an United Kingdom, France and Japan. the first sequenced species for gnetophytes. unprecedented landscape, we should never Despite only partial sequencing data being They revealed unique genomic features of forget the historic path that has led those available, gene annotation and positional this species that seem to place it closer to the possibilities, nor fail to keep in mind how cloning were already being pursued to basal lineage of angiosperms, indicating an important it is to offer shoulders for younger understand the functions of different genes. early evolutionary path for seed plants. generations to stand on, and see further. ❐ At this point, the limited resources and In addition to these high-quality tools of functional genomics were serious genomes, revolutionary technologies and Published online: 31 January 2018 obstacles for gene studies. It is a favourite tools used for functional genomic analysis https://doi.org/10.1038/s41477-018-0109-x joke among early-career scientists today are constantly emerging, including new that “if we could take a time machine back transformation methods, gene-editing References 1. e A Th rabidopsis Genome Initiative. Nature 408, 796–815 (2000). to the decade when cloning a gene was tools, yeast two-hybrid systems, mass 2. Alonso, J. M. et al. Science 301, 653–657 (2003). sufficient to publish a high-impact article, spectrometry and high-throughput 3. Yu, J. et al. Science 296, 79–92 (2002). research life will be much easier”. However, bioinformatics. Combining different 4. Go, S. A. et a ff l. Science 296, 92–100 (2002). 5. Zeng, D. et al. Nat. Plants 3, 17031 (2017). the expanding demand for new tools also methods for functional research is becoming 6. Mascher, M. et al. Nature 544, 427–433 (2017). generated great potential for innovations in popular, providing a powerful toolkit for 7. Daccord, N. et al. Nat. Genet. 49, 1099–1106 (2017). methodology and biotechnology. digging into the hidden nature of genome 8. Zhao, G. et al. Nat. Plants 3, 946–955 (2017). 9. Wan, T. et al. Nat. Plants https://doi.org/10.1038/s41477-017- The first genome-wide transfer DNA sequences. In an article in this issue, Xu 10 0097-2 (2018). mutagenesis of A. thaliana in 2003, led by and coworkers identify a key heterodimer 10. Xu, C. et al. Nat. Plants https://doi.org/10.1038/s41477-017- the Salk Institute, was a major breakthrough that controls cell reprogramming during 0095-4 (2018). in plant functional genomics . This Arabidopsis organ regeneration. To test 11. Wang, M. et al. Nat. Plants https://doi.org/10.1038/s41477-017- 0096-3 (2018). enormous effort directly triggered the the hypothesis, they performed high-quality blossoming of plant molecular genetics in analyses using mutant lines from ABRC, Acknowledgements the past 15 years, and its influence is still transgenic plants, confocal microscopy The editorial team acknowledges the support of the Cold strong today. For Arabidopsis researchers, and approaches to identify both Spring Harbor Laboratory, and the Meetings & Courses it is now hard to imagine how experiments protein–protein interactions and Department in particular, for allowing access to the could be designed and conducted without protein–DNA interactions. abstract books of the historical meetings. Nature PlaNts | VOL 4 | FEBRUARY 2018 | 55 | www.nature.com/natureplants © 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. © 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Nature Plants Springer Journals

From genes to networks

Nature Plants , Volume 4 (2) – Jan 31, 2018
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Life Sciences; Life Sciences, general; Plant Sciences
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Abstract

editorial Sixty years ago, Francis Crick articulated the central dogma of molecular biology to explain the sequential information flow between genes and proteins. Nowadays our understanding of genes and the information they convey is no longer limited to the single-molecule level. he Cold Spring Harbor Laboratory the seed collection in the Arabidopsis Such newly developed technologies (CSHL), recently hosted their 11th Biological Resource Center (ABRC) or liberate researchers from conventional TPlant Genomes meeting while also access to the Arabidopsis Information research scenarios and open a new dimension celebrating the 20th anniversary of their Resource (TAIR). of network thinking. But translating biennial Plant meeting series. This year also Rice (Oryza sativa) was the second information from genes to proteins is not an marks the 20th anniversary of the National plant species to have its whole genome easy road. Simply analysing the sequences 3,4 Plant Genome Initiative (NPGI), which has sequenced . The release of the reference of genes will never tell the true stories of been dedicated to accelerating the basic and genome of rice and other important gene regulation. Using high-throughput translational research of plant genomics. crops has provided great opportunities chromosome confirmation capture (Hi-C) With the support of the NPGI and various to understand the history of crop and chromatin interaction analysis through global collaborations, Arabidopsis thaliana domestication and identify landmarks paired-end tag sequencing (ChIA-PET), 1 11 became the first sequenced plant . for crop improvement. Combining the Wang et al. present the 3D genome The publication of its genome in 2000 knowledge gained from functional genomics architecture of cotton and show how its was three years ahead of the completion of and modern plant breeding, scientists have evolutionary dynamics altered the networks the Human Genome Project, marking the successfully designed and developed new of gene regulation, again in this issue. dawn of the genome era in plant research. rice varieties with high-yield and superior- If there were a time machine, it would Now there are at least 264 plant species with quality grains . Similar improvements in be fascinating to shuttle back to 1997, to their reference genomes sequenced and other crops are also ongoing. fact-check the memories of the scientists published (http://www.plabipd.de), from These achievements and foundations who attended the first CSHL Plant meeting: superficially simple algae and bryophytes to have pushed plant research into the fast The Arabidopsis Genome: From Sequence complex gymnosperms and angiosperms. lane. The sequencing and assembly of to Function. Whether you regard the 6–8 Opening the abstract book of the first high-quality ‘platinum’ genomes further intervening 20 years as long or short, they CSHL Plant Genomes meeting (1997), we empowers plant scientists to pursue the have seen a remarkable accumulation of can still feel the beat of the Arabidopsis details of genetic regulation and deepen knowledge and technologies in plant science. genome project. The sequencing updates our understanding of plant evolution. For The scope of the recent CSHL Plant meeting of Chromosome 1-5 were made by at least example, in this issue, Wan and colleagues Plant Genomes & Biotechnology: From Genes eight international research groups from report a high-quality draft genome of to Networks reflected those changes. With our regions including the United States, the Gnetum montanum, a gymnosperm and current ability to do incredible research in an United Kingdom, France and Japan. the first sequenced species for gnetophytes. unprecedented landscape, we should never Despite only partial sequencing data being They revealed unique genomic features of forget the historic path that has led those available, gene annotation and positional this species that seem to place it closer to the possibilities, nor fail to keep in mind how cloning were already being pursued to basal lineage of angiosperms, indicating an important it is to offer shoulders for younger understand the functions of different genes. early evolutionary path for seed plants. generations to stand on, and see further. ❐ At this point, the limited resources and In addition to these high-quality tools of functional genomics were serious genomes, revolutionary technologies and Published online: 31 January 2018 obstacles for gene studies. It is a favourite tools used for functional genomic analysis https://doi.org/10.1038/s41477-018-0109-x joke among early-career scientists today are constantly emerging, including new that “if we could take a time machine back transformation methods, gene-editing References 1. e A Th rabidopsis Genome Initiative. Nature 408, 796–815 (2000). to the decade when cloning a gene was tools, yeast two-hybrid systems, mass 2. Alonso, J. M. et al. Science 301, 653–657 (2003). sufficient to publish a high-impact article, spectrometry and high-throughput 3. Yu, J. et al. Science 296, 79–92 (2002). research life will be much easier”. However, bioinformatics. Combining different 4. Go, S. A. et a ff l. Science 296, 92–100 (2002). 5. Zeng, D. et al. Nat. Plants 3, 17031 (2017). the expanding demand for new tools also methods for functional research is becoming 6. Mascher, M. et al. Nature 544, 427–433 (2017). generated great potential for innovations in popular, providing a powerful toolkit for 7. Daccord, N. et al. Nat. Genet. 49, 1099–1106 (2017). methodology and biotechnology. digging into the hidden nature of genome 8. Zhao, G. et al. Nat. Plants 3, 946–955 (2017). 9. Wan, T. et al. Nat. Plants https://doi.org/10.1038/s41477-017- The first genome-wide transfer DNA sequences. In an article in this issue, Xu 10 0097-2 (2018). mutagenesis of A. thaliana in 2003, led by and coworkers identify a key heterodimer 10. Xu, C. et al. Nat. Plants https://doi.org/10.1038/s41477-017- the Salk Institute, was a major breakthrough that controls cell reprogramming during 0095-4 (2018). in plant functional genomics . This Arabidopsis organ regeneration. To test 11. Wang, M. et al. Nat. Plants https://doi.org/10.1038/s41477-017- 0096-3 (2018). enormous effort directly triggered the the hypothesis, they performed high-quality blossoming of plant molecular genetics in analyses using mutant lines from ABRC, Acknowledgements the past 15 years, and its influence is still transgenic plants, confocal microscopy The editorial team acknowledges the support of the Cold strong today. For Arabidopsis researchers, and approaches to identify both Spring Harbor Laboratory, and the Meetings & Courses it is now hard to imagine how experiments protein–protein interactions and Department in particular, for allowing access to the could be designed and conducted without protein–DNA interactions. abstract books of the historical meetings. Nature PlaNts | VOL 4 | FEBRUARY 2018 | 55 | www.nature.com/natureplants © 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. © 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

Journal

Nature PlantsSpringer Journals

Published: Jan 31, 2018

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