© 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. © 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.
From genes to networks
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
(CSHL), recently hosted their 11th
Plant Genomes meeting while also
celebrating the 20th anniversary of their
biennial Plant meeting series. This year also
marks the 20th anniversary of the National
Plant Genome Initiative (NPGI), which has
been dedicated to accelerating the basic and
translational research of plant genomics.
With the support of the NPGI and various
global collaborations, Arabidopsis thaliana
became the first sequenced plant
The publication of its genome in 2000
was three years ahead of the completion of
the Human Genome Project, marking the
dawn of the genome era in plant research.
Now there are at least 264 plant species with
their reference genomes sequenced and
published (http://www.plabipd.de), from
superficially simple algae and bryophytes to
complex gymnosperms and angiosperms.
Opening the abstract book of the first
CSHL Plant Genomes meeting (1997), we
can still feel the beat of the Arabidopsis
genome project. The sequencing updates
of Chromosome 1-5 were made by at least
eight international research groups from
regions including the United States, the
United Kingdom, France and Japan.
Despite only partial sequencing data being
available, gene annotation and positional
cloning were already being pursued to
understand the functions of different genes.
At this point, the limited resources and
tools of functional genomics were serious
obstacles for gene studies. It is a favourite
joke among early-career scientists today
that “if we could take a time machine back
to the decade when cloning a gene was
sufficient to publish a high-impact article,
research life will be much easier”. However,
the expanding demand for new tools also
generated great potential for innovations in
methodology and biotechnology.
The first genome-wide transfer DNA
mutagenesis of A. thaliana in 2003, led by
the Salk Institute, was a major breakthrough
in plant functional genomics
enormous effort directly triggered the
blossoming of plant molecular genetics in
the past 15 years, and its influence is still
strong today. For Arabidopsis researchers,
it is now hard to imagine how experiments
could be designed and conducted without
the seed collection in the Arabidopsis
Biological Resource Center (ABRC) or
access to the Arabidopsis Information
Rice (Oryza sativa) was the second
plant species to have its whole genome
. The release of the reference
genome of rice and other important
crops has provided great opportunities
to understand the history of crop
domestication and identify landmarks
for crop improvement. Combining the
knowledge gained from functional genomics
and modern plant breeding, scientists have
successfully designed and developed new
rice varieties with high-yield and superior-
. Similar improvements in
other crops are also ongoing.
These achievements and foundations
have pushed plant research into the fast
lane. The sequencing and assembly of
high-quality ‘platinum’ genomes
empowers plant scientists to pursue the
details of genetic regulation and deepen
our understanding of plant evolution. For
example, in this issue, Wan and colleagues
report a high-quality draft genome of
Gnetum montanum, a gymnosperm and
the first sequenced species for gnetophytes.
They revealed unique genomic features of
this species that seem to place it closer to the
basal lineage of angiosperms, indicating an
early evolutionary path for seed plants.
In addition to these high-quality
genomes, revolutionary technologies and
tools used for functional genomic analysis
are constantly emerging, including new
transformation methods, gene-editing
tools, yeast two-hybrid systems, mass
spectrometry and high-throughput
bioinformatics. Combining different
methods for functional research is becoming
popular, providing a powerful toolkit for
digging into the hidden nature of genome
sequences. In an article in this issue, Xu
identify a key heterodimer
that controls cell reprogramming during
Arabidopsis organ regeneration. To test
the hypothesis, they performed high-quality
analyses using mutant lines from ABRC,
transgenic plants, confocal microscopy
and approaches to identify both
protein–protein interactions and
Such newly developed technologies
liberate researchers from conventional
research scenarios and open a new dimension
of network thinking. But translating
information from genes to proteins is not an
easy road. Simply analysing the sequences
of genes will never tell the true stories of
gene regulation. Using high-throughput
chromosome confirmation capture (Hi-C)
and chromatin interaction analysis through
paired-end tag sequencing (ChIA-PET),
Wang et al.
present the 3D genome
architecture of cotton and show how its
evolutionary dynamics altered the networks
of gene regulation, again in this issue.
If there were a time machine, it would
be fascinating to shuttle back to 1997, to
fact-check the memories of the scientists
who attended the first CSHL Plant meeting:
The Arabidopsis Genome: From Sequence
to Function. Whether you regard the
intervening 20 years as long or short, they
have seen a remarkable accumulation of
knowledge and technologies in plant science.
The scope of the recent CSHL Plant meeting
Plant Genomes & Biotechnology: From Genes
to Networks reflected those changes. With our
current ability to do incredible research in an
unprecedented landscape, we should never
forget the historic path that has led those
possibilities, nor fail to keep in mind how
important it is to offer shoulders for younger
generations to stand on, and see further. ❐
Published online: 31 January 2018
1. e Arabidopsis Genome Initiative. Nature 408, 796–815 (2000).
2. Alonso, J. M. et al. Science 301, 653–657 (2003).
3. Yu, J. et al. Science 296, 79–92 (2002).
4. Go, S. A. et al. Science 296, 92–100 (2002).
5. Zeng, D. et al. Nat. Plants 3, 17031 (2017).
6. Mascher, M. et al. Nature 544, 427–433 (2017).
7. Daccord, N. et al. Nat. Genet. 49, 1099–1106 (2017).
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-
10. Xu, C. et al. Nat. Plants https://doi.org/10.1038/s41477-017-
11. Wang, M. et al. Nat. Plants https://doi.org/10.1038/s41477-017-
The editorial team acknowledges the support of the Cold
Spring Harbor Laboratory, and the Meetings & Courses
Department in particular, for allowing access to the
abstract books of the historical meetings.
Nature PlaNts | VOL 4 | FEBRUARY 2018 | 55 | www.nature.com/natureplants