DOI: 10.1002/ppp3.8
OPINION
Beautiful genes, beautiful plants Huanming Yang | Xiaoling Wang | Juan Tian BGI‐Shenzhen, China Correspondence Huanming Yang, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China. Email:
[email protected]
Societal Impact Statement We all have reason to acknowledge plants, as humans, together with all other animals, breathe the oxygen produced by plants every second of the day, and we need the diversity of plants to maintain a balanced ecological environment. Plants also help us to understand the secrets of life and contribute to our understanding of ourselves. The Earth BioGenome Project (EBP), announced in February 2017, has the ambitious mission to sequence “all life on Earth,” of which plants are of course a major part. Summary Research into plants has led to many vital contributions to science in general. International collaborations are now the lifeblood of scientific research, particularly in the field of genomics. From humble, underfunded beginnings as the only developing nation in the Human Genome Project (HGP), China has emerged as a powerhouse of genomics research with major involvement in a whole host of genome‐sequencing projects worldwide. Today, the cutting‐edge international research projects are focused on genome writing and edit‐ ing, allowing us to engineer organisms to produce bioproducts or to display a new suite of phenotypic characteristics. It is possible to bioengineer anything if all the constituent parts of the metabolic/signaling pathways and the regulation network are understood. Decoding the secrets of life is vital for enhancing our appreciation of plants, our understanding of how we can benefit from them, and our ability to protect them. Once again, plant science is driving our understanding of the world in general, which may enable us to protect both plant biodiversity and to create a beautiful and brilliant future for humankind. KEYWORDS
Earth BioGenome Project, genome sequencing, genome writing, genomics, Human Genome Project, Life 3.0, Shenzhen Declaration, Three Million Genomes Project
1 | I NTRO D U C TI O N
in 1984. … An incredibly beautiful tapestry of blue and white, tan, black and green seems to glide beneath you at an elegant, stately
Humankind has achieved a great deal in the last century. One of
pace.” We are passionate about our planet and the life it sustains;
the greatest achievements was that we looked at Earth from a
for example, at least half of the poems written during the Chinese
new direction, observing life on our green planet from a greater
Tang dynasty (618–907) focus on the beauty of life.
distance than ever before. Yang Liwei, China’s first astronaut, was
Plants make this planet colorful and beautiful. They are part of
spellbound by space and his view of our beautiful home. Kathryn
our ecological civilization. We are surrounded by plants and can‐
Sullivan (2002), the first American woman to walk in space, noted,
not live without them; we breathe oxygen they produce, eat food
“I first saw the Earth—the whole Earth—from the shuttle Challenger
and take medicines derived from them, and use them for textiles,
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2018 The Authors, Plants, People, Planet © New Phytologist Trust Plants, Planet, People. 2019;1:27–31.
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building materials and fuel. In China, tea is embedded within the cul‐
but China’s contribution was acknowledged by the leaders of the
ture, and innovative ideas for architecture have been derived from
United States and the United Kingdom, as well as in the announce‐
plants; for example, the China National GeneBank building, takes the
ment of the completion of the HGP by the government leaders of
form of a beautiful rice field (Figure 1b).
the six member countries.
Despite their absolute importance, many plants are under threat. The consequences of our continued destruction of eco‐ systems are unimaginable, although plants are already warn‐ ing us. The XIX International Botanical Congress was held in
3 | O N G O I N G I N FLU E N C E O F TH E H U M A N G E N O M E PROJ EC T
Shenzhen, China, to discuss the importance of plants and their roles in sustaining life and making it more beautiful, as well as
The HGP had three major impacts on life sciences and society. The
their use in research.
first is that it has nurtured a culture of collaboration, as the data produced was generated under an ethos of “Owned by All, Done
2 | PL A NT S A N D S C I E NTI FI C R E VO LU TI O N S
by All, and Shared by All.” The leader of the HGP in the UK, Nobel Laureate John Sulston, noted, “I especially salute the Chinese Colleagues who have contributed so much to the international genome effort … and affirmed its common ownership by all man‐
Plants have been used to make important contributions to science for
kind” (Wang, Xia, Chen, & Yang, 2018). Today, vast international
centuries. Gregor Mendel’s work on peas was crucial for the discovery
collaboration has become a major part of the scientific culture,
of genes, while Barbara McClintock’s discovery of “jumping genes” in
including ongoing projects such as the Earth BioGenome project
maize (Zea mays) was another ground‐breaking moment in genetics.
(EBP), which aims to sequence the genomes of all known eukary‐
More recently, Youyou Tu discovered artemisinin, a compound pro‐
otic organisms over the next 10 years (Lewin et al., 2018), and the
duced by sweet wormwood (Artemisia annua) that can be used to treat
African Orphan Crops Consortium, which aims to enhance the
malaria (Tu, 2011). There are so many examples of plants benefitting
nutritional content of over 100 traditional African food crops by
science; Arabidopsis thaliana as a model organism helps us to under‐
sequencing, assembling, and annotating their genomes (https://
stand genomics more broadly, highlighting that an understanding of
africanorphancrops.org/; Fox, 2013). In the Nature Index 2015 of
plants enables us to understand ourselves (Meinke et al., 1998).
Collaborations, the BGI in Shenzhen, China, was listed as the high‐
The discovery of DNA’s structure by Watson and Crick (1953)
est‐scoring organization for collaborations, with the widest net‐
was the first revolution in life sciences in the 20th century. The
work of colleagues in many countries across the world (Grayson
double helix has become something of a logo for the past century,
& Pincock, 2015). Today, it is almost impossible for researchers
at least for the natural sciences. Further discoveries about how
working in the field of genomics not to be involved in international
DNA is packaged into chromosomes and how genes can be mod‐
collaborations, as big goals cannot be achieved alone.
ified epigenetically to affect their expression showed us how the
The second impact of the HGP is that it led to the creation of a
genome of a species defines its every characteristic. This led to the
new field of science—“omics” research. In 2013, Monya Baker noted
second revolution, the sequencing of genomes, and specifically the
“Where once there was only the genome, now there are thousands
Human Genome Project (HGP). This was initially conceived in the
of omes,” and Stephen Friend commented that, “Today, we’ve got‐
USA, and British, Japanese, French, German and Chinese research‐
ten to the point where almost no biological phenomenon can escape
ers joined the project in 1999, with China being the only developing
‘omicsization,’ and within the next 25 years, ‘omics’ will be the big‐
country to take a role in sequencing the human genome. It is dif‐
gest, if not the only, game in town” (Friend, 2011).
ficult to imagine how poor and under resourced Chinese research
The third impact of the HGP was the development of new
laboratories were in 1999; we could not afford a laboratory bench
technologies for life sciences, particularly for genome sequencing.
or table, making the job extremely difficult. It was hard and tiring,
Early career researchers may advocate such a slogan, “sequencing,
(a)
(b)
F I G U R E 1 (a) The April 2002 issue of Science, featuring the publication of the draft genomes of Oryza japonica (Goff et al., 2002) and Oryza indica (Yu et al., 2002), the cover image is a photograph of the Honghe Hani rice terraces in Yunnan Province, by Liwen Ma and Baoxing Qiu; (b) The China National GeneBank building which takes the distinctive form of a rice field (image courtesy of the China National GeneBank, https://www.cngb. org/index.html)
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YANG ET AL.
sequencing, sequencing,” but its concept was taken from the father
a logical development, and the ultimate stage of genomics. Of the
of sequencing technology, Frederick Sanger (1988). The language of
truly revolutionary technologies around today, we consider the most
information science uses 0s and 1s, while the language of life com‐
important to be genome writing and editing. Currently, genome writ‐
prises four letters: ATCG. In a sense, sequencing is the digitization
ing is at the stage where we can redesign and synthesize new com‐
of life. Francis Crick (1958) called it a “sequentialisation,” enabling us
ponents within a genome or metabolic pathway. This revolution in
to read life like a book; however, we are still not in a position to fully
bioindustry means the genes of any specific metabolic pathway can
understand this book in its entirety.
be transformed into yeast to synthesize a bioproduct. One example
It has been said that everyone comes to the land of the United
is the biosynthesis of the antimalarial artemisinin, which is naturally
States of America with a dream. We would say that everyone comes
produced by either wild or cultivated varieties of sweet wormwood
to the field of genomics with two dreams or a dream with two parts;
(Artemisia annua). Genome sequencing and subsequent biochemi‐
the first is to sequence every living thing on the planet, including an‐
cal analyses led to the identification of the genes involved in the
imals, plants, fungi, bacteria and other microorganisms. Our mission
metabolic pathway that produces artemisinin. These genes have
is to collect and preserve all living things on the planet before it is
been transformed into yeast (Saccharomyces cerevisiae), causing it to
too late—before extinction. Many animals and microorganisms have
biosynthesize high levels of artemisinin; a small fermentation tank
been sequenced by international collaborations of researchers, and
can produce tons of artemisinin for a low cost (Paddon et al., 2013).
plants are most important subjects for sequencing. The genomes of
A second example is the production of morphine, the precursors of
many plant species have already been sequenced, but this work will
which have been successfully biosynthesized from sugars in geneti‐
be taken much further over the next decade by the EBP, described
cally engineered yeast (DeLoache et al., 2015). Although morphine
above (Lewin et al., 2018).
is more difficult to biosynthesize than artemisinin, this research was
The second dream of genomicists is to sequence everybody
another very important milestone in genome writing. Lammens,
in the world. At the 6th International Conference on Genomics in
Spekreijse, Puente, Chinthapalli, and Crnomarkovic (2017) listed 120
Shenzhen, China, Huanming Yang announced the Three Million
high‐value chemicals that could be bio‐manufactured in the future.
Genomes Project, in which we will sequence the genomes of one
Synthetic agriculture and bio‐manufacturing may also play major
million humans, one million plant and animal species, and a million
roles in feeding the growing human population; therefore, sequenc‐
microorganisms. China is now considered a world leader in genome
ing more plants to elucidate their metabolic/signaling pathways is
sequencing: we will complete the Three Million Genomes Project,
vital for the development of technologies we are likely to rely on in
but like all major genomics projects, we cannot do it alone.
the future. These data could one day facilitate the production of any and all biological products in fermenting tanks, assuming the meta‐
4 | G E N O M E W R ITI N G
bolic and signaling pathways are fully elucidated. Producing known compounds is just the beginning, however. In the future, we could redesign and synthesize whole prokaryotic
The next revolution in life sciences will probably be genome writ‐
genomes, such as bacteria. So far, researchers have been able to
ing. In other words, going from genome reading to genome design.
produce simple partially synthetic cells with predicted phenotypes,
This is also called Life 3.0. The redesign and synthesis of genomes is
the first of which was nicknamed Synthia (Mycoplasma laboratorium;
F I G U R E 2 The assignments of yeast chromosomes across the international Sc2.0 consortium. Image reproduced with permission from Richardson et al. (2017)
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30
Gibson et al., 2010). The next phase is the redesign and synthesis
to protect plants is to protect ourselves, to save plants is to save
of a monocellular eukaryotic whole genome, which began in yeast.
ourselves. We cannot excuse ourselves because of ignorance, make
The First International Synthetic Yeast Genome Meeting, Sc2.0,
mistakes because of hesitation, and keep using plants solely for our
was held in Beijing, China, in 2012, during which each of yeast’s 16
own sake. It is not difficult to imagine what the world would become
chromosomes were assigned to research groups around the world
if we continue to abuse our relationship with plants.
(Figure 2). As a result of this international collaboration, a highly
At the same time, we have never been as confident of the fu‐
modified synthetic Sc2.0 genome was reported in 2017 (Richardson
ture for plants and nature as we are today. Our ancestors passed
et al., 2017). The redesign and synthesis of multicellular eukaryotic
on an innate knowledge of nature that has been accumulated over
whole genomes are also currently underway, with an initial focus on
millennia. Our scientific expertise has been built on foundations
the model organisms Caenorhabditis elegans and Arabidopsis thaliana.
laid for centuries by pioneering predecessors, enabling us to make
We cannot say we fully understand life until we are able to create it.
so many scientific achievements in the last decades, especially the
Creating synthetic genomes inevitably raises questions about
newly emerging discoveries in genomics, information science and
biosafety and bioethics; however, the process is controllable and
big data. At the XIX International Botanical Congress, we reached
all potential issues are covered by the regulatory frameworks and
a consensus on the sober and wise missions we must undertake,
principles already in place. Of course, we must still be cautious; sci‐
based on our strong belief of ecological civilization and biodiver‐
entists surely have freedom in research, but we are responsible for
sity, outlined in the Shenzhen Declaration (Crane et al., 2017, and in
any safety issues. The responsibilities and freedoms of scientists re‐
this issue). We should not hesitate to stand up and act now, before
garding the synthetic yeast project is discussed in a previous report
it is too late!
(Sliva, Yang, Boeke, & Mathews, 2015).
Ultimately, to succeed, we need broad international collabora‐ tion within plant sciences. We need new and coordinated actions
5 | D ECO D I N G TH E S EC R E T S O F LI FE
that will expand and enlarge our ability to accomplish our botanical research. In the Shenzhen Declaration, we particularly call for in‐ creased associations with our colleagues from developing countries,
If the 20th century was the century of physics, this century might
in which the richest plant resources and diversity are found, and who
be called “the century of the gene.” It seems clear that the life sci‐
have the biggest potential for future research development.
ences will shake up the world in the 21st century, shaping and re‐ shaping the future of humans and all other life on Earth. The 1968 book Biology and the Future of Man, edited by Philip Handler, outlined the advances that had been made in life sciences at that time, and at‐ tempted to create a dream of the future. One quotation particularly resonates “Homo sapiens, the creation of Nature, has transcended her. From a product of circumstances, he has risen to a product of responsibility” (Handler, 1968). We are confident of the brilliant fu‐ ture of humankind, and have confidence in the young people who will help to shape it. Let us appreciate the beauty of life and decode its secrets. Over 7,000 scientists from around the world came together in Shenzhen, China, at the XIX International Botanical Congress to sing the praises of plants and share innovative ideas, call for collaborative and co‐ ordinated actions, and dream of an even better future together. No words can ever express our respect and admiration for plants, be‐ cause without plants we as humans could not survive. It is plants, silent and active, that offer the oxygen that we breathe and the food that sustains us and all other animals. Plants are major factors of ecology and biodiversity, and teach us the concepts and signifi‐ cance of harmony, colorfulness, and beauty, inspiring us to cherish and embrace nature as one of the origins of our knowledge, culture, and civilization. Plants and humans evolved together. As plant scientists, we cannot hide our concern and worry for the future of plants and the planet any further; we must confess and rethink our attitudes and behaviors toward plants. To care for plants is to care for ourselves,
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How to cite this article: Yang H, Wang X, Tian J. Beautiful genes, beautiful plants. Plants, People, Planet, 2019;1:27–31. https://doi.org/10.1002/ppp3.8
