Molecular evolution connects a broad range of fields andsheds light on what life isKURAKU, Shigehiro Professor

Molecular Life History Laboratory,
Department of Genomics and Evolutionary Biology

Professor Kuraku graduated from the Faculty of Science at Kyoto University in 1999. After receiving his PhD from the Graduate School of Kyoto University in 2005,
he served as a research scientist at RIKEN. He obtained a junior faculty position at the University of Konstanz (Germany) in 2007. He became the Unit Leader atRIKEN CDB in 2012 and became Team Leader, also at RIKEN BDR in 2019. He was appointed Professor at the National Institute of Genetics (NIG) in April 2021.

Molecular evolution is a branch of biology that studies how organisms evolve based on molecular information
including DNA and protein sequences. Professor Shigehiro Kuraku has been investigating the origins of biologicalphenomena, mainly in developmental biology, using DNA sequence analysis of diverse vertebrates. He states that
"Molecular evolution is an essential tool for all fields of life science.”

Shark research is critical to overview
vertebrates

rarity in that it was completed in one laboratory from start to finish.

I am planning two directions for my research at NIG. First, I would liketo analyze groups of animals for which there is not a lot of genome
sequence information, in order to make them equally comparablewith other groups. Second, after comparing genomes, I plan on
finding any distinct differences and clarifying how these differences
contribute to the characteristics that make up the identity of an organism.
I would like to explain this by introducing some of my research. This
includes research I carried out on sharks, which I published in 2018.
There were two groups of vertebrates that were severely lacking indetailed genome information: cartilaginous fish and reptiles.
Cartilaginous fish mainly comprise sharks and rays. We analyzed thegenomes of three species: the bamboo shark, the catshark, and thewhale shark. Genome analysis of shark species was lagging behind
partly because their genome is large and difficult to analyze. However,we were able to achieve a highly comprehensive analysis that no one
else could match at the time. I think the work we carried out was aWe approached the question "what in the shark genome really makesa shark?" from various angles, using the genome sequence information.
We examined the genes that produce hormones that control appetite,growth, reproduction, etc. and pinpointed those that are specific to1

I entered Kyoto University where Professor Miyata conducted his
research and attended his lectures at every opportunity. I had noreservations about joining Professor Miyata's laboratory for myundergraduate research, and there I learned how to conduct researchon molecular evolution.

sharks. We also looked at organisms that have been well studied,such as humans, and clarified how their hormone repertoires areestablished.
We also investigated opsin gene repertoires that control vision andfound that the catshark may not see in colour. Nowadays, catsharks
can reside in shallow water. However, our findings suggested that
their ancestors were likely to have lived deep in the sea. We also
revealed that a whale shark opsin gene can absorb light of wavelengths
that can penetrate the deep sea. This knowledge regarding their
deep-sea habitat was obtained through experiments where proteins
were synthesized based on the genome sequences. This was allaccomplished without the need to sacrifice living organisms.

In the study of molecular evolution, an evolutionary pathway is deduced
after the inference of a phylogenetic tree based on DNA and protein
sequences of biological species. To be specific, it is necessary to build
a phylogenetic tree by comparing the sequences of a broad range ofspecies. Since a vast number of calculations are required, you sometimes
have to write your own programs and carry out calculations using acomputer specialized for large-scale analysis. At the Miyata Laboratory,
I was able to learn about molecular evolutionary analysis startingfrom the basics. This included using a computer to compare sequences,calculating the divergence time (age) of particular species, andbuilding phylogenetic trees.

The National Institute of Genetics is located close to Suruga Bay—awell-known deep-sea area. Here, we will continue to push forwardwith our research into sharks. Cartilaginous fish have a unique
phylogenetic position among vertebrates, and yet little molecularresearch has been done on them. By analyzing these species, we will
not only elucidate the evolutionary process of early vertebrates thatexisted on Earth 500 million years ago but also explore the conditionsof ecological systems in the sea that need to be protected.

Taking the plunge into the world ofdevelopmental biology
When I was a graduate student, the availability of animal genome
sequences was very limited. I sometimes performed experiments toclone gene fragments of the organisms I was interested in. However,most of my time was spent sitting in front of a computer analyzing thenucleotide sequences of the DNA, consisting of A, T, G, and C. Before
long, I thought I should also train myself with hypothesis-based
experiments using cells and tissues. That is what most other researchers
were working on.
In my doctoral program, I decided to join a laboratory that wasconducting research into developmental biology. From there, I
commenced my own research in the laboratory of Dr. Shigeru Kurataniof the RIKEN CDB (RIKEN Center for Developmental Biology). The
Kuratani laboratory specializes in comparative developmental biology
studies, in particular, EvoDevo (which means "evolutionary developmentalbiology"). My research was focused on the evolution of the shells ofsoft-shelled turtles, and I obtained my PhD based on this research
theme.

The research presented here includes the two directions I previously
mentioned: organizing information that is the basis for comparison ata molecular level, and shedding light on biological phenomena. Thereis also another common characteristic behind my research methods
that I would like to emphasize—a means to connect with different
scientific disciplines through research on molecular evolution. I would
like to explain this while introducing my career to you.

First encounter with molecular evolution
When I first learned about molecular evolution, I was still a high school
student preparing for my university entrance exams. It was just one
week before the National Center Test for University Admissions. Bychance, I was drawn to a book in a bookstore authored by Professor
Takashi Miyata of Kyoto University (Now professor emeritus of Kyoto
University) called "Invitation to the Study of Molecular Evolution," andended up reading it from start to finish in one sitting. The following isa quotation from the book: "Conventional research on evolution waslimited to comparing superficial phenomena, such as morphology, andtended to be subjective. However, the study of molecular evolution
will make the research quantitative and objective for the first time.”

At that time, methods exploring functional changes of developmental
regulatory genes while keeping in mind the evolution of those genes
were not established. I was already familiar with molecular evolution
and felt as though a fresh perspective had opened up in front of me. I
realized that if I were to link developmental biology together with2

This is how I was able to secure a position abroad where I could
conduct research based on my own ideas. Initially, I spent all of mytime preparing for teaching. Fortunately, I was in charge of a class
where I could communicate in English, and not in German. Despite
having an interest in language and being proficient in English, it was
not easy to teach. First and foremost, I had no prior teaching experienceeven in Japanese, and it took more than two years before I was able
to adjust and think through things calmly.

molecular evolution, I could play a role of my own in the field.
At the Kuratani Lab, I had many opportunities to get involved in othermembers' research. I started considering how I could solve problems
by applying my skills, and what was required to move the wholeproject forward. This experience trained me well and thereafter it
became a fundamental part of my research style.
Another valuable aspect of my time there was the frequent discussions
I had with Dr. Kuratani. He would ask me various questions such as"How do you think you can outperform that researcher?" It was as if
he was testing me to see if I could become a more independent
researcher. I think these experiences helped form the foundations ofmy attitude toward research today.

It was only after I had a few PhD students under my wing and could
hire part-time students that I was able to focus on my research.

Conducting research based on my own
plan
After I received my Ph.D., I still had some research to do, so I stayedat the Kuratani Lab for two more years as a postdoctoral researcher. Ihad already been looking for a postdoctoral position before I got mydegree. My primary goal was to study abroad, but I guess I was lacking
something since I missed out on all the opportunities I applied for. At
this stage, I was aiming to get a fellowship and carry out research on
my initiative, rather than getting paid to do lab work. I think this idea
narrowed my opportunities to get accepted.
At that time, genome analysis of species other than conventional
experimental animals was gaining traction. Taking advantage of thistrend, I joined the International Genome Consortium of Sea Lamprey.
I also got the opportunity to have a say in the overall direction ofprojects by producing most of the figures for the published paper.
Through this experience, I was able to get a feel for the direction thatgenome analysis was going in around the world and could use thisknowledge to my advantage in my own research. Using the sequence
information developed by the Consortium, my research was mainly
focused on the evolution of the gene repertoire that controls thedevelopment of vertebrates. This covered many vertebrates, including
lampreys.

In my second year, I changed my mind and decided to look for PI(Principal Investigator) positions. I figured this was best if wanted totry working with my ideas. There was a public offering for a juniorleader position at University of Konstanz in Germany which I thought
was a perfect fit. It was posted on a job site run by Nature, and I felt it
was an opportunity I couldn't pass up.
Dr. Axel Meyer, a professor at the university who posted the position,
specializes in evolutionary biology. By chance, I had met him at a mixer
at an international conference just three months previously, where wesat down and had a conversation. I applied for the job immediately,and fortunately, I was hired.

Humans and experimental animals alone comprise only a small
proportion of the broad range of vertebrates. The inclusion of information
on cartilaginous fish like sharks as well as lampreys will enable us todelve into the genetic makeup of the ancestors of vertebrates. Only
after doing this will we be able to understand changes that haveoccurred in the phylogeny leading up to humans and experimental
animals. As a result of a series of studies, it became clear that many
genes have been retained throughout the evolution of animals. Many
genes disappeared after the main vertebrate groups branched out.

I worked as a junior leader for five years at University of Konstanz,
located near the Swiss border, starting in 2007. The University wasselected as the target for a national excellence initiative project thatyear. As a junior leader, I was treated as a member of a large researchgroup led by the professor and was responsible for undergraduate
education including practical training courses in addition to generallectures. I was able to freely pursue research themes based on myown ideas, while communicating with the professor.
From the second year of my appointment, I applied for the German
Research Foundation (DFG) grant, which is similar to the Japanese
Grant-in-Aid for Scientific Research. As a result, I was successful insecuring research funding. There are no categories based on age orexperience, and applications are accepted year-round. I felt that thisis very different from the Japanese system.

Having a job in data production in Japan
Around my fourth year at University of Konstanz, I started looking formy next position. I was particularly conscious about current trends,and up until that point I was using genome information prepared byothers in my research. The continuity of genomic DNA sequences
was often lacking, and in order to make my analyses more accurate, I
figured it was necessary to become familiar with DNA sequencing
technology—something that had already achieved huge progress atthe time. As a result, I was hired for a leadership role by RIKEN CDB

My time in Germany:
preparing for lectures3

overview of the entire genome. People may think that to study evolution
is to study the past. However, to study evolution is to investigate howa living organism has evolved into what it is today and how it differsfrom other organisms that make up the ecosystem. In other words, itis also a study that teaches the "now" of biodiversity.

that was setting up a new division using this cutting-edge technology.
So, after five years of life in Germany, I decided to move back to Japan.
The main role of the position at RIKEN was to support NGS(next-generation sequencer) analysis at the request of the researchers
in the institute. I was a former employee of RIKEN, but this time aroundit was an entirely different position. I started my life thereby learning
about new advanced technologies, putting off my research. In mynine years of service there, I gained extensive experience in analyzing
different information, from sequencing genomes to profiling gene
expression. Researchers from various fields of developmental biology
were working around me, and I tried my best to fulfil the role ofsupporting DNA information analysis through a number of collaborative
research projects. Using the experience I gained in my doctoral course,
where I worked with the approach of incorporating different fields ofstudy into developmental biology, I felt I was applying the same approachon a broader scale in my work.

Another method of research I am focusing on is analysis at the cellularlevel. As technology advances, acquiring omics information at thesingle-cell level has become an increasingly active field around theworld. These techniques determine how genome information is beingexpressed. Much as the key concept behind the Neutral Theory ofMolecular Evolution is that there are functional constraints on genefunctions, functional constraints to achieving cellular activity should
also exist. However, our knowledge is limited to organisms that haveshort lives and small genomes. If we apply a molecular evolutionary
approach to omics information, I think we will be able to come close
to answering various questions, such as what are the factors that
determine the size of the genome? —something we don't yet have ananswer for. It is important to compare and explore not only modelorganisms but also various organisms in nature, using a molecular
evolutionary approach.

Recently, there is something I have begun to feel quite strongly about.
Large-scale information analysis technology has become very popularand there is an increasing number of people who can use it. However,there is a shortage of people who have both the skills to perform thisanalysis and an understanding of the concept of molecular evolution.
This poses a problem since it has become possible to compare a broad
range of species in various fields of life science, and the need forinterpretations based on the understanding of evolutionary biology
has never been greater.

Planning a new type of research on
molecular evolution at NIG
I began to think that setting up laboratories focused on molecular
evolution and providing guidance to young people was the responsibilityof those who specialize in the field. I came to NIG with that idea.
Today, I feel that molecular evolution is not only a single academic
field, but also a valuable tool for all life science researchers. In theshark research I explained at the beginning of this interview, molecular
evolutionary analysis techniques were used in discoveries related todevelopmental biology, comparative endocrinology, and ecology.

Message to young people
It is my motto not to narrow down my research subjects. Many
researchers narrow down their themes and concentrate on a focused
topic. This creates a gap between one research field and another. I
always want to keep my eyes open and connect these gaps using anapproach I'm good at. I think connecting fields and elements together
is a process that helps push science forward, and it is something I am
particularly enthusiastic about.
I think molecular evolution plays a role in making these connections.
With this in mind, I believe it is critical to have a broad perspective. I
named my laboratory the "Molecular Life History" Lab with the ideathat we would not limit ourselves to a particular field or, conversely,
exclude any other fields. When we try to elucidate the origins of life ata molecular level, which is very complex, we must face the problem
head-on by incorporating techniques and knowledge from all research
fields. Those interested in joining my laboratory are expected to learn
how to develop a perspective that goes beyond a single field of study
and to expand their networks for this purpose.

Many interesting animals have undergone striking phenotypicevolution. For example, whales live in the sea even though they aremammals, and turtles have evolved to have shells. In this regard, Iwould like to find out how the genome determines the characteristics
of each organism by looking at a variety of organisms and having an

If you are going to be a researcher, my wish is that you develop yourcommunication skills to engage in creative activities. It is important to4

have the ability to deepen your research through communication withothers, including using English.
One more important thing I would like you to remember is that you
are a person before you are a researcher. Please use your time wellnot only in research but for other things, too. This will lead to better
research.
I like to watch baseball and soccer myself. There's a special place inmy heart for team play even in research, and I always get the mostjoy when I achieve something as a team. This is because I get theopportunity to achieve things that go beyond my own imagination. Iwould like to work with members of my laboratory to form an effective
team.

Interviewer:
Yoshiko Fujikawa, Science writer
Photographer:
Mitsuhiko Kurusu, NIG ORD
July 2021