京都大学教育研究振興財団助成事業
成 果 報 告 書
2019年5月31日

公益財団法人京都大学教育研究振興財団会 長

藤洋 作

助 成 の 種 類

様

所属部局

化学研究所

職名助教

氏

名

Romain Blanc-Mathieu
30 年度 ・研究活動推進助成

申請時の科研費
研 究 課 題 名

珪藻類の多様化を支える進化メカニズムの解明

上記以外で助成金を 充 当 し た
研 究 内 容Not applicable

助成金充当に関わる共同研究者

発表学会文献等成 果 の 概 要

（所属・職名・氏名）
Not applicable（この研究成果を発表した学会・文献等）
None

研究内容・研究成果・今後の見通しなどについて、 簡略に、A４版・和文で作成し、添付して下さい。（タイトルは「成果の概要／報告者名」）

1,000,000 円
1,000,000 円
0円

交付 を 受 けた 助成 金額
使 用 し た 助 成 金 額返納すべき助成金額費会

計報

告
助成金の使途内訳

目金額

RNA sequencing (March 2019)25,332 JPY

Business trip Fukui (March 2019)18,000 JPY

Business trip + conference
Lyon (France) (2-11 July2019)
Conference Yamanashi(Japan) (10-13 September2019)
Business Trip + Conference
Aussois (France) (6-12October 2019)
Sequencing of diatoms +diverse (books, etc)

300,000 JPY (estimate)
100,000 JPY (estimate)
300,000 JPY (estimate)
256,668 JPY (estimate)（今回の助成に対する感想、今後の助成に望むこと等お書き下さい。助成事業の参考にさせていただきます。）

当財団の助成について珪藻類の多様化を支える進化メカニズムの解明
Romain Blanc-Mathieu
Summary of research aim and results:
Diatoms are unicellular phytoplankton that contribute to 20% of the global primaryproduction; they have colonized all marine and freshwater habitats and diversified into
thousands of species. Investigation of their evolutionary success and prediction of their fate inresponse to the ongoing global environmental changes is critical to understand thesustainability of our environment. In this perspective we engaged in comparative population
genomic of diatoms and their sister group Parmales. The use of Parmales genomic data gives
us a strong advantage to infer what features (genes, genome organization, ploidy level, etc)
were present in the diatoms-Parmales last common ancestor and which ones have been
derived in Diatoms. This can give us hint as to what functional innovation (e.g. urea cycle) or
phenotypic characteristics (e.g. ploidy change) may be responsible for the success of diatoms.
As a part of a collaborative work with the Parmales genome group led by Dr. Kuwata, I
performed an in silico analysis to infer the ploidy level of the reference Triparma laevis(Parmales) strain (NIES-2565) whose cells are armed with silicate plates and deprived offlagella. Our results reveal an extremely low amount of segregating genetic variation within
the culture of the reference Triparma laevis strain. This result itself is somewhat inconclusive(absence of evidence is not evidence of absence) as it is compatible with either Parmales
armed cells being haploid or nearly-fully homozygous polyploid. Hence my collaborators
performed additional workbench experiments to measure the relative amount of DNA inParmales cells compared to other species whose genome size and ploidy level is known.
Result revealed a DNA amount twice larger than the size of the reference genome assembly(40Mb) of Triparma laevis, thereby indicating that these cells are diploid.
This suggests that the ancestor of Diatoms and Parmales was already an organism
alternating between a diploid and a haploid stage. Diatoms are known diplontic organisms(i.e. most of the life cycle is diploid). In the case of Parmales some cultures are made of
naked flagellated cells (e.g. Triparma pacifica and this culture is haploid) and hence may behaplontic (spend most of their life cycle as haploids) while others (e.g. Triparma laevis) aremade of armed cells and hence are though to be diplontic. Parsimony would suggest that thediatoms ancestor was diplontic but a more carful mapping of the ploidy phase onto theParmales phylogeny would be required to confirm such a hypothesis. This result will bevalued as paragraph in a manuscript in preparation for a peer reviewed journal reporting thegenome characteristics of Triparma laevis (led by Dr. kuwata).
Four additional Triparma laevis strains were isolated from water samples collected by Dr.
Kuwata in the sea of Okhotsk (TL4 and TL3) and Oyashio (TL5, TL6, NIES-2565). Total
DNA for these strains was sequenced. I used these sequence data to call polymorphisms along
the reference genome of NIES25-65. Polymorphisms analysis revealed that among the fivestrains of Triparma laevis, only 2 distinct lineages exist: NIES-2565, TL3, TL6 weregenetically identical over the full genome and TL4 and TL5 were identical. This near absenceof genetic diversity between strains isolated from different oceanic regions suggests that theTriparma laevis is evolving clonally or with very limited gene exchange. This is a rather
surprising result that will deserve deeper investigation and would probably be of interest forthe plankton scientific community.
In this fiscal year we started to investigate genetic diversity for Triparma laevis by using alarger sample size (we already generated sequence data for two additional strains and will addmore). Clonal evolution is expected to less efficiently purge deleterious mutations andprevents the spread of beneficial mutations. The dynamic of transposable elements is also
known to be affected by the level of recombination in a genome, although the direction of theeffect is still matter of debate. We will therefore investigate the state of these genomic
features (deleterious mutations and transposable element dynamic), which are usuallyassociated with clonal evolution, in Triparma laevis.
In parallel we will continue our effort to obtain the genome sequence of the diatom T.
nordenskioeldii. We could not generate axenic strain yet so we decided to use transcript
sequencing to have a first insight into to functional potential of this species. RNA extraction
and sequencing was performed using the Global Unit grant and was successful. We assembled
the sequence data into 26,368 contigs from which 19,904 proteins were predicted. Careful
gene content analysis will be performed latter this year and this transcriptomes can be used areference for future plan population genomics study. We will next engage in a comparative
genomics analysis of T. nordenskioeldii with other diatom genome sequences to pinpointinteresting genomics features and relate it to its peculiar ecology and evolutionary history.

Planned usage of grant:
The amounts listed below are estimates that may change when booking.
I/ Travel expenses to participate the annual conference of the Japanese Society ofMicrobial Ecology to be help in Yamanashi from 10 to 13th September 2019. Results
obtained for this project will be presented as a talk or poster.
Registration: 10,000 JPY
Train/bus (return): 50,000 JPY
Hotel (4 nights): 40,000 JPY
Total 1: 100,000 JPY
II/ Travel expenses for a trip to Europe to present my results obtained with this grant in aconference and to collaborators from ~23rd September to -11th October 2019 as follow:
1) Participate to the “evolutionary biology meeting in Marseille” (France) from 24 to 27
Septembre:
Registration: 55,000 JPY
Hotel (4 nights): 40,000 JPY
2) Meet with Dr. Gwenael Piganeau in Banyuls-sur-Mer (France) to discuss my results andpotential collaboration on the population genomics of Parmales and Diatoms algae from 28
September to 5th October.
Train from Marseille to Banyuls-sur-Mer: 7,000 JPY
Hotel (7 nights): 70,000 JPY
3) Participate to a collaborative meeting of the Tara Oceans project to be held in Barcelona(Spain) between 6th to 10th October (exact dates are not fixed yet) to meet collaborators
working on Diatoms and related algae and discuss my results.
Train or Bus from Banyuls-sur-Mer to Barcelone: 6,000 JPY
Hotel (5 nights): 50,000 JPY
Flight from Marseille to Osaka and from Barcelone to Osaka: 150,000 JPY.
Daily allowance for a total of 16 days: 40,000 JPY
Total 2: 418,000 JPY

Total for travel expenses: 518,000 JPY
Usage of the rest of the grants will be used to buy consumable and equipment.