FY2022 Annual Report

Genomics and Regulatory Systems Unit
Professor Nicholas M. Luscombe

Abstract

1. Staff

• Nicholas M. Luscombe, Professor 
• Charles Plessy, Staff Scientist
• Michael J. Mansfield, Research Scientist
• Jiashun Miao, Research Scientist
• Charlotte Capitanchik, JSPS Research Fellow (The Francis Crick Institute, London UK)
• Nicolas Dierckxsens, Joint Post-Doctoral fellow (with Tim Ravasi's Unit)
• Gaspar Sánchez Serna, Visiting Research Scientist (University of Barcelona, Spain)
• Andrew W. Liu, Senior Technician
• Aki Masunaga, Technician
• Yongkai Tan, Technician
• Aleksandra Bliznina, Graduate Student
• Makiko Sanabe, Research Unit Administrator

2. Collaborations

2.1 The Title or Name or Topic of the Collaboration

• Description:
• Type of collaboration: Joint research
• Researchers:
  • Associate Professor, Cristian Cañestro, Barcelona University
  • PhD Student, Gaspar Sánchez Serna, Barcelona University (Visiting Research Student at OIST 2022 Aug - 2023 Jan)

3. Activities and Findings

4. Publications

4.1 Journals

1. Masunaga, A., Mansfield, M.J., Tan, Y., Liu, A.W., Bliznina, A., Barzaghi, P., Hodgetts, T.L., Ferrández-Roldán, A., Cañestro, C., Onuma, T., Plessy, C., Luscombe, N.M. 
   The cosmopolitan appendicularian Oikopleura dioica reveals hidden genetic diversity around the globe.
   Marine Biology169, 157; doi: 10.1007/s00227-022-04145-5 (2022)

2. Wei, X., Wentz, T., Lobb, B., Mansfield, M.J., Zhen, W., Tan, H., Wu, Z., Pellett, S., Dong, M., Doxey, A.C.
   Identification of divergent botulinum neurotoxin homologs in Paeniclostridium ghonii.
   bioRxiv 2022.08.17.504336; doi: 10.1101/2022.08.17.504336 (2022)

3. Bhat, D., Hauf, S., Plessy, C., Yokobayashi, Y., Pigolotti, S.
   Speed variations of bacterial replisomes.
   Elife 2022 Jul 25;11:e75884. doi: 10.7554/eLife.75884 (2022)

4. de Hoon, M., Bonetti, A., Plessy, C., Ando, Y., Hon, C.C., Ishizu, Y., Itoh, M., Kato, S., Lin, D., Maekawa, S., Murata, M., Nishiyori, H., Shin, J.W., Stolte, J., Suzuki, A.M., Tagami, M., Takahashi, H., Thongjuea, S., Forrest, A.R.R., Hayashizaki, Y., Kere, J., Carninci, P.
   Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs.
   Genome Research 2022 Aug 12;32(9):1727–35. doi: 10.1101/gr.276647.122 (2022)

5. Sugiman-Marangos, S.N., Gill, S.K., Mansfield, M.J., Orrell, K.E., Doxey, A.C., Melnyk, R.A.
   Structures of distant diphtheria toxin homologs reveal functional determinants of an evolutionarily conserved toxin scaffold.
   Communications Biology5, 375. doi: 10.1038/s42003-022-03333-9 (2022)

6. Martin-Zamora, M., Liang, Y., Guynes, K., Carillo-Baltodano, A.M., Davies, B.E., Donnellan, D., Tan, Y., Moggiloi, G., Seudre, O., Tran, M., Mortiner, K., Luscombe, N.M., Henjol, A., Marlétaz, F.
   Annelid functional genomics reveal the origins of bilaterian lifecycles.
   Nature615, 105-110; doi: 10.1038/s41586-022-05636-7 (2023)

7. Hodgins, H.P., Chen, P., Lobb, B., Tremblay B.J.M., Mansfield M.J., Lee, V.C.Y., Lee, P-G., Coffin, J., Wei, X., Duggan, A.T., Dolphin, A.E., Renaud, G., Dong, M., Doxey, A.C.
   Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains.
   bioRxiv 2022.06.30.498301; doi: 10.1101/2022.06.30.498301 (2023)

4.2 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations

1. Masunaga, A., Oikopleura dioica, the cosmopolitan appendicularian hides multiple cryptic species around the globe.
   11th International Tunicate Meeting, Kobe, Japan. From 12th -15th July (2022)

2. Plessy, C., Drastic genome remodeling across Oikopleura dioica worldwide.
   11th International Tunicate Meeting, Kobe, Japan. From 12th -15th July (2022)

3. Mansfield, M.J., Gene expression in the context of genomic rearrangement in Oikopleura dioica
   11th International Tunicate Meeting, Kobe, Japan. From 12th -15th July (2022)

4. Plessy, C., Massively scrambled genomes producing animals with conserved morphology
   45th Annual Meeting of the Molecular Biology Society of Japan, Chiba, Japan. From 30th Nov - 3rd Dec (2022)

5. Plessy, C., Related animals with small genomes, conserved morphology, but flexible gene order: Oikopleura dioica
   "Oceans – and the impact of humans and climate change” - OIST-Tohoku University. 2nd Joint Workshop on Marine Science, Sendai, Japan. From 24th - 26th Oct (2022)

6. Masunaga, A., Uncovering speciation and population structures in the marine zooplankton, Oikopleura dioica
   "Oceans – and the impact of humans and climate change” - OIST-Tohoku University. 2nd Joint Workshop on Marine Science, Sendai, Japan. From 24th - 26th Oct (2022)

7. Plessy, C., Drastic genome remodeling across Oikopleura dioica worldwide, Invited seminar at Konan University, Japan. Nov (2022)

8. Mansfield, M.J., Poster presentation title: Molecular clock estimation of divergence times in populations of "Oikopleura dioica.
   Event title "Oceans - and the impact of humans and climate change". Onna-son, Japan. April (2022)

9. Mansfield, M.J., Invited talk title: Conservation of gene expression amidst genomic rearrangement in two species of Oikopleura dioica.
   Konan University, Department of Biology Seminar, Kobe, Japan. Nov (2022)

10. Mansfield, M.J., Poster presentation title: Conservation of gene expression amidst genomic rearrangement in two species of Oikopleura dioica.
    Keystone Symposium: Epigenetics, Chromatin, Development, and Disease. Vancouver, Canada. From 12th - 15th Mar (2023)

5. Intellectual Property Rights and Other Specific Achievements

Nothing to report

6. Meetings and Events

Nothing to report.

7. Other

Nothing to report.