2019 Fiscal Year Annual Research Report
Interplay between speciation and adaptation: an 'Omics' study on the effects of human impacts on Mediterranean and Indo-Pacific Zoantharia
| Project/Area Number |
18F18755
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| Research Institution | University of the Ryukyus |
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Principal Investigator |
Reimer J・D 琉球大学, 理学部, 准教授 (20452956)
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| Co-Investigator(Kenkyū-buntansha) |
POLISENO ANGELO 琉球大学, 理学部, 外国人特別研究員
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| Project Period (FY) |
2018-11-09 – 2021-03-31
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| Keywords | Zoantharians / population genetics / whole genome sequencing / phylogenomics |
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| Outline of Annual Research Achievements |
Fifty-two (52) individuals of Savalia savaglia, belonging five Mediterranean populations and one Eastern Atlantic population have been successfully processed using Restricted-site associated DNA sequencing (RAD-seq) on Illumina platform. The sequencing led to a number of reads per individual ranging from 9M to 18M. Demultiplexing, quality check and filtering of the reads as well as SNP calling has been performed using the Stacks pipeline installed in the computer server of the host Institution. Further population genetics analyses will be done by May 2020. The WGS of Savalia savaglia and P. tuberculosa led to 610M and 900M DNA reads, respectively. Regarding Umimayanthus spp., 24 specimens have been preliminarly investigated. Of these, 21 were considered for molecular analysis, 14 for morphological observations and 17 for chemical characterisations. For DNA barcoding, to date, partial COI and two fragments of the 28S ribosomal RNA gene were considered with more than 100 DNA sequences obtained through Sanger sequencing. Over the last fiscal year one paper and a book chapter were published. Another book chapter has been accepted for pubblication and two manuscripts have been submitted for publication in international peer-reviewed journals.
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| Current Status of Research Progress |
Current Status of Research Progress
1: Research has progressed more than it was originally planned.
Reason
Laboratory activities for the Mediterranean project have been successfully completed as planned. For population genetics, 60% of the analyses have been performed, the remaning will be done by the end of May 2020. For genome assembly, annotation and phylogenomics, the analyses will be completed by the end of the fellowship (October 2020). Regarding the Indo-Pacific project, most of the field work has been completed, although further sampling might be planned once new specimens will be required for DNA and RNA sequencing. 95% of the molecular work of the specimens collected was completed. Morphological and chemical characterisations of the sponges hosting Umimayanthus spp. will be performed in collaboration with European and Japanese researchers thorugh the year.
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| Strategy for Future Research Activity |
The use 'fresh' newly collected material will contribute to obtain hmw DNA suitable for library preparation and HTS. Similarly, using specific protocols for tissue- preservation and nucleic acids extraction, will increase the chances to recover non-degraded RNA of zoantharians and other cnidarians. Regarding bioinformatics, aiming to speed-up and optimize the analytical process, part of the data and computational information will be shared among research groups within Japan and abroad. This way, building an international network will increase the efficiency and speed of budget use and obtaining results, as well as broadening collaborations with Japan and overseas researchers.
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Research Products
(5 results)
