2015 Fiscal Year Annual Research Report
| Project/Area Number |
15J01101
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| Research Institution | Okinawa Institute of Science and Technology Graduate University |
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Principal Investigator |
LUO YIーJYUN 沖縄科学技術大学院大学, 科学技術研究科, 特別研究員(DC1)
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| Project Period (FY) |
2015-04-24 – 2018-03-31
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| Keywords | Lingula / Brachiopod / Lophotrochozoan / Biomineralization / Genome / Transcriptome / Evolution / Phylogenomics |
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| Outline of Annual Research Achievements |
During the first year, I improved the genome assembly of the brachiopod Lingula anatina by incorporating PacBio long-read data. I performed an extensive annotation of the genome, and conducted comparative genomics especially to those available genomes within lophotrochozoans. Because Lingula shells and vertebrate bones are both made by calcium phosphate, I focused on analyzing biomineralization-related genes to understand the evolution of phosphate biominerals. The accomplished works are listed as the followings:
1.I have showed a recent gene family expansion in the Lingula genome. The expansion of one biomineralization-related gene, such as chitin synthases, has been identified. These findings suggest that the Lingula genome is rather evolving but not like a genuine “living fossil.”
2.I have compared the gene content for those transcription factors, signaling, and differentiation genes that are related to biomineralization. A genome-scale comparison has been performed, and I found that there is very little similarity in terms of molecular machinery of phosphate biomineralization between vertebrates and Lingula.
3.I have identified 65 shell matrix proteins from the shell proteomic data based on genome gene models and mantle transcriptome. By comparing to vertebrates and molluscs, I have proposed a model for shell formation in Lingula.
The results mentioned above has been published in Nature Communications. In addition, a large-scale comparative studies of mitochondrial genomes including the one from Lingula has been published in Marine Genomics.
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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
The research progress was going well. I have finished all the first-year plans in the proposal. During the first year, I have learned how to use the computer cluster and to write Perl and R scripts. These abilities allow me to analyze large scale genomic information. By having newly available genomic data from a relatively unexplored taxon, I then asked how these data can improve our understanding about their phylogenetic position and evolution of biomineralization toolkits. The annotation of genome together with the questions mentioned above have been finished and answered.
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| Strategy for Future Research Activity |
After having a good and well annotated genome assembly, I am planning to use this resource to study the Lingula embryonic development. I am particularly interested in axial patterning and cell type specification. Since brachiopods have dorsal-ventral oriented shells rather than left-right as in bivalves, I will focus on a signaling pathway, BMP, which is important for regulating dorsal-ventral axis conserved across bilaterians. Preliminary data using an antibody, phosphorylated Smad1/5, have shown that BMP signals are active at the animal side of the embryos started from blastula stage. I am wondering to know how BMP signals pattern the formation of the larval organs, such as shells and lophophores.
By perturbation of BMP signaling with small molecules, I will perform an unbiased transcriptomic approach using RNA-seq to identify BMP signaling downstream genes. The roles of BMP signals in body axis formation and cell type specification will be studied in detail by examining the expression pattern of germ layer marker genes and neuronal markers under different perturbation condition.
So far, our understanding of dorsal-ventral patterning in non-spiral cleavage lophotrochozoans is very limited. Information from annelids shows that they have quite different mechanisms in terms of short-range BMP signals transmission unlike other animal groups. As the protostome with radial cleavage pattern, the results from brachiopods will be comparable to deuterostomes such as sea urchins and amphioxus. Together, this will provide insights into the evolution of dorsal-ventral patterning.
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[Presentation] The brachiopod genome of Lingula anatina provides insight into the evolution of lophotrochozoans and calcium-phosphate-based biomineralization2015
Author(s)
Luo YJ, Takeuchi T, Koyanagi R, Yamada L, Kanda M, Khalturina M, Fujie M, Yamasaki S, Endo K, Satoh N
Organizer
Inaugural Meeting of Pan-American Society for Evolutionary Developmental Biology
Place of Presentation
Berkeley, USA
Year and Date
2015-08-05 – 2015-08-09
Int'l Joint Research
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[Presentation] The brachiopod genome of Lingula anatina and the evolution of lophotrochozoans and biomineralization2015
Author(s)
Luo YJ, Takeuchi T, Koyanagi R, Yamada L, Kanda M, Khalturina M, Fujie M, Yamasaki S, Endo K, Satoh N
Organizer
The 7th International Brachiopod Congress
Place of Presentation
Nanjing, China
Year and Date
2015-05-23 – 2015-05-25
Int'l Joint Research
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[Presentation] The brachiopod genome of Lingula anatina provides insight into the evolution of lophotrochozoans and calcium-phosphate-based biomineralization2015
Author(s)
Luo YJ, Takeuchi T, Koyanagi R, Yamada L, Kanda M, Khalturina M, Fujie M, Yamasaki S, Endo K, Satoh N
Organizer
2015 CSHL Conference on The Biology of Genomes
Place of Presentation
Cold Spring Harbor, USA
Year and Date
2015-05-05 – 2015-05-09
