2016 Fiscal Year Annual Research Report
Decoding the genome of the brachiopod Lingula anatina
| 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 | Nemertea / Phoronida / Brachiopoda / Lophotrochozoa / Genome / Transcriptome / Evolution / Phylogenomics |
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| Outline of Annual Research Achievements |
In the second year, I was focusing on analyzing two new lophotrochozoan genomes, namely the nemertean Notospermus geniculatus and the phoronid Phoronis australis. These two genomes are closely related to the brachiopod Lingula anatina. However, their phylogenetic positions and evolutionary origins remain unclear. Although lophophores are feeding apparatuses that can be found in brachiopods and phoronids, whether their lophophores share the same origin at the molecular level is unknown.
To explore lophotrochozoan evolution and morphological novelties of lophophores, I conducted comparative genomics and transcriptomics of the new genomes. To improve genome assembly quality, I prepared genomic DNA and mRNA for genome scaffolding and tissue transcriptomes. I assembled the genomes and transcriptomes, and then prepared gene models based on transcript information. In addition, I improved the quality of the Lingula genome assembly by removing the allele scaffolds. I have finished the analyses and submitted a manuscript about the nemertean and phoronid genomes.
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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. For the new genome project, the major progress is as follows:
1. I performed phylogenetic analyses with one-to-one orthologs using available lophotrochozoan genomes and found that Nemertea is close to the group of Brachiopoda and Phoronida. I also conducted transcriptome-based phylogenetic analyses. And I found evidence to support that Ectoprocta (Bryozoa) is sister to Phoronida. These results favor the traditional classification of the clade, Lophophorata (Brachiopoda, Phoronida, and Ectoprocta).
2. I analyzed the gene families of lophotrochozoans and discovered that lophotrochozoans share many gene families with deuterostomes. Interestingly, many these gene families are lost in ecdysozoans and remaining spiralians, suggesting that lophotrochozoans retain a core set of bilaterian genes. Gene ontology analysis shows that these shared gene families are associated with cell cycle and cell adhesion, reflecting a conserved gene repertoire of multicellularity.
3. I found that although lophophores are morphologically not similar to the bilaterian heads, many head marker genes, such as six3/6 and lhx1/5, are highly expressed in the lophophores. Thus, my results suggest that a conserved common head patterning system is used for patterning the lophophores.
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| Strategy for Future Research Activity |
I am working on the dorsal-ventral patterning of Lingula embryos. This project is mainly to understand the evolution of brachiopod body plans and the role of BMP signals in neural induction. I conducted embryological experiments during the Lingula spawning season in last August. And I performed pharmaceutical treatments to manipulate BMP signaling. Afterward, I analyzed the differential expression patterns of BMP up-regulated and down-regulated genes using a functional RNA-seq with biological replications. I identified several developmental genes that are regulated by BMP signals. I am currently working on in situ hybridization to examine the spatial pattern of candidate genes.
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