Comparative genome and transcriptome analysis of diatom, Skeletonema costatum, reveals evolution of genes for harmful algal bloom
License
http://creativecommons.org/licenses/by/4.0/Type
ArticleAuthors
Ogura, AtsushiAkizuki, Yuki
Imoda, Hiroaki
Mineta, Katsuhiko
Gojobori, Takashi
Nagai, Satoshi
KAUST Department
Computational Bioscience Research Center (CBRC)Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Biological and Environmental Sciences and Engineering (BESE) Division
Bioscience Program
Online Publication Date
2018-10-22Print Publication Date
2018-12Date
2018-10-22Abstract
BACKGROUND:Diatoms play a great role in carbon fixation with about 20% of the whole fixation in the world. However, harmful algal bloom as known as red tide is a major problem in environment and fishery industry. Even though intensive studies have been conducted so far, the molecular mechanism behind harmful algal bloom was not fully understood. There are two major diatoms have been sequenced, but more diatoms should be examined at the whole genome level, and evolutionary genome studies were required to understand the landscape of molecular mechanism of the harmful algal bloom. RESULTS:Here we sequenced the genome of Skeletonema costatum, which is the dominant diatom in Japan causing a harmful algal bloom, and also performed RNA-sequencing analysis for conditions where harmful algal blooms often occur. As results, we found that both evolutionary genomic and comparative transcriptomic studies revealed genes for oxidative stress response and response to cytokinin is a key for the proliferation of the diatom. CONCLUSIONS:Diatoms causing harmful algal blooms have gained multi-copy of genes related to oxidative stress response and response to cytokinin and obtained an ability to intensive gene expression at the blooms.Citation
Ogura A, Akizuki Y, Imoda H, Mineta K, Gojobori T, et al. (2018) Comparative genome and transcriptome analysis of diatom, Skeletonema costatum, reveals evolution of genes for harmful algal bloom. BMC Genomics 19. Available: http://dx.doi.org/10.1186/s12864-018-5144-5.Acknowledgements
This work was funded by Grants-in-Aid for Scientific Research (KAKENHI) 17H06399 and Grant for Basic Science Research Projects from the Sumitomo Foundation to AO, and Science and Technology Research Partnership for sustainable Development to SN. This work has been supported partly by funding from King Abdullah University of Science and Technology (KAUST) to TG.Publisher
Springer NatureJournal
BMC GenomicsDOI
10.1186/s12864-018-5144-5Additional Links
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5144-5Relations
Is Supplemented By:- [Dataset]
. DOI: 10.6084/m9.figshare.c.4275500.v1 HANDLE: 10754/664220
- [Dataset]
. DOI: 10.6084/m9.figshare.7238906 HANDLE: 10754/664221