Dataset Information

Comparative genome and transcriptome analysis of diatom, Skeletonema costatum, reveals evolution of genes for harmful algal bloom.

ABSTRACT: 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.

SUBMITTER: Ogura A

PROVIDER: S-EPMC6198448 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Comparative genome and transcriptome analysis of diatom, Skeletonema costatum, reveals evolution of genes for harmful algal bloom.

Ogura Atsushi A Akizuki Yuki Y Imoda Hiroaki H Mineta Katsuhiko K Gojobori Takashi T Nagai Satoshi S

BMC genomics 20181022 1

<h4>Background</h4>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 ...[more]

PMID: 30348078

Similar Datasets

Project description:Recently, harmful algal bloom (HAB), also termed "red tide", has been recognized as a serious problem in marine environments according to climate changes worldwide. Many novel materials or methods to prevent HAB have not yet been employed except for clay dispersion, in which can the resulting sedimentation on the seafloor can also cause alteration in marine ecology or secondary environmental pollution. In the current study, we investigated that antimicrobial peptide have a potential in controlling HAB without cytotoxicity to harmless marine organisms. Here, antimicrobial peptides are proposed as new algicidal compounds in combating HAB cells. HPA3 and HPA3NT3 peptides which exert potent antimicrobial activity via pore forming action in plasma membrane showed that HPA3NT3 reduced the motility of algal cells, disrupted their plasma membrane, and induced the efflux of intracellular components. Against raphidoflagellate such as Heterosigma akashiwo, Chattonella sp., and C. marina, it displayed a rapid lysing action in cell membranes at 1~4 µM within 2 min. Comparatively, its lysing effects occurred at 8 µM within 1 h in dinoflagellate such as Cochlodium polykrikoides, Prorocentrum micans, and P. minimum. Moreover, its lysing action induced the lysis of chloroplasts and loss of chlorophyll a. In the contrary, this peptide was not effective against Skeletonema costatum, harmless algal cell, even at 256 µM, moreover, it killed only H. akashiwo or C. marina in co-cultivation with S. costatum, indicating to its selective algicidal activity between harmful and harmless algal cells. The peptide was non-hemolytic against red blood cells of Sebastes schlegeli, the black rockfish, at 120 µM. HAB cells were quickly and selectively lysed following treatment of antimicrobial peptides without cytotoxicity to harmless marine organisms. Thus, the antibiotic peptides examined in our study appear to have much potential in effectively controlling HAB with minimal impact on marine ecology.

Dataset Information

Comparative genome and transcriptome analysis of diatom, Skeletonema costatum, reveals evolution of genes for harmful algal bloom.

Publications

Comparative genome and transcriptome analysis of diatom, Skeletonema costatum, reveals evolution of genes for harmful algal bloom.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets