Presentation Information
[P04-563]Comparative genomic analysis of the diatom Chaetoceros toward revealing acquisition of nutrient for resting spore formation
○Sawaka Umehara1, Hikaru Tago1, Tsuyoshi Tanaka1, Kosuke Kataoka1,2 (1. Graduate School of Engineering, Tokyo University of Agriculture and Technology (Japan), 2. Comprehensive Research Organization, Waseda University (Japan))
Keywords:
Resting spores,Diatoms,Silicon transporter,Genome analysis
[Purpose]
Diatoms are widespread marine microalgae that account for a large fraction of oceanic CO2 fixation and drive marine primary production. Notably, some species form resting spores under environmental stress. These spores arrest growth and form a thick, heavily silicified frustule that enhances survival, sinks to the seafloor, and can persist for long periods, potentially contributing to carbon sequestration. Although this process may influence diatom-driven carbon cycling, the molecular basis of resting spore formation remains poorly understood. Because spore formation requires high nutrient inputs for silicification and the accumulation of storage reserves, we hypothesized that resting spore-forming lineages are enriched in nutrient uptake transporters. To test this, we performed comparative genomics of nutrient transporter gene families in the genus Chaetoceros, a lineage in which resting spore formation is frequently reported.
[Method]
Protein sequences from 12 diatom genomes, including seven species from Chaetoceros and five other diatom species, were analysed. The orthologous were inferred using OrthoFinder. Interspecies copy number variation was assessed for six nutrient transporters, including silicic acid transporters (SITs) based on the constructed phylogeny.
[Results and Consideration]
Comparative genomics revealed no significant expansion of nutrient transporters between Chaetoceros spp. and other diatoms, except for SITs. On average, Chaetoceros spp. had 10.5 SIT copies per species, versus 7.0 in other diatoms. In model diatoms, three SIT subfamilies (SIT1–SIT3) have been described. Subfamily-level quantification showed that this increase was concentrated in a Phaeodactylum tricornutum SIT1/2 (PtSIT1/2)-related lineage, with 5–17 copies per species across Chaetoceros spp. (mean = 8.1), whereas the PtSIT3-related lineage showed no comparable increase. Previous studies suggest that PtSIT1/2 form a closely related lineage from relatively recent duplications and are major, highly expressed silicon transporters, whereas PtSIT3 is more divergent from PtSIT1/2 and expressed at lower levels. SIT1/2 have also been proposed to function not only in silicic acid uptake but also in extracellular silicon sensing. This expansion of PtSIT1/2 implies lineage-specific reinforcement of silicon sensing and downstream response regulation under silicon limitation, rather than a simple increase in transport capacity. These findings are consistent with the high silicon demand required to produce the thick, heavily silicified frustule characteristic of resting spores.
[Conclusion]
This study suggests that nutrient transporter families have not expanded uniformly in resting-spore-forming diatoms. Instead, we detected a selective expansion of specific SIT subfamilies in Chaetoceros. This selective expansion is consistent with an evolutionary response to the high silicon demand associated with resting spore formation.
Diatoms are widespread marine microalgae that account for a large fraction of oceanic CO2 fixation and drive marine primary production. Notably, some species form resting spores under environmental stress. These spores arrest growth and form a thick, heavily silicified frustule that enhances survival, sinks to the seafloor, and can persist for long periods, potentially contributing to carbon sequestration. Although this process may influence diatom-driven carbon cycling, the molecular basis of resting spore formation remains poorly understood. Because spore formation requires high nutrient inputs for silicification and the accumulation of storage reserves, we hypothesized that resting spore-forming lineages are enriched in nutrient uptake transporters. To test this, we performed comparative genomics of nutrient transporter gene families in the genus Chaetoceros, a lineage in which resting spore formation is frequently reported.
[Method]
Protein sequences from 12 diatom genomes, including seven species from Chaetoceros and five other diatom species, were analysed. The orthologous were inferred using OrthoFinder. Interspecies copy number variation was assessed for six nutrient transporters, including silicic acid transporters (SITs) based on the constructed phylogeny.
[Results and Consideration]
Comparative genomics revealed no significant expansion of nutrient transporters between Chaetoceros spp. and other diatoms, except for SITs. On average, Chaetoceros spp. had 10.5 SIT copies per species, versus 7.0 in other diatoms. In model diatoms, three SIT subfamilies (SIT1–SIT3) have been described. Subfamily-level quantification showed that this increase was concentrated in a Phaeodactylum tricornutum SIT1/2 (PtSIT1/2)-related lineage, with 5–17 copies per species across Chaetoceros spp. (mean = 8.1), whereas the PtSIT3-related lineage showed no comparable increase. Previous studies suggest that PtSIT1/2 form a closely related lineage from relatively recent duplications and are major, highly expressed silicon transporters, whereas PtSIT3 is more divergent from PtSIT1/2 and expressed at lower levels. SIT1/2 have also been proposed to function not only in silicic acid uptake but also in extracellular silicon sensing. This expansion of PtSIT1/2 implies lineage-specific reinforcement of silicon sensing and downstream response regulation under silicon limitation, rather than a simple increase in transport capacity. These findings are consistent with the high silicon demand required to produce the thick, heavily silicified frustule characteristic of resting spores.
[Conclusion]
This study suggests that nutrient transporter families have not expanded uniformly in resting-spore-forming diatoms. Instead, we detected a selective expansion of specific SIT subfamilies in Chaetoceros. This selective expansion is consistent with an evolutionary response to the high silicon demand associated with resting spore formation.
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