Presentation Information
[P04-547]Transposon dynamics across haplotypes reveal the hybrid origin of the allodiploid diatom Fistulifera solaris
○Hikaru Tago1, Kosuke Kataoka1,2, Chris Bowler3, Tsuyoshi Tanaka1 (1. Graduate School of Engineering, Tokyo University of Agriculture and Technology (Japan), 2. Comprehensive Research Organization, Waseda University (Japan), 3. Institut de Biologie de l'Ecole Normale Supérieure (France))
Keywords:
Microalgae,Diatom,Hybridization,Genomics,Transposon
[Purpose]
Diatoms, a major group of microalgae, are promising platforms for sustainable bioproduction because they can synthesize lipids and pharmaceutical precursors from CO2. To enable industrial application, further improvements in strain resilience and yield are required for productive cultivation. In addition to genome editing, crossbreeding may contribute to strain improvement in diatoms, given their high diversity and capacity for sexual reproduction. However, because previous artificial crosses have failed to produce stable hybrids, the feasibility of this approach remains unresolved. In this study, we show that the allodiploid diatom Fistulifera solaris derived from hybridization and has persisted over time, indicating the potential of crossbreeding for diatom.
[Method]
A genome-wide search for 18S rDNA in F. solaris was conducted by BLAST-based homology screening. Phylogeny was inferred with BEAST using 18S rDNA sequences from F. solaris and 18 related diatom species. To estimate hybridization timing, transposable elements (TEs) were identified with RepeatMasker using a de novo library generated by RepeatModeler with Repbase as a reference. TE insertion ages were calculated from Kimura distances and converted to absolute time using a neutral substitution rate inferred from the 18S rDNA phylogeny.
[Results&Consideration]
Hybrid organisms can retain two distinct nuclear 18S rDNA ribotypes, so the presence of divergent rDNA lineages supports hybridization (Casteleyn et al., Protist, 2009). A genome-wide analysis of F. solaris identified 16 18S rDNA coding regions (eight per haplotype). Phylogenetic analysis of 18S rDNA sequences resolved two reciprocally monophyletic clades that segregated by haplotype, indicating distinct ancestral origins.To date the hybridization event, we analyzed TE insertion dynamics. Because TEs serve as lineage-specific markers, insertions shared between the two haplotypes can be used to constrain the timing of divergence and hybridization (Session et al., Nature, 2016). In F. solaris, most TE families were haplotype-specific, whereas nine families showed evidence of TE exchange between haplotypes. Insertion-age distributions revealed a temporal gap, with TE exchange occurring at ~1.60 million years ago (MYA), followed by restricted exchange until activity resumed at ~0.12 MYA. These results suggest that the parental lineages diverged after ~1.60 MYA and subsequently hybridized before ~0.12 MYA.To our knowledge, this represents the first report of an interspecific hybrid diatom that can be stably maintained in the laboratory. It may serve as an important model organism for elucidating the mechanisms that enable stable interspecific hybridization in diatoms.
[Conclusion]
This study validates the hybrid origin of F. solaris and establishes it as a model for investigating hybrid formation and long-term persistence. These insights provide a foundation for exploring the potential of crossbreeding in diatoms.
Diatoms, a major group of microalgae, are promising platforms for sustainable bioproduction because they can synthesize lipids and pharmaceutical precursors from CO2. To enable industrial application, further improvements in strain resilience and yield are required for productive cultivation. In addition to genome editing, crossbreeding may contribute to strain improvement in diatoms, given their high diversity and capacity for sexual reproduction. However, because previous artificial crosses have failed to produce stable hybrids, the feasibility of this approach remains unresolved. In this study, we show that the allodiploid diatom Fistulifera solaris derived from hybridization and has persisted over time, indicating the potential of crossbreeding for diatom.
[Method]
A genome-wide search for 18S rDNA in F. solaris was conducted by BLAST-based homology screening. Phylogeny was inferred with BEAST using 18S rDNA sequences from F. solaris and 18 related diatom species. To estimate hybridization timing, transposable elements (TEs) were identified with RepeatMasker using a de novo library generated by RepeatModeler with Repbase as a reference. TE insertion ages were calculated from Kimura distances and converted to absolute time using a neutral substitution rate inferred from the 18S rDNA phylogeny.
[Results&Consideration]
Hybrid organisms can retain two distinct nuclear 18S rDNA ribotypes, so the presence of divergent rDNA lineages supports hybridization (Casteleyn et al., Protist, 2009). A genome-wide analysis of F. solaris identified 16 18S rDNA coding regions (eight per haplotype). Phylogenetic analysis of 18S rDNA sequences resolved two reciprocally monophyletic clades that segregated by haplotype, indicating distinct ancestral origins.To date the hybridization event, we analyzed TE insertion dynamics. Because TEs serve as lineage-specific markers, insertions shared between the two haplotypes can be used to constrain the timing of divergence and hybridization (Session et al., Nature, 2016). In F. solaris, most TE families were haplotype-specific, whereas nine families showed evidence of TE exchange between haplotypes. Insertion-age distributions revealed a temporal gap, with TE exchange occurring at ~1.60 million years ago (MYA), followed by restricted exchange until activity resumed at ~0.12 MYA. These results suggest that the parental lineages diverged after ~1.60 MYA and subsequently hybridized before ~0.12 MYA.To our knowledge, this represents the first report of an interspecific hybrid diatom that can be stably maintained in the laboratory. It may serve as an important model organism for elucidating the mechanisms that enable stable interspecific hybridization in diatoms.
[Conclusion]
This study validates the hybrid origin of F. solaris and establishes it as a model for investigating hybrid formation and long-term persistence. These insights provide a foundation for exploring the potential of crossbreeding in diatoms.
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