Asuka Arimoto's research while affiliated with Hiroshima University and other places

... Owing to the lack of a chromosome-level reference genome for P. japonicas, it was difficult to directly impute missing genotypes. Therefore, based on our previously constructed linkage map and the scaffold-level genome sequences (Kawato et al., 2021), markers were assigned to the corresponding linkage groups and ordered approximately. Initially, contig sequences harboring markers in the linkage groups were aligned to the genome sequences, and these scaffolds were then ordered according to the alignment results. ...

... In this study, we examined R. viridis and Tetraselmis sp. using transcriptomics, plastid genomics and time-course observations with transmission electron microscopy in order to evaluate the level of integration between the plastids and the host cell. We demonstrate that R. viridis has no canonical plastids but has only transient kleptoplasts (kP) that have been previously reported also from other systems (11)(12)(13)(14)(15)(16)(17)(18) (SI Appendix, section 1.1), which are regularly acquired by consuming Tetraselmis sp. We also show that R. viridis expresses a series of nucleus-encoded proteins with apparent "plastid"-targeting signals that are homologous to those found in the Euglenophyceae and are probably transported into the kleptoplasts. ...

... Knowledge generated from this research will complement the delineation of alternatively spliced transcript variants and other idiosyncratic genomic features of dinoflagellates such as non-canonical splice sites and splice leader trans-splicing in the transcriptomes of Symbiodiniaceae and other species (González-Pech et al. 2021;Stephens et al. 2020); distinct lineages or genera of Symbiodiniaceae may exhibit slightly different patterns for each of these features, which may help explain niche specialization. These results are also foundational for developing a customized, more-accurate gene-prediction workflow (Beedessee et al. 2020;Chen et al. 2020;González-Pech et al. 2021;Stephens et al. 2020). ...

... In addition, other brown macroalgae were studied, including differences in photosynthetic rates and carbon assimilation (Undaria pinnatifida; Gao et al. 2013), nutrient uptake kinetics (U. pinnatifida; Sato et al. , 2017, and high temperature tolerance (Saccharina latissima; Gerard 1997). For C. okamuranus, sporophytes cultivated at each locality have been used as mother plants, with several strains selected as cultivars by the Okinawa Prefectural authorities (Nishitsuji et al. 2020). However, the physiological characteristics for each sample from different localities remains to be revealed. ...

... Sacoglossan sea slugs (Gastropoda: Heterobranchia) sequester plastids from their food algae (mainly Ulvophyceae) and may maintain the plastids in their digestive cells for photosynthesis (functional kleptoplasty) (Evertsen et al., 2007;Maeda et al., 2020;Pelletreau et al., 2011;Rumpho et al., 2008). Kleptoplasty has been reported in many unicellular organisms such as foraminiferans and dinoflagellates (Johnson, 2011). ...

... The high extent of phylogenetic diversity of Symbiodiniaceae is highlighted by the recent systematic revision (LaJeunesse et al. 2018), comparative genomic analyses (González-Pech et al. 2021;Shoguchi et al. 2018), and intragenomic variation of the commonly used phylogenetic marker, the internally transcribed spacer 2 (ITS2) region (Arif et al. 2014;Hume et al. 2019;Stat et al. 2011;Thornhill et al. 2007). Variation in genetic content can be introduced at the transcriptional level through RNA editing (Mungpakdee et al. 2014;Shoguchi et al. 2020) and alternatively spliced transcripts (Lin 2011;Mendez et al. 2015). RNA editing is a ubiquitous feature of dinoflagellates (Klinger et al. 2018;Lin 2011;Wisecaver and Hackett 2011). ...

... The pattern of mitochondrial inheritance has not been studied in Alaria genus. Among the brown algae where the organelle inheritance has been studied so far, both plastids and mitochondria of oogamous species, such as Laminariales and Fucales, are maternally inherited ( [15] and references within). However, if the inheritance of both plastids and mitochondria was strictly maternal in Alaria esculenta, we should not see such a discrepancy between the MDS plots obtained using the plastidial and mitochondrial SNPs ( Fig. 2B and C). ...

... The stolon acts as a creeping, anchoring structure and is usually rather protected from the light. Additionally, gene expression differs between stolon and frond, showing a slightly higher amount of expressed genes in the stolon with functions generally related to translation and DNA replication [76]. Besides, the elongation of stolons could be a strategy to slowly change the alga's position, as observed by for C. prolifera under nutrient-limited conditions [77]. ...

... Therefore, we determined differential protein expression by LC-MS/MS under 4× condition compared to other conditions. Although the Caulerpa protein database is available from the Okinawa Institute of Science and Technology (OIST) website [27] it lacks of functional description of proteins, complicating the following proteomics analysis. Therefore, we used the model organism Arabidopsis protein database to analyze LC-MS/MS data. ...

... However, valuable insights into the construction and dynamics of the symbiotic ecosystem require successful separation of the host, symbiont, and contaminant data (Cornet and Baurain, 2022). Complicated and laborious experimental approaches have been developed to isolate host sequences from prokaryotic contamination (Arimoto et al., 2019;Cheng et al., 2019;Wang et al., 2020). Current bioinformatic methods rely on the species differentiation in statistical features (Woyke et al., 2006;Alneberg et al., 2014), or nucleotide and protein similarity of pre-assemblies to known genomes or public databases (Coghlan et al., 2019). ...