Adaptation to life at different oxygen tensions plays a role in protozoan ecology and controls the distribution of different species in anoxic habitats. The ciliate genus Spirostomum inhabiting fresh or low salinity water globally where these species are considered as bioindicators. Under anaerobic or low oxygen conditions, the rhodoquinol-dependent pathway has been reported in the species from the class Heterotrichea. With the help of RNA sequencing (RNAseq) data, Spirostomum spp., are suitable for deep molecular investigations on rquA for rhodoquinone (RQ) biosynthesis. In this study, Spirostomum ambiguum, Spirostomum subtilis, and Spirostomum teres collected from densely vegetated freshwater habitat in Fuzhou, China, explored the evidence of rquA. Based on transcriptome analysis, two to three RquA proteins were identified in S. ambiguum, S. teres, and S. subtilis, respectively. The presence of a key Motif-I of RquA and mitochondrial targeting signals (MTS), also confirmed the identity of these as RquA. Furthermore, Spirostomum RquA proteins could be sorted into two groups based on their conserved amino acid (CAA) residues. Phylogenetic analysis also exhibited RquA division into two subclades contained RquA1 and RquA2/RquA3 and supports two to three paralogs of rquA genes in the genomes Spirostomum spp. Additional transcriptomes and genomes analysis of Blepharisma spp., and Stentor spp., respectively, also revealed at least two paralogs of rquA in members of the class Heterotrichea. The present study provides evidence for the presence of RquA and rhodoquinol dependent fumarate reduction pathway in Spirostomum species potentially use to respire in the oxygen-depleted habitats and two to three diverse rquA genes.
Regeneration capability varies in the phylum Annelida making them an excellent group to investigate the differences between closely related organisms. Several studies have described the process of regeneration, while the underlying molecular mechanism remains unclear, especially during the early stage (wound healing and blastema formation). In this study, the newly identified Ophryotrocha xiamen was used to explore the early regeneration. The detailed morphological and molecular analyses positioned O. xiamen within ‘labronica’ clade. We analyzed the morphological changes during regeneration process (0–3 days post amputation) and molecular changes during the early regeneration stage (1 day post amputation). Wound healing was achieved within one day and a blastema formed one day later. A total of 243 DEGs were mainly involved in metabolism and signal transduction. Currently known regeneration-related genes were identified in O. xiamen which could help with exploring the functions of genes involved in regeneration processes. According to their conserved motif, we identified 8 different Hox gene fragments and Hox5 and Lox2 were found to be absent in early regeneration and during regular growth. Our data can promote further use of O. xiamen which can be used as an experimental model for resolving crucial problems of developmental biology in marine invertebrates.
BackgroundIn recent years, significant progress has been made using powerful genetic approaches with newly developed models for understanding on regeneration, however, the molecular and cellular basis of early regeneration remains unclear. Annelids of the genus Ophryotrocha have long been subjects of research use as model species in ecological, toxicological, reproductive, and regenerative investigations. Although, Ophryotrocha spp., are amenable to molecular, cellular, and functional analyses, still in need to explore new model organisms in this genus to understand regeneration mechanisms. Here, we focus on a newly identified Ophryotrocha species for its early regeneration developmental mode.ResultsBased on detailed morphological (K-maxillae, rosette gland, and chromosome number) and molecular analyses, we present, O. xiamen as a new suitable model species to investigate the early regeneration mechanism. The comparative transcriptome analysis showed the gene expression patterns were related to transcriptional regulation, energy metabolism profiles and structure and signal transduction during early stages of regeneration. Data also exhibited that genes such as neurotrypsin, Nos2, DMBT1, SCO spondin, and endotubin associated to regulate inflammation, enterocyte differentiation, apoptosis, and neuroepithelial, were up-regulated during early regeneration stages (wound healing and blastema formation). Additionally, most of the known regeneration-related genes of annelids were also identified in O. xiamen which enabled to explore the precise functions of genes involved in regeneration process.ConclusionsThis study enriches the identification of genus Ophryotrocha in Chinese coastal zones, an area with high abundances of annelids. The comparative transcriptome analysis provided the whole expression changes during early regeneration process. Morphology and molecular shred of evidences in O. xiamen revealed similar features of early regeneration with other invertebrates. Information on potential candidate genes associated with early regeneration in O. xiamen, will be useful for further studies.
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