The Draft Genome of Chinese Endemic Species Phascolosoma esculenta (Sipuncula, Phascolosomatidae) Reveals the Phylogenetic Position of Sipuncula.
Ontology highlight
ABSTRACT:
SUBMITTER: Zhong S
PROVIDER: S-EPMC9354978 | biostudies-literature | 2022
REPOSITORIES: biostudies-literature
Publications
The Draft Genome of Chinese Endemic Species <i>Phascolosoma esculenta</i> (Sipuncula, Phascolosomatidae) Reveals the Phylogenetic Position of Sipuncula.
Zhong Shengping S Ma Xiaowan X Jiang Yan Y Qiao Ying Y Zhao Longyan L Huang Lianghua L Huang Guoqiang G Zhao Yongzhen Y Liu Yonghong Y Chen Xiuli X
Frontiers in genetics 20220722
Similar Datasets
Project description:BackgroundThere are many advantages to the application of complete mitochondrial (mt) genomes in the accurate reconstruction of phylogenetic relationships in Metazoa. Although over one thousand metazoan genomes have been sequenced, the taxonomic sampling is highly biased, left with many phyla without a single representative of complete mitochondrial genome. Sipuncula (peanut worms or star worms) is a small taxon of worm-like marine organisms with an uncertain phylogenetic position. In this report, we present the mitochondrial genome sequence of Phascolosoma esculenta, the first complete mitochondrial genome of the phylum.ResultsThe mitochondrial genome of P.esculenta is 15,494 bp in length. The coding strand consists of 32.1% A, 21.5% C, 13.0% G, and 33.4% T bases (AT = 65.5%; AT skew = -0.019; GC skew = -0.248). It contains thirteen protein-coding genes (PCGs) with 3,709 codons in total, twenty-two transfer RNA genes, two ribosomal RNA genes and a non-coding AT-rich region (AT = 74.2%). All of the 37 identified genes are transcribed from the same DNA strand. Compared with the typical set of metazoan mt genomes, sipunculid lacks trnR but has an additional trnM. Maximum Likelihood and Bayesian analyses of the protein sequences show that Myzostomida, Sipuncula and Annelida (including echiurans and pogonophorans) form a monophyletic group, which supports a closer relationship between Sipuncula and Annelida than with Mollusca, Brachiopoda, and some other lophotrochozoan groups.ConclusionThis is the first report of a complete mitochondrial genome as a representative within the phylum Sipuncula. It shares many more similar features with the four known annelid and one echiuran mtDNAs. Firstly, sipunculans and annelids share quite similar gene order in the mitochondrial genome, with all 37 genes located on the same strand; secondly, phylogenetic analyses based on the concatenated protein sequences also strongly support the sipunculan + annelid clade (including echiurans and pogonophorans). Hence annelid "key-characters" including segmentation may be more labile than previously assumed.
| S-EPMC2667193 | biostudies-literature
Project description:Phascolosoma esculenta, an economically important species inhabiting the high tide areas of the intertidal zone, is particularly sensitive to water pollution. Considering its potential as a bioindicator, studies on the ecotoxicology of P. esculenta are imperative. The toxic effects of cadmium (Cd) were analyzed by exposing P. esculenta to different concentrations of Cd (6, 24, 96 mg/L). In this study, the changes in the antioxidative indexes of total superoxide dismutase (T-SOD), glutathione s-transferase (GST), reduced glutathione (GSH), and microscale malondialdehyde (MDA) were recorded. Copper/zinc superoxide dismutase (Cu/Zn SOD) is one of the most important free radical scavenging members. To reveal the antioxidative function of P. esculenta, an important member of the antioxidative system, designated Pe-Cu/Zn SOD, was cloned and analyzed. Phylogenic analysis revealed that Pe-Cu/Zn SOD was located in the invertebrate evolutionary branch of intracellular Cu/Zn SOD (icCu/Zn SOD). The quantitative real-time polymerase chain reaction results showed that Pe-Cu/Zn SOD messenger ribonucleic acid was widely expressed in all tissues examined. The highest expression levels in coelomic fluid after Cd exposure indicated its function in the stress response. Using a prokaryotic expression system, we obtained a Pe-Cu/Zn SOD recombinant protein, which enhanced the heavy metal tolerance of Escherichia coli. In vivo assays also confirmed that the Pe-Cu/Zn SOD recombinant protein had an antioxidative and free radical scavenging ability. A Cd toxicity experiment, in which purified Pe-Cu/Zn SOD protein was injected into the body cavities of P. esculenta, showed that the reactive oxygen species content in the coelomic fluid of the experimental group was significantly lower compared with the control group. These results suggest that Pe-Cu/Zn SOD played a role in Cd detoxification by chelating heavy metal ions and scavenging reactive oxygen free radicals, and that P. esculenta could be used as a bioindicator to evaluate heavy metal pollution.
| S-EPMC9602484 | biostudies-literature
Project description:Phascolosoma esculenta Raw sequence reads
| PRJNA1115933 | ENA
Project description:Phascolosoma esculenta Raw sequence reads
| PRJNA1130545 | ENA
Project description:Phascolosoma esculenta Genome sequencing and assembly
| PRJNA819496 | ENA
Project description:Phascolosoma (P.) varians, a sipunculan species known from the Greater Caribbean, was designated as a synonym of Phascolosoma (P.) nigrescens, which was originally described from Fiji. Their synonymy was primarily based upon an interpretation that these two species were morphologically indistinguishable. After its designation as a synonym, no further detailed analyses of morphological or molecular characteristics were performed to corroborate the assumed widespread distribution of Phascolosoma (P.) nigrescens. In this study, Phascolosoma (P.) varians is redescribed, and notable differences between this species and its proposed senior synonym are presented. These two species differ in the shape of their hooks, the spatial attachment of nephridia to the body wall, and the morphology of the contractile vessel. Additionally, there is high genetic divergence between nucleotide sequences within their respective cytochrome c oxidase subunit 1 (COI) genes, which supports the morphological data. Herein, the synonymy of Phascolosoma (P.) varians with Phascolosoma (P.) nigrescens is rejected due to morphological and molecular differences. Furthermore, the assumed widespread distribution of Phascolosoma (P.) nigrescens is still considered as questionable.
| S-EPMC7597625 | biostudies-literature
Project description:Sipuncula (peanut worms) is a traditional phylum which consists of unsegmented bilateral symmetric marine worms. Although it is accepted as a phylum, the phylogenetic position of Sipuncula has been questionable. There is lack of molecular record on Sipuncula species while morphological data is not enough to distinguish the closer relationships between Annelida and Sipuncula. In order to add more data to genomic library of sipunculan species, Phascolosoma pacificum (Keferstein, 1866) was collected from seagrass area of Chuuk lagoon/Micronesia and its complete mitochondrial genome sequenced. Furthermore, phylogenetic relationship of the phylum Sipuncula and the other Trochozoan phyla investigate due to mitochondrial protein coding genes. Although there is lack of recorded data, our results support the idea that Sipuncula are nested within Annelida according to phylogenetic analyses of mitochondrial protein coding genes.
| S-EPMC7800858 | biostudies-literature
Project description:In this study a Sipuncula species Phascolosoma sp. was collected from seagrass area from Chuuk lagoon Micronesia and its complete mitochondrial genome analyzed. This is the second complete mitochondrial genome record from the genus after Phascolosoma esculenta. The total length of mitochondrial genome of the species is 16,571 bp, which is longer than P. esculenta record. Also, locations of tRNA-Gly and putative control region are different between two records. Furthermore, phylogenetic relationship of Phascolosoma sp. are investigated due to protein-coding genes of mitochondrial genome. Due to the lack of recorded data, P. esculenta has been observed is the closest species to Phascolosoma sp. and they are belonging to the monophyletic group.
| S-EPMC7799974 | biostudies-literature
Project description:For marine invertebrates with no adaptive immune system, ferritin is a major intracellular iron-storage protein with a critical role in innate immunity. Here, we present the crystal structures of two novel ferritins [Fer147 and Phascolosoma esculenta ferritin (PeFer)] from the marine invertebrate P. esculenta, which resides in muddy-bottom coastal regions. Fer147 and PeFer exhibit the 4-3-2 symmetry of cage-like hollow shells containing 24 subunits, similar to other known ferritins. Fer147 and PeFer contain both the conserved ferroxidase center and threefold channels. Subtle structural differences in the putative nucleation sites suggest possible routes of metal ion movement in the protein shells. However, the marked variation in the electrostatic potential of the threefold channels in Fer147 and the fourfold channels in PeFer suggests significant diversity between Fer147 and PeFer in terms of metal ion aggregation and cation exclusion. In summary, the presented crystal structures may serve as references for studies of the iron-storage mechanism of additional ferritins from marine invertebrates.
| S-EPMC7931202 | biostudies-literature