Retraction Note to: The complete mitochondrial genomes of two freshwater snails provide new protein-coding gene rearrangement models and phylogenetic implications.
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ABSTRACT:
SUBMITTER: Mu X
PROVIDER: S-EPMC5522592 | biostudies-literature | 2017 Jul
REPOSITORIES: biostudies-literature
Publications
Retraction Note to: The complete mitochondrial genomes of two freshwater snails provide new protein-coding gene rearrangement models and phylogenetic implications.
Mu Xidong X Yang Yexin Y Liu Yi Y Luo Du D Xu Meng M Wei Hui H Gu Dangen D Song Hongmei H Hu Yinchang Y
Parasites & vectors 20170721 1
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Project description:BackgroundMitochondrial (mt) genome sequences are widely used for species identification and to study the phylogenetic relationships among Gastropoda. However, to date, limited data are available as taxon sampling is narrow. In this study we sequenced the complete mt genomes of the freshwater gastropods Radix swinhoei (Lymnaeidae) and Planorbarius corneus (Planorbidae). Based on these sequences, we investigated the gene rearrangement in these two species and the relationships with respect to the ancestral gene order and assessed their phylogenetic relationships.MethodsThe complete mt genomes of R. swinhoei and P. corneus were sequenced using Illumina-based paired-end sequencing and annotated by comparing the sequence information with that of related gastropod species. Putative models of mitochondrial gene rearrangements were predicted for both R. swinhoei and P. corneus, using Reishia clavigera mtDNA structure as the ancestral gene order. The phylogenetic relationships were inferred using thirteen protein sequences based on Maximum likelihood and Bayesian inference analyses.ResultsThe complete circular mt genome sequences of R. swinhoei and P. corneus were 14,241 bp and 13,687 bp in length, respectively. Comparison of the gene order demonstrated complex rearrangement events in Gastropoda, both for tRNA genes and protein-coding genes. The phylogenetic analyses showed that the family Lymnaeidae was more closely related to the family Planorbidae, consistent with previous classification. Nevertheless, due to the position recovered for R. swinhoei, the family Lymnaeidae was not monophyletic.ConclusionThis study provides the complete mt genomes of two freshwater snails, which will aid the development of useful molecular markers for epidemiological, ecological and phylogenetic studies. Additionally, the predicted models for mt gene rearrangement might provide novel insights into mt genome evolution in gastropods.
| S-EPMC5219674 | biostudies-literature
Project description:[This retracts the article DOI: 10.5114/wiitm.2017.66025.].
| S-EPMC5502346 | biostudies-other
Project description:The apple snails Pomacea canaliculata, Pomacea diffusa and Pomacea maculate (Gastropoda: Caenogastropoda: Ampullariidae) are invasive pests causing massive economic losses and ecological damage. We sequenced and characterized the complete mitochondrial genomes of these snails to conduct phylogenetic analyses based on comparisons with the mitochondrial protein coding sequences of 47 Caenogastropoda species. The gene arrangements, distribution and content were canonically identical and consistent with typical Mollusca except for the tRNA-Gln absent in P. diffusa. An identifiable control region (d-loop) was absent. Bayesian phylogenetic analysis indicated that all the Ampullariidae species clustered on the same branch. The genus Pomacea clustered together and then with the genus Marisa. The orders Architaenioglossa and Sorbeoconcha clustered together and then with the order Hypsogastropoda. Furthermore, the intergenic and interspecific taxonomic positions were defined. Unexpectedly, Ceraesignum maximum, Dendropoma gregarium, Eualetes tulipa and Thylacodes squamigerus, traditionally classified in order Hypsogastropoda, were isolated from the order Hypsogastropoda in the most external branch of the Bayesian inference tree. The divergence times of the Caenogastropoda indicated that their evolutionary process covered four geological epochs that included the Quaternary, Neogene, Paleogene and Cretaceous periods. This study will facilitate further investigation of species identification to aid in the implementation of effective management and control strategies of these invasive species.
| S-EPMC6274680 | biostudies-literature
Project description:BackgroundDue to their great species and ecological diversity as well as their capacity to produce hundreds of different toxins, cone snails are of interest to evolutionary biologists, pharmacologists and amateur naturalists alike. Taxonomic identification of cone snails still relies mostly on the shape, color, and banding patterns of the shell. However, these phenotypic traits are prone to homoplasy. Therefore, the consistent use of genetic data for species delimitation and phylogenetic inference in this apparently hyperdiverse group is largely wanting. Here, we reconstruct the phylogeny of the cones endemic to Cabo Verde archipelago, a well-known radiation of the group, using mitochondrial (mt) genomes.ResultsThe reconstructed phylogeny grouped the analyzed species into two main clades, one including Kalloconus from West Africa sister to Trovaoconus from Cabo Verde and the other with a paraphyletic Lautoconus due to the sister group relationship of Africonus from Cabo Verde and Lautoconus ventricosus from Mediterranean Sea and neighboring Atlantic Ocean to the exclusion of Lautoconus endemic to Senegal (plus Lautoconus guanche from Mauritania, Morocco, and Canary Islands). Within Trovaoconus, up to three main lineages could be distinguished. The clade of Africonus included four main lineages (named I to IV), each further subdivided into two monophyletic groups. The reconstructed phylogeny allowed inferring the evolution of the radula in the studied lineages as well as biogeographic patterns. The number of cone species endemic to Cabo Verde was revised under the light of sequence divergence data and the inferred phylogenetic relationships.ConclusionsThe sequence divergence between continental members of the genus Kalloconus and island endemics ascribed to the genus Trovaoconus is low, prompting for synonymization of the latter. The genus Lautoconus is paraphyletic. Lautoconus ventricosus is the closest living sister group of genus Africonus. Diversification of Africonus was in allopatry due to the direct development nature of their larvae and mainly triggered by eustatic sea level changes during the Miocene-Pliocene. Our study confirms the diversity of cone endemic to Cabo Verde but significantly reduces the number of valid species. Applying a sequence divergence threshold, the number of valid species within the sampled Africonus is reduced to half.
| S-EPMC5702168 | biostudies-literature
Project description:Resident microbes (microbiota) can shape host organismal function and adaptation in the face of environmental change. Invasion of new habitats exposes hosts to novel selection pressures, but little is known about the impact on microbiota and the host-microbiome relationship (e.g., how rapidly new microbial associations are formed, whether microbes influence invasion success). We used high-throughput 16S rRNA sequencing of New Zealand (native) and European (invasive) populations of the freshwater snail Potamopyrgus antipodarum and found that while invaders do carry over some core microbial taxa from New Zealand, their microbial community is largely distinct. This finding highlights that invasions can result in the formation of novel host-microbiome relationships. We further show that the native microbiome is composed of fewer core microbes than the microbiome of invasive snails, suggesting that the microbiota is streamlined to a narrower set of core members. Furthermore, native snails exhibit relatively low alpha diversity but high inter-individual variation, whereas invasive snails have higher alpha diversity but are relatively similar to each other. Together, our findings demonstrate that microbiota comparisons across native and invasive populations can reveal the impact of a long coevolutionary history and specialization of microbes in the native host range, as well as new associations occurring after invasion. We lay essential groundwork for understanding how microbial relationships affect invasion success and how microbes may be utilized in the control of invasive hosts.
| S-EPMC7980272 | biostudies-literature
Project description:Psilidae (Diptera: Brachycera) is a moderate-sized family currently placed in the superfamily Diopsoidea and contains some destructive agricultural and forestry pests. The systematic position and intrafamilial classification of rust flies are in need of further study, and the available molecular data of Psilidae are still limited. In this study, we present the mitochondrial genomes of 6 Psilidae species (Chamaepsilatestudinaria Wang and Yang, Chyliza bambusae Wang and Yang, Chy. chikuni Wang, Loxocera lunata Wang and Yang, L. planivena Wang and Yang and L. sinica Wang and Yang). Comparative analyses show a conserved genome structure, in terms of gene composition and arrangement, and a highly Adenine plus Thymine biased nucleotide composition of the 6 psilid mitogenomes. Mitochondrial evolutionary rates vary among the 6 species, with species of Chylizinae exhibiting a slower average rate than species of Psilinae. The length, the nucleotide composition, and the copy number of repeat units of the control region are variable among the 6 species, which may offer useful information for phylogenetic and evolutionary studies of Psilidae. Phylogenetic analyses based on 4 mitogenomic datasets (AA, PCG, PCG12RNA, and PCGRNA) support the monophyly of Psilidae, and the sister relationship between Chylizinae and Psilinae, while Diopsoidea is suggested to be non-monophyletic. Our study enlightens the future application of mitogenomic data in the phylogenetic and evolutionary studies of Psilidae, based on denser taxon sampling.
| S-EPMC9224655 | biostudies-literature
Project description:BackgroundPhylogenetic relationships among Asian and African colobine genera have been disputed and are not yet well established. In the present study, we revisit the contentious relationships within the Asian and African Colobinae by analyzing 44 nuclear non-coding genes (>23 kb) and mitochondrial (mt) genome sequences from 14 colobine and 4 non-colobine primates.Principal findingsThe combined nuclear gene and the mt genome as well as the combined nuclear and mt gene analyses yielded different phylogenetic relationships among colobine genera with the exception of a monophyletic 'odd-nosed' group consisting of Rhinopithecus, Pygathrix and Nasalis, and a monophyletic African group consisting of Colobus and Piliocolobus. The combined nuclear data analyses supported a sister-grouping between Semnopithecus and Trachypithecus, and between Presbytis and the odd-nosed monkey group, as well as a sister-taxon association of Pygathrix and Rhinopithecus within the odd-nosed monkey group. In contrast, mt genome data analyses revealed that Semnopithecus diverged earliest among the Asian colobines and that the odd-nosed monkey group is sister to a Presbytis and Trachypithecus clade, as well as a close association of Pygathrix with Nasalis. The relationships among these genera inferred from the analyses of combined nuclear and mt genes, however, varied with the tree-building methods used. Another remarkable finding of the present study is that all of our analyses rejected the recently proposed African colobine paraphyly and hybridization hypothesis and supported reciprocal monophyly of the African and Asian groups.SignificanceThe phylogenetic utility of large-scale new non-coding genes was assessed using the Colobinae as a model, We found that these markers were useful for distinguishing nodes resulting from rapid radiation episodes such as the Asian colobine radiation. None of these markers here have previously been used for colobine phylogenetic reconstruction, increasing the spectrum of molecular markers available to mammalian systematics.
| S-EPMC3338693 | biostudies-literature
Project description:Efforts to catalog viral diversity in the gut microbiome have largely focused on DNA viruses, while RNA viruses remain understudied. To address this, we screened assemblies of previously published mouse gut metatranscriptomes for the presence of RNA viruses. We identified the coding-complete genomes of an astrovirus and five mitovirus-like viruses.
| S-EPMC7082449 | biostudies-literature
Project description:The Yangtze River basin is one of the most species-rich regions for freshwater mussels on Earth, but is gravely threatened by anthropogenic activities. However, conservation planning and management of mussel species has been hindered by a number of taxonomic uncertainties. In order to clarify the taxonomic status and phylogenetic position of these species, mitochondrial genomes of four species (Acuticostachinensis, Schistodesmuslampreyanus, Cuneopsisheudei and Cuneopsiscapitatus) were generated and analyzed along with data from 43 other mitogenomes. The complete F-type mitogenomes of A.chinensis, S.lampreyanus, C.heudei, and C.capitatus are 15652 bp, 15855 bp, 15892 bp, and 15844 bp, respectively, and all four F-type mitogenomes have the same pattern of gene arrangement. ML and BI trees based on the mitogenome dataset are completely congruent, and indicate that the included Unionidae belong to three subfamilies with high bootstrap and posterior probabilities, i.e., Unioninae (Aculamprotula, Cuneopsis, Nodularia, and Schistodesmus), Anodontinae (Cristaria, Arconaia, Acuticosta, Lanceolaria, Anemina, and Sinoanodonta), and Gonideinae (Ptychorhynchus, Solenaia, Lamprotula, and Sinohyriopsis). Results also indicate that A.chinensis has affinities with Arconaialanceolata and Lanceolariagrayii and is a member of the subfamily Anodontinae.
| S-EPMC6328525 | biostudies-literature
Project description:BackgroundThe genus Zingiber of the Zingiberaceae is distributed in tropical, subtropical, and in Far East Asia. This genus contains about 100-150 species, with many species valued as important agricultural, medicinal and horticultural resources. However, genomic resources and suitable molecular markers for species identification are currently sparse.ResultsWe conducted comparative genomics and phylogenetic analyses on Zingiber species. The Zingiber chloroplast genome (size range 162,507-163,711 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 86,986-88,200 bp), a small single copy (SSC, 15,498-15,891 bp) and a pair of inverted repeats (IRs, 29,765-29,934 bp). The genomes contain 113 unique genes, including 79 protein coding genes, 30 tRNA and 4 rRNA genes. The genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats and long repeats are conservative in the genomes of Zingiber. The analysis of sequence divergence indicates that the following genes undergo positive selection (ccsA, ndhA, ndhB, petD, psbA, psbB, psbC, rbcL, rpl12, rpl20, rpl23, rpl33, rpoC2, rps7, rps12 and ycf3). Eight highly variable regions are identified including seven intergenic regions (petA-pabJ, rbcL-accD, rpl32-trnL-UAG, rps16-trnQ-UUG, trnC-GCA-psbM, psbC-trnS-UGA and ndhF-rpl32) and one genic regions (ycf1). The phylogenetic analysis revealed that the sect. Zingiber was sister to sect. Cryptanthium rather than sect. Pleuranthesis.ConclusionsThis study reports 14 complete chloroplast genomes of Zingiber species. Overall, this study provided a solid backbone phylogeny of Zingiber. The polymorphisms we have uncovered in the sequencing of the genome offer a rare possibility (for Zingiber) of the generation of DNA markers. These results provide a foundation for future studies that seek to understand the molecular evolutionary dynamics or individual population variation in the genus Zingiber.
| S-EPMC9848714 | biostudies-literature