Dataset Information

First mitogenome of Anthomyia illocata (Diptera, Anthomyiidae) yielded by next-generation sequencing.

ABSTRACT: The mitochondrial genome of Anthomyia illocata Walker, 1857 belonging to the Anthomyiidae, was obtained using a next-generation sequencing approach. This 16,236 bp complete mitogenome consists of 13 protein-coding, two ribosomal RNA, and 22 transfer RNA genes, as well as a non-coding control region. The Anthomyiidae are reconstructed as a paraphyletic group, with the genera Pegomya recovered as a sister group of the Scathophagidae.

SUBMITTER: Li H

PROVIDER: S-EPMC9176329 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

First mitogenome of Anthomyia illocata (Diptera, Anthomyiidae) yielded by next-generation sequencing.

Li Henan H Yan Liping L Pei Wenya W Hu Yang Y Wang Aidong A Wang Zhiyuan Z Zhang Dong D

Mitochondrial DNA. Part B, Resources 20220526 5

The mitochondrial genome of Anthomyia illocata Walker, 1857 belonging to the Anthomyiidae, was obtained using a next-generation sequencing approach. This 16,236 bp complete mitogenome consists of 13 protein-coding, two ribosomal RNA, and 22 transfer RNA genes, as well as a non-coding control region. The Anthomyiidae are reconstructed as a paraphyletic group, with the genera Pegomya recovered as a sister group of the Scathophagidae. ...[more]

PMID: 35692704

Similar Datasets

Project description:BACKGROUND: This study describes how the complete mitogenome of a terrestrial snail, Cylindrus obtusus (Draparnaud, 1805) was sequenced without PCRs from a collection specimen that had been in 70% ethanol for 8 years. The mitogenome was obtained with Illumina GAIIx shot gun sequencing. Although the used specimen was collected relatively recently and kept in a DNA-friendly preservative (not formalin as frequently used with old museum specimens), we believe that the exclusion of PCRs as facilitated by NGS (Next Generation Sequencing) removes a great obstacle in DNA sequencing of collection specimens. A brief comparison is made between our Illumina GAIIx approach and a similar study that made use of the Roche 454-FLX platform. RESULTS: The mtDNA sequence of C. obtusus is 14,610 bases in length (about 0.5 kb larger than other stylommatophoran mitogenomes reported hitherto) and contains the 37 genes (13 protein coding genes, two rRNAs and 22 tRNAs) typical for metazoans. Except for a swap between the position of tRNA-Pro and tRNA-Ala, the gene arrangement of C. obtusus is identical to that reported for Cepaea nemoralis. The 'aberrant' rearrangement of tRNA-Thr and COIII compared to that of other Sigmurethra (and the majority of gastropods), is not unique for C. nemoralis (subfamily Helicinae), but is also shown to occur in C. obtusus (subfamily Ariantinae) and might be a synapomorphy for the family Helicidae. CONCLUSIONS: Natural history collections potentially harbor a wealth of information for the field of evolutionary genetics, but it can be difficult to amplify DNA from such specimens (due to DNA degradation for instance). Because NGS techniques do not rely on primer-directed amplification (PCR) and allow DNA to be fragmented (DNA gets sheared during library preparation), NGS could be a valuable tool for retrieving DNA sequence data from such specimens. A comparison between Illumina GAIIx and the Roche 454 platform suggests that the former might be more suited for de novo sequencing of mitogenomes.

Project description:BackgroundRecent reports have demonstrated that the entire mitochondrial genome can be secreted in extracellular vesicles (EVs), but the biological attributes of this cell-free mitochondrial DNA (mtDNA) remain insufficiently understood. We used next-generation sequencing to compare plasma EV-derived mtDNA to that of whole blood (WB), peripheral blood mononuclear cells (PBMCs), and formalin-fixed paraffin-embedded (FFPE) tumor tissue from eight rectal cancer patients and WB and fresh-frozen (FF) tumor tissue from eight colon cancer patients.MethodsTotal DNA was isolated before the mtDNA was enriched by PCR with either two primer sets generating two long products or multiple primer sets (for the FFPE tumors), prior to the sequencing. mtDNA diversity was assessed as the total variant number, level of heteroplasmy (mutant mtDNA copies mixed with wild-type copies), variant distribution within the protein-coding genes, and the predicted functional effect of the variants in the different sample types. Differences between groups were compared by paired Student's t-test or ANOVA with Dunnett's multiple comparison tests when comparing matched samples from patients. Mann-Whitney U test was used when comparing differences between the cancer types and patient groups. Pearson correlation analysis was performed.ResultsIn both cancer types, EV mtDNA presented twice as many variants and had significantly more low-level heteroplasmy than WB mtDNA. The EV mtDNA variants were clustered in the coding regions, and the proportion of EV mtDNA variants that were missense mutations (i.e., estimated to moderately affect the mitochondrial protein function) was significantly higher than in WB and tumor tissues. Nonsense mutations (i.e., estimated to highly affect the mitochondrial protein function) were only observed in the tumor tissues and EVs.ConclusionTaken together, plasma EV mtDNA in CRC patients exhibits a high degree of diversity.Trial registrationClinicalTrials.gov: NCT01816607 . Registered 22 March 2013.

Dataset Information

First mitogenome of Anthomyia illocata (Diptera, Anthomyiidae) yielded by next-generation sequencing.

Publications

First mitogenome of <i>Anthomyia illocata</i> (Diptera, Anthomyiidae) yielded by next-generation sequencing.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets