Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis最新文献

Authentication of traditional Chinese medicine (TCM) is challenging due to DNA degradation in Chinese medicinal materials, which are usually processed and stored dry. The standard DNA barcoding length (648 bp) or longer are difficult to amplify, which makes it difficult to identify adulterants in Chinese medicinal materials. In this study, we used the mitochondrial 16S rRNA gene (< 200bp) as a barcode to differentiate black-spotted tokay geckoes (Gekko reevesii) from the related species used as counterfeits. We collected 63 specimens from 17 species of G. reevesii and their counterfeits, and each specimen generated a 189 bp 16S rRNA gene sequence. The average uncorrected p-distances within genuine G. reevesii was 0.9%, while the average uncorrected p-distances between G. reevesii and their counterfeits was 6.3% (at a minimum). According to phylogenetic analysis and genetic distances, the genuine G. reevesii samples collected in this study constitute a monophyly that can be distinguished from its counterfeits in TCM formulations, including G. gecko (red-spotted tokay geckos), which have very similar morphology. Thus, the short 16S rRNA barcode provides an effective tool for distinguishing G. reevesii from its counterfeits, ensuring the safety and efficacy of clinical medications containing components from G. reevesii in TCM.

Dictyostelia exhibits high diversity; however, mitochondrial genome data remain scarce for many genera. Although key features of some dictyostelid mitogenomes have been identified, several aspects remain unclear, including core gene content, segmental arrangement, and differences between 18S rRNA and mitochondrial gene phylogenies. To address these gaps, we reconstructed two complete mitogenomes-from Cavenderia subdiscoidea and Dictyostelium sp. (TH18CC)-and analyzed mitochondrial genes from ten genera and six additional complete mitogenomes from public databases. A comparison of eight complete mitogenomes revealed a conserved core of 39 protein-coding genes, 17 tRNA genes, and three rRNA genes. Two distinct segmental arrangements were identified: Dictyostelium (except D. purpureum) exhibits an A-C-B pattern, while other genera display an A-B-C pattern defined by the clusters nad9-atp1, trnC(GCA)-atp9, and rnl-nad3. Phylogenetic analyses based on 18S rDNA and mitochondrial rns suggest the transposition between segments B and C occurred after D. purpureum diverged from other Dictyostelium species, potentially involving tRNA gene displacement. In contrast, the mitochondrial protein-coding gene phylogeny differs from the rRNA trees, indicating that these gene sets may have evolved independently. These findings advance our understanding of dictyostelid mitogenome structure and evolution.

A recently discovered nemertean egg predator, Carcinonemertes conanobrieni, inhabiting Panulirus argus egg masses poses a potential threat to this ecologically and commercially relevant lobster. This study assessed the prevalence of C. conanobrieni in the southwestern Caribbean Sea; Costa Rica and Panama. Brooding females of P. argus were collected by fishermen near Punta Uva beach, Costa Rica (n = 17), and Guna Yala, Panama (n = 19) and examined for the presence of C. conanobrieni. Prevalence of C. conanobrieni in brooding lobsters, determined as the presence/absence of adults, juveniles, encysted juvenile worms, or carcinonemertid egg masses was 47.06% and 31.58% in Costa Rica and Panama, respectively. Moreover, when indirect evidence (empty capsules and/or dead embryos presumably attacked/consumed by worms) of the presence of C. conanobrieni in brooding lobsters is considered in addition to direct evidence, prevalence of C. conanobrieni in brooding lobsters was 64.71% and 47.37% in Costa Rica and Panama, respectively. The observations suggest that this parasitic worm completes its life cycle locally in the southwestern Caribbean. Notably, a Maximum Likelihood phylogenetic analysis based on a fragment of the mitochondrial cox1 gene clustered two specimens collected in Costa Rica together with four other specimens previously collected in Saint Kitts into a single fully supported monophyletic clade that segregated from a second clade containing six specimens of C. conanobrieni collected in Colombia, Florida, and Saint Kitts. The barcoding analysis suggests that there is an undescribed species of Carcinonemertes, anatomically like C. conanobrieni, infecting P. argus in Costa Rica.

The genus Origanum is taxonomically complex and often considered an underutilized group despite its economic and medicinal significance. Origanum vulgare L., the most variable species within the genus, is widely utilized as a culinary spice and medicinal herb, exhibiting considerable morphological diversity across its six recognized subspecies. In this study, we assembled and annotated the complete chloroplast (cp) genome of a wilt-resistant Saudi Arabian accession of O. vulgare. The cp genome measures 151,826 bp in length and displays the typical circular quadripartite structure, consisting of a large single copy (LSC) region (83,014 bp), a small single copy (SSC) region (17,620 bp), and a pair of inverted repeats (IRs) (25,596 bp each). It contains 129 genes, including 85 protein-coding genes, 36 transfer RNA genes, and 8 ribosomal RNA genes. Notably, the Saudi accession possesses a duplicated rps19 gene, and its cp genome length differs from that of other O. vulgare accessions. Phylogenetic analysis clustered all O. vulgare accessions into a single well-supported clade, revealing considerable genetic divergence among populations. Furthermore, the genus Origanum was strongly supported as sister to Thymus. This study provides a valuable chloroplast genome resource for evolutionary, taxonomic, and conservation studies in O. vulgare and related taxa within the Lamiaceae.

The Ribbontail stingray Taeniura lymma is an economically important fish and attractive species for the aquarium trade industry. Overfishing, habitat degradation, and pollution, however, pose a threat to this species. This study used partial mitochondrial cytochrome oxidase subunit I (COI) sequences (603 base pairs long) from 96 samples of T. lymma collected at five fish-landing sites (Deep Sea-Tanga, Malindi-Unguja, Kaole-Bagamoyo, Kivukoni-Dar es Salaam, and Bandarini-Mtwara) located along the coast of Tanzania to determine the species' genetic diversity, population genetic structure, and demographic history. The findings revealed an average nucleotide diversity of 0.24 ± 0.16% and a haplotype diversity of 0.75 ± 0.04. Nucleotide and haplotype diversities were relatively low at Kaole-Bagamoyo compared to the other studied localities. An Analysis of Molecular Variance (AMOVA) indicated limited but statistically significant genetic differences among populations (Overall F_ST = 0.09, p < 0.01). Pairwise AMOVA revealed genetic difference between the Deep Sea-Tanga population and all other populations studied with exception of Malindi-Unguja. Analyses of mismatch distribution, demographic history, and a haplotype network support a scenario of historical population expansion in the studied species. Immediate effort is required to protect population exhibiting low genetic diversity in this commercially important ray.

Trichoderma Persoon (1794) is a genus of fungus found in soils and decaying wood all over the world. We present the assembly and annotation of the mitochondrial genome of Trichoderma cerinum Bissett, Kubicek & Szakacs (2003) and an assessment of the phylogeny of the group, discussing the loss and gain of shared genes in the evolutionary history of fungi. We downloaded the raw data of T. cerinum from the NCBI database and exported it to the Galaxy Europe platform, where we performed the mitogenome assembly using the NOVOplasty tool. We used three tools for annotation. The phylogeny was conducted with 12 Trichoderma species and the T. cerinum. Fusarium oxysporum was used as an outgroup. We got a circularized mitochondrial genome of 26,696 bp, with 15 protein-coding genes, 25 tRNAs, two rRNAs, two endonuclease sequences, and an orf40. This species contains only one intron in the cob gene. In our phylogenetic reconstruction, T. cerinum was recovered as a sister group of a clade containing Trichoderma lixii, Trichoderma afroharzianum, Trichoderma simmonsii, and Trichoderma harzianum.

The subject of this study is Aegilops aucheri Boiss. 1844: a member of the section Sitopsis, subsection Truncata. This species is infrequently included in phylogenetic studies and is commonly regarded as a heterotypic synonym of Aegilops speltoides Tausch. The aim of this study was to detect genetic differences between Ae. aucheri and Ae. speltoides using the phylogenetic signal retrieved from chloroplast genomes. Plastomes of five Ae. aucheri accessions from different geographical locations were sequenced, annotated, and subjected to a phylogenetic analysis. Plastome sizes were found to range between 135,666 and 135,668 bp in Ae. aucheri. Comparative analysis of the chloroplast genome sequences from five Ae. aucheri accessions revealed single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels) relative to the Ae. speltoides plastome. To gain a more comprehensive understanding of the genetic divergence within the Truncata subsection, sequencing the nuclear genome of Ae. aucheri and comparing it to that of Ae. speltoides is essential.

We sequenced and assembled mitochondrial genomes of three tenthredinid sawflies (Euura poecilonota, E. striata, and Dolerus timidus) using Oxford Nanopore Technologies' MinION. The Canu assembler produced circular assemblies (23,000-40,000 bp). Still, errors were found in the highly repetitive non-coding control region because of the fragmented DNA which led to no reads spanning the complete control region, preventing its reliable assembly. Based on the non-repetitive coding region's sequencing coverage, we estimate the lengths of mitochondrial genomes of E. poecilonota, D. timidus, and E. striata to be about 30,000 bp, 31,000 bp, and 37,000 bp and control region to be 15,000 bp, 16,000 bp, and 22,000 bp respectively. All standard bilaterian mitochondrial genes are in the same order and orientation, except trnQ, which is on the minus strand in Euura and the plus strand in Dolerus. Using published tenthredinid genome data, we show that control region lengths are often underestimated.

The populations of the loggerhead turtles, Caretta caretta, present four main D-loop mitochondrial haplogroups that are distributed across the Indo-Pacific, Mediterranean, and Atlantic oceans. The Southwestern Atlantic (SWA) is one of the Regional Management Units (RMUs) of loggerheads, characterized by unique haplotypes, high nest density, and distinct life history traits. Detecting new D-loop haplogroups is important, particularly endemic ones, as they can enhance our understanding of their life history within the RMUs and contribute to the resolution of mixed stock analysis. In this study, we conducted a series of phylogenetic delimitation and network analyses to identify, validate, and infer the origin of four new D-loop haplotypes detected in the loggerhead populations from the SWA. Our findings demonstrate that these new D-loop haplotypes are valid and unique to the SWA lineage, potentially aiding in the delimitation of individuals' origins and the inference of their lineage.

Chorthippus dubius (Zub.) is one of the dominant grasshopper species. The limited data on Ch. dubius (Zub.) has impeded further understanding of its genetic characteristics and molecular detection. In this study, we analyzed the mitogenome of Ch. dubius (Zub.), which was 15,561 bp in length and contained 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and an AT-rich region. The entire mtDNA exhibited a strong AT bias, with an overall A+T content of 74.8%. The relative synonymous codon usage (RSCU) analysis revealed UUA (L) as the most frequently used codon. All the PCGs evolved under purifying selection (Ka/Ks <0.5), with ATP8 gene exhibited the highest Ka/Ks ratio. Maximum likelihood (ML) and Bayesian inference (BI) analyses reconstructed two topologically similar phylogenetic trees, and supported the monophly of the six subfamilies in Acrididae. Our results indicated two stable clades of the six subfamilies, with Oedipodinae emerging as the ancestral taxon and being sister group to the remaining taxa. In the alternative phylogenetic lineage, the remaining five subfamilies clustered the following relationship: Gomphocernae + (Acridinae + (Calliptaminae + (Melanoplinae + Oxyinae))). Both phylogenetic trees exhibited a closer relationship between Chorthippus dubius (Zub.) and Chorthippus aethalinus, members from the same genus.