Identification Of Molecular Species Research Articles

Prevalence and molecular identification of Plasmodium falciparum in symptomatic individuals in Nyala city, Sudan

Background: Malaria is one of the most important infectious diseases in tropical and subtropical regions, and 45% of the population living in areas that suffer from stable malaria transmission in Sudan. The prevalence of symptomatic Plasmodium infection based on microscopy and RDTs is poorly documented in Nyala city. This study was conducted to determine the prevalence of plasmodium infection and molecular identification of plasmodium species in Nyala city, Sudan.
 Methods: A cross-sectional study was conducted from July 2018 to December 2018 to determine the prevalence of malaria and molecular identification of plasmodium species in Nyala city, Sudan. A total of 300 suspected patients were enrolled in this study. Microscopy and RDTs were performed to estimate the prevalence and nPCR to detect the plasmodium genus and species.
 Results: Of 300 patients, 113 (37.7%) were positive for malaria. Plasmodium falciparum was the only prevalent species detected amongst the study population. The prevalence of plasmodium infection by microscopy and RDTs was 113 (37.7 %) and 106 (35.3 %), respectively. While PCR result showed prevalence of 47 (47%).
 Conclusions: This study showed that the only prevalent species identified was P. falciparum, the findings demonstrate no existence of non-falciparum malaria, and children less than five years old were the most infected patients. The diagnostic performance of microscopy was better than RDTs in the diagnosis of malaria infection.

Molecular identification of Sarcocystis species in sika deer (Cervus nippon) of free-ranging populations in Germany and Austria.

In this study, for the first time, Sarcocystis species were identified molecularly in sika deer (Cervus nippon) that form free-ranging populations in several countries of Europe. Diaphragm muscle samples from 151 deer from 10 populations in Germany and Austria were examined for sarcocysts. By one-gram methylene-blue staining, sarcocysts were recorded in samples of 114 animals (75.5%) which originated from all populations. Sarcocysts were more often (p < 0.0001) recorded in yearling and adult deer than in calves. Infection intensity was generally low with ~ 70% of the sarcocyst positive deer harbouring ≤ 10 sarcocysts per 1-gram diaphragm muscle. Based on cox1 sequence comparison, 10 species of Sarcocystis, all previously reported parasitizing cervids, were identified: S. elongata, S. entzerothi, S. hjorti, S. iberica, S. japonica, S. linearis, S. morae, S. pilosa, S. silva and S. truncata. The prevailing S. hjorti was detected in sika deer of all 10 populations. The identification in sika deer of S. hjorti, S. iberica, S. elongata, S. linearis, S. morae and S. silva constitutes new host records. With the additional species records of this study, the highest number of Sarcocystis species, at least 16, was identified in this host.

Evidence for intrinsic defects and nanopores as hotspots in 2D PdSe2 dendrites for plasmon-free SERS substrate with a high enhancement factor

Surface-enhanced Raman spectroscopy (SERS), a very powerful tool for the identification of molecular species, has relied mostly on noble metal-based substrates to obtain a high enhancement factor. In this work, we demonstrate that self-driven intrinsic defects in 2D palladium di-selenide (PdSe2) dendrites grown at low temperature (280 °C) act as hotspots for high SERS enhancement. We grow 2D dendritic PdSe2 with ample intrinsic defects to exploit it for SERS application. X-ray electron spectroscopy (XPS) analysis reveals 9.3% outer layer and 4.7% interior Se vacancies. A detailed examination of atomic-scale defects revealed Se vacancy (VSe) coupled with Se–Pd–Se vacancy (VSe-Pd-Se) in monolayer PdSe2, and an array of line defects (Se vacancies) and nanopores in bilayer PdSe2 dendrites. Interestingly, our studies reveal that Se vacancy-rich PdSe2 gives rise to line defects that act like hotspots for SERS enhancement. Remarkably, the vacancy-rich dendritic PdSe2 shows a SERS enhancement factor >105 and can detect RhB at a concentration down to 10−8 M. We speculate that the topological line defects and the edge construction in PdSe2 dendrites act as metallic wire or edge, which is partly responsible for the high enhancement in the SERS signal. The high SERS sensitivity is explained on the basis of multiple charge transfer processes combined with the predicted metal-like behavior of the defected 2D PdSe2. Our conclusions are fully supported by the density functional theory calculation of the electronic density of states of the defective bilayer (2L) PdSe2, which remarkably exhibits metallic character. Being a defect-enabled SERS substrate, dendritic 2D PdSe2 fills the gap between conventional plasmonic SERS substrate and plasmon-free SERS substrate.

Prevalence and molecular identification of Plasmodium falciparum

Background: Malaria is one of the most important infectious diseases in tropical and subtropical regions, and 45% of the population living in areas that suffer from stable malaria transmission in Sudan. The prevalence of symptomatic Plasmodium infection based on microscopy and RDTs is poorly documented in Nyala city. This study was conducted to determine the prevalence of plasmodium infection and molecular identification of plasmodium species in Nyala city, Sudan.&#x0D; Methods: A cross-sectional study was conducted from July 2018 to December 2018 to determine the prevalence of malaria and molecular identification of plasmodium species in Nyala city, Sudan. A total of 300 suspected patients were enrolled in this study. Microscopy and RDTs were performed to estimate the prevalence and nPCR to detect the plasmodium genus and species.&#x0D; Results: Of 300 patients, 113 (37.7%) were positive for malaria. Plasmodium falciparum was the only prevalent species detected amongst the study population. The prevalence of plasmodium infection by microscopy and RDTs was 113 (37.7 %) and 106 (35.3 %), respectively. While PCR result showed prevalence of 47 (47%).&#x0D; Conclusions: This study showed that the only prevalent species identified was P. falciparum, the findings demonstrate no existence of non-falciparum malaria, and children less than five years old were the most infected patients. The diagnostic performance of microscopy was better than RDTs in the diagnosis of malaria infection.

Ribosomal RNA (rRNA) sequences from 33 globally distributed mosquito species for improved metagenomics and species identification.

Total RNA sequencing (RNA-seq) is an important tool in the study of mosquitoes and the RNA viruses they vector as it allows assessment of both host and viral RNA in specimens. However, there are two main constraints. First, as with many other species, abundant mosquito ribosomal RNA (rRNA) serves as the predominant template from which sequences are generated, meaning that the desired host and viral templates are sequenced far less. Second, mosquito specimens captured in the field must be correctly identified, in some cases to the sub-species level. Here, we generate mosquito rRNA datasets which will substantially mitigate both of these problems. We describe a strategy to assemble novel rRNA sequences from mosquito specimens and produce an unprecedented dataset of 234 full-length 28S and 18S rRNA sequences of 33 medically important species from countries with known histories of mosquito-borne virus circulation (Cambodia, the Central African Republic, Madagascar, and French Guiana). These sequences will allow both physical and computational removal of rRNA from specimens during RNA-seq protocols. We also assess the utility of rRNA sequences for molecular taxonomy and compare phylogenies constructed using rRNA sequences versus those created using the gold standard for molecular species identification of specimens-the mitochondrial cytochrome c oxidase I (COI) gene. We find that rRNA- and COI-derived phylogenetic trees are incongruent and that 28S and concatenated 28S+18S rRNA phylogenies reflect evolutionary relationships that are more aligned with contemporary mosquito systematics. This significant expansion to the current rRNA reference library for mosquitoes will improve mosquito RNA-seq metagenomics by permitting the optimization of species-specific rRNA depletion protocols for a broader range of species and streamlining species identification by rRNA sequence and phylogenetics.

Molecular Investigation of Theileria and Babesia Species in Domestic Mammals from Sardinia, Italy.

Piroplasmoses are tick-borne diseases caused by hemoprotozoan parasites of veterinary and public health significance. This study focuses on the molecular identification and characterization of species belonging to the Theileria/Babesia genera in 152 blood samples, collected from 80 horses and 72 cattle from several farms in Sardinia, by targeting the 18S rRNA gene. The PCR results highlighted that 72% of the samples were positive for Theileria/Babesia spp., with a rate of infection of 68% and 75% for the horses and cattle, respectively. Sequencing and the BLASTn analysis showed that the 18S rRNA generated in this study has 99-100% homology with the B. bigemina, T. orientalis/sergenti/buffeli, T. equi and T. annulata strains isolated from different hosts worldwide. These findings improve the knowledge on Babesia and Theileria infections in domestic mammals and confirm the significant prevalence of piroplasmosis among subclinical and carrier animals throughout the island. Furthermore, the presence of T. annulata, reported for the first time in the study area, expands the repertoire of pathogens already detected in Sardinia. Our results gather updates on the diversity and distribution of piroplasms in Sardinia and suggest the need to develop procedures to improve animal and public health safety.

Molecular Identification of Neoechinorhynchus chrysemydis (Acanthocephala: Neoechinorhynchidae) of Eastern River Cooters, Pseudemys concinna concinna (Testudines: Emydidae), from Arkansas and Oklahoma, U.S.A., Provides Insight into Host Specificity

Turtle acanthocephalans (genus Neoechinorhynchus) reside in the intestine of their definitive hosts and have been reported from a wide variety of turtle species. However, few reports exist of acanthocephalans in river cooters (Pseudemys concinna). We examined several eastern river cooters, P. c. concinna, from Arkansas and Oklahoma for acanthocephalans and generate the first sequence data for specimens of Neoechinorhynchus chrysemydis from this host. Molecular species identification was achieved by sequencing the complete internal transcribed spacer (ITS) gene and comparing it to ITS sequences for other species of Neoechinorhynchus from turtles and fishes available in GenBank. We also document a new state report for Neoechinorhynchus chrysemydis in Arkansas, as well as a new host record for N. chrysemydis in eastern river cooters in Oklahoma. Neoechinorhynchus chrysemydis appears to have relatively low host specificity among the species of turtle Neoechinorhynchus, and DNA sequencing can be a useful tool for investigating these host–parasite relationships.

Application of direct PCR for phylogenetic analysis of Fusarium fujikuroi species complex isolated from rice seeds.

Plant pathogenic fungi cause severe yield losses and mycotoxin contamination in crops. The precise and rapid detection of fungal pathogens is essential for effective disease management. Sequencing universal DNA barcodes has become the standard method for the diagnosis of fungal diseases, as well as for identification and phylogenetic analysis. A major bottleneck in obtaining DNA sequence data from many samples was the laborious and time-consuming process of sample preparation for genomic DNA. Here, we describe a direct PCR approach that bypasses the DNA extraction steps to streamline the molecular identification of fungal species. Using a direct PCR approach, we successfully sequenced the nuclear ribosomal internal transcribed spacer (ITS) region for the representatives of major fungal lineages. To demonstrate the usefulness of this approach, we performed a phylogenetic analysis of the Fusarium fujikuroi species complex, which causes bakanae ("foolish seedling") disease of rice and mycotoxin contamination. A total of 28 candidate strains were isolated from rice seeds in the Republic of Korea, and the identity of the isolates was determined using the DNA sequence of both ITS and translation elongation factor 1-α regions. In addition, 17F. fujikuroi isolates were examined for fumonisin (FB) production in rice medium using an enzyme-linked immunosorbent assay. Phylogenetic and toxigenic analyses showed that the F. fujikuroi strains could be distinguished into two groups: FB producers (B14-type) and non-producers (B20-type). These results will accelerate the molecular identification of fungal pathogens and facilitate the effective management of fungal diseases.

Comparison of DNA extraction methods on CITES-listed timber species and application in species authentication of commercial products using DNA barcoding

Quality and quantity of DNA extracted from wood is important for molecular identification of wood species, which can serve for conservation of wood species and law enforcement to combat illegal wood trading. Rosewood (Dalbergia and Pterocarpus) and agarwood (Aquilaria) are the most commonly found hardwood in timber seizure incidents. To monitor international trade of timber and commercial wood products and to protect these endangered wood species from further population decline, in this study, we have compared three extraction protocols for DNA extraction from 12 samples of rosewood and agarwood timber logs, and later applied the best DNA extraction protocol on 10 commercial wood products claimed to be rosewood and agarwood. We also demonstrated the applicability of DNA mini-barcoding with multi-loci combination with reference library for identifying the species of timber and commercial wood products. We found that a silica column-based method with guanidine thiocyanate-containing binding buffer served the best in DNA extraction from different parts of wood in all three genera with good quality and quantity. Single barcode region ITS2 or multi-loci combinations including ITS2 barcode region generally provide better discriminatory power for species identification for both rosewood and agarwood. All 10 products were identified to species-level using multi-loci combination. In terms of accuracy in labelling, 80% of them were labelled correctly. Our work has shown the feasibility of extracting good quality of DNA from authentic wood samples and processed wood products and identifying them to species level based on DNA barcoding technology.

Molecular identification and phylogenetic confirmation of Sarcocystis species in slaughtered camels in Al-Najif province, Iraq.

Sarcocystis is an intracellular parasite of particular importance as it infects many domestic animals as camels that play the role of intermediate host for the parasite. This study aimed to identify Sarcocystis species in camels by molecular assay with confirmation of local isolates by phylogenetic analysis. A total of 200 slaughtered camels (Camelus dromedarius) that were slaughtered in Al-Najaf province (Iraq) abattoirs from October (2021) to July (2022) were subjected to collect the fresh tissues from four organs (esophagus, diaphragm, skeletal muscle, and heart), to be tested later by the conventional polymerase chain reaction (PCR). Then, a total of 20 positive genomic DNA samples were sequenced, named, got specific access numbers (OP785703.1 to OP785722.1), and compared with the NCBI-GenBank isolates. Targeting Cox1 gene, 80% of collected tissues were found positive by the conventional PCR assay. Phylogenetic tree analysis revealed that the local Sarcocystis isolates were identical to Indian S. cameli isolates at 99.70%-99.90%. Significantly, an increase in Sarcocystis infection was seen in the esophagus compared to the diaphragm, skeletal muscle, and heart; older (>4 years) than younger (≤4 years) camels, and in females more than males. To the best of our knowledge, this represents the first molecular study in Iraq that identifies Sarcocystis cameli in camels. However, additional epidemiological and molecular studies in camel populations as well as in other domestic and wild animals appeared to be necessary.

Histopathology and molecular identification of Sarcocystis species forming macrocysts in slaughtered sheep and goats of Duhok, Iraq.

This study aimed to identify Sarcocystis species isolated from macroscopic sarcocysts of naturally infected sheep and goats using histopathological and molecular studies. A total of 260 macrosarcocyst samples were randomly collected from 1,337 infected sheep and goats slaughtered at different abattoirs in Duhok province, Iraq, from May 2021 to June 2022. The macroscopic cysts, which were found in the esophagus, diaphragm, and abdominal muscles, were classified into fat and thin cysts. Histopathological examination of the observed fat and thin cysts showed a thick eosinophilic wall, several internal septa-forming compartments enclosing numerous bradyzoites, and mild mononuclear inflammatory cells infiltrating around the cysts. The 18 Subunit ribosomal RNA (18S rRNA) and 28 Subunit ribosomal RNA (28S rRNA) genes of Sarcocystis spp. were amplified by polymerase chain reaction (PCR) from 200 macrosarcocysts samples. Molecularly, the DNA sequencing results obtained from fat macrocysts of sheep and goats were found to be identical to Sarcocystis gigantea, and from thin cysts of sheep proved to be similar to Sarcocystis medusiformis, while from thin macrocysts of goats were found to be identical to Sarcocystis moulei. Alignment and phylogenetic analysis observed a very close relationship between identified species of Sarcocystis and other Sarcocystis DNA sequences of sheep and goats across the world. To our knowledge, this is the first histopathological and molecular study for identification of Sarcocystis spp. isolated from different macroscopic forms of sarcocysts of sheep and goats in Iraq.

Molecular species identification of Rockskipper (Pisces: Blenniidae) from Porok Beach (Yogyakarta, Indonesia) based on 16S rRNA and COI genes

Rockskipper belongs to the species-rich family of Blenniidae (Combtooth blenny) and is known for its cryptic and species complexes presence. Identifying cryptic species based solely on morphological features is challenging due to their similar morphological characteristics. As a result, molecular genetic techniques based on two partial mtDNA genes, COI and 16S rRNA, were employed to identify fish accurately. This study aimed to evaluate the effectiveness of COI and 16S rRNA gene for the identification of Rockskipper fish and investigate the genetic relationship between species of Rockskipper from Porok Beach. The result revealed that the thirteen Rockskipper samples from Porok Beach that belong to six species (E. vermiculatus, E. striatus, I. lineatus, I. dussumieri, I. edentulus, and B. caudolineata) with more than 99% similarity. In contrast, the 16S analysis identified five species. A Bayesian phylogenetic tree demonstrated that six species of Rockskipper from Porok Beach are genetically distinct and separated into two clusters. We also found that two samples (RS-9 and RS-10) form a monophyletic group with B. caudolineata with maximum bootstrap (NJ and ML: 100%) and posterior probability (1.00). We hypothesized that B. caudolineata is a species complex with at least two lineages: one was genetically closer to RS-8, and another was more closely related to RS-9 and RS-10. Both the COI and 16S rRNA genes were found to be capable of delineating species and revealing genetic variation among Rockskipper samples in this study. However, our findings demonstrated that the COI gene is a more accurate and reliable marker for identifying Rockskipper species from Porok Beach, Gunungkidul, Yogyakarta, Indonesia.

Identity of the numerous bloodstains at the murder scene: molecular identification of fly artifacts and fly species by CO1 analysis.

Crime scenes may contain insect artifacts as well as samples of human origin. While the presence of insects can be important evidence in forensic medicine and forensic entomology, the insect artifacts sometimes interfere with the interpretation of bloodstain pattern analysis (BPA) which can be critical for accurate crime reconstruction. Fly artifacts are especially complicated to distinguish from true bloodstains. Indeed, we encountered a murder scene with numerous bloodstains inconsistent with the cause of death and had trouble interpreting them. The morphological method has been developed to distinguish them, but this method has to rely on the analyst's experience and opinion. This study aims not only to distinguish fly artifacts from true bloodstains but also to identify fly species by detecting fly DNA in small amounts of bloodstains at the scenes. Melt curve analysis of real-time PCR (qPCR) targeting cytochrome c oxidase subunit 1 (CO1) of mitochondrial DNA (mtDNA) was able to detect fly DNA in bloodstains from a murder scene. The fly DNA was sequenced from the qPCR product, and the fly species were identified by BLAST search. Fluorescence-labeled specific primers for four species of necrophagous flies were designed based on the sequences of the CO1 region, and differences in the length of the amplification products were used to identify fly species from trace amounts of fly DNA in the artifacts.

50%, not great, not terrible: Pan-European gap-analysis shows the real status of the DNA barcode reference libraries in two aquatic invertebrate groups and points the way ahead

The essential key to routine molecular species identification (DNA barcoding/metabarcoding) is the existence of an error-free DNA barcode reference library providing full coverage of all species. Published studies generally state the need to produce more barcodes, and control their quality, but unfortunately, the number of barcoded species is still low. However, to initiate real progress, we need to know where the gaps lie, how big they are and why they persist. Our aims were to draw and understand the current state of knowledge regarding species diversity, distribution, and barcode coverage, and offer solutions for improvement. In this study, we used two groups of aquatic insects, beetles and true bugs. We have compiled and critically evaluated an essentially complete and up-to-date European list, containing 1527 species. The list served as a basis for the barcode gap analyses in the Barcode-of-Life-Data-System (BOLD) conducted in three subsequent years (2020–2022). The overall barcode coverage of the pan-European fauna was around 50 % in both groups. The lowest coverage was in the Mediterranean, the Balkans and South-eastern Europe. The coverage in each country depended significantly on the local diversity, the number of rare, endemic species and the similarity of its fauna to that of the most active barcoding European countries. Gap analyses showed a very small increase in species coverage (<1 % in European aquatic beetles) despite an ~25 % increase in the number of barcodes. Hence, it is clear that future barcoding campaigns must prioritise quality over quantity. To visibly improve reference libraries, we need to increase the involvement of taxonomic experts and focus on targeted studies and underexplored but biodiversity-rich areas.

New record of Tylodelphys metacercariae (Diplostomidae) from Perccottus glenii (Odontobutidae) and their phylogenetic assessment.

Metacercariae of Tylodelphys sp. were found in the abdominal cavity of the Chinese sleeper (Perccottus glenii) collected in Liaoning Province and Inner Mongolia Autonomous Region of China. The sequences of the mitochondrial cox1 gene and ribosomal ITS1-5.8S rDNA-ITS2 region were obtained and used for molecular identification and phylogenetic assessment of this parasite species. Results of phylogenetic analyses based on ITS and cox1 markers showed that the metacercariae of Tylodelphys sp.ex P. glenii from China were conspecific with specimens of Tylodelphys sp. collected by Sokolov etal. (2013) from the same fish-host species captured earlier in West Siberia, Russia. The examined Tylodelphys sp. ex. P. glenii is the only member of the genus whose metacercariae parasitise the abdominal cavity of fish in northern Eurasia. Tylodelphys sp. ex P. glenii clustered with T. darbyi, T. immer, T.podicipina, and Tylodelphys sp. of Soldánová etal., 2017 based on mitochondrial DNA markers, and with T. darbyi, T. immer, T. kuerepus, and T. schreuringi using nuclear DNA markers.

Super-Mitobarcoding in Plant Species Identification? It Can Work! The Case of Leafy Liverworts Belonging to the Genus Calypogeia

Molecular identification of species is especially important where traditional taxonomic methods fail. The genus Calypogeia belongs to one of the tricky taxons. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. The finding of the universal single-locus DNA barcode in plants seems to be 'the Holy Grail'; therefore, researchers are increasingly looking for multiloci DNA barcodes or super-barcoding. Since the mitochondrial genome has low sequence variation in plants, species delimitation is usually based on the chloroplast genome. Unexpectedly, our research shows that super-mitobarcoding can also work! However, our outcomes showed that a single method of molecular species delimitation should be avoided. Moreover, it is recommended to interpret the results of molecular species delimitation alongside other types of evidence, such as ecology, population genetics or comparative morphology. Here, we also presented genetic data supporting the view that C. suecica is not a homogeneous species.

Molecular Identification and Phylogenetic Relationship of Some Plant Species In Ashdagh Mountain, Sangaw, Kurdistan Of Iraq

Phylogenetic and molecular perspective of plant identification can reveal the plant composition of areas. Many new species have been identified based on morphological characters in different area of Kurdistan, but few have been identified through DNA barcoding method. In this study, Internal transcribed spacers 1 and 2 (ITS1 and ITS2) were used to identify some species in Ashdagh Mountain. The identified taxa were belonged to different families and clades and not recorded in any studies. The nucleotide sequences of identified species were 98-100% identical with species in the genebank database. The phylogenetic analysis showed diversity in phylogenetic relationships among coexisting species. In addition, the existing of Chara sp. in the acidic stream of Awa spi is a new record and not observed before. The finding of this study show the importance of using molecular and phylogenetic technique to identify and understand phylogenetic relationship among coexisting species because Kurdistan is a hot spot and need more emphasis. In addition, new species occurrence data has been added to flora of Kurdistan.

Evaluation of Candida colonization index, molecular identification, and antifungal susceptibility pattern of Candida species isolated from critically ill pediatric patients: A single-center study in Iran.

Given the high mortality rate of invasive candidiasis in hospitalized pediatric patients, it is crucial to establish a predictive system to achieve early diagnosis and treatment of patients who are likely to benefit from early antifungal treatment. This study aimed to assess the Candida colonization index, species distribution, and antifungal susceptibility pattern of Candida strains isolated from pediatric patients with high Candida colonization index (CI). This study was carried out at the Children's Medical Center in Tehran-Iran. In total, 661 samples were collected from 83 patients. The Candida CI was calculated according to the descriptions of previous studies. The isolates were identified using polymerase chain reaction-based techniques. The Clinical and Laboratory Standard Institute protocol M60 was used to conduct the antifungal susceptibility test. A colonization index greater than 0.5 was confirmed in 29 cases (58% of positive samples) with two children developing candidemia. Candida albicans (n=53, 49.5%) was the most common Candida species in patients with CI > 0.5. Except for acute lymphoblastic leukemia, no risk factors were linked to a high index in colonized children (P > 0.05). Twelve isolates (7.01%) were multi-azole resistant with high MICs against both isavuconazole and ravuconazole and seven strains (4.09%) were echinocandins resistant. In pediatric intensive care units, patients are at risk of fungal infection, particularly candidemia. In this study, more than half of the children with positive yeast cultures had CI > 0.5, and 6.8% developed candidemia.

Comparative analysis of mitochondrial genomes of Broussonetia spp. (Moraceae) reveals heterogeneity in structure, synteny, intercellular gene transfer, and RNA editing.

The genus Broussonetia (Moraceae) is comprised of three non-hybrid recognized species that all produce high quality fiber essential in the development of papermaking and barkcloth-making technology. In addition, these species also have medicinal value in several countries. Despite their important economical, medicinal, and ecological values, the complete mitogenome of Broussonetia has not been reported and investigated, which would greatly facilitate molecular phylogenetics, species identification and understanding evolutionary processes. Here, we assembled the first-reported three complete Broussonetia (B. papyrifera, B. kaempferi, and B. monoica) mitochondrial genomes (mitogenome) based on a hybrid strategy using Illumina and Oxford Nanopore Technology sequencing data, and performed comprehensive comparisons in terms of their structure, gene content, synteny, intercellular gene transfer, phylogeny, and RNA editing. Our results showed their huge heterogeneities among the three species. Interestingly, the mitogenomes of B. monoica and B. papyrifera consisted of a single circular structure, whereas the B. kaempferi mitogenome was unique and consisted of a double circular structure. Gene content was consistent except for a few transfer RNA (tRNA) genes. The Broussonetia spp. mitogenomes had high sequence conservation but B. monoica with B. kaempferi contained more synteny blocks and were more related, a finding that was well-supported in organellar phylogeny. Fragments that had been transferred between mitogenomes were detected at plastome hotspots that had integrated under potential mediation of tRNA genes. In addition, RNA editing sites showed great differences in abundance, type, location and efficiency among species and tissues. The availability of these complete gap-free mitogenomes of Broussonetia spp. will provide a valuable genetic resource for evolutionary research and understanding the communications between the two organelle genomes.

Genetic identification of submersed dodder (Cuscuta: Convolvulaceae) in Texas, U.S.A.

Cuscuta plants that were observed growing entirely submersed and parasitizing the aquatic macrophyte Hygrophila polysperma in the San Marcos and Comal Rivers in Texas, are identified genetically as C. obtusiflora. This note documents the first molecular identification of any Cuscuta species naturally growing underwater or parasitizing a submersed aquatic plant.