Development of genomic simple sequence repeat markers for Glycyrrhiza lepidota and cross-amplification of other Glycyrrhiza species
Background Licorice (Glycyrrhiza spp. L.) is used as a natural sweetener and medicinal herb in European and Asian countries. Molecular studies have been conducted to find differences between wild and cultivated species because most wild species are highly resistant to abiotic and biotic stresses compared with their cultivated species. However, few molecular markers have been developed for studying the genetic diversity and population structure of licorice species and to identify differences between cultivars. Thus, the present study aimed to develop a set of genomic simple sequence repeat (SSR) markers for molecular studies of these species. Methods In the present study, we developed polymorphic SSR markers based on whole-genomesequence data of Glycyrrhiza lepidota. Then, based on the sequence information, the polymorphic SSR markers were developed. The SSR markers were applied to 23 Glycyrrhiza individual plants. We also evaluated the phylogenetic relationships and interspecies transferability among samples. Results The genetic diversity analysis using these markers identified 2–23 alleles, and the major allele frequency, observed heterozygosity, genetic diversity, and polymorphism information content were 0.11–0.91, 0–0.90, 0.17–0.94, and 0.15–0.93, respectively. Interspecies transferability values were 93.5%, 91.6%, and 91.1% for G. echinata, G. glabra, and G. uralensis, respectively. Phylogenetic analysis clustered cultivated (group 1) and wild (group 2) species into three and two subgroups, respectively. The reported markers represent a valuable resource for the genetic characteri z ation of Glycyrrhiza spp. for theanalysis of its genetic variability, and as a tool for licorice transferability. This is the first intraspecific study in a collection of Glycyrrhiza spp. germplasm using SSR markers.
Bang et al. (2019) Development of genomic simple sequence repeat markers for Glycyrrhiza lepidota and cross-amplification of other Glycyrrhiza species. PeerJ 7:e7479 https://doi.org/10.7717/peerj.7479
Pangenomic type III effector database of the plant pathogenic Ralstonia spp.
Background The bacterial plant pathogenic Ralstonia species belong to the beta-proteobacteria class and are soil-borne pathogens causing vascular bacterial wilt disease, affecting a wide range of plant hosts. These bacteria form a heterogeneous group considered as a “species complex” gathering three newly defined species. Like many other Gram negative plant pathogens, Ralstonia pathogenicity relies on a type III secretion system, enabling bacteria to secrete/inject a large repertoire of type III effectors into their plant host cells. Type III-secreted effectors (T3Es) are thought to participate in generating a favorable environment for the pathogen (countering plant immunity and modifying the host metabolism and physiology). Methods Expert genome annotation, followed by specific type III-dependent secretion, allowed us to improve our Hidden-Markov-Model and Blast profiles for the prediction of type III effectors. Results We curated the T3E repertoires of 12 plant pathogenic Ralstonia strains, representing a total of 12 strains spread over the different groups of the species complex. This generated a pangenome repertoire of 102 T3E genes and 16 hypothetical T3E genes. Using this database, we scanned for the presence of T3Es in the 155 available genomes representing 140 distinct plant pathogenic Ralstonia strains isolated from different host plants in different areas of the globe. All this information is presented in a searchable database. A presence/absence analysis, modulated by a strain sequence/gene annotation quality score, enabled us to redefine core and accessory T3E repertoires.
Sabbagh et al. (2019) Pangenomic type III effector database of the plant pathogenic Ralstonia spp.. PeerJ 7:e7346 https://doi.org/10.7717/peerj.7346
262 Voyages Beneath the Sea: a global assessment of macro- and megafaunal biodiversity and research effort at deep-sea hydrothermal vents
For over 40 years, hydrothermal vents and the communities that thrive on them have been a source of profound discovery for deep-sea ecologists. These ecosystems are found throughout the world on active plate margins as well as other geologically active features. In addition to their ecologic interest, hydrothermal vent fields are comprised of metallic ores, sparking a nascent industry that aims to mine these metal-rich deposits for their mineral wealth. Here, we provide the first systematic assessment of macrofaunal and megafaunal biodiversity at hydrothermal vents normalized against research effort. Cruise reports from scientific expeditions as well as other literature were used to characterize the extent of exploration, determine the relative biodiversity of different biogeographic provinces, identify knowledge gaps related to the distribution of research effort, and prioritize targets for additional sampling to establish biodiversity baselines ahead of potential commercial exploitation. The Northwest Pacific, Southwest Pacific, and Southern Ocean biogeographic provinces were identified as high biodiversity using rarefaction of family-level incidence data, whereas the North East Pacific Rise, Northern East Pacific, Mid-Atlantic Ridge, and Indian Ocean provinces had medium biodiversity, and the Mid-Cayman Spreading Center was identified as a province of relatively low biodiversity. A North/South divide in the extent of biological research and the targets of hydrothermal vent mining prospects was also identified. Finally, we provide an estimate of sampling completeness for each province to inform scientific and stewardship priorities.
Thaler et al. (2019) 262 Voyages Beneath the Sea: a global assessment of macro- and megafaunal biodiversity and research effort at deep-sea hydrothermal vents. PeerJ 7:e7397 https://doi.org/10.7717/peerj.7397
Genetic structure of two sympatric gudgeon fishes (Xenophysogobio boulengeri and X. nudicorpa) in the upper reaches of Yangtze River Basin
Background Xenophysogobio boulengeri and X. nudicorpa are the only two species within the genus Xenophysogobio (Cyprinidae, Cypriniformes), and both are endemic to the upper reaches of the Yangtze River. In recent years, due to human activities, the natural resources available to both species have declined sharply. Sympatric species with overlapping niches inevitably compete for their habitats, and genetic structure and diversity can reflect population history and their potential for adaptation to changing environments, which is useful for management decisions. Methods In the present study, microsatellite DNA and mitochondrial DNA (mtDNA) markers were used to investigate the patterns of population genetic structure for X. boulengeri and X. nudicorpa. Microsatellite DNA data, jointly with traditional summary statistics including FST and Fis, were used to assess the population genetic structure by structure analysis. The mtDNA sequences were then used to examine these patterns through time to detect demographic history. Results Xenophysogobio boulengeri and X. nudicorpa exhibited high levels of genetic diversity in Yangtze River populations, except for two populations of X. nudicorpa in the Jinsha River, which were low in mtDNA diversity. X. boulengeri showed genetic homogeneity among populations, whereas X. nudicorpa appeared to have significant geographic genetic divergence. Both species experienced a late-Pleistocene sudden population expansion in Yangtze River populations, but not in the Jinsha River populations of X. nudicorpa. Discussion The genetic homogeneity of X. boulengeri populations might result from similar population expansion events and environment features. The geographic genetic subdivision for X. nudicorpa between the Jinsha and Yangtze Rivers might be caused by the geographic isolation in the middle Pliocene, as well as climate and environmental heterogeneity.
Dong et al. (2019) Genetic structure of two sympatric gudgeon fishes (Xenophysogobio boulengeri and X. nudicorpa) in the upper reaches of Yangtze River Basin. PeerJ 7:e7393 https://doi.org/10.7717/peerj.7393
Molecular evidence that the Channel Islands populations of the orange-crowned warbler (Oreothlypis celata; Aves: Passeriformes: Parulidae) represent a distinct evolutionary lineage
We used molecular data to assess the degree of genetic divergence across the breeding range of the orange-crowned warbler (Oreothlypis celata) in western North America with particular focus on characterizing the divergence between O. celata populations on the mainland of southern California and on the Channel Islands. We obtained sequences of the mitochondrial gene ND2 and genotypes at ten microsatellite data for 192 O. celata from populations spanning all four recognized subspecies. We recovered shallow, but significant, levels of divergence among O. celata populations across the species range. Our results suggest that island isolation, subspecies (delineation by morphology, ecological, and life-history characteristics), and isolation-by-distance, in that order, are the variables that best explain the geographic structure detected across the range of O. celata. Populations on the Channel Islands were genetically divergent from those on the mainland. We found evidence for greater gene flow from the Channel Islands population to mainland southern California than from the mainland to the islands. We discuss these data in the context of differentiation in phenotypic and ecological characters.
Hanna et al. (2019) Molecular evidence that the Channel Islands populations of the orange-crowned warbler (Oreothlypis celata; Aves: Passeriformes: Parulidae) represent a distinct evolutionary lineage. PeerJ 7:e7388 https://doi.org/10.7717/peerj.7388
Large pelvic tubercle in orangutans relates to the adductor longus muscle
Orangutan pelves commonly exhibit a large, projecting tubercle in the iliopubic region, historically assumed to homologous to the pubic tubercle in humans. However, it is not clear whether this tubercle is a unique feature of Pongo, or if it is anatomically homologous with the human pubic tubercle when considered as a soft tissue attachment point. To clarify this issue, we dissected orangutan and other ape cadaveric specimens to evaluate the pelvic brim soft tissues and how they may relate to the tubercle (when present). We additionally conducted a broad osteological survey of pelvic brim morphology across 28 primate genera (n = 294 specimens) to document the presence of the tubercle in primate pelves. Cadaveric dissections revealed that the tubercle is exclusively associated with the proximal attachment of the adductor longus muscle tendon in orangutans. Our osteological survey confirms that the tubercle is both constantly present and very prominent in orangutans. We observed that the tubercle is consistently situated along the pectineal line, lateral to where the pubic tubercle in humans is found, thereby making its structural homology unlikely. The osteological survey documented the tubercle at polymorphic frequencies in all hominoid taxa, though generally less protuberant than observed in Pongo. We argue that this further excludes its possibility of homology with the pubic tubercle, and that it may therefore be more appropriately be considered an adductor longus tubercle. We discuss possible functional and phylogenetic implications for this feature.
Shearer et al. (2019) Large pelvic tubercle in orangutans relates to the adductor longus muscle. PeerJ 7:e7273 https://doi.org/10.7717/peerj.7273
miRDRN—miRNA disease regulatory network: a tool for exploring disease and tissue-specific microRNA regulatory networks
Background MicroRNA (miRNA) regulates cellular processes by acting on specific target genes, and cellular processes proceed through multiple interactions often organized into pathways among genes and gene products. Hundreds of miRNAs and their target genes have been identified, as are many miRNA-disease associations. These, together with huge amounts of data on gene annotation, biological pathways, and protein–protein interactions are available in public databases. Here, using such data we built a database and web service platform, miRNA disease regulatory network (miRDRN), for users to construct disease and tissue-specific miRNA-protein regulatory networks, with which they may explore disease related molecular and pathway associations, or find new ones, and possibly discover new modes of drug action. Methods Data on disease-miRNA association, miRNA-target association and validation, gene-tissue association, gene-tumor association, biological pathways, human protein interaction, gene ID, gene ontology, gene annotation, and product were collected from publicly available databases and integrated. A large set of miRNA target-specific regulatory sub-pathways (RSPs) having the form (T, G1, G2) was built from the integrated data and stored, where T is a miRNA-associated target gene, G1 (G2) is a gene/protein interacting with T (G1). Each sequence (T, G1, G2) was assigned a p-value weighted by the participation of the three genes in molecular interactions and reaction pathways. Results A web service platform, miRDRN (http://mirdrn.ncu.edu.tw/mirdrn/), was built. The database part of miRDRN currently stores 6,973,875 p-valued RSPs associated with 116 diseases in 78 tissue types built from 207 diseases-associated miRNA regulating 389 genes. miRDRN also provides facilities for the user to construct disease and tissue-specific miRNA regulatory networks from RSPs it stores, and to download and/or visualize parts or all of the product. User may use miRDRN to explore a single disease, or a disease-pair to gain insights on comorbidity. As demonstrations, miRDRN was applied: to explore the single disease colorectal cancer (CRC), in which 26 novel potential CRC target genes were identified; to study the comorbidity of the disease-pair Alzheimer’s disease-Type 2 diabetes, in which 18 novel potential comorbid genes were identified; and, to explore possible causes that may shed light on recent failures of late-phase trials of anti-AD, BACE1 inhibitor drugs, in which genes downstream to BACE1 whose suppression may affect signal transduction were identified.
Liu et al. (2019) miRDRN—miRNA disease regulatory network: a tool for exploring disease and tissue-specific microRNA regulatory networks. PeerJ 7:e7309 https://doi.org/10.7717/peerj.7309
First report of cestode infection in the crustacean Artemia persimilis from Southern Chilean Patagonia and its relation with the Neotropical aquatic birds
The brine shrimp genus Artemia Leach (Crustacea, Branchiopoda), a keystone group in hipersaline wetlands all over the world, offers an excellent model to study species interactions (parasitism) and to explore “hidden fauna” (avian endoparasites). The present study is the first report on the parasite infection of the South American species Artemia persimilis from the Southern Chilean Patagonia (50°S–53°S). Samples were collected in Los Cisnes and Amarga lagoons, the two most austral populations of this crustacean described to date, during two seasons (spring and autumn). A total of 98 larvae of cestodes of the family Hymenolepididae (Cestoda, Cyclophyllidea) were found and identified as belonging to the following taxa: Confluaria podicipina (adult parasitic in grebes), Flamingolepis sp. (a cestode parasite of flamingos), Fimbriarioides (?) sp. (adults of the species of this genus infect waterfowl and shorebirds) and Wardium sp. (definitive host unknown, most probably charadriiform birds). This is a new geographical record of C. podicipina and the genus Fimbriarioides for the Neotropical Region, the latter being the most widely distributed species at both localities and seasons surveyed, and the only species recorded in autumn (April). Cestode community composition in Los Cisnes population was characterised by dominance of Flamingolepis sp., representing more than 65% of the total cestode species recorded, whereas in the Amarga population the most abundant parasite (>83%) was Fimbriarioides (?) sp. Significant seasonal variations were detected in Los Cisnes lagoon for Flamingolepis sp. and C. podicipina, with exclusive presence of them in spring (November). Besides providing novel information on cestodes infection in A. persimilis, this study provides new data on the life cycle of cestodes of Neotropical aquatic birds such as South American flamingos and grebes. Our finding expands the knowledge on the biodiversity and population dynamics of extreme and unique environments from high latitudes (Patagonia) and makes evident the need of further taxonomical and ecological studies for better understanding the life cycles of avian helminth parasites in the Neotropics and the role of aquatic invertebrates in them.
Redón et al. (2019) First report of cestode infection in the crustacean Artemia persimilis from Southern Chilean Patagonia and its relation with the Neotropical aquatic birds. PeerJ 7:e7395 https://doi.org/10.7717/peerj.7395
Road traffic injuries in China from 2007 to 2016: the epidemiological characteristics, trends and influencing factors
Background Road traffic accidents are one of the serious disasters that cause public injury, fatality and great economic loss. They are a growing public health problem around the world. Objectives The aim of this study was to determine epidemiological characteristics, tendency and possible influencing factors of road traffic injuries (RTIs) in China, so as to give target suggestions on preventative measures. Methods Road traffic accident data were obtained from National Bureau of Statistics of China and Ministry of Transport of the People’s Republic of China. Descriptive statistic such as RTIs frequency, trends of different accident types from 2007 to 2016; the RTIs difference between different regions and road surfaces were compared; and the possible influencing factors of RTIs were also explored. Results Over the past decade, with the mileage of constructed highway increased, the frequency of road traffic accidents have declined substantially in China, and the death toll from road traffic accidents with motor vehicles has declined from 2007 to 2015, Conversely, the number of deaths from non-motor vehicle accidents has risen rapidly since 2012. Our study showed that the traffic accident related mortality in Guizhou province was different from the level of the whole nation, and the Eastern, Central and Western areas of China were all significantly different (P < 0.001). Linear regression suggested a significant affected of gross domestic product (GDP)-per-capita, education level, the number of health institutions, populations, and car ownership status on traffic accident death tolls (P < 0.001). Moreover, cement concrete pavement roads were associated with the highest occurrence rates of RTI, and RTIs was statistically significant (P < 0.001) on different road surfaces. Conclusion Even though the frequency of road traffic accidents has declined, RTIs remain an urgent public health problem in China. Thus, the government should give some target preventative measures to reduce RTIs, aiming at different regions, the increasing trend of the death toll related to non-motor vehicles and the highest occurrence on cement concrete pavement roads.
Wang et al. (2019) Road traffic injuries in China from 2007 to 2016: the epidemiological characteristics, trends and influencing factors. PeerJ 7:e7423 https://doi.org/10.7717/peerj.7423
Application of cell-free DNA sequencing in characterization of bloodborne microbes and the study of microbe-disease interactions
It is an important issue whether microorganisms can live harmoniously with normal cells in the cardiovascular system. The answer to the question will have enormous impact on medical microbiology. To address the issue, it is essential to identify and characterize the bloodborne microbes in an efficient and comprehensive manner. Due to microbial sequence complexity and the composition of significant number of unknown microbial species in the circulatory system, traditional approaches using cell culture, PCR, or microarray are not suitable for the purpose. Recent reports indicate that cell-free DNA (cfDNA) sequencing using next-generation sequencing (NGS) or single-molecule sequencing (SMS), together with bioinformatics approaches, possesses a strong potential enabling us to distinguish microbial species at the nucleotide level. Multiple studies using microbial cfDNA sequencing to identify microbes for septic patients have shown strong agreement with cell culture. Similar approaches have also been applied to reveal previously unidentified microorganisms or to demonstrate the feasibility of comprehensive assessment of bloodborne microorganisms for healthy and/or diseased individuals. SMS using either SMRT (single-molecule real-time) sequencing or Nanopore sequencing are providing new momentum to reinforce this line of investigation. Taken together, microbial cfDNA sequencing provides a novel opportunity allowing us to further understand the involvement of bloodborne microbes in development of diseases. Similar approaches should also be applicable to the study of metagenomics for sufficient and comprehensive analysis of microbial species living in various environments. This article reviews this line of research and discuss the methodological approaches that have been developed, or are likely to be developed in the future, which may have strong potential to facilitate cfDNA- and cfRNA-based studies of cancer and acute/chronic diseases, in the hope that a better understanding of the hidden microbes in the circulatory system will improve diagnosis, prevention and treatment of problematic diseases.
Chiu et al. (2019) Application of cell-free DNA sequencing in characterization of bloodborne microbes and the study of microbe-disease interactions. PeerJ 7:e7426 https://doi.org/10.7717/peerj.7426