Intraspecific DNA Barcoding and Variation Analysis for Citri Reticulatae Pericarpium of Citrus reticulata “Chachi”

Citri Reticulatae Pericarpium, the desiccative mature peel of Citrus reticulata Blanco or its cultivated varieties, is a national geographical indicated product that has the concomitant function of both medicine and foodstuff. The primary source of Citri Reticulatae Pericarpium is Citrus reticulata “Chachi,” called “Guang chenpi,” while it differs in variety, propagation, grafting rootstock, and tree age, and the hereditary stability of its biological information between intraspecific plants is worthy of our attention. Homologous analysis result of 4 DNA barcodings in the ribosome or the chloroplast showed that the homology of them (ITS2, rbcl, matK, and psbA-trnH) of 22 samples was 100.00%, 99.97%, 99.99%, and 99.81%, respectively, which indicated that 4 DNA barcodes maintained a high degree of genetic stability in Citrus reticulata “Chachi.” Also, ITS2 was considered to identify Citrus reticulata “Chachi” from other varieties because it presented not only low variability within a certain taxon but also a high level of interspecies variability. Simultaneously, variant site detection of Citrus reticulata “Chachi” was analyzed by comparing with the reference Citrus reticulata genome, and 2652697 SNP sites and 533906 InDel sites were detected from whole-genome resequencing data of 22 samples, providing the data resources and theoretical foundation for the future study about the relevant molecular makers of “Guang chenpi.”

Development of genic SSR marker resources from RNA-seq data in Camellia japonica and their application in the genus Camellia

Camellia is a genus of flowering plants in the family Theaceae, and several species in this genus have economic importance. Although a great deal of molecular makers has been developed for molecular assisted breeding in genus Camellia in the past decade, the number of simple sequence repeats (SSRs) publicly available for plants in this genus is insufficient. In this study, a total of 28,854 potential SSRs were identified with a frequency of 4.63 kb. A total of 172 primer pairs were synthesized and preliminarily screened in 10 C. japonica accessions, and of these primer pairs, 111 were found to be polymorphic. Fifty-one polymorphic SSR markers were randomly selected to perform further analysis of the genetic relationships of 89 accessions across the genus Camellia. Cluster analysis revealed major clusters corresponding to those based on taxonomic classification and geographic origin. Furthermore, all the genotypes of C. japonica separated and consistently grouped well in the genetic structure analysis. The results of the present study provide high-quality SSR resources for molecular genetic breeding studies in camellia plants.

DISTINCTION BETWEEN CRINUM LATIFOLIUM AND CRINUM ASIATICUM (AMARYLLIDACEAE) USING MOLECULAR DATA

Crinum latifolium and C. asiaticum are the two species of genus Crinum, Amaryllidaceae family and they have highly medicinal values. Distinction between two species is challenging due to many similar morphological characteristics. In this study, we used molecular makers to distinguish the two species Crinum latifolium and C. asiaticum. The phylogenetic tree was constructed based on the DNA sequence data of the ITS (internal transcribed spacer) nuclear ribosomal DNA (nrDNA) sequences of Crinum latifolium and C. asiaticum. As a result, C. latifolium and C. asiaticum were sorted into two different groups in the phylogenetic tree. Therefore, C. latifolium and C. asiaticum were carried out to solve the taxonomic ambiguity.

Unveiling the mystery: assessing the evolutionary trajectory of the Apaporis caiman population (Caiman crocodilus apaporiensis, Medem 1955) via mitochondrial molecular makers

The Apaporis caiman (Caiman crocodilus apaporiensis) has been of particular interest due to its highly differentiated morphology. However, no molecular research has been done to clarify its taxonomy. We characterized the genetic variation within C. crocodilus by assessing the evolutionary trajectory of Apaporis caiman populations using mitochondrial molecular markers. We collected ten Apaporis caiman samples from the middle basin of the Apaporis River, Colombia, sequenced two mitochondrial genes [cytochrome oxidase I (COI) and cytochrome B (CytB)], and analysed them together with all available sequences from homologous gene fragments at GenBank for the species. Phylogenetic reconstructions revealed three main clades clearly differentiated across the C. crocodilus complex. These clades matched genetically and geographically with three of the four subspecies currently recognized (C. c. chiapasius, C. c. fuscus and C. c. crocodilus). However, we found low to almost non-existent genetic differentiation between C. c. crocodilus and the until-now morphologically recognized C. c. apaporiensis, suggesting that the latter is part of the genetic spectrum present within C. c. crocodilus. We reject the hypothesis of an expected elevated level of genetic variation due to isolation (supported by morphological differentiation) and support the idea of Apaporis caiman populations as a C. crocodilus ecomorph.

The substitution of T271A in PB2 protein could enhance the infectivity and pathogenicity of Eurasian avian-like H1N1 swine influenza viruses in mice

BackgroundCurrently, Eurasian avian-like H1N1 (EA H1N1) swine influenza viruses (SIVs) are widely prevalent in pigs in China, with sporadic human cases reported as well. As one of the key molecular makers detected in avian H5N1 and H 7N9 viruses and pandemic H1N1 2009 virus, contributions of T271A in PB2 protein to the EA H1N1 viruses are still unknown. In this study, we investigated the effects of residue 271 in PB2 protein on the viral properties of EA H1N1 viruses.MethodsInfectivity, replication, virulence and pathogenicity of the recombinant viruses containing A or T in position 271 in PB2 protein were studied in cells and mice.ResultsThe results showed that the substitution PB2-T271A increased the viral replication in mammalian and avian cell lines. In addition, the mutation enhanced the viral infectivity, virulence and pathogenicity in mice. The viral titers of lung tissue in the rgHuN271A virus were higher than that of the rgHuN271T at 1, 4, and 7 dpi. The MID50 of the rgHuN271A and rgHuN271T virus were 101.1 TCID50 and 101.9 TCID50, respectively. Besides, the substitution of PB2-T271A enhanced the viral polymerase activity in mammalian cells.ConclusionsThe pathogenicity and replication of EA H1N1 virus containing 271A in PB2 protein were higher than the EA H1N1 virus containing 271T in PB2 protein in vivo and in vitro. Therefore, the PB2-T271A mutation should be continually monitored in influenza viruses circulating in pigs and humans.

Source apportionment of PM_2.5 in Shanghai based on hourly molecular organic markers and other source tracers

Identification of various sources and quantification of their contributions are a necessary step to formulating scientifically sound pollution control strategies. Receptor model is widely used in source apportionment of fine particles. However, most of the previous studies are based on traditional filter collection and lab analysis of aerosol chemical species (usually ions, elemental carbon (EC), organic carbon (OC) and elements) as inputs. In this study, we conducted robust online measurements of a range of organic molecular makers and trace elements, in addition to the major aerosol components (ions, OC and EC), in urban Shanghai in the Yangtze River Delta region, China. The large suite of molecular and elemental tracers, together with water-soluble ions, OC and EC, provide data for establishing measurement-based source apportionment methodology for PM2.5. We conducted source apportionment using positive matrix factorization (PMF) and compared PMF solutions with molecular makers added (i.e. MM-PMF) and those without organic markers. MM-PMF identified 11 types of pollution sources, with biomass burning, cooking and secondary organic aerosol (SOA) as the additional sources identified. The three sources accounted for 4.9 %, 2.6 % and 14.7 % of the total PM2.5 mass, respectively. During the whole campaign, the secondary source is an important source of atmospheric pollution, the average contribution of secondary pollution sources is as high as 63.8 % of the total PM2.5 mass. Grouping different sources to secondary and primary, we note that SOC and POC contributed 45.1 % and 54.9 %, respectively. It is worth noting that the contribution of cooking to PM2.5 mass only account for 2.6 %, but it contributed to 10.7 % of OC. Episodic analysis indicated that secondary nitrate was the always the main cause of PM2.5 pollution, while during non-episodic hours, vehicle exhaust made a significant contribution. Through the application of the above-mentioned techniques to the Yangtze River Delta, more insights are gained on the sources, formation mechanism and pollution characteristics of PM2.5 in this region.

Phylogeny and species delimitations in the entomopathogenic genus Beauveria (Hypocreales, Ascomycota), including the description of B. peruviensis sp. nov.

The genus Beauveria is considered a cosmopolitan anamorphic and teleomorphic genus of soilborne necrotrophic arthropod-pathogenic fungi that includes ecologically and economically important species. Species identification in Beauveria is difficult because of its structural simplicity and the lack of distinctive phenotypic variation. Therefore, the use of multi-locus sequence data is essential to establish robust species boundaries in addition to DNA-based species delimitation methods using genetic distance, coalescent, and genealogical concordance approaches (polyphasic approaches). In this regard, our study used multilocus phylogeny and five DNA-based methods to delimit species in Beauveria using three molecular makers. These polyphasic analyses allowed for the delimitation of 20–28 species in Beauveria, confirming cryptic diversity in five species (i.e. B. amorpha, B. bassiana, B. diapheromeriphila, and B. pseudobassiana) and supporting the description of B. peruviensis as a new taxon from northeastern Peru. The other five species were not evaluated as they did not have enough data (i.e. B. araneola, B. gryllotalpidicola, B. loeiensis, B. medogensis, and B. rudraprayagi). Our results demonstrate that the congruence among different methods in a polyphasic approach (e.g. genetic distance and coalescence methods) is more likely to show reliably supported species boundaries. Among the methods applied in this study, genetic distance, coalescent approaches, and multilocus phylogeny are crucial when establishing species boundaries in Beauveria.

Breeding groundnut for rust resistance: A review

Sustainable groundnut production can be realised through development and adoption of high yielding cultivars possessing durable rust resistance. Integrating conventional breeding with genomic tools in identifying candidate rust resistance genes, and introgressing the genes into adapted elite germplasm, with the aid of molecular makers, could enhance breeding for rust resistance. This review highlights breeding approaches for groundnut rust resistance, with emphasis on integrating conventional breeding with marker-assisted selection. The life cycle, symptoms and epidemiology of the pathogen are also discussed to understand the host-pathogen interaction and guide groundnut rust resistance breeding