Research advance of genetic diversity of Chinese traditional herb Gentianae Macrophyllae Radix / 中草药

Gentianae Macrophyllae Radix is a Chinese traditional Tibetan herb, belonging to Sect. Cruciata Gaudin of Gentiana genus. Which originated from Qinghai-Tibetan Plateau and adjacent regions and had significant pharmaceutical effect on lots of disease. In this review, we summarized the research advance studies on morphologic, biochemical, and genetic diversity on this species in the past 20 years, which could provide the help for germplasm protection, identification, and evolutionary adaptation works in the future.

Assessment of the Diversity of Lactic Acid Bacteria Involved in Cocoa Fermentation of Six Main Cocoa Producing Regions of Côte d’ivoire

Aims: The variability of lactic acid bacteria (LAB) species involved in cocoa bean fermentation would cause inconsistency in the quality of cocoa. The aims of this study is to investigate the physicochemical parameters of cocoa bean fermentation in order to assess the activity and the molecular diversity of LAB involved in cocoa fermentation from six other regions of Côte d’Ivoire. Place and Duration of Study: Laboratory of Biotechnology, UFR Biosciences, University Félix Houphouet-Boigny (Côte d’Ivoire), between October 2016 and September 2017. Methodology: Spontaneous heap fermentations were conducted in six cocoa producing regions during 6 days. Physicochemical analysis of cocoa mass such as temperature, pH, titratable acidity and reducing sugars were carried out. In addition, LAB isolation was performed using plate culture on MRS medium and their fermentative type as well as their profile were determined. In addition, LAB species were determined by restriction profile analysis of the 16S gene. Results: a total of 568 LAB were isolated from cocoa fermentation. Biochemical and morphological identification of these germs revealed the clear dominance of the bacilli form (81.16%) and the heterofermentative type (over 80%) with facultative heterofermentative type recording more than half (54.4%) of the isolated population. Their molecular identification by sequencing the hypervariable zone of the 16S rDNA gene of a few representatives from each restriction group revealed 08 species with a predominance of Lactobacillus plantarum (76.76%) and Leuconostoc mesenteroides (15.31%) associated with minority species. This species diversity could be exploited for selecting appropriate starter cultures. Conclusion: This diversity of LAB species could be responsible for the variability of cocoa quality in Côte d’Ivoire.

The complete mitochondrial genome of Corydoras nattereri (Callichthyidae: Corydoradinae)

The complete mitogenome of Corydoras nattereri , a species of mailed catfishes from southeastern Brazil, was reconstructed using next-generation sequencing techniques. The mitogenome was assembled using mitochondrial transcripts from the liver transcriptomes of three individuals, and produced a circular DNA sequence of 16,557 nucleotides encoding 22 tRNA genes, two rRNA genes, 13 protein-coding genes and two noncoding control regions (D-loop, OrigL). Phylogeographic analysis of closely related sequences of Cytochrome Oxydase C subunit I (COI) demonstrates high diversity among morphologically similar populations of C. nattereri . Corydoras nattereri is nested within a complex of populations currently assigned to C. paleatus and C. ehrhardti . Analysis of mitogenome structure demonstrated that an insertion of 21 nucleotides between the ATPase subunit-6 and COIII genes may represent a phylogenetically informative character associated with the evolution of the Corydoradinae.

O mitogenoma completo de Corydoras nattereri , uma espécie de bagres encouraçados do sudeste do Brasil, foi reconstruído através de técnicas de sequencimento de DNA de próxima geração. O mitogenoma foi produzido a partir de produtos de transcrição mitocondrial dos transcriptomas hepáticos de três indivíduos, resultando numa sequência de DNA circular de 16.557 nucleotídeos abrangendo 22 genes de tRNA, dois genes de rRNA, 13 genes codificadores de proteínas e duas regiões de controle não codificadoras (D-loop, OrigL). A análise filogenética de sequências proximamente relacionadas da subunidade I do gene Citocrome Oxidase C (COI) demonstrou a existência de elevada diversidade entre populações morfologicamente similares de C. nattereri . Corydoras nattereri está inserida num complexo de populações atualmente identificadas como C. paleatus e C. ehrhardti . A análise da estrutura do mitogenoma demonstra que a inserção de uma sequência de 21 nucleotídeos entre os genes da subunidade 6 da ATPase e do COIII representa um caráter filogeneticamente informativo associado à evolução de Corydoradinae.

Penicillium menonorum: A Novel Fungus to Promote Growth and Nutrient Management in Cucumber Plants

The present study is the first report on the isolation of Penicillium menonorum from rhizosphere soil in Korea and its identification based on morphological characteristics and internal transcribed spacer gene sequence. The fungal isolate was named KNU-3 and was found to exhibit plant growth-promoting (PGP) activity through indole acetic acid (IAA) and siderophore production, as well as P solubilization. KNU-3 produced 9.7 mg/L IAA and solubilized 408 mg of Ca3PO4/L, and inoculation with the isolate significantly (p < 0.05) increased the dry biomass of cucumber roots (57%) and shoots (52%). Chlorophyll, starch, protein, and P contents were increased by 16%, 45%, 22%, and 14%, respectively, compared to plants grown in uninoculated soil. The fungus also increased soil dehydrogenase (30%) and acid phosphatase (19%) activities. These results demonstrate that the isolate KNU-3 has potential PGP attributes, and therefore it can be considered as a new fungus to enhance soil fertility and promote plant growth. Moreover, the discovery of PGP ability and traits of this fungus will open new aspects of research and investigations. In this study, plant growth promotion by P. menonorum KNU-3 is reported for the first time in Korea after its original description.

Genetic diversity of Korean Bacillus anthracis isolates from soil evaluated with a single nucleotide repeat analysis

Bacillus (B.) anthracis, the etiological agent of anthrax, is one of the most genetically monomorphic bacteria species in the world. Due to the very limited genetic diversity of this species, classification of isolates of this bacterium requires methods with high discriminatory power. Single nucleotide repeat (SNR) analysis is a type of variable-number tandem repeat assay that evaluates regions with very high mutation rates. To subtype a collection of 21 isolates that were obtained during a B. anthracis outbreak in Korea, we analyzed four SNR marker loci using nucleotide sequencing analysis. These isolates were obtained from soil samples and the Korean Center for Disease Control and Prevention. The SNR analysis was able to detect 13 subgenotypes, which allowed a detailed evaluation of the Korean isolates. Our study demonstrated that the SNR analysis was able to discriminate between strains with the same multiple-locus variable-number tandem repeat analysis genotypes. In summary, we obtained SNR results for four SNR marker loci of newly acquired strains from Korea. Our findings will be helpful for creating marker systems and help identify markers that could be used for future forensic studies.

Development of cDNA-derived ssr markers and their efficiency in diversity assessment of cymbidium accessions

Cymbidium spp. are popular flowering plants. Assessment of the genetic diversity in cultivated Cymbidium facilitates conservation of germplasm and subsequent cultivar improvement. Thus, it is important to develop more efficient polymorphic DNA markers. Although more motifs (403) were identified and more primers (206) were designed in the genomic library compared to the cDNA library, a larger number of successful primers were obtained from the cDNA library (59.9 percent) than from genomic DNA library (51.1 percent). However, higher PIC and gene diversity were identified in genomic SSRs. The average allele number per locus was also higher in genomic SSRs (7.3) than EST-SSRs (5.2), among the 24 evaluated Cymbidium accessions. AT/TA was comparatively high in EST-SSRs, while this motif was not as common in genomic SSRs. The CTT/AAG/TCT/AGA/TTC/GAA and TGC/GCA/GCT/AGC/CTG/CAG motifs were the most abundant tri-nucleotide sequences in EST-SSRs, while GTT/AAC/TGT/ACA/TTG/CAA was the most frequent in genomic SSRs. The number of repeats ranged from 3 to 12 in EST-SSRs. Currently, 52 novel polymorphic SSR markers have been evaluated, which will be useful for germplasm assessments, core set construction, evaluation of genetic diversity, and marker assisted selection (MAS) based Cymbidium breeding.

Preliminary study on the galectin molecular diversity in Moroccoan Phlebotomus papatasi sandfly populations.

Context: Galactose binding protein (PpGalec) plays an important role in the specificity of Phlebotomus papatasi sandfly for Leishmania major. The molecular diversity of this ligand is currently unknown but might have some influence on the ability of PpGalec to efficiently recognize L. major in natural sandfly populations. Objective: To explore the molecular diversity of the P. papatasi Galectin gene (PpGalec) in natural sandfly population of Morocco. Results & Conclusions: Sequence variations of PpGalec was analyzed in 31 P. papatasi specimens collected from endemic and non-endemic zoonotic cutaneous leishmaniasis foci of Morocco. Among the 211 amino acid positions analyzed, 11 are subjected to mutation. Interestingly, we observe that one mutation directly affect an amino acid known to be involved in the substrate recognition by galectin. The repercussion of this polymorphism on the capacity of the galectin to efficiently bind the L. major Lipophosphoglycane (LPG) awaits further investigations.

Molecular diversity in rice genotypes differing in physiological mechanisms of salt tolerance through SSR and ISSR markers.

Two different DNA-based techniques viz, simple sequence repeat (SSR) and inter simple sequence repeat (ISSR) markers were used to estimate genetic diversity among 20 rice genotypes possessing different physiological mechanisms contributing to salt tolerance. A total of 11 clear and repeatable bands were amplified from ten selected SSR primers pairs and 43 fragments were detected from nine ISSR primers. The level of polymorphism was 1.1% with SSR compared to 90.7% with ISSRs. Mean genetic similarity of 0.88 based on SSRs and 0.85 using ISSRs was observed. A total of 43 (39 polymorphic) and 11 bands were detected using 9 ISSR primers and 10 well distributed mapped SSR markers, respectively. Estimates of genetic similarity of ISSRs based on the 39 polymorphic markers between 20 rice cultivars ranged from 0.55 for PR108/CSR19 to 0.94 for Pokkali/CSR20 with an average of 0.81. The estimates revealed by the 11 polymorphic SSR bands showed the average value (0.94) and also the range of genetic similarity (from 0.86 to 1.00 for CSR22/CSR18 and CSR24/CSR20, respectively) reflecting their hyper variability and their high resolution power. The findings are likely to expedite breeding new salt tolerant cultivars by involving parents from diverse molecular clusters.