scholarly journals Infraspecific Variation of Huperzine A and B in Icelandic Huperzia selago Complex

Planta Medica ◽  
2018 ◽  
Vol 85 (02) ◽  
pp. 160-168 ◽  
Author(s):  
Maonian Xu ◽  
Starri Heidmarsson ◽  
Margret Thorsteinsdottir ◽  
Pawel Wasowicz ◽  
Hang Sun ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Large Subunit ◽  
Intergenic Spacer ◽  
Good Alternative ◽  
Huperzine A ◽  
Genotype 3 ◽  
Bisphosphate Carboxylase ◽  
Intergenic Spacer Region ◽  
Genotype 2 ◽  
Plant Sources

AbstractThe alkaloids huperzine A and huperzine B were originally isolated from the Chinese club moss Huperzia serrata. They are known inhibitors of acetylcholinesterase, and especially huperzine A shows pharmaceutical potential for the treatment of Alzheimerʼs disease. Its supply heavily relies on natural plant sources belonging to the genus Huperzia, which shows considerable interspecific huperzine A variations. Furthermore, taxonomic controversy remains in this genus, particularly in the Huperzia selago group. With focus on Icelandic H. selago taxa, we aimed to explore the relatedness of Huperzia species using multi-locus phylogenetic analysis, and to investigate correlations between huperzine A contents, morphotypes, and genotypes. Phylogenetic analysis was performed with five chloroplastic loci (the intergenic spacer between the photosystem II protein D1 gene and the tRNA-His gene, maturase K, ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, tRNA-Leu, and the intergenic spacer region between tRNA-Leu and tRNA-Phe). Huperzine A and huperzine B contents were determined using an HPLC-UV method. The phylogenetic analysis suggests that previously proposed Huperzia appressa and Huperzia arctica should not be considered species, but rather subspecies of H. selago. Three genotypes of Icelandic H. selago were identified and presented in a haplotype networking diagram. A significantly (p < 0.05) higher amount of huperzine A was found in H. selago genotype 3 (264 – 679 µg/g) than genotype 1 (20 – 180 µg/g), where the former shows a typical green and reflexed “selago” morphotype. The huperzine A content in genotype 3 is comparable to Chinese H. serrata and a good alternative huperzine A source. Genotype 2 contains multiple morphotypes with a broad huperzine A content (113 – 599 µg/g). The content of huperzine B in Icelandic taxa (6 – 13 µg/g) is much lower than that in Chinese H. serrata (79 – 207 µg/g).

Isolation and Phylogenetic Analysis of Avian Mycoplasmas from Poultry Affected with Respiratory Infections in India

2020 ◽  
Author(s):  
Y. Singh ◽  
P. Tomar ◽  
N. K. Mahajan ◽  
N. Jindal
Keyword(s):  
Phylogenetic Analysis ◽  
Broiler Chicken ◽  
Respiratory Infections ◽  
Intergenic Spacer ◽  
Mycoplasma Gallisepticum ◽  
Epidemiological Investigation ◽  
Wild Type ◽  
Tissue Samples ◽  
Growth Inhibition Test ◽  
Intergenic Spacer Region

Mycoplasma gallisepticum (MG) and Mycoplasma synoviae (MS) are the two most pathogenic avian mycoplasmas. In the present study, examination of 92 pooled tissue samples from broiler chicken of 92 different poultry flocks of Haryana (India) exhibiting respiratory infections resulted in isolation of 13 (14%) Mollicutes. Based on biochemical reactions, growth inhibition test, PCR and/or sequencing, 8 (8.6%) isolates could be characterized as MG, 1 (1.08%) as MS, 3 (3.24%) as M. gallinarum and 1 (1.08%) as Acholeplasma laidlawii. The phylogenetic analysis using Intergenic spacer region (IGSR) of these MG isolates revealed that they clustered with USA strain whereas the vaccine strains were in different clade. Single locus sequence typing (SLST) revealed considerable nucleotides variation between 8 MG isolates and vaccine strains. Conclusively, Sequencing of IGSR region of MG can be used as a valuable epidemiological investigation tool for the differentiation of wild-type MG strains from vaccine strains.

scholarly journals The Species Identification in Traditional Herbal Patent Medicine, Wuhu San, Based on Shotgun Metabarcoding

2021 ◽  
Vol 12 ◽  
Author(s):  
Jinxin Liu ◽  
Weishan Mu ◽  
Mengmeng Shi ◽  
Qing Zhao ◽  
Weijun Kong ◽  
...  
Keyword(s):  
Species Identification ◽  
Raw Materials ◽  
Intergenic Spacer ◽  
Carthamus Tinctorius ◽  
Sequencing Data ◽  
Bisphosphate Carboxylase ◽  
Sequencing Platform ◽  
Intergenic Spacer Region ◽  
Saposhnikovia Divaricata ◽  
Patent Medicine

Traditional herbal patent medicine typically consists of multiple ingredients, making it challenging to supervise contamination by impurities and the improper use of raw materials. This study employed shotgun metabarcoding for the species identification of biological ingredients in traditional herbal patent medicine, Wuhu San. The five prescribed herbal materials found in Wuhu San were collected, and their reference sequences were obtained by traditional DNA barcoding using Sanger sequencing. Two lab-made and three commercial Wuhu San samples were collected, and a total of 37.14 Gb of shotgun sequencing data was obtained for these five samples using the Illumina sequencing platform. A total of 1,421,013 paired-end reads were enriched for the Internal Transcribed Spacer 2 (ITS2), psbA and trnH intergenic spacer region (psbA-trnH), maturase k (matK), and ribulose-1, 5-bisphosphate carboxylase (rbcL) regions. Furthermore, 80, 11, 9, and 8 operational taxonomic units were obtained for the ITS2, psbA-trnH, matK, and rbcL regions, respectively, after metagenomic assembly, annotation, and chimeric detection. In the two lab-made mock samples, all labeled ingredients in the Wuhu San prescription were successfully detected, and the positive control, Panax quinquefolius L., was detected in the HSZY172 mock sample. Three species, namely Angelica sinensis (Oliv.) Diels, Saposhnikovia divaricata (Turcz. ex Ledeb.) Schischk., and Carthamus tinctorius L., belonging to three labeled ingredients, Angelicae Sinensis Radix (Danggui), Saposhnikoviae Radix (Fangfeng), and Carthami Flos (Honghua), were detected in the three commercial samples. Angelica dahurica (Hoffm.) Benth. &amp; Hook. f. ex Franch. &amp; Sav., the original Angelicae Dahuricae Radix (Baizhi) species, was only detected in WHS003. Arisaema erubescens (Wall.) Schott, Arisaema heterophyllum Blume, or Arisaema amurense Maxim., the original Arisaematis Rhizoma (Tiannanxing) species, were not detected in any of the commercial samples, which could be attributed to the fact that this medicinal material underwent extensive processing. In addition, the Saposhnikovia divaricata adulterant was detected in all the commercial samples, while 24 fungal genera, including Aspergillus, were identified in both the lab-made and commercial samples. This study showed that shotgun metabarcoding provided alternative strategy and technical means for identifying prescribed ingredients in traditional herbal patent medicine and displayed the potential to effectively complement traditional methods.

scholarly journals Genetic Diversity of Fusarium oxysporum f. sp. cubense in East and Central Africa

Plant Disease ◽  
2018 ◽  
Vol 102 (3) ◽  
pp. 552-560 ◽  
Author(s):  
Patrick Karangwa ◽  
Diane Mostert ◽  
Privat Ndayihanzamaso ◽  
Thomas Dubois ◽  
Björn Niere ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Disease Management ◽  
Fusarium Oxysporum ◽  
Fusarium Wilt ◽  
Management Practices ◽  
Management Strategies ◽  
Central Africa ◽  
Elongation Factor ◽  
Intergenic Spacer ◽  
Intergenic Spacer Region

Banana Fusarium wilt is a major production constraint globally and a significant threat to the livelihoods of millions of people in East and Central Africa (ECA). A proper understanding of the diversity and population dynamics of the causal agent, Fusarium oxysporum f. sp. cubense (Foc), could be useful for the development of sustainable disease management strategies for the pathogen. The current study investigated the diversity of Foc in ECA using vegetative compatibility group (VCG) analysis, PCR-RFLPs of the ribosomal DNA’s intergenic spacer region, as well as phylogenetic analysis of the elongation factor-1α gene. Six VCGs (0124, 0125, 0128, 01212, 01220, and 01222), which all belong to one lineage (Foc lineage VI), were widely distributed throughout the region. VCGs 0128 and 01220 are reported for the first time in Burundi, the Democratic Republic of Congo (DRC), Rwanda, Tanzania, and Uganda, while VCG 01212 is reported in the DRC and Rwanda. Isolates that did not belong to any of the known VCGs were identified as Foc lineage VI members by phylogenetic analysis and may represent novel VCGs. CAV 2734, a banana pathogen collected in Rwanda, clustered with nonpathogenic F. oxysporum isolates in lineage VIII. Results from this study will contribute significantly toward the implementation of banana Fusarium wilt disease management practices in the region, such as the restricted movement of infected planting material and the selective planting of resistant banana varieties.

scholarly journals Selection of suitable fragment from rbcL gene for DNA barcode analysis of family Halymeniaceae, Rhodophyta

2019 ◽  
Vol 19 (4A) ◽  
pp. 201-213
Author(s):  
Nguyen Xuan Vy ◽  
Nguyen Nhat Nhu Thu ◽  
Nguyen Trung Hieu ◽  
Nguyen Thi Xuan Thuy
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Trees ◽  
Large Subunit ◽  
Dna Barcode ◽  
Full Length ◽  
Species Classification ◽  
Gene Encoding ◽  
Bisphosphate Carboxylase ◽  
Marine Algal ◽  
The Cost

Among the members of Halymeniaceae family, Grateloupia sensu lato occupies the largest composition in species. Classification based on morphological traits is difficult due to the highly variable terete to blade-like thalli among the members of this genus that usually leads to misidentification. Molecular systematics has been applied to classify Grateloupia sensu lato so that the taxonomists acquire a better understanding of the species diversity in general. The plastid gene encoding the large subunit of ribulose-1,5-bisphosphate-carboxylase-oxygenase (rbcL) was the focus of numerous marine algal studies concerning phylogeny and molecular evolution. However, using the full length of rbcL showed disadvantages such as cost and time consuming due to two times of sequencing and two times of PCR. In the present study, the shorter sequence, fragment 773 bp at 5’ end and fragment 579 bp at 3’ end of rbcL were applied and compared for the phylogenetic analysis of Halymeniaceae members. The results indicated there are no differences of topological phylogenetic trees, species resolution within genus and genus resolution within the family between fragment 773 bp at 5’ and the full length of rbcL. Therefore, we conclude that fragment 773 bp at 5’ should be used as DNA barcodes for the Halymeniaceae to reduce the cost and time during phylogenetic analysis. Two taxa Grateloupia newly collected in Vietnam were grouped to the known Phyllymenia, a new genus in Vietnam.

scholarly journals Phylogenetic analysis of human parvovirus B19, indicating two subgroups of genotype 1 in Vietnamese patients

2006 ◽  
Vol 87 (10) ◽  
pp. 2941-2949 ◽  
Author(s):  
Nguyen L. Toan ◽  
Anja Duechting ◽  
Peter G. Kremsner ◽  
Le H. Song ◽  
Martin Ebinger ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Hepatitis B Virus ◽  
Parvovirus B19 ◽  
Human Parvovirus B19 ◽  
Genotype 1 ◽  
Genotype 3 ◽  
Nucleotide Difference ◽  
Genotype 2 ◽  
B Virus ◽  
The Mean

Recently, three distinct genotypes (1, 2 and 3) of human parvovirus B19 (B19) have been identified. However, the characteristics and distribution of B19 genotypes in Vietnam have not been investigated. Phylogenetic analysis using 49 subgenomic NS1/VP1u regions and two coding NS1–VP1/VP2 regions has been applied to investigate the prevalence of B19 genotypes in Vietnamese patients co-infected with Hepatitis B virus. Genetic analysis of the subgenomic NS1/VP1u region of B19 revealed that two genotypes of B19 were identified in these populations, with predominance of genotype 1 (47/49, 96 %) followed by genotype 2 (2/49, 4 %), but not genotype 3. Further, phylogenetic analysis of subgenomic B19 genomes revealed two major subgroups within genotype 1 (B19-1A and B19-1B) with an estimated nucleotide difference of >5 % between each subgroup, forming different branches. The mean percentage of amino acid variation between subgroup B19-1A and B19-1B was >2 % of the NS1, VP1 and VP2 proteins. Our results indicated that two of the three known genotypes of B19 were present in Vietnamese patients, with genotype 1 predominating, and that this genotype can be classified into at least two subgroups, B19-1A and B19-1B.

scholarly journals Structural and phylogenetic analysis of the rDNA intergenic spacer region ofVerticillium dahliae

2013 ◽  
Vol 347 (1) ◽  
pp. 23-32 ◽  
Author(s):  
Ioannis A. Papaioannou ◽  
Chrysoula D. Dimopoulou ◽  
Milton A. Typas
Keyword(s):  
Phylogenetic Analysis ◽  
Intergenic Spacer ◽  
Intergenic Spacer Region ◽  
Rdna Intergenic Spacer

scholarly journals Prevalence and phylogenetic analysis of Mycoplasma synoviae strains isolated from Polish chicken layer flocks

2019 ◽  
Vol 63 (1) ◽  
pp. 41-49 ◽  
Author(s):  
Olimpia Kursa ◽  
Grzegorz Tomczyk ◽  
Anna Sawicka
Keyword(s):  
Phylogenetic Analysis ◽  
Real Time ◽  
Real Time Pcr ◽  
Genetic Material ◽  
Clinical Signs ◽  
Intergenic Spacer ◽  
Lamp Method ◽  
Conventional Pcr ◽  
Mycoplasma Synoviae ◽  
Intergenic Spacer Region

AbstractIntroduction:Mycoplasma synoviae(MS) is a chicken pathogen of major economic importance.Material and Methods:Between 2010 and 2016, 906 commercial layer chicken flocks in Poland were examined for MS, and the phylogenetic relationship among the strains was established. Regionally dispersed samples were collected and tested with the use of real-time PCR to detect the 16S–23S intergenic spacer region. Positive samples were also tested with LAMP and conventional PCR to detect thevlhAgene.Results:MS genetic material was detected in 265 (29%) of the tested flocks by real-time PCR, in 227 by the LAMP method and in 202 (22%) by conventional PCR. The by-year percentage of positive samples began at 34% in 2010, rose to 44% in 2012, and declined to 29% in 2016. A phylogenetic analysis of PolishM. synoviaestrains using a partial sequence of thevlhAgene showed nine genotypes (A–I), the most frequently occurring being F and C. Pathogenic Polish MS field isolates (n = 27) collected from chickens with clinical signs of infection were grouped for their characteristic symptoms: respiratory for genotypes C, E, F, and I (n = 13), EAA and a drop in laying for genotypes F, E, and C (n = 12), and synovitis for genotype A (n = 2).Conclusion:These data showed the country’s isolate diversity. The high prevalence suggests the need to introduce appropriate control programmes. This is the first report of molecular epidemiological data onM. synoviaeinfection in layer chickens in Poland.

scholarly journals Taxonomy of the canine Mollicutes by 16S rRNA gene and 16S/23S rRNA intergenic spacer region sequence comparison

2004 ◽  
Vol 54 (2) ◽  
pp. 537-542 ◽  
Author(s):  
Victoria J. Chalker ◽  
Joe Brownlie
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Comparison ◽  
Intergenic Spacer ◽  
23S Rrna ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Intergenic Spacer Region ◽  
The 16S Rrna Gene

The taxonomy of canine Mollicutes is described, based on phylogenetic analysis of 16S rRNA gene and 16S/23S rRNA intergenic spacer (IGS) region sequences. The nucleotide sequences of the 16S rRNA gene of two untyped mycoplasmas and the IGS region of 11 Mycoplasma species were determined and used for phylogenetic analysis. The two untyped Mycoplasma strains, HRC 689 and VJC 358, were found to be distinct from all known canine mycoplasmas and all published mycoplasma 16S rRNA gene sequences.

scholarly journals Origin and Evolution of Emerging Liaoning Virus（genus Seadornavirus, family Reoviridae) 

2020 ◽  
Author(s):  
Jun Zhang ◽  
Hong Liu ◽  
Jiahui Wang ◽  
Jiheng Wang ◽  
Jianming Zhang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Population Variation ◽  
Central China ◽  
Liaoning Province ◽  
Western China ◽  
Shanxi Province ◽  
Genotype 1 ◽  
Genotype 3 ◽  
Long Distance ◽  
Genotype 2

Abstract Background:Liaoning virus(LNV) is a member of the genus Seadornavirus, family Reoviridae and has been isolated from kinds of sucking insects in Asia and Australia. However, there are no systematic studies describe the molecular genetic evolution and migration of LNVs isolated from different time, regions and vectors.Methods:Here, a phylogenetic analysis using Bayesian Markov chain Monte Carlo simulations was conducted on the LNVs isolated from a variety of vectors during 1990-2014,worldwide. Results:The phylogenetic analysis demonstrated that the LNV could be divided into 3 genotypes, of which genotype 1 mainly composed of LNVs isolated from Australia during 1990 to 2014 as well as the original LNV strain(LNV-NE97-31) isolated from Liaoning province in northern China in 1997,genotype 2 comprised of the isolates all from Xinjiang province in western China and genotype 3 consisted the isolates from Qinghai and Shanxi province of central China. LNVs emerged about 272 years ago in Australia and gradually evolved into three LNV lineages in the order genotype1(at 73.0 years ago),genotype2(at 46.5 years ago)and genotype 3(at 25.3 years ago). Following further phylogeographic analysis, we proposed that Australia (113°E-153°E,10°S-42°S) was the source of LNVs and the genotype 1 LNVs transmitted from this region to Liaoning province(118°E-125°E,38°N-43°N) in Northeast Asian continent then further spread across the central part of China to Xinjiang province in western China(75°E-95°E,35°N-50°N).Conclusion: LNVs were initially isolated from Liaoning province of China in the Northeast Asia, however, the present study demonstrated that LNVs were originated from Australia in the South Pacific region and transmitted to mainland China then rapidly spread across China and evolved three different genotypes.The above results suggested that LNV had the characteristics of long-distance transmission and there were great genetic diversity existed in the LNV population. Therefore, it is of great importance to strengthen the monitoring of the population variation of LNV and maintain vigilance to avoid LNV breaking through the species barrier and further clarify its relationship to human and animal infection.

scholarly journals Epidemiology of Hepatitis B, C, E, and G Virus Infections and Molecular Analysis of Hepatitis G Virus Isolates in Bolivia

1999 ◽  
Vol 37 (10) ◽  
pp. 3291-3295 ◽  
Author(s):  
Nami Konomi ◽  
Chiaki Miyoshi ◽  
Carlos La Fuente Zerain ◽  
Tian-Cheng Li ◽  
Yasuyuki Arakawa ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Hepatitis B ◽  
Blood Donors ◽  
Full Length ◽  
Hcv Rna ◽  
Genotype 3 ◽  
Hepatitis G Virus ◽  
Genotype 2

Prevalence of hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis G virus (HGV), and hepatitis E virus (HEV) was investigated among 574 healthy blood donors in Bolivia. HCV RNA and HGV RNA in the serum were identified by a nested reverse transcription-PCR using primers derived from the 5′ untranslated region (5′ UTR). We also tested for hepatitis B surface antigen (HBsAg) and for the antibody to HEV. The results revealed that HGV RNA was present in 84 of 574 (14.6%) tested blood donors, whereas HBsAg was detected in only 2 (0.3%) donors, and no individuals positive for HCV RNA were found. Anti-HEV immunoglobulin G (IgG) was detected in 93 (16.2%) individuals and anti-HEV IgM was found in 10 (1.7%) individuals among the same population. Phylogenetic analysis of 44 HGV isolates in the 5′ UTR showed that 27 (61%) isolates were genotype 3 (Asian type) and the remaining 17 (39%) isolates were genotype 2 (United States and European type). Moreover, we obtained a full-length nucleotide sequence of the HGV genome (designated HGV-BL230) recovered from a Bolivian blood donor. The BL230 was composed of 9,227 nucleotides and had a single open reading frame, encoding 2,842 amino acid residues. Interestingly, the BL230 belonged to genotype 2 of HGV at the level of a full-length sequence, although this was classified as genotype 3 by a phylogenetic analysis based on the 5′ UTR sequence. The BL230 differed from previously reported HGV/hepatitis GB virus type C isolates by 12 to 13% of the nucleotide sequence and 4% of the amino acid sequence. Our data indicate a high prevalence of HGV in native Bolivians, and the major genotype of HGV was type 3.

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