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Internal transcribed spacer guided multiplex PCR for species identification of Convolvulus prostratus and Evolvulus alsinoides

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Acta Pharmaceutica Sinica B 2016年第3期6卷 253-258页

作者： Sonal Sharma Neeta Shrivastava B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre Sarkhej-Gandhinagar Highway Nirma University

Shankhpushpi is a reputed drug from an Indian system of medicine for treating mental disorders and enhancing memory. Two herbs, namely Convolvulus prostratus Forssk. and Evolvulus alsinoides(L.) L., are commonly known as Shankhpushpi. Ambiguous vernacular identity can affect the scientific validity of the Shankpushpi-based herbal drug therapy. In the present investigation, a novel and sensitive multiplex PCR method based on polymorphism in the internal transcribed spacer(ITS) region was developed to establish the molecular identity of C. prostratus and E. alsinoides. DNA was isolated and the ITS region was amplified, sequenced and assembled. Sequences were aligned to identify variable nucleotides in order to develop plant-specific primers. Primers were validated in singleplex reactions and eventually a multiplex assay was developed. This assay was tested for sensitivity and validated by amplifying DNA isolated from the simulated blended powdered plant material. Primers developed for C. prostratus resulted into a 200 bp amplicon and 596 bp for E. alsinoides. The assay was found to be sensitive enough for amplification of low quantities of DNA. The method can detect 10% of the mixing of plants with each other in blended material. This PCR assay can be used for rapid botanical identification of Shankhpushpi plant materials and will improve evidence-based herbal drug therapy.

关键词： PCR Internal transcribed spacers Shankhpushpi Botanical identification Adulteration Substitution Herbal drugs DNA barcoding

Molecular phylogeny of Pneumocystis based on 5.8S rRNA gene and the internal transcribed spacers of rRNA gene sequences

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Science China(Life Sciences) 2008年第5期51卷 445-452页

作者： LI ZiHui1,2, FENG XianMin1, LU SiQi1, ZHANG Fan1, WANG FengYun1 & HUANG Song1 1 Department of Pathogenic Biology, Capital Medical University, Beijing 100069, China 2 Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101100, China Department of Pathogenic Biology Capital Medical University Beijing China Beijing Tuberculosis and Thoracic Tumor Research Institute Beijing China

To clarify the phylogenetic relationships and species status of Pneumocystis, the 5.8S rRNA gene and the internal transcribed spacers (ITS, 1 and 2) of Pneumocystis rRNA derived from rat, gerbil and human were amplified, cloned and sequenced. The genetic distance matrix of six Pneumocystis species compared with other fungi like Taphrina and Saccharomyces indicated that the Pneumocystis genus contained multiple species including Pneumocystis from gerbil. The phylogenetic tree also showed that Pneumocystis from human and monkey formed one group and four rodent Pneumocystis formed another group. Among the four members, Pneumocystis wakefieldiae was most closely related to Pneumocystis murina and Pneumocystis carinii, and was least related to gerbil Pneumocystis.

关键词： Pneumocystis phylogeny 5.8S rRNA gene internal transcribed spacers

DNA Barcoding of Ricinus communisfrom Different Geographical Origin by Using Chloroplast matKand Internal transcribed Spacers

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American Journal of Plant Sciences 2012年第9期3卷 1304-1310页

作者： Mohamed Enan Mohammad Al-Deeb Nael Fawzy Khaled Amiri Department of Biology UAE University Al-Ain UAE Flora and Phyto-Taxonomy Research Department Horticultural Research Institute Agricultural Research Center Giza Egypt

Ricinus communis have attracted considerable attention because of its specific industrial and pharmacological activities. DNA barcodes can be used as reliable tools to facilitate the identification of medicinal plants for the safe use, quality control and forensic investigation. In this study, the differential identification of eight accessions of R. com-munis was investigated through DNA sequence analysis of two candidate DNA barcodes. The nucleotide sequence of internal transcribed spacers (ITS2) and chloroplast maturase gene (matK) have been determined to construct the phylogenetic tree. The phylogenetic relationships of accessions based on the nrITS2 region and partial matK region showed that all accessions in this study were related to three geographical origins. Based on sequence align-ment and phylogenetic analyses we concluded that the ITS2 sequences can distinguish R. communis accessions from different geographical distributions.

关键词： DNA Barcoding Internal transcribed Spacer Maturase K Ricinus communis

Phylogenetic Relationships of Termitomyces aurantiacusInferred from Internal transcribed Spacers DNA Sequences

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Advances in Bioscience and Biotechnology 2015年第5期6卷 358-367页

作者： Shafiquzzaman Siddiquee Kobun Rovina Laila Naher Kenneth F. Rodrigues Md Akhter Uzzaman Biotechnology Research Institute Universiti Malaysia Sabah Kota Kinabalu Malaysia Faculty of Agro-Based Industry Universiti Malaysia Kelantan Jeli Campus-17600 Kelantan Malaysia Planning and Development Division Bangladesh Atomic Energy Commission Dhaka Bangladesh

Fungus-growing termites cultivate species of the mutualistic basidiomycete genus Termitomyces on a substrate called the fungal comb. Identification of fungal species based on morphological features is complicated, tedious, and prone to errors. As an alternative, nuclear ribosomal DNA sequences consisting of the internal transcribed spacers (ITS1 and ITS2) and 5.8S rDNA were used to identify Malaysian isolates of Termitomyces sp. The morphological characteristics and molecular data indicate that Malaysian Termitomyces isolated is clearly monophyletic and belongs to the Tricholomataceae family. The Malaysian isolates analyzed in this study represent the termite fungus species called T. aurantiacus.

关键词： Fungal Comb Internal transcribed Spacers Morphological Feature Phylogenetic Relationship

A re-investigation of the bloom-forming unarmored dinoflagellate Karenia longicanalis(*** umbella)from Chinese coastal waters

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Journal of Oceanology and Limnology 2018年第6期36卷 2202-2215页

作者：王建艳岑竞仪李思吕颂辉 MOESTRUP ?jvind 陈健嘉江涛雷向东 Department of Science Research Beijing Museum of Natural History College of Life Science and Technology Jinan University Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes Jinan University Marine Biological Section Department of BiologyUniversity of Copenhagen School of Science & Technology Open University of Hong Kong Key Laboratory of Sustainable Development of Marine Fisheries Ministry of AgricultureYellow Sea Fisheries Research InstituteChinese Academy of Fishery Sciences Wenzhou Marine Environmental Monitoring Center Station State Oceanic Administration

The dinoflagellate genus K arenia is known for recurrent harmful blooms worldwide. However, species diversity of the genus is generally overlooked owing to the difficulty of identifying small unarmored dinoflagellates. We have established four clonal cultures of K arenia longicanalis isolated from the type locality, Hong Kong harbor(strain HK01) and other three locations along the Chinese coasts(strains YB01, DT01, and NJ01). The morphology of the strain was studied by light and scanning electron microscopy(LM and SEM) and the pigment composition analyzed by high-performance liquid chromatography. We provide the first molecular data of K. longicanalis based on the large subunit(LSU) rRNA gene sequence and internal transcribed spacer(ITS). The four strains showed identical LSU rDNA sequences with a similarity of 99.4% to the holotype of K arenia umbella(strain KUTN05) from Australia. In the ITS phylogeny, the sequence of K. umbella branched between the Chinese strains of K. longicanalis. A careful comparison of the morphology of K. longicanalis and K. umbella reveals the similarity in the diagnostic characters. Diff erences may appear due to the sample treatment for SEM. We conclude that K. umbella is a junior synonym of K. longicanalis.

关键词： harmful algal blooms(HABs) phytoplankton morphology phylogeny large subunit(LSU)rRNA internal transcribed spacer(ITS)

Exploitation of genetic resources based on regulome and gene editing in crops

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Science China(Life Sciences) 2020年第9期63卷 1406-1409页

作者： Yunzhen Li Wenhao Yan National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China

Future breeding programs have to meet diverse demands of different consumers, which require massive genetic resources and variations. However, the number of natural existing haplotypes is always limited due to domestication and breeding process (Tanksley and Mc Couch, 1997). Compared with traditional genetic cloning approaches, elucidating how one gene is transcribed and how it regulates downstream workhorses will generate more information on the casual mutation(s) of the gene and its downstream targets.

关键词： breeding crops transcribed

Phylogenetic status of Pneumocystis from corticosteroid-treated gerbils

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Science China(Life Sciences) 2010年第10期53卷 1239-1246页

作者： RODNEY D Adam Department of Medicine and Immunobiology University of Arizona College of Medicine

Pneumocystis spp. infect the lungs of multiple mammalian species and cause disease in immunosuppressed individuals. The Pneumocystis isolates that have been studied to date fall into two major clades, those from primates and those from rodents. Within each of these clades, different species have been described on the basis of host specificity and differences in sequence and morphology. Here, we demonstrate that dexamethasone immunosuppression consistently results in histologically apparent lung infection in gerbils (28/35 animals). Sequence analysis of the 18S, 5.8S and internal transcribed spacer regions of the rDNA and a portion of the mitochondrial large subunit rDNA demonstrated that this gerbil Pneumocystis is grouped with other rodent Pneumocystis spp., but is distinct from them. Our results suggest that gerbil Pneumocystis differs sufficiently from Pneumocystis species found in other rodents to be considered a separate species.

关键词： 5.8S rRNA gene gerbil internal transcribed spacers (ITS) mitochondrial large subunit (mtLS) rRNA gene 18S rRNA gene Pneumocystis

Protocruzia,a highly ambiguous ciliate(Protozoa;Ciliophora):Very likely an ancestral form for Heterotrichea,Colpodea or Spirotrichea? With reevaluation of its evolutionary position based on multigene analyses

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中国科学：生命科学英文版 2010年第1期53卷 131-138页

作者： Thorsten STOECK Shin Mann Kyoon Al-Rasheid Khaled A. S. Al-Khedhairy Abdulaziz A. Department of Ecology University of Kaiserslautern Department of Biology University of Ulsan Zoology Department King Saud University

The ciliate genus Protocruzia belongs to one of the most ambiguous taxa considering its systematic position,possibly as a member of the classes Heterotrichea,Spirotrichea or Karyorelictea,which is tentatively placed into Spirotrichea in Lynn’s 2008 *** test these hypotheses,multigene trees(Bayesian inference,evolutionary distance,maximum parsimony,and maximum likelihood) were constructed using the small subunit rRNA(SSU rRNA) gene,internal transcribed spacer 2(ITS2) and a protein coding gene(histone H4).All analyses agree that:(1) four morphotypes of Protocruzia from different geographical origins group together and form a monophyletic clade,which cannot be assigned to any of the eleven described ciliate classes;(2) it is invariably positioned on an isolated branch separated from the class Spirotrichea suggesting that this clade should be clearly removed from Spirotrichea;(3) this leads us to hypothesize that this taxon may indeed represent a lineage on a class *** on the fact that it is,both morphologically and in molecular features,closely related to the heterotrichs,Colpodea and Oligohymenophorea,Protocruziida might be an ancestral form for the subphylum Intramacronucleata in the evolutionary line from the class Heterotrichea(subphylum Postciliodesmatophora) to higher taxa.

关键词： SSU rRNA gene internal transcribed spacer 2(ITS2) gene histone H4 gene phylogenetic position Protocruzia Protocruziidea new class

A Mitochondria-Targeted PPR Protein Restores pol Cytoplasmic Male Sterility by Reducing orF224 Transcript Levels in Oilseed Rape

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Molecular Plant 2016年第7期9卷 1082-1084页

作者： Liu, Zhi Yang, Zonghui Wang, Xiang Li, Kaidi An, Hong Liu, Jie Yang, Guangsheng Fu, Tingdong Yi, Bin Hong, Dengfeng Huazhong Agr Univ Natl Ctr Rapeseed Improvement Wuhan Natl Key Lab Crop Genet Improvement Wuhan 430070 Peoples R China Huazhong Agr Univ Coll Plant Sci & Technol Wuhan 430070 Peoples R China

Cytoplasmic male sterility （CMS） in plants is a maternally inherited inability to produce functional pollen. CMS is generally caused by aberrant mitochondrial genes that are often chimeric in structure and frequentl... 详细信息

关键词： inability mitochondrial transcribed