scholarly journals Molecular Autograph of Maturase-K Gene in Isodon rugosus (Lamiaceae)

Botanica ◽  
2020 ◽  
Vol 26 (1) ◽  
pp. 95-100
Author(s):  
Devendra Kumar Srivastava ◽  
Pekhna Bansal ◽  
Pradeep Kumar Singh ◽  
Manjit Inder Singh Saggoo
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Medicinal Plants ◽  
Dna Sequence ◽  
Accession Number ◽  
Candidate Marker ◽  
Isodon Rugosus ◽  
Dna Sequence Alignment ◽  
Species Specific ◽  
First Time

AbstractMolecular autograph of trn/mat-K gene was used as one of the important candidate marker in addressing the questions of systematics and barcoding of medicinal plants. Features of trn/mat-K gene in Isodon rugosus (Lamiaceae) were assessed for the first time (NCBI GenBank Accession Number: MH939199.1). Sequence of 756 bp length was amplified by the universal matK primers (matK472F and matK1248R) in the cpDNA of the plant. It was reported to contain trnK gene (>1…..50; >746…..756), partial sequence; and matK gene (>51…..745), partial coding DNA sequence. Alignment search and analysis showed that only nine different Isodon species are currently available for matK sequences with repeated copy of submissions in GenBank. The matK sequences of I. rugosus was reported with 34.2 (G + C)% and 17 variable sites (VS), out of which seven were singleton (ST) and 10 sites were species-specific parsimoniously-informative (PI) that could be used to differentiate I. rugosus from other species as well as to authenticate the taxon. Phylogenetic analysis resulted into monophyletic clustering of I. rugosus near to the clade having I. coetsa by both maximum likelihood (ML) and maximum parsimony (MP) methods. Clades obtained in ML tree were more informative as compared to MP tree.

New species of Mycena (Mycenaceae, Agaricales) with colored lamellae and three new species records from China

Phytotaxa ◽  
2018 ◽  
Vol 361 (3) ◽  
pp. 266 ◽  
Author(s):  
QIN NA ◽  
TOLGOR BAU
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
North America ◽  
Morphological Characters ◽  
Its Sequences ◽  
Monophyletic Clade ◽  
Three New Species ◽  
First Time

Four species of Mycena possessing a colored lamellar are reported. Of these, Mycena entolomoides is described as new and is distinguished by an incarnate color of the whole lamellae, and M. citrinomarginata, M. purpureofusca, and M. strobilinoidea are recorded for the first time in China. A complete description, drawings and photographs of the morphological characters of M. entolomoides sp. nov. are accompanied by comparisons with closely related taxa. The three species newly recorded in China are considered in agreement with those species in Europe and North America. Phylogenetic analysis based on ITS sequences showed that M. entolomoides sp. nov. forms a monophyletic clade, well supported by maximum likelihood and Bayesian inference.

scholarly journals A new species of the genus Euxaldar Fennah, 1978 (Hemiptera, Fulgoromorpha, Issidae) from China and revision on the molecular phylogeny of the family

ZooKeys ◽  
2021 ◽  
Vol 1021 ◽  
pp. 19-35
Author(s):  
Liang-Jing Yang ◽  
Zhi-Min Chang ◽  
Lin Yang ◽  
Xiang-Sheng Chen
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Molecular Phylogenetic Analysis ◽  
The Family ◽  
Molecular Phylogenetic ◽  
First Time ◽  
A New Species

A new species Euxaldar daweishanensis Yang, Chang & Chen, sp. nov. is described and illustrated from southwestern China. The female genitalia of the genus Euxaldar is described and presented for the first time. A checklist and key to the known species of the genus are provided. A revised molecular phylogenetic analysis of the family Issidae based on combined partial sequences of 18S, 28S, COI, and Cytb is provided using both Maximum likelihood and Bayesian inference analyses.

scholarly journals Bartonella vinsonii subsp. berkhoffii andB.henselaein dogs

2018 ◽  
Vol 146 (9) ◽  
pp. 1202-1204 ◽  
Author(s):  
A. Müller ◽  
F. Soto ◽  
M. Sepúlveda ◽  
P. Bittencourt ◽  
J. L. Benevenute ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Infection Risk ◽  
Southern Chile ◽  
Quantitative Real Time Pcr ◽  
Accession Number ◽  
Conventional Pcr ◽  
Canine Population ◽  
Pcr Assays ◽  
First Time ◽  
Positive Results

AbstractThis study aimed to molecularly surveyBartonellain dogs from Chile. Quantitative real-time PCR (qPCR) forBartonellaspp. based onnuoGgene was performed in 139 blood samples taken from dogs belonging to rural localities of the Valdivia Province, Los Ríos region, southern Chile.nuoGqPCR-positive samples were submitted to conventional PCR assays forftsZ,gltA,rpoBandnuoGgenes and sequencing for speciation and phylogenetic analysis. Based upon qPCR results,Bartonellaspp. occurrence in dogs was 4.3% (6/139). Out of sixnuoGqPCR-positive samples, six, three, two and none showed positive results in cPCR assays based ongltA,ftsZ,rpoBandnuoGgenes, respectively. Consistent sequencing results were obtained only for theftsZgene from sample #1532 (GeneBank accession number: MG252491), andgltAgene from samples #1535 (MG252490) and #1532 (148 bp fragment that was not deposited in GenBank). Phylogenetic analysis offtsZandgltAgenes allowed speciation of twonuoG-positive samples, one asBartonella vinsoniisubsp. berkhoffii and the other asB. henselae. Bartonella vinsoniisubsp. berkhoffii andB. henselaeare detected for the first time in dogs from Chile, highlighting the importance of the canine population as a source of zoonotic agents and potential infection risk to humans.

scholarly journals Detection and Characterization of Distinct Alphacoronaviruses in Five Different Bat Species in Denmark

Viruses ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 486 ◽  
Author(s):  
Christina Lazov ◽  
Mariann Chriél ◽  
Hans Baagøe ◽  
Esben Fjederholt ◽  
Yu Deng ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Rt Pcr ◽  
The United Kingdom ◽  
Faecal Samples ◽  
Myotis Daubentonii ◽  
Pcr Assays ◽  
Species Specific ◽  
First Time ◽  
Geographical Locations

Bat populations harbour a multitude of viruses; some of these are pathogenic or potentially pathogenic in other animals or humans. Therefore, it is important to monitor the populations and characterize these viruses. In this study, the presence of coronaviruses (CoVs) in different species of Danish bats was investigated using active surveillance at different geographical locations in Denmark. Faecal samples were screened for the presence of CoVs using pan-CoV real-time RT-PCR assays. The amplicons, obtained from five different species of bats, were sequenced. Phylogenetic analysis revealed a species-specific clustering with the samples from Myotis daubentonii, showing a close resemblance to coronavirus sequences obtained from the same species of bat in Germany and the United Kingdom. Our results show, for the first time, that multiple, distinct alphacoronaviruses are present in the Danish bat populations.

scholarly journals Halanonchus scintillatulus sp. nov. from New Zealand and a review of the suborder Trefusiina (Nematoda: Enoplida)

2020 ◽  
Author(s):  
Daniel Leduc ◽  
Zeng Qi Zhao ◽  
Frederic Sinniger
Keyword(s):  
Phylogenetic Analysis ◽  
New Zealand ◽  
Maximum Likelihood ◽  
18S Rdna ◽  
Valid Species ◽  
Female Reproductive System ◽  
Rdna Sequences ◽  
18S Rdna Sequences ◽  
First Time

We provide a review of the enoplid suborder Trefusiina Siddiqi, 1983, based on morphological considerations and analyses of new and published 18S rDNA sequences. We also describe Halanonchus scintillatulus Leduc sp. nov. from the Hauraki Gulf, northern New Zealand, as well as females of Trefusialaimus idrisi Leduc, 2013 from the continental slope of New Zealand. We show for the first time that the structure of the female reproductive system of Trefusialaimus Riemann, 1974 consists of two opposed and outstretched ovaries, an unusual feature for the Enoplida. The Trefusiina did not form a monophyletic group in the 18S rDNA phylogeny due to the placement of Lauratonema Gerlach, 1953 and Trefusialaimus sequences well away from the main Trefusiina clade. However, due to generally weak Maximum Likelihood support values, we refrain from changing the classification of these taxa until more comprehensive analyses can be conducted. Our phylogenetic analysis supports the inclusion of the Trischistomatidae Andrássy, 2007 within the Trefusiina, meaning that all of the enoplid suborders now include at least some terrestrial/freshwater representatives. The Trefusiina currently comprises five families, 14 genera and 92 valid species.

A description of eleven new species of Agaricus sections Xanthodermatei and Hondenses collected from Tibet and the surrounding areas

Phytotaxa ◽  
2016 ◽  
Vol 257 (2) ◽  
pp. 99 ◽  
Author(s):  
Jun-Liang Zhou ◽  
Sheng-Yu Su ◽  
Hong-Yan Su ◽  
Bo Wang ◽  
Philippe Callac ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Maximum Likelihood ◽  
Sequence Data ◽  
Molecular Phylogenetic Analysis ◽  
Likelihood Methods ◽  
Maximum Likelihood Methods ◽  
Molecular Phylogenetic ◽  
Surrounding Areas ◽  
First Time

Specimens of Agaricus sections Xanthodermatei and Hondenses were collected in Tibet and the surrounding areas. All specimens were morphologically described and subjected to molecular phylogenetic analysis of the ITS and combined ITS, LSU and tef-1α sequence data using Bayesian and Maximum Likelihood methods. Twelve species were identified in this study, eleven of which were new species and one of which was identified in China for the first time. All of the identified species are described and illustrated with photo plates.

New and noteworthy lichen-forming and lichenicolous fungi 10

2020 ◽  
Vol 62 (1-2) ◽  
pp. 69-108
Author(s):  
S. Y. Kondratyuk ◽  
D. K. Upreti ◽  
G. K. Mishra ◽  
S. Nayaka ◽  
K. K. Ingle ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
South Korea ◽  
Eastern Europe ◽  
South Asia ◽  
New Combinations ◽  
Eastern Asia ◽  
Forest Zone ◽  
Mediterranean Europe ◽  
First Time ◽  
India And China

Eight species, new for science, i.e.: Lobothallia gangwondoana S. Y. Kondr., J.-J. Woo et J.-S. Hur and Phyllopsora dodongensis S. Y. Kondr. et J.-S. Hur from South Korea, Eastern Asia, Ioplaca rinodinoides S. Y. Kondr., K. K. Ingle, D. K. Upreti et S. Nayaka, Letrouitia assamana S. Y. Kondr., G. K. Mishra et D. K. Upreti, and Rusavskia indochinensis S. Y. Kondr., D. K. Upreti et S. Nayaka from India and China, South Asia, Caloplaca orloviana S. Y. Kondr. and Rusavskia drevlyanica S. Y. Kondr. et O. O. Orlov from Ukraine, Eastern Europe, as well as Xanthoria ibizaensis S. Y. Kondr. et A. S. Kondr. from Ibiza Island, Spain, Mediterranean Europe, are described, illustrated and compared with closely related taxa. Fominiella tenerifensis S. Y. Kondr., Kärnefelt, A. Thell et Feuerer is for the first time recorded from Mediterranean Europe, Huriella loekoesiana S. Y. Kondr. et Upreti is provided from Russia for the first time, and H. pohangensis S. Y. Kondr., L. Lőkös et J.-S. Hur for the first time from China, Phoma candelariellae Z. Kocakaya et Halıcı is new to Ukraine, and Staurothele frustulenta Vain. is recorded from the Forest Zone of Ukraine for the first time. Twelve new combinations, i.e.: Bryostigma apotheciorum (for Sphaeria apotheciorum A. Massal.), Bryostigma biatoricola (for Arthonia biatoricola Ihlen et Owe-Larss.), Bryostigma dokdoense (for Arthonia dokdoensis S. Y. Kondr., L. Lőkös, B. G. Lee, J.-J. Woo et J.-S. Hur), Bryostigma epiphyscium (for Arthonia epiphyscia Nyl.), Bryostigma lobariellae (for Arthonia lobariellae Etayo), Bryostigma lapidicola (for Lecidea lapidicola Taylor), Bryostigma molendoi (for Tichothecium molendoi Heufl. ex Arnold), Bryostigma neglectulum (for Arthonia neglectula Nyl.), Bryostigma parietinarium (for Arthonia parietinaria Hafellner et Fleischhacker), Bryostigma peltigerinum (for Arthonia vagans var. peltigerina Almq.), Bryostigma phaeophysciae (for Arthonia phaeophysciae Grube et Matzer), Bryostigma stereocaulinum (for Arthonia nephromiaria var. stereocaulina Ohlert), are proposed based on results of combined phylogenetic analysis based on mtSSU and RPB2 gene sequences. Thirty-one new combinations for members of the genus Polyozosia (i.e.: Polyozosia actophila (for Lecanora actophila Wedd.), Polyozosia agardhiana (for Lecanora agardhiana Ach.), Polyozosia altunica (for Myriolecis altunica R. Mamut et A. Abbas), Polyozosia antiqua (for Lecanora antiqua J. R. Laundon), Polyozosia bandolensis (for Lecanora bandolensis B. de Lesd.), Polyozosia behringii (for Lecanora behringii Nyl.), Polyozosia caesioalutacea (for Lecanora caesioalutacea H. Magn.), Polyozosia carlottiana (for Lecanora carlottiana C. J. Lewis et Śliwa), Polyozosia congesta (for Lecanora congesta Clauzade et Vězda), Polyozosia eurycarpa (for Lecanora eurycarpa Poelt, Leuckert et Cl. Roux), Polyozosia expectans (Lecanora expectans Darb.), Polyozosia flowersiana (Lecanora flowersiana H. Magn.), Polyozosia fugiens (for Lecanora fugiens Nyl.), Polyozosia invadens (for Lecanora invadens H. Magn.), Polyozosia juniperina (for Lecanora juniperina Śliwa), Polyozosia latzelii (for Lecanora latzelii Zahlbr.), Polyozosia liguriensis (for Lecanora liguriensis B. de Lesd.), Polyozosia massei (for Myriolecis massei M. Bertrand et J.-Y. Monnat), Polyozosia mons-nivis (for Lecanora mons-nivis Darb.), Polyozosia oyensis (for Lecanora oyensis M.-P. Bertrand et Cl. Roux), Polyozosia percrenata (for Lecanora percrenata H. Magn.), Polyozosia persimilis (for Lecanora hagenii subsp. persimilis Th. Fr.), Polyozosia poeltiana (for Lecanora poeltiana Clauzade et Cl. Roux), Polyozosia prominens (for Lecanora prominens Clauzade et Vězda), Polyozosia prophetae-eliae (for Lecanora prophetae-eliae Sipman), Polyozosia salina (for Lecanora salina H. Magn.), Polyozosia schofieldii (for Lecanora schofieldii Brodo), Polyozosia sverdrupiana (for Lecanora sverdrupiana Øvstedal), Polyozosia torrida (for Lecanora torrida Vain.), Polyozosia wetmorei (for Lecanora wetmorei Śliwa), Polyozosia zosterae (for Lecanora subfusca? zosterae Ach.)) are proposed.

LegumeDB: Development of Legume Medicinal Plant Database and Comparative Molecular Evolutionary Analysis of matK Proteins of Legumes and Mangroves

2019 ◽  
Vol 15 (4) ◽  
pp. 353-362
Author(s):  
Sambhaji B. Thakar ◽  
Maruti J. Dhanavade ◽  
Kailas D. Sonawane
Keyword(s):  
Phylogenetic Analysis ◽  
Medicinal Plants ◽  
Homology Modeling ◽  
Sequence Alignment ◽  
Vigna Unguiculata ◽  
Multiple Sequence Alignment ◽  
Legume Species ◽  
Mangrove Species ◽  
Multiple Sequence ◽  
Thespesia Populnea

Background: Legume plants are known for their rich medicinal and nutritional values. Large amount of medicinal information of various legume plants have been dispersed in the form of text. Objective: It is essential to design and construct a legume medicinal plants database, which integrate respective classes of legumes and include knowledge regarding medicinal applications along with their protein/enzyme sequences. Methods: The design and development of Legume Medicinal Plants Database (LegumeDB) has been done by using Microsoft Structure Query Language Server 2017. DBMS was used as back end and ASP.Net was used to lay out front end operations. VB.Net was used as arranged program for coding. Multiple sequence alignment, phylogenetic analysis and homology modeling techniques were also used. Results: This database includes information of 50 Legume medicinal species, which might be helpful to explore the information for researchers. Further, maturase K (matK) protein sequences of legumes and mangroves were retrieved from NCBI for multiple sequence alignment and phylogenetic analysis to understand evolutionary lineage between legumes and mangroves. Homology modeling technique was used to determine three-dimensional structure of matK from Legume species i.e. Vigna unguiculata using matK of mangrove species, Thespesia populnea as a template. The matK sequence analysis results indicate the conserved residues among legume and mangrove species. Conclusion: Phylogenetic analysis revealed closeness between legume species Vigna unguiculata and mangrove species Thespesia populnea to each other, indicating their similarity and origin from common ancestor. Thus, these studies might be helpful to understand evolutionary relationship between legumes and mangroves. : LegumeDB availability: http://legumedatabase.co.in

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