Tag: dnasp
Phylogenomic analysis, cryptic species discovery, and DNA barcoding of the genus Cibotium in China based on plastome data
Introduction Traditional Chinese herbal medicine plays an indispensable role in the treatment of multiple diseases in China and other developing countries (Newman et al., 2008). Apart from the traditional usage, many medicinal plants, such as Artemisia annua L. (artemisinin, Tu, 2016), Huperzia javanica (Sw.) C. Y. Yang (Huperzine A, Zangara, 2003;…
Characterization of nuclear DNA diversity in an individual Leymus chinensis
Introduction The definition of an individual organism, traditionally defined by the invariable presence of a physiological unit and genetic homogeneity, is challenged by situations such as intraorganismal genetic heterogeneity (IGH), which refers to the presence of more than one genotype in a single organism (Schweinsberg et al., 2015). Cells within a…
Molecular evolution and phylogenomic analysis of complete chloroplast genomes of Cotinus (Anacardiaceae)
Abstract Cotinus is an oligo‐specific ornamentally valuable genus with a disjunct distribution in the Northern Hemisphere. Traditionally, the taxonomy of Cotinus was mainly based on leaf morphological characteristics. However, the limited availability of genomic information greatly hindered the study of molecular evolution and phylogeny of this genus. This study sequenced…
Evolution and biogeography of apple stem grooving virus | Virology Journal
New Iranian isolates ASGV was detected in 18 (10.3%) of samples in both west and north west Iran (Table S1). All nine full-CP sequences contained open reading frames (ORFs) 714 nt in length with 237 deduced amino acid residues. ASGV has the codon UAG as stop codon in all sequences….
A Comparative Phylogeographic Analysis of Mitochondrial DNA Variability in Four Fish Species (Salmonidae and Cyprinidae) in the Northwest Pacific
Bol’shakov, S.G., Some features of biology, growth, and age of Far Eastern redfins—Pacific redfin Tribolodon brandti and big-scaled redfin Tribolodon hakonensis—in southern Primorskii krai, Izv. Tikhookean. Nauchno-Issled. Inst. Rybn. Khoz. Okeanogr., 2013, pp. 141–158. Google Scholar Brykov, V.A., Polyakova, N.E., and Semina, A.V., Comparative analysis of mitochondrial DNA variability in four…
Comparative plastome genomics, taxonomic delimitation and evolutionary divergences of Tetraena hamiensis var. qatarensis and Tetraena simplex (Zygophyllaceae)
Liu, J. et al. Integrating a comprehensive DNA barcode reference library with a global map of yews (Taxus L.) for forensic identification. Mol. Ecol. Resour. 18, 1115–1131 (2018). Article CAS Google Scholar Parveen, I., Singh, H. K., Raghuvanshi, S., Pradhan, U. C. & Babbar, S. B. DNA barcoding of endangered…
Possible origins and implications of atypical morphologies and domestication-like traits in wild golden jackals (Canis aureus)
Camera surveillance and spatial analyses Camera surveillance took place between August and December 2020, at twelve ~ 30 km2 sites located in the central and northern Golan Heights (Supplementary Table 1). The sampling sites designated for this study belonged to four different land-use categories: “high culling risk”, “low culling risk”, nature reserves…
Protocols to Study Host-Pathosystems | SpringerLink
Alkooranee JT, Liu S, Aledan TR, Yin Y, Li M (2015) First report of powdery mildew caused by erysiphe cruciferarum on brassica napus in China. Plant Dis 99(11):1651 CrossRef Google Scholar Al-Lami HFD, You MP, Barbetti MJ (2019a) Incidence, pathogenicity and diversity of Alternaria spp. associated with alternaria leaf spot…
Molecular characterization of oriental eyeworm (Thelazia callipaeda) detected from raccoon (Procyon lotor) and Japanese raccoon dog (Nyctereutes viverrinus) in Kanto region, Japan | Parasites & Vectors
Shen J, Gasser RB, Chu D, Wang Z, Cantacessi C, Otranto D. Human thelaziasis—a neglected parasitic disease of the eye. J Parasitol. 2006;92:872–5. Article PubMed Google Scholar Otranto D, Mendoza-Roldan JA, Dantas-Torres F. Thelazia callipaeda. Trends Parasitol. 2021;37:263–4. Article PubMed Google Scholar Otranto D, Lia RP, Buono V, Traversa D,…
Extensive prevalence and significant genetic differentiation of Blastocystis in high- and low-altitude populations of wild rhesus macaques in China | Parasites & Vectors
Andersen LO, Stensvold CR. Blastocystis in health and disease: are we moving from a clinical to a public health perspective? J Clin Microbiol. 2016;54:524–8. Article CAS PubMed PubMed Central Google Scholar Hublin JSY, Maloney JG, Santin M. Blastocystis in domesticated and wild mammals and birds. Res Vet Sci. 2021;135:260–82. Article …
Phylogeny and Genetic Diversity of Philippine Native Pigs (Sus scrofa) as Revealed by Mitochondrial DNA Analysis
Ai H, Fang X, Yang B, Huang Z, Chen H, Mao L, Zhang F, Zhang L, Cui L, He W, Yang J, Yao X, Zhou L, Han L, Li J, Sun S, Xie X, Lai B, Su Y, Lu Y, Yang H, Huang T, Deng W, Nielsen R, Ren J,…
Novel equi merozoite antigen (ema-1) gene heterogeneity in a geographically isolated Theileria equi population in Croatia | Parasites & Vectors
Richter S. Vrste haemosporidia u konja i goveda NR Hrvatskoj. Thesis: Veterinary faculty university of zagreb; 1954. Google Scholar Rothschild CM. Equine piroplasmosis. J Equine Vet Sci. 2013;33:497–508. Article Google Scholar Ueti MW, Palmer GH, Scoles GA, Kappmeyer LS, Knowles DP. Persistently infected horses are reservoirs for intrastadial tick-borne transmission…
Remarkably low host specificity in the bat fly Penicillidia fulvida (Diptera: Nycteribiidae) as assessed by mitochondrial COI and nuclear 28S sequence data | Parasites & Vectors
Zachos FE. Species concepts in biology: historical development, theoretical foundations and practical relevance. Berlin: Springer; 2016. Google Scholar Perkins SL. Species concepts and malaria parasites: detecting a cryptic species of Plasmodium. Proc Biol Sci. 2000;267:2345–50. CAS PubMed PubMed Central Google Scholar Mayr E. Systematics and the origin of species. New…
Comparative chloroplast genome and phylogenetic analyses of Chinese Polyspora
Choo, L. M., Niissalo, M. A., Leong, P. K. F. & Khew, G. S. The complete plastome sequence of Gordonia penangensis Ridl. supports the transfer of Asian Gordonia into Polyspora (Theaceae). Phytotaxa 458, 159–166 (2020). Nguyet, H. N. L. et al. An updated checklist of Theaceae and a new species…
Plastomes of limestone karst gesneriad genera Petrocodon and Primulina, and the comparative plastid phylogenomics of Gesneriaceae
Features of the newly sequenced Petrocodon and Primulina plastomes Sizes of the nine newly sequenced plastomes of Petrocodon and Primulina range from 152,323 bp in Pr. medica (D.Fang ex W.T.Wang) Yin Z.Wang to 153,786 bp in Pr. cordata Mich.Möller & A.Weber (Tables 1, S1). These nine plastomes display the typical quadripartite structure…
Unveiling new perspective of phylogeography, genetic diversity, and population dynamics of Southeast Asian and Pacific chickens
Food and Agriculture Organization. The state of the world’s animal genetic resources for food and agriculture (Rome, 2007). Lawler, A. Dawn of the chicken revealed in Southeast Asia. Science 368, 1411 (2020). ADS CAS PubMed Article Google Scholar Sykes, N. A social perspective on the introduction of exotic animals: the…
Antiplatelet response to clopidogrel is associated with a haplotype in CYP2C19 gene in Pakistani patients
Amsterdam, E. A. et al. 2014 AHA/ACC guideline for the management of patients with non-ST-elevation acute coronary syndromes: Executive summary: A report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines. Circulation 130, 2354–2394 (2014). Google Scholar Kernan, W. N. et al. Guidelines for the prevention…
The Clam Cyclina sinensis (Gmelin) Phylogeography Study with 28S rRNA Gene and Potential of Nuclear rRNA Genes in Genetic Assessments of Molluscs
Avise, J. C., 2009. Phylogeography: Retrospect and prospect. Journal of Biogeography, 36: 3–15. Article Google Scholar Beheregaray, L. B., 2008. Twenty years of phylogeography: The state of the field and the challenges for the Southern Hemisphere. Molecular Ecology, 17: 3754–3774. Google Scholar Clement, M., Posada, D., and Crandall, K. A.,…
New insight into the taxonomic resolution of the genus Bythotrephes Leydig (Crustacea: Cladocera) based on molecular data from Central Europe
1. Therriault, T. W. et al. Taxonomic resolution of the genus Bythotrephes Leydig using molecular markers and re-evaluation of its global distribution. Divers. Distrib. 8, 67–84 (2002). Google Scholar 2. Karpowicz, M., Ejsmont-Karabin, J., Kozłowska, J., Feniova, I. & Dzialowski, A. R. Zooplankton community responses to oxygen stress. Water 12,…
Two divergent haplogroups of a sacsin-like gene in Acropora corals
Verification of coding sequence (CDS) of a sacsin-like gene The genomic assembly version 2.01 of A. millepora13 was downloaded from the web site (przeworskilab.com/acropora-millepora-genome/). RNA-seq reads of one A. millepora (accession: SRR2086157) were mapped (similarity fraction > 0.8, length fraction > 0.9) to the genome assembly using CLC Genomics Workbench (www.qiagenbioinformatics.com/). Mapping results were…
The mtDNA Control Region Variability of Microtus rossiaemeridionalis (Rodentia, Arvicolini) from Two Invasive Populations of the Russian Far East
1 Hobbs, R.J., Arico, S., Aronson, J., et al., Novel ecosystems: theoretical and management aspects of the new ecological world order, Global Ecol. Biogeography, 2006, vol. 15, pp. 1–7. doi.org/10.1111/j.1466-822x.2006.00212.x Article Google Scholar 2 Bellard, C., Cassey, P., and Blackburn, T.M., Alien species as a driver of recent extinctions, Biol….
Drug resistance mutations & genetic diversity of HIV1 in ART
Introduction At the end of 2018, 19.5 million people living with HIV were accessing ART globally.1 However, virological failure and development of drug resistance are becoming a bottleneck for the success of ART program. A global study involving 36 countries and 1926 patients with treatment failure from 1998–2015 reported that…
Organelle DNA sequence data provide new insights into the maternal and paternal lineages of Musa species germplasms
Argent GCG (1976) The wild bananas of Papua new Guinea. Notes Roy Bot Gard Edinb 35:77–114 Google Scholar Baker JG (1893) A synopsis of the genera and species of Musaceae. Ann Bot 7:189–229. doi.org/10.1093/aob/os-7.2.189 Article Google Scholar Barrett CF, Specht CD, Leebens-Mack J, Stevenson DW, Zomlefer WB, Davis JI (2014)…
Following the Trace of HVS II Mitochondrial Region Within the Nine Iranian Ethnic Groups Based on Genetic Population Analysis
Akbari MT, Izadi P, Izadyar M, Kyriacou K, Kleanthous M (2008) Molecular basis of thalassemia intermedia in Iran. Hemoglobin 32:462–470 CAS Article Google Scholar Al-Allawi NA, Jubrael JM, Hughson M (2006) Molecular characterization of β-thalassemia in the Dohuk region of Iraq. Hemoglobin 30:479–486 CAS Article Google Scholar Alibakhshi R, Kianishirazi…
Haplotype Diversity of Mongolian and Tuvan Goat Breeds (Capra hircus) Based on mtDNA and Y-Chromosome Polymorphism
1 Zonaed Siddiki, A., Miah, G., Islam, M.S., et al., Goat genomic resources: the search for genes associated with its economic traits, Int. J. Genomics, 2020, 5940205. doi.org/10.1155/2020/5940205 2 Amills, M., Capote, J., and Tosser-Klopp, G., Goat domestication and breeding: a jigsaw of historical, biological and molecular data with missing…
Cenozoic climatic changes drive evolution and dispersal of coastal benthic foraminifera in the Southern Ocean
1. Thomson, M. R. A. Geological and palaeoenvironmental history of the Scotia Sea region as a basis for biological interpretation. Deep Sea Res. II 51, 1467–1487 (2004). Article ADS Google Scholar 2. Maldonado, A. et al. A model of oceanic development by ridge jumping: Opening of the Scotia Sea. Glob….
Connectivity, diversity, and hybridization between two endemic fish species (Percilia spp.) in a complex temperate landscape
Anderson EC, Thompson EA (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160:1217–1229. doi.org/10.1175/1520-0442(1992)0052.0.CO;2 CAS Article PubMed PubMed Central Google Scholar Arratia G (1982) A Review of freshwater percoids from South America (Pisces, Osteichthyes, Perciformes, Percichthyidae, and Peciliidae). Abh Senckenb Naturforsch Ges 15:1–52 Google Scholar …
Dnasp Tutorial For Beginner
Dnasp Tutorial For Beginner 1 Hi Can someone help me? I need to know which data is required to perform different test with DNAsp: intra or interspecies sequences thank you • 6.1k views The “sp” in DNAsp stands for “sequence polymorphism” which reflects that this software is principally designed for…
