keyword
MENU ▼
Read by QxMD icon Read
search

intergenic spacer region

keyword
https://www.readbyqxmd.com/read/28713393/the-complete-chloroplast-genome-of-chinese-bayberry-morella-rubra-myricaceae-implications-for-understanding-the-evolution-of-fagales
#1
Lu-Xian Liu, Rui Li, James R P Worth, Xian Li, Pan Li, Kenneth M Cameron, Cheng-Xin Fu
Morella rubra (Myricaceae), also known as Chinese bayberry, is an economically important, subtropical, evergreen fruit tree. The phylogenetic placement of Myricaceae within Fagales and the origin of Chinese bayberry's domestication are still unresolved. In this study, we report the chloroplast (cp) genome of M. rubra and take advantage of several previously reported chloroplast genomes from related taxa to examine patterns of evolution in Fagales. The cp genomes of three M. rubra individuals were 159,478, 159,568, and 159...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28684375/complete-mitochondrial-genome-of-triatoma-infestans-hemiptera-reduviidae-triatominae-main-vector-of-chagas-disease
#2
Sebastián Pita, Francisco Panzera, Jesús Vela, Pablo Mora, Teresa Palomeque, Pedro Lorite
The complete mitogenome of Triatoma infestans, the main vector of Chagas disease in South America, was obtained by combining Illumina and Sanger sequencing sequence data. The 17,301bp long genome contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a control region. The number, order and orientation of mitochondrial genes are the same as in T. dimidiata, the only Triatominae mt genome published so far. The main differences between both mitogenomes are found in the control region and in the intergenic spacer between the nd1 gene and the tRNA-Ser...
July 3, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28642589/multiple-origins-and-a-narrow-genepool-characterise-the-african-tea-germplasm-concordant-patterns-revealed-by-nuclear-and-plastid-dna-markers
#3
Moses Cheloti Wambulwa, Muditha Kasun Meegahakumbura, Samson Kamunya, Alice Muchugi, Michael Möller, Jie Liu, Jian-Chu Xu, De-Zhu Li, Lian-Ming Gao
Despite the highly economic value of tea in Africa, its genetic and geographic origins remain largely unexplored. Here we address this by collecting 439 samples across 11 countries in Africa and Asia to investigate the origin and genepool composition of African tea based on 23 nuclear microsatellites loci (nSSRs) and three cpDNA intergenic spacer regions. Our results indicated that the African tea represents a potpourri originating from multiple introductions over time. The nSSR analysis revealed that the majority (79%) of tea accessions collected in Africa belong to Indian Assam tea which have likely originated from India and/or Sri Lanka...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28620408/quality-control-of-the-traditional-patent-medicine-yimu-wan-based-on-smrt-sequencing-and-dna-barcoding
#4
Jing Jia, Zhichao Xu, Tianyi Xin, Linchun Shi, Jingyuan Song
Substandard traditional patent medicines may lead to global safety-related issues. Protecting consumers from the health risks associated with the integrity and authenticity of herbal preparations is of great concern. Of particular concern is quality control for traditional patent medicines. Here, we establish an effective approach for verifying the biological composition of traditional patent medicines based on single-molecule real-time (SMRT) sequencing and DNA barcoding. Yimu Wan (YMW), a classical herbal prescription recorded in the Chinese Pharmacopoeia, was chosen to test the method...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28608849/the-complete-chloroplast-genome-sequences-of-fritillaria-ussuriensis-maxim-and-fritillaria-cirrhosa-d-don-and-comparative-analysis-with-other-fritillaria-species
#5
Inkyu Park, Wook Jin Kim, Sang-Min Yeo, Goya Choi, Young-Min Kang, Renzhe Piao, Byeong Cheol Moon
The genus Fritillaria belongs to the widely distributed Liliaceae. The bulbs of Fritillaria, F. ussuriensis and F. cirrhosa are valuable herbaceous medicinal ingredients. However, they are still used indiscriminately in herbal medicine. Identification and molecular phylogenic analysis of Fritillaria species are therefore required. Here, we report the complete chloroplast (CP) genome sequences of F. ussuriensis and F. cirrhosa. The two Fritillaria CP genomes were 151,524 and 151,083 bp in length, respectively, and each included a pair of inverted repeated regions (52,678 and 52,156 bp) that was separated by a large single copy region (81,732 and 81,390 bp), and a small single copy region (17,114 and 17,537 bp)...
June 13, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28598968/comparative-mitochondrial-genome-analysis-of-daphnis-nerii-and-other-lepidopteran-insects-reveals-conserved-mitochondrial-genome-organization-and-phylogenetic-relationships
#6
Yu Sun, Chen Chen, Jin Gao, Muhammad Nadeem Abbas, Saima Kausar, Cen Qian, Lei Wang, Guoqing Wei, Bao-Jian Zhu, Chao-Liang Liu
In the present study, the complete sequence of the mitochondrial genome (mitogenome) of Daphnis nerii (Lepidoptera: Sphingidae) is described. The mitogenome (15,247 bp) of D.nerii encodes13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and an adenine (A) + thymine (T)-rich region. Its gene complement and order is similar to that of other sequenced lepidopterans. The 12 PCGs initiated by ATN codons except for cytochrome c oxidase subunit 1 (cox1) gene that is seemingly initiated by the CGA codon as documented in other insect mitogenomes...
2017: PloS One
https://www.readbyqxmd.com/read/28582433/travelling-to-the-south-phylogeographic-spatial-diffusion-model-in-monttea-aphylla-plantaginaceae-an-endemic-plant-of-the-monte-desert
#7
Matias C Baranzelli, Andrea Cosacov, Gabriela Ferreiro, Leigh A Johnson, Alicia N Sérsic
Effects of Pleistocene climatic oscillations on plant phylogeographic patterns are relatively well studied in forest, savanna and grassland biomes, but such impacts remain less explored on desert regions of the world, especially in South America. Here, we performed a phylogeographical study of Monttea aphylla, an endemic species of the Monte Desert, to understand the evolutionary history of vegetation communities inhabiting the South American Arid Diagonal. We obtained sequences of three chloroplast (trnS-trnfM, trnH-psbA and trnQ-rps16) and one nuclear (ITS) intergenic spacers from 272 individuals of 34 localities throughout the range of the species...
2017: PloS One
https://www.readbyqxmd.com/read/28566081/-a-rarely-isolated-bacterium-in-microbiology-laboratories-streptococcus-uberis
#8
Canan Eryıldız, Şebnem Bukavaz, Şaban Gürcan, Osman Hatipoğlu
Streptococcus uberis is a gram-positive bacterium that is mostly responsible for mastitis in cattle. The bacterium rarely has been associated with human infections. Conventional phenotyphic methods can be inadequate for the identification of S.uberis; and in microbiology laboratories S.uberis is confused with the other streptococci and enterococci isolates. Recently, molecular methods are recommended for the accurate identification of S.uberis isolates. The aim of this report is to present a lower respiratory tract infection case caused by S...
April 2017: Mikrobiyoloji Bülteni
https://www.readbyqxmd.com/read/28549151/borrelia-species-detected-in-ticks-feeding-on-wild-korean-water-deer-hydropotes-inermis-using-molecular-and-genotypic-analyses
#9
D VanBik, S H Lee, M G Seo, B R Jeon, Y K Goo, S J Park, M H Rhee, O D Kwon, T H Kim, P J L Geraldino, D Kwak
Lyme borreliosis is a vector-borne disease transmitted through the bite of ticks infected by Borrelia burgdorferi sensu lato group, including B. burgdorferi sensu stricto, B. afzelii, and B. garinii. The goal of the present study was to detect Borrelia species in ticks infesting wild Korean water deer (KWD; Hydropotes inermis Swinhoe), using molecular and genotypic analyses. In total, 48 ticks were collected from KWD, all of which were morphologically identified as Haemaphysalis longicornis Neumann that is dominant in Korea...
May 26, 2017: Journal of Medical Entomology
https://www.readbyqxmd.com/read/28534230/trueperella-pyogenes-isolated-from-a-brain-abscess-of-an-adult-roebuck-capreolus-capreolus
#10
Jörn-Peter Wickhorst, Abdulwahed Ahmed Hassan, Omar Hashim Sheet, Tobias Eisenberg, Osama Sammra, Mazen Alssahen, Christoph Lämmler, Ellen Prenger-Berninghoff, Michael Zschöck, Markus Timke, Amir Abdulmawjood
The present study was designed to characterize phenotypically and genotypically a Trueperella pyogenes strain isolated from a brain abscess of an adult roebuck (Capreolus capreolus). The species identity could be confirmed by phenotypical investigations, by MALDI-TOF MS analysis, and by sequencing the 16S ribosomal RNA (rRNA) gene, the 16S-23S rRNA intergenic spacer region (ISR); by sequencing the target genes rpoB, gap, and tuf; and by detection of T. pyogenes chaperonin-encoding gene cpn60 with a previously developed loop-mediated isothermal amplification (LAMP) assay...
May 23, 2017: Folia Microbiologica
https://www.readbyqxmd.com/read/28521734/higher-order-organisation-of-extremely-amplified-potentially-functional-and-massively-methylated-5s-rdna-in-european-pikes-esox-sp
#11
Radka Symonová, Konrad Ocalewicz, Lech Kirtiklis, Giovanni Battista Delmastro, Šárka Pelikánová, Sonia Garcia, Aleš Kovařík
BACKGROUND: Pikes represent an important genus (Esox) harbouring a pre-duplication karyotype (2n = 2x = 50) of economically important salmonid pseudopolyploids. Here, we have characterized the 5S ribosomal RNA genes (rDNA) in Esox lucius and its closely related E. cisalpinus using cytogenetic, molecular and genomic approaches. Intragenomic homogeneity and copy number estimation was carried out using Illumina reads. The higher-order structure of rDNA arrays was investigated by the analysis of long PacBio reads...
May 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28502098/-fix-me-another-marguerite-species-delimitation-in-a-group-of-intensively-hybridising-lineages-of-ox-eye-daisies-leucanthemum-mill-compositae-anthemideae
#12
Florian Wagner, Sabine Härtl, Robert Vogt, Christoph Oberprieler
Delineating species boundaries in the framework of the multi-species coalescent (MSC) proves to be a reliable, objective, and reproducible method in an increasing number of studies. However, the underlying model assumes the lack of gene flow after speciation; an assumption which may be frequently violated in plant evolution. The present study evaluates the robustness of currently available species delimitation methods implemented in beast (BFD, BFD*, and dissect) in the closely-knit ox-eye daisy group around Leucanthemum ageratifolium Pau...
May 14, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28486518/complete-mitochondrial-genomes-of-two-blattid-cockroaches-periplaneta-australasiae-and-neostylopyga-rhombifolia-and-phylogenetic-relationships-within-the-blattaria
#13
Jinnan Ma, Chao Du, Chuang Zhou, Yongmei Sheng, Zhenxin Fan, Bisong Yue, Xiuyue Zhang
Complete mitochondrial genomes (mitogenomes) of two cockroach species, Periplaneta australasiae and Neostylopyga rhombifolia, 15,605 bp and 15,711 bp in length, respectively, were determined. As reported for other cockroach mitogenomes, the two mitogenomes possessed typical ancestral insect mitogenome gene composition and arrangement. Only several small intergenic spacers were found: one, which was common in all sequenced cockroach mitogenomes except for the genus Cryptocercus, was between tRNA-Ser (UCN) and ND1 and contained a 7bp highly conserved motif (WACTTAA)...
2017: PloS One
https://www.readbyqxmd.com/read/28467379/mycoviruses-in-the-plant-pathogen-ustilaginoidea-virens-are-not-correlated-with-the-genetic-backgrounds-of-its-hosts
#14
Jie Zhong, Chuan Yuan Cheng, Bi Da Gao, Qian Zhou, Hong Jian Zhu
Ustilaginoidea virens, the causal agent of rice false smut, is one of the most devastating grain diseases that causes loss of yield in most rice-growing areas worldwide. In this study, we performed a dsRNA screen to isolate mycoviruses from 35 U. virens strains. The results revealed that 34 of the tested isolates were infected by various dsRNA elements, displaying highly viral diversity and mixed infections. We characterized a 5.3 kbp dsRNA from a typical isolate containing dsRNA segments with sizes ranging from 0...
May 3, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28448637/45s-rdna-external-transcribed-spacer-organization-reveals-new-phylogenetic-relationships-in-avena-genus
#15
Joana Rodrigues, Wanda Viegas, Manuela Silva
The genus Avena comprises four distinct genomes organized in diploid (AA or CC), tetraploid (AABB or AACC) and hexaploid species (AACCDD), constituting an interesting model for phylogenetic analysis. The aim of this work was to characterize 45S rDNA intergenic spacer (IGS) variability in distinct species representative of Avena genome diversity-A. strigosa (AA), A. ventricosa (CvCv), A. eriantha (CpCp), A. barbata (AABB), A. murphyi (AACC), A. sativa (AACCDD) and A. sterilis (AACCDD) through the assessment of the 5' external transcribed spacer (5'-ETS), a promising IGS region for phylogenetic studies poorly studied in Avena genus...
2017: PloS One
https://www.readbyqxmd.com/read/28437593/tabula-rasa-in-the-patagonian-channels-the-phylogeography-of-oreobolus-obtusangulus-cyperaceae
#16
Simon Pfanzelt, Dirk C Albach, Klaus Bernhard von Hagen
The extent of the Pleistocene glaciations in the Patagonian Channel region (southwesternmost South America) and their impact on the vegetation there is largely unknown. Whether the regional flora was wiped out completely (tabula rasa) or survived in ice-free pockets (in situ survival) is still an open question. The molecular imprint of either scenario should still be visible in extant populations. Therefore, DNA sequence data of Oreobolus obtusangulus Gaudich. (Cyperaceae) were analyzed. This species is an abundant constitutent of Patagonian cushion peat bogs, one of the Patagonian Channel region's major vegetation types...
April 24, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28435087/the-complete-mitochondrial-genome-of-clostera-anachoreta-lepidoptera-notodontidae-and-phylogenetic-implications-for-noctuoidea-species
#17
Xiao-Yu Zhu, Zhao-Zhe Xin, Ying Wang, Hua-Bin Zhang, Dai-Zhen Zhang, Zheng-Fei Wang, Chun-Lin Zhou, Bo-Ping Tang, Qiu-Ning Liu
In this study, the complete mitochondrial genome (mitogenome) of Clostera anachoreta (Lepidoptera: Notodontidae) was sequenced. It comprises 15,456 base pairs (bp), including 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and one non-coding control region (CR), as found in other lepidopterans. Gene order is identical to that of typical lepidopterans. There are 15 intergenic spacers ranging from 2 to 49bp, and 9 overlapping regions ranging from 1 to 8bp, occurring throughout the genome...
July 2017: Genomics
https://www.readbyqxmd.com/read/28421039/population-structure-of-sclerotinia-subarctica-and-sclerotinia-sclerotiorum-in-england-scotland-and-norway
#18
John P Clarkson, Rachel J Warmington, Peter G Walley, Matthew Denton-Giles, Martin J Barbetti, Guro Brodal, Berit Nordskog
Sclerotinia species are important fungal pathogens of a wide range of crops and wild host plants. While the biology and population structure of Sclerotinia sclerotiorum has been well-studied, little information is available for the related species S. subarctica. In this study, Sclerotinia isolates were collected from different crop plants and the wild host Ranuculus ficaria (meadow buttercup) in England, Scotland, and Norway to determine the incidence of Sclerotinia subarctica and examine the population structure of this pathogen for the first time...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28402789/rust-fungi-on-panicum
#19
Jill E Demers, Miao Liu, Sarah Hambleton, Lisa A Castlebury
Rusts are economically important diseases of switchgrass (Panicum virgatum) and other Paniceae grasses. Phylogenetic analyses based on sequences of the nuc rDNA 5.8S internal transcribed spacer 2 region (ITS2), partial 28S region, and intergenic spacer region (IGS) of nuc rDNA showed that species of rust fungi infecting switchgrass are closely related within Puccinia. Variation among rbcLa sequences for the associated hosts sampled concurred with the original identifications. Five species infecting switchgrass were recognized: Puccinia graminicola (≡ Uromyces graminicola), P...
2017: Mycologia
https://www.readbyqxmd.com/read/28381961/investigation-of-genetic-diversity-of-fusarium-oxysporum-f-sp-fragariae-using-pcr-rflp
#20
Ji-Su Kim, Nam Jun Kang, Youn-Sig Kwak, Choungkeun Lee
Fusarium wilts of strawberry, caused by Fusarium oxysporum f. sp. fragariae, is a serious soil-borne disease. Fusarium wilt causes dramatic yield losses in commercial strawberry production and it is a very stubborn disease to control. Reliable chemical control of strawberry Fusarium wilt disease is not yet available. Moreover, other well-known F. oxysporum have different genetic information from F. oxysporum f. sp. fragariae. This analysis investigates the genetic diversity of strawberry Fusairum wilt pathogen...
April 2017: Plant Pathology Journal
keyword
keyword
75803
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"