17,472 results match your criteria average nucleotide

Genomic Prediction of Average Daily Gain, Back-Fat Thickness, and Loin Muscle Depth Using Different Genomic Tools in Canadian Swine Populations.

Front Genet 2021 3;12:665344. Epub 2021 Jun 3.

Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.

Improvement of prediction accuracy of estimated breeding values (EBVs) can lead to increased profitability for swine breeding companies. This study was performed to compare the accuracy of different popular genomic prediction methods and traditional best linear unbiased prediction (BLUP) for future performance of back-fat thickness (BFT), average daily gain (ADG), and loin muscle depth (LMD) in Canadian Duroc, Landrace, and Yorkshire swine breeds. In this study, 17,019 pigs were genotyped using Illumina 60K and Affymetrix 50K panels. Read More

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Cellulosimicrobium fucosivorans sp. nov., isolated from San Elijo Lagoon, contains a fucose metabolic pathway linked to carotenoid production.

Arch Microbiol 2021 Jun 20. Epub 2021 Jun 20.

College of Science and Technology, Bellevue University, 1000 Galvin Rd. S., Bellevue, NE, 68005, USA.

Cellulosimicrobium strain SE3 was isolated from the San Elijo coastal lagoon near San Diego. A whole genome-based phylogenetic comparison shows great heterogeneity within the Cellulosimicrobium genus. Based on average nucleotide identity, whole genome-based comparison, and the presence of a unique L-fucose metabolic pathway, strain SE3 was shown to belong to a novel species within the genus, together with five other strains. Read More

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Pontibaca salina sp. nov., isolated from marine sediment.

Arch Microbiol 2021 Jun 19. Epub 2021 Jun 19.

Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China.

A Gram-stain-negative, oval or short rod-shaped, non-motile, aerobic bacterium, designated strain S1109L, was isolated from a marine sediment in Weihai, PR China. Cells were oxidase positive and catalase positive. Growth of strain S1109L occurred at 10-40 °C (optimum, 30-33 °C), pH 6. Read More

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Standardization of a SNP panel for parentage verification and identification in the domestic cat (Felis silvestris catus).

Anim Genet 2021 Jun 18. Epub 2021 Jun 18.

Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.

The domestic cat (Felis silvestris catus) is a valued companion animal throughout the world. Over 60 different cat breeds are accepted for competition by the cat fancy registries in different countries. Genetic markers, including short tandem repeats and SNPs, are available to evaluate and manage levels of inbreeding and genetic diversity, population and breed structure relationships, and individual identification for forensic and registration purposes. Read More

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A High-Density SNP Genetic Map Construction Using ddRAD-Seq and Mapping of Capsule Shattering Trait in Sesame.

Front Plant Sci 2021 1;12:679659. Epub 2021 Jun 1.

Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Turkey.

The seed-bearing capsule of sesame shatters at harvest. This wildish trait makes the crop unsuitable for mechanized harvesting and also restricts its commercial potential by limiting the cultivation for countries that have no access to low-cost labor. Therefore, the underlying genetic basis of the capsule shattering trait is highly important in order to develop mechanization-ready varieties for sustainable sesame farming. Read More

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Somatic variations led to the selection of acidic and acidless orange cultivars.

Nat Plants 2021 Jun 17. Epub 2021 Jun 17.

Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China.

Somatic variations are a major source of genetic diversification in asexual plants, and underpin clonal evolution and the breeding of asexual crops. Sweet orange is a model species for studying somatic variation because it reproduces asexually through apomixis and is propagated asexually through grafting. To dissect the genomic basis of somatic variation, we de novo assembled a reference genome of sweet orange with an average of three gaps per chromosome and a N50 contig of 24. Read More

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A comparison of genotyping arrays.

Eur J Hum Genet 2021 Jun 18. Epub 2021 Jun 18.

Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands.

Array technology to genotype single-nucleotide variants (SNVs) is widely used in genome-wide association studies (GWAS), clinical diagnostics, and linkage studies. Arrays have undergone a tremendous growth in both number and content over recent years making a comprehensive comparison all the more important. We have compared 28 genotyping arrays on their overall content, genome-wide coverage, imputation quality, presence of known GWAS loci, mtDNA variants and clinically relevant genes (i. Read More

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Flavobacterium difficile sp. nov., isolated from a freshwater waterfall.

Arch Microbiol 2021 Jun 16. Epub 2021 Jun 16.

Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City, 811, Taiwan.

A bacterial strain designated KDG-16 is isolated from a freshwater waterfall in Taiwan and characterized to determine its taxonomic affiliation. Cells of strain KDG-16 are Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and form light yellow colonies. Optimal growth occurs at 20-25 °C, pH 6-7, and with 0% NaCl. Read More

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Simulation study and comparative evaluation of viral contiguous sequence identification tools.

BMC Bioinformatics 2021 Jun 16;22(1):329. Epub 2021 Jun 16.

Center for Genes, Environment, and Health, National Jewish Health, 1400 Jackson Street, Denver, CO, 80206, USA.

Background: Viruses, including bacteriophages, are important components of environmental and human associated microbial communities. Viruses can act as extracellular reservoirs of bacterial genes, can mediate microbiome dynamics, and can influence the virulence of clinical pathogens. Various targeted metagenomic analysis techniques detect viral sequences, but these methods often exclude large and genome integrated viruses. Read More

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First report of infecting white clover () in Finland.

Plant Dis 2021 Jun 15. Epub 2021 Jun 15.

Finnish Food Authority, Laboratory and Research, Mustialankatu 3, Helsinki, Finland, 00790;

Soybean dwarf virus (SbDV, genus ) is a single-stranded positive-sense RNA virus able to infect several legume species. SbDV was first reported in Japan where it was associated with significant yield losses in soybean (Tamada, 1969). Since then the virus has been detected worldwide. Read More

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First Report of Bacterial Rot Caused by Pantoea endophytica on Tobacco in Liuyang, China.

Plant Dis 2021 Jun 15. Epub 2021 Jun 15.

Chinese Academy of Agricultural Sciences Institute of Tobacco Research, 243822, Qingdao, Shandong, China;

Tobacco, Nicotiana tabacum L., is produced largely in China (~1/3 of the global market). In the monsoon summer of 2020, tobacco plant petioles, where axillary buds were removed, became black-rotten, and thick ooze appeared, when squeezed. Read More

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Phocaeicola faecalis sp. nov., a strictly anaerobic bacterial strain adapted to the human gut ecosystem.

Antonie Van Leeuwenhoek 2021 Jun 15. Epub 2021 Jun 15.

State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Binhu District, Wuxi, 214122, Jiangsu, China.

A novel strictly anaerobic, Gram-negative bacterium, designated as strain FXJYN30E22, was isolated from the feces of a healthy woman in Yining county, Xinjiang province, China. This strain was non-spore-forming, bile-resistant, non-motile and rod-shaped. It was found to belong to a single separate group in the Phocaeicola genus based on its 16 S ribosomal RNA (rRNA) gene sequence. Read More

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sp. nov. a novel actinobacterium isolated from the coral .

Int J Syst Evol Microbiol 2021 Jun;71(6)

Key Laboratory of Tropical Biological Resources of the Ministry of Education of China, Hainan University, Haikou 570228, PR China.

Strain HNM0947, representing a novel actinobacterium, was isolated from the coral collected from the coast of Wenchang, Hainan, China. The strain was found to have morphological and chemotaxonomic characteristics consistent with the genus . The organism formed abundant fragmented substrate mycelia and aerial mycelia which differentiated into non-motile, rod-shaped spores. Read More

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Description of sp. nov., based on phylogenomic analysis.

Int J Syst Evol Microbiol 2021 Jun;71(6)

Department of Biotechnology, Institute of Life Sciences, Nalco Square, Bhubaneswar - 751023, India.

A novel strain of a member of the genus strain PS-1, was isolated from the skin of fresh water pufferfish () collected from Mahanadi River, India. Cells were Gram-stain-negative, aerobic, coccoid and non-motile. The predominant polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE) and phospholipid (PL) and the cell wall sugars were glucose, galactose and ribose. Read More

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Cytosine Base Editor-Mediated Multiplex Genome Editing to Accelerate Discovery of Novel Antibiotics in and .

Front Microbiol 2021 28;12:691839. Epub 2021 May 28.

Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.

Genome-based identification of new antibiotics is emerging as an alternative to traditional methods. However, uncovering hidden antibiotics under the background of known antibiotics remains a challenge. To over this problem using a quick and effective genetic approach, we developed a multiplex genome editing system using a cytosine base editor (CBE). Read More

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A case of peritoneal dialysis-associated peritonitis caused by Rhodococcus kroppenstedtii.

BMC Infect Dis 2021 Jun 13;21(1):565. Epub 2021 Jun 13.

Department of Infectious Diseases, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, 321# Zhongshan Road, Gulou District, Nanjing City, Jiangsu Province, 210008, P. R. China.

Background: Rhodococcus kroppenstedtii is an aerobic, gram-positive bacterium firstly identified in the environment, which has not been reported in human-related infection. Herein, we reported the first case of peritoneal dialysis (PD)-associated peritonitis caused by R. kroppenstedtii which was identified by whole genome sequencing. Read More

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Development and application of the Faba_bean_130K targeted next-generation sequencing SNP genotyping platform based on transcriptome sequencing.

Theor Appl Genet 2021 Jun 12. Epub 2021 Jun 12.

National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

Key Message: Large-scale faba bean transcriptome data are available, and the first genotyping platform based on liquid-phase probe targeted capture technology was developed for genetic and molecular breeding studies. Faba bean (Vicia faba L., 2n = 12) is an important food legume crop that is widely grown for multiple uses worldwide. Read More

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Citrobacter arsenatis sp. nov., an arsenate-reducing bacterium isolated from freshwater sediment.

Antonie Van Leeuwenhoek 2021 Jun 11. Epub 2021 Jun 11.

School of Environmental Science and Engineering, Hubei Key Laboratory of Mine Environmental Pollution Control and Remediation, Hubei Polytechnic University, Huangshi, China.

A novel arsenate-reducing bacterium, LY-1, was isolated from freshwater sediment in Huangshi, China. Morphological analysis indicated that the cells were shaped like rods and were gram-negative. The major fatty acids (> 10%) were C, summed feature 3 (C ω7c, C ω6c) and summed feature 8 (C ω7c, C ω6c). Read More

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Genomic adaptations enabling Acidithiobacillus distribution across wide-ranging hot spring temperatures and pHs.

Microbiome 2021 Jun 11;9(1):135. Epub 2021 Jun 11.

School of Biological Sciences, The University of Auckland, Auckland, New Zealand.

Background: Terrestrial hot spring settings span a broad spectrum of physicochemistries. Physicochemical parameters, such as pH and temperature, are key factors influencing differences in microbial composition across diverse geothermal areas. Nonetheless, analysis of hot spring pools from the Taupo Volcanic Zone (TVZ), New Zealand, revealed that some members of the bacterial genus, Acidithiobacillus, are prevalent across wide ranges of hot spring pHs and temperatures. Read More

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Major genetic discontinuity and novel toxigenic species in taxonomy.

Elife 2021 Jun 11;10. Epub 2021 Jun 11.

School of Biomedical Sciences, University of Western Australia, Nedlands, Australia.

infection (CDI) remains an urgent global One Health threat. The genetic heterogeneity seen across underscores its wide ecological versatility and has driven the significant changes in CDI epidemiology seen in the last 20 years. We analysed an international collection of over 12,000 genomes spanning the eight currently defined phylogenetic clades. Read More

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The impact of codon choice on translation process in Saccharomyces cerevisiae: folding class, protein function and secondary structure.

Daniele Santoni

J Theor Biol 2021 Jun 7;526:110806. Epub 2021 Jun 7.

Institute for System Analysis and Computer Science "Antonio Ruberti", National Research Council of Italy, Via dei Taurini 19, Rome 00185, Italy. Electronic address:

The genetic code consists in a set of rules used by living organisms to translate genomic information, contained in genes, into proteins; every amino acid is coded by a set of nucleotide triplets or codons. We refer to codon choice as the choice of a given codon, among the synonymous available ones, to code a given amino acid occurrence. The aim of this work is to shed light on the pivotal role that codon choice plays in regulating the timing of translation process, through patterns of low and high translation efficiency codons. Read More

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SNP detection and population structure evaluation of Y. L. Chang et Skv. in Hunshandake Sandland, Inner Mongolia, China.

Physiol Mol Biol Plants 2021 May 24;27(5):997-1005. Epub 2021 Apr 24.

Faculty of Resources and Environment, Baotou Teachers' College, Inner Mongolia University of Science and Technology, Baotou, 014030 China.

Single nucleotide polymorphisms (SNPs) are the most abundant and richest form of genomic polymorphism and, hence, are highly favorable markers for genetic map construction and genome-wide association studies. Based on the DNA specific-locus amplified fragment sequencing (SLAF-seq) for large-scale SNP detection, the genetic diversity and population structure of Y. L. Read More

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sp. nov., an endophytic actinomycete isolated from the root of (L.).

Int J Syst Evol Microbiol 2021 Jun;71(6)

Actinobacterial Research Unit, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand.

An endophytic actinobacterium, designated strain CA1R205, was isolated from the surface-sterilized root of L. collected from Ratchaburi province, Thailand. The taxonomic position of this strain was evaluated using a polyphasic approach. Read More

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sp. nov. (sv. septentrionale) and sp. nov. (sv. septentrionale) associated with legumes native to Canada possess rearranged symbiosis genes and numerous insertion sequences.

Int J Syst Evol Microbiol 2021 Jun;71(6)

Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A OC6, Canada.

Six bacterial strains isolated from root nodules of soybean plants that had been inoculated with root-zone soil of legumes native to Canada were previously characterized and 1) placed in two novel lineages within the genus and 2) assigned to symbiovar septentrionale. Here we verified the taxonomic status of these strains using genomic and phenotypic analyses. Phylogenetic analyses of five protein encoding partial gene sequences as well as 52 full length ribosome protein subunit gene sequences confirmed placement of the novel strains in two highly supported lineages distinct from named species. Read More

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Complete mitochondrial genome and phylogenetic analysis of the copper shark (Günther, 1870).

Mitochondrial DNA B Resour 2021 May 18;6(6):1659-1661. Epub 2021 May 18.

Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.

Copper shark ( Günther, 1870) is one of the most widely distributed but least known species in the family Carcharhinidae. Herein, we report the first complete mitogenome of . The overall structure of the 16,704 bp mitogenome was similar to that of other species and showed the highest average nucleotide identity (97. Read More

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sp. nov., isolated from rhizosphere soil of .

Int J Syst Evol Microbiol 2021 Jun;71(6)

Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China.

A novel Gram-stain positive, facultatively anaerobic, motile, irregularly rod-shaped bacterium, designated GY 10621, was isolated from rhizosphere soil of in Beihai City, Guangxi Province, PR China, and characterized using a polyphasic taxonomic approach. GY 10621 was positive for catalase and oxidase. Growth occurred at 4-42 °C (optimum 30-37 °C), at pH 5. Read More

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Identification and Characterization of Genes for the Allo A Lectins in Japanese Rhinoceros Beetle (Trypoxylus dichotomus [Allomyrina dichotoma]).

Biochem Genet 2021 Jun 7. Epub 2021 Jun 7.

Department of Chemistry and Life Sciences, Graduate School of Science and Engineering, Ibaraki University, Ibaraki, 316-8511, Japan.

The Japanese rhinoceros beetle (Trypoxylus dichotomus [Allomyrina dichotoma]) produces the lectins allo A-I and allo A-II, which have strong N-acetyllactosamine (Galβ1-4GlcNAc)-binding activity. It has been suggested that the two lectins are formed from three subunits (α, β, and γ), with allo A-I comprising α and γ subunits and allo A-II comprising β and γ subunits. Here, we determined the cDNA sequences of these subunits using both conventional polymerase chain reaction (PCR)-cloning-sequencing and transcriptome-sequencing analyses. Read More

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Molecular Analysis of Bacterial Isolates From Necrotic Wheat Leaf Lesions Caused by , and Description of Three Putative Novel Species, sp. nov., sp. nov. and sp. nov.

Front Microbiol 2021 19;12:666689. Epub 2021 May 19.

Crop Diversification Centre South, Alberta Agriculture and Forestry, Brooks, AB, Canada.

is the etiological agent of the wheat bacterial leaf streak (BLS) disease. The isolation of this pathogen is usually based on the Wilbrink's-boric acid-cephalexin semi-selective medium which eliminates 90% of other bacteria, some of which might be novel species. In our study, a general purpose nutrient agar was used to isolate 49 bacterial strains including from necrotic wheat leaf tissues. Read More

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sp. nov., a Nitrogen-Fixing Bacterium Isolated From Forest Soil by Using Optimized Culture Method.

Front Microbiol 2021 21;12:647132. Epub 2021 May 21.

Department of Life Sciences, College of Natural Sciences, Kyonggi University, Suwon-si, South Korea.

A bacterial strain, designated strain G-1-1-14, was isolated from Kyonggi University forest soil during a study of previously uncultured bacterium. The cells of strain G-1-1-14 were motile by means of peritrichous flagella, Gram-stain-negative, rod-shaped, and able to grow autotrophically with hydrogen and fix nitrogen. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain G-1-1-14 belonged to the genus . Read More

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The Impacts of and Genetic Variants on Rheumatoid Arthritis Risk in the Chinese Han Population: A Case-Control Study.

Int J Gen Med 2021 28;14:2147-2159. Epub 2021 May 28.

Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, People's Republic of China.

Background: Rheumatoid arthritis (RA), an autoimmune systemic inflammatory disease, largely resulted from genetic factor. Our purpose was to explore the association for and genetic variants with RA susceptibility in the Chinese Han population.

Patients And Methods: A total of 508 RA patients and 494 controls were involved in this case-control study; single-nucleotide polymorphisms (SNPs) genotyping was identified by the Agena MassARRAY platform. Read More

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