scholarly journals Syntenizer 3000: Synteny-based analysis of orthologous gene groups

2019 ◽  
Author(s):  
Camous Moslemi ◽  
Cathrine Kiel Skovbjerg ◽  
Sara Moeskjær ◽  
Stig Uggerhøj Andersen
Keyword(s):  
Sequence Similarity ◽  
Orthologous Gene ◽  
Homologous Gene ◽  
Syntenic Relationship ◽  
Gene Group ◽  
Amorphous Nature ◽  
Duplication Events ◽  
Areas Of Interest ◽  
Relationship Of

AbstractMotivationThe amorphous nature of genes combined with the prevalence of duplication events makes establishing correct genetic phylogenies challenging.Since homologous gene groups are traditionally formed on basis of sequence similarity, both orthologs and paralogs are often placed in the same gene group by existing tools. Certain tools such as PoFF take syntenic relationship of genes into consideration when forming gene groups. However, a method to form gene groups consisting of only true syntelogs has not yet been developed.In order to obtain orthologous gene groups consisting of the most likely syntelogs we need a method to filter out paralogs. If one strain has two or more copies of the same gene in a gene group we want to keep only the true syntelog in the group, and remove the paralogous copies by distinguishing between the two using synteny analysis.ResultsWe present a novel algorithm for measuring the degree of synteny shared between two genes and successfully disambiguate gene groups. This synteny measure is the basis for a number of other useful functions such as gene neighbourhood visualisation to inspect suspect gene groups, strain visualisation for assessing assembly quality and finding genomic areas of interest, and chromosome/plasmid classification of contigs in partially classified datasets.AvailabilityThe latest version of Syntenizer 3000 can be downloaded from the GitHub repository at https://github.com/kamiboy/Syntenizer3000/Consult the manual.pdf file in the repository for instructions on how to build and use the tool, as well as a in depth explanation of the algorithms utilised.

Codon usage inCryptosporidium parvumdiffers from that in other Eimeriorina

Parasitology ◽  
1996 ◽  
Vol 112 (4) ◽  
pp. 357-362 ◽  
Author(s):  
S. Char ◽  
P. Kelly ◽  
A. Naeem ◽  
M. J. G. Farthing
Keyword(s):  
Codon Usage ◽  
18S Rrna ◽  
Homologous Gene ◽  
Rrna Sequence ◽  
Synonymous Codons ◽  
Current Classification ◽  
Close Relationship ◽  
Relationship Of ◽  
Β Tubulin

SUMMARYCodon usage ofCrytosporidium parvumwas compared with those of other EimeriorinaToxoplasma gondiiandEimeria tenellaand revealed a biased use of synonymous codons with a preference for NNU (40·0%) and NNA (33·4%). There was no close resemblance of the codon usage ofC. parvumtoT. gondii(correlation coefficient, r = 0·14) orE. tenella(r = 0·14) but it was similar toEntamoeba histolytica(r = 0·75) andPlasmodium falciparum(r = 0·5). Analysis of the codon usage in homologous gene sequences (actin, β-tubulin) also failed to reveal a close relationship betweenC. parvumandT. gondiiorE. tenella. The low usage codons inC. parvumwere most frequently used codons inT. gondiiandE. tenella. These observations are consistent with 18S rRNA sequence analysis which shows no close relationship ofCryptosporidiumwith other Eimeriorina (Sarcocystis, ToxoplasmaandEimeria) and questions the validity of the current classification ofC. parvum.

scholarly journals Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas sp. AAP5

2021 ◽  
Vol 9 (4) ◽  
pp. 768
Author(s):  
Karel Kopejtka ◽  
Yonghui Zeng ◽  
David Kaftan ◽  
Vadim Selyanin ◽  
Zdenko Gardian ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Close Phylogenetic Relationship

An aerobic, yellow-pigmented, bacteriochlorophyll a-producing strain, designated AAP5 (=DSM 111157=CCUG 74776), was isolated from the alpine lake Gossenköllesee located in the Tyrolean Alps, Austria. Here, we report its description and polyphasic characterization. Phylogenetic analysis of the 16S rRNA gene showed that strain AAP5 belongs to the bacterial genus Sphingomonas and has the highest pairwise 16S rRNA gene sequence similarity with Sphingomonas glacialis (98.3%), Sphingomonas psychrolutea (96.8%), and Sphingomonas melonis (96.5%). Its genomic DNA G + C content is 65.9%. Further, in silico DNA-DNA hybridization and calculation of the average nucleotide identity speaks for the close phylogenetic relationship of AAP5 and Sphingomonas glacialis. The high percentage (76.2%) of shared orthologous gene clusters between strain AAP5 and Sphingomonas paucimobilis NCTC 11030T, the type species of the genus, supports the classification of the two strains into the same genus. Strain AAP5 was found to contain C18:1ω7c (64.6%) as a predominant fatty acid (>10%) and the polar lipid profile contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, six unidentified glycolipids, one unidentified phospholipid, and two unidentified lipids. The main respiratory quinone was ubiquinone-10. Strain AAP5 is a facultative photoheterotroph containing type-2 photosynthetic reaction centers and, in addition, contains a xathorhodopsin gene. No CO2-fixation pathways were found.

scholarly journals Relationship of Hull Mesocarp Color to Seed Germination and Vigor in Large-Seeded Virginia-Type Peanuts

1995 ◽  
Vol 22 (1) ◽  
pp. 22-26 ◽  
Author(s):  
J. F. Spears ◽  
G. A. Sullivan
Keyword(s):  
Accelerated Aging ◽  
Dry Weight ◽  
Seed Moisture Content ◽  
Physiological Maturity ◽  
Seed Maturity ◽  
Seed Moisture ◽  
Arachis Hypogaea L ◽  
Maturity Class ◽  
Relationship Of

Abstract Classification of peanuts (Arachis hypogaea L.) based on pod mesocarp color has become a popular means of estimating maturity of runner peanuts. This study was initiated to determine if the hull mesocarp color is related to seed maturity of virginia-type peanuts and to evaluate changes in quality as seed mature. Cultivars NC 7 and NC 9 peanuts were harvested by hand in 1990, 1991, and 1992. Pods were separated according to mesocarp color. Seed moisture content and dry weight within a maturity class varied with cultivar and production year. Germination of NC 7 seed grown in 1990 and 1992 increased as seed approached maturity. Immature NC 9 seed grown in 1991 and 1992 had substantially lower germination than seed from mature pods. There was no increase in germination during maturation of NC 7 seed harvested in 1991 or NC 9 from 1990. Seed leakage during imbibition, measured by electrical conductivity, decreased as seed matured. The lowest leakage levels occurred when seed had reached physiological maturity. Germination following accelerated aging (AA) increased as seed matured. Maximum AA germination of NC 7 occurred when seed had reached 77, 84, and 100% of their final dry weight in 1990, 1991, and 1992, respectively. NC 9 seed achieved maximum germination following AA after the seed amassed at least 90% of their final dry weight.

scholarly journals Psychroserpens Luteus Sp. Nov., Isolated fFrom Red Algae

2021 ◽  
Author(s):  
Xiu-Ya Ping ◽  
Kai Wang ◽  
Jin-Yu Zhang ◽  
Shu-Xin Wang ◽  
Zong-Jun Du ◽  
...  
Keyword(s):  
Red Algae ◽  
Genomic Dna ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gram Stain ◽  
Optimum Ph ◽  
The 16S Rrna Gene

Abstract A Gram-stain-negative, gliding-motile, positive for catalase, facultative anaerobic, designated strain XSD401T, was isolated from the red algae of Xiaoshi Island, Shandong Province, China. Growth occurred at 20–37 °C (optimum, 33 °C), pH 5.5–9.5 (optimum, pH 6.5–7.5), and with 0.5–5% (w/v) NaCl (optimum, 3%). The main fatty acids are iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH, iso-C15:0 3-OH, C16:0. Phosphatidylethanolamine (PE), three unidentified aminolipids (AL1, AL2, AL3) and one unidentified lipid (L) were the major polar lipids. The G+C content of the genomic DNA was 33.9 mol%. Strain XSD401T had the highest sequence similarity (96.88%) to the 16S rRNA gene of Psychroserpens damuponensis KCTC 23539T. The similarities with Psychroserpens burtonensis DSM 12212T was 96.31%. The dDDH values between strain XSD401T and P. damuponensis KCTC 23539T, P. burtonensis DSM 12212T, were 20.40% and 20.30%, respectively. The average nucleotide identity (ANI) values between strain XSD401T and P. damuponensis KCTC 23539T, P. burtonensis DSM 12212T were 76.91%, 76.88%, respectively. The differences in morphology, physiology and genotype from the previously described taxa support the classification of strain XSD401T as a representative of a novel species of the genus Psychroserpens, for which the name Psychroserpens luteus sp. nov. is proposed. The type strain is XSD401T (= MCCC 1H00396T = KCTC 72684T = JCM 33931T).

scholarly journals Pseudomonas taeanensis sp. nov., isolated from a crude oil-contaminated seashore

2010 ◽  
Vol 60 (12) ◽  
pp. 2719-2723 ◽  
Author(s):  
Dong-Heon Lee ◽  
Sung-Ran Moon ◽  
Young-Hyun Park ◽  
Jung-Ho Kim ◽  
Hoon Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Crude Oil ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Low Levels

A novel Gram-negative, aerobic, motile, short rod-shaped bacterium, designated MS-3T, was isolated from a crude oil-contaminated seashore in Taean, Korea. Strain MS-3T grew at 4–30 °C, at pH 6.0–9.5 and with 0–5 % NaCl and was oxidase- and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MS-3T was most similar to Pseudomonas marincola KMM 3042T (97.9 % 16S rRNA gene sequence similarity), P. cuatrocienegasensis 1NT (97.8 %), P. borbori R-20821T (97.3 %) and P. lundensis ATCC 49968T (97.1 %). Relatively low levels of DNA–DNA relatedness were found between strain MS-3T and P. cuatrocienegasensis LMG 24676T (57.2 %), P. borbori LMG 23199T (39.7 %), P. marincola KMM 3042T (32.2 %) and P. lundensis KACC 10832T (32.1 %), which support the classification of strain MS-3T within a novel species of the genus Pseudomonas. The G+C content of the genomic DNA of strain MS-3T was 57.6 mol% and the major isoprenoid quinone was Q-9. Strain MS-3T contained summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 38.0 %), C16 : 0 (24.4 %), C18 : 1 ω7c (12.8 %), C12 : 0 (9.6 %) and C10 : 0 3-OH (4.9 %) as the major cellular fatty acids. On the basis of the phenotypic, genotypic and phylogenetic data, strain MS-3T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas taeanensis sp. nov. is proposed. The type strain is MS-3T (=KCTC 22612T =KACC 14032T =JCM 16046T =NBRL 105641T).

scholarly journals A New Paralog Removal Pipeline Resolves Conflict between RAD-seq and Enrichment

2020 ◽  
Author(s):  
Wenbin Zhou ◽  
John Soghigian ◽  
Qiu-yun (Jenny) Xiang
Keyword(s):  
High Throughput Sequencing ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Disjunct Distribution ◽  
Divergence Times ◽  
Target Enrichment ◽  
Sequencing Technologies ◽  
Duplication Events ◽  
The Witch ◽  
Phylogenomic Analyses

ABSTRACTTarget enrichment and RAD-seq are well-established high throughput sequencing technologies that have been increasingly used for phylogenomic studies, and the choice between methods is a practical issue for plant systematists studying the evolutionary histories of biodiversity of relatively recent origins. However, few studies have compared the congruence and conflict between results from the two methods within the same group of organisms, especially in plants, where extensive genome duplication events may complicate phylogenomic analyses. Unfortunately, currently widely used pipelines for target enrichment data analysis do not have a vigorous procedure for remove paralogs in Hyb-Seq data. In this study, we employed RAD-seq and Hyb-Seq of Angiosperm 353 genes in phylogenomic and biogeographic studies of Hamamelis (the witch-hazels) and Castanea (chestnuts), two classic examples exhibiting the well-known eastern Asian-eastern North American disjunct distribution. We compared these two methods side by side and developed a new pipeline (PPD) with a more vigorous removal of putative paralogs from Hyb-Seq data. The new pipeline considers both sequence similarity and heterozygous sites at each locus in identification of paralogous. We used our pipeline to construct robust datasets for comparison between methods and downstream analyses on the two genera. Our results demonstrated that the PPD identified many more putative paralogs than the popular method HybPiper. Comparisons of tree topologies and divergence times showed significant differences between data from HybPiper and data from our new PPD pipeline, likely due to the error signals from the paralogous genes undetected by HybPiper, but trimmed by PPD. We found that phylogenies and divergence times estimated from our RAD-seq and Hyb-Seq-PPD were largely congruent. We highlight the importance of removal paralogs in enrichment data, and discuss the merits of RAD-seq and Hyb-Seq. Finally, phylogenetic analyses of RAD-seq and Hyb-Seq resulted in well-resolved species relationships, and revealed ancient introgression in both genera. Biogeographic analyses including fossil data revealed a complicated history of each genus involving multiple intercontinental dispersals and local extinctions in areas outside of the taxa’s modern ranges in both the Paleogene and Neogene. Our study demonstrates the value of additional steps for filtering paralogous gene content from Angiosperm 353 data, such as our new PPD pipeline described in this study. [RAD-seq, Hyb-Seq, paralogs, Castanea, Hamamelis, eastern Asia-eastern North America disjunction, biogeography, ancient introgression]

GONADAL DYSGENESIS WITH XX-ISOCHROMOSOME CONSTITUTION AND ABNORMAL THYROID PATTERNS

1967 ◽  
Vol 54 (4) ◽  
pp. 609-617 ◽  
Author(s):  
R. G. Milet ◽  
E. R. Plunkett ◽  
D. H. Carr
Keyword(s):  
Autoimmune Disease ◽  
X Chromosome ◽  
Gonadal Dysgenesis ◽  
Ridge Count ◽  
Suppurative Otitis Media ◽  
Lyon Hypothesis ◽  
Relationship Of ◽  
The Relationship ◽  
Thyroid Abnormalities

ABSTRACT The authors report a female patient with XXi constitution for the long arm of the X chromosome associated with thyroid abnormalities, high digital ridge count and chronic suppurative otitis media. This is followed by a discussion of the correlation between genotype and phenotype, comment on the Lyon hypothesis, the relationship of thyroid abnormalities to this condition, autoimmune disease, unbalanced sex chromosomal constitution and the association with a high total digital ridge count. Finally a single hypothesis is proposed for the associated clinical entities that have been found and the suggestion that the classification of this particular type of gonadal dysgenesis be considered as a new syndrome, the »XX-isochromosome syndrome«.

SYSTEMIC LUPUS ERYTHEMATOSUS AND SYNDROMES POSSIBLY RELATED

PEDIATRICS ◽  
1957 ◽  
Vol 19 (6) ◽  
pp. 1109-1123
Author(s):  
M. A. Ogryzlo ◽  
H. A. Smythe
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Lupus Erythematosus ◽  
Serum Proteins ◽  
Clinical Manifestations ◽  
Electrophoretic Pattern ◽  
Chemotherapeutic Agents ◽  
Systemic Lupus ◽  
Relationship Of ◽  
The Relationship

Attention is drawn to the difficulties that may be encountered in the positive identification and classification of many patients suspected of suffering from systemic lupus erythematosus. Much of this is due to a lack of specific criteria, either clinical or pathologic, for the diagnosis of the disease. The problem has been made more difficult by the recognition of a number of other syndromes that bear a superficial resemblance to systemic lupus erythematosus, yet differ in clinical manifestations, natural course, prognosis and other respects. A feature common to the group is the presence of the L.E. cell phenomenon. The related conditions differ from lupus enythematosus in that the L.E. phenomenon may only be demonstrable intermittently especially during severe exacerbations of the disease, while at the same time disturbances in the electrophoretic pattern of the serum proteins may be much more profound. In systemic rheumatoid disease the prognosis without steroid therapy is better than in systemic lupus erythematosus, although the morbidity may be great. The reactions which follow administration of certain chemotherapeutic agents are of considerable interest, particularly in view of the similarity to lupus erythematosus and rheumatoid arthritis, and the reversibility on withdrawal of the offending agent. The relationship of these syndromes to each other and to classical systemic lupus erythematosus has not yet been resolved, and inclusion of them under the diagnosis of systemic lupus erythematosus at this time must be regarded as premature.

Accounting theories and their impact on the formation and development of social expenditure accounting

2020 ◽  
pp. 251-258
Author(s):  
Vera Savchenko ◽  
◽  
Oleksandr Gai ◽  
Oksana Yurchenko ◽  
◽  
...  
Keyword(s):  
Social Development ◽  
Point Of View ◽  
Social Costs ◽  
Social Expenditure ◽  
Economic Theories ◽  
The Subject ◽  
Accounting Theory ◽  
Relationship Of ◽  
The Relationship

The article considers the essence of accounting theories, approaches to their separation, the relationship of accounting and economic theories, and the direction of development of accounting theories in accordance with the needs of economic and social development. The approaches to the classification of accounting theories are generalized, as well as the approaches to the interpretation of «accounting theory», the peculiarities of the interpretation of the subject of accounting from the point of view of different accounting theories are revealed and the objectivity of expansion of accounting objects is substantiated. In the context of the formation and development of accounting theories, the category of «social costs» is considered as an accounting object.

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