scholarly journals The Highly Conserved Family of Tetrahymena thermophila Chromosome Breakage Elements Contains an Invariant 10-Base-Pair Core

2006 ◽  
Vol 5 (4) ◽  
pp. 771-780 ◽  
Author(s):  
Eileen P. Hamilton ◽  
Sondra Williamson ◽  
Sandra Dunn ◽  
Virginia Merriam ◽  
Cindy Lin ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Sequence Variation ◽  
Tetrahymena Thermophila ◽  
Germ Line ◽  
Chromosome Breakage ◽  
Whole Genome Sequence ◽  
Unicellular Eukaryote ◽  
Whole Genome ◽  
Chromosome Fragmentation ◽  
Necessary And Sufficient

ABSTRACT As a typical ciliate, Tetrahymena thermophila is a unicellular eukaryote that exhibits nuclear dimorphism: each cell contains a diploid, germ line micronucleus (MICN) and a polyploid, somatic macronucleus (MACN). During conjugation, when a new MACN differentiates from a mitotic descendant of the diploid fertilization nucleus, the five MICN chromosomes are site-specifically fragmented into 250 to 300 MACN chromosomes. The classic chromosome breakage sequence (CBS) is a 15-bp element (TAAACCAACCTCTTT) reported to be necessary and sufficient for chromosome breakage. To determine whether a CBS is present at every site of chromosome fragmentation and to assess the range of sequence variation tolerated, 31 CBSs were isolated without preconception as to the sequence of the chromosome breakage element. Additional CBS-related sequences were identified in the whole-genome sequence by their similarities to the classic CBS. Forty CBS elements behaved as authentic chromosome breakage sites. The CBS nucleotide sequence is more diverse than previously thought: nearly half of the CBS elements identified by unbiased methods have a variant of the classic CBS. Only an internal 10-bp core is completely conserved, but the entire 15-bp chromosome breakage sequence shows significant sequence conservation. Our results suggest that any one member of the CBS family provides a necessary and sufficient cis element for chromosome breakage. No chromosome breakage element totally unrelated to the classic CBS element was found; such elements, if they exist at all, must be rare.

scholarly journals Whole-Genome Sequence of Toxic Freshwater Cyanobacterium Chrysosporum ovalisporum Strain UAM-MAO

2018 ◽  
Vol 7 (14) ◽  
Author(s):  
Soledad Sanz-Alférez ◽  
Carolina E. Rodríguez-Sanz ◽  
Ángel Barón-Sola ◽  
Francisca F. del Campo
Keyword(s):  
Nucleotide Sequence ◽  
Genome Sequence ◽  
Complete Nucleotide Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Freshwater Systems ◽  
Freshwater Cyanobacterium ◽  
Artificial Pond ◽  
Mao A

Here, we report the complete nucleotide sequence of Chrysosporum ovalisporum UAM-MAO, a filamentous, cylindrospermopsin-producing cyanobacterium involved in bloom forming in freshwater systems worldwide. It was isolated from an artificial pond in Madrid, Spain.

Nucleotide sequence structure and consistency of a developmentally regulated DNA deletion in Tetrahymena thermophila

1987 ◽  
Vol 7 (1) ◽  
pp. 435-443 ◽  
Author(s):  
C F Austerberry ◽  
M C Yao
Keyword(s):  
Tetrahymena Thermophila ◽  
Germ Line ◽  
Dna Recombination ◽  
Chromosome Breakage ◽  
Base Pairs ◽  
Developmentally Regulated ◽  
Junction Sequence ◽  
Macronuclear Development ◽  
Dna Deletion ◽  
Minor Degree

DNA deletion by site-specific chromosome breakage and rejoining occurs extensively during macronuclear development in the ciliate Tetrahymena thermophila. We have sequenced both the micronuclear (germ line) and rearranged macronuclear (somatic) forms of one region from which 1.1 kilobases of micronuclear DNA are reproducibly deleted during macronuclear development. The deletion junctions lie within a pair of 6-base-pair direct repeats. The termini of the deleted sequence are not inverted repeats. The precision of deletion at the nucleotide level was also characterized by hybridization with a synthetic oligonucleotide matching the determined macronuclear (rejoined) junction sequence. This deletion occurs in a remarkably sequence-specific manner. However, a very minor degree of variability in the macronuclear junction sequences was detected and was shown to be inherent in the mechanism of deletion itself. These results suggest that DNA deletion during macronuclear development in T. thermophila may constitute a novel type of DNA recombination and that it can create sequence heterogeneity on the order of a few base pairs at rejoining junctions.

scholarly journals Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Strains Circulating in East African Smallholder Pig Farms

Viruses ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 1262
Author(s):  
Joshua O. Amimo ◽  
Eunice M. Machuka ◽  
Edward O. Abworo ◽  
Anastasia N. Vlasova ◽  
Roger Pelle
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Sequence ◽  
Epitope Prediction ◽  
Whole Genome Sequence ◽  
Diagnostic Tools ◽  
Whole Genome ◽  
Potential Candidate ◽  
Whole Genome Analysis ◽  
Porcine Astrovirus ◽  
Sequence Identities

Astroviruses (AstVs) are widely distributed and are associated with gastroenteritis in human and animals. The knowledge of the genetic diversity and epidemiology of AstVs in Africa is limited. This study aimed to characterize astroviruses in asymptomatic smallholder piglets in Kenya and Uganda. Twenty-four samples were randomly selected from a total of 446 piglets aged below 6 months that were initially collected for rotavirus study and sequenced for whole genome analysis. Thirteen (13/24) samples had contigs with high identity to genus Mamastrovirus. Analysis of seven strains with complete (or near complete) AstV genome revealed variable nucleotide and amino acid sequence identities with known porcine astrovirus (PoAstV) strains. The U083 and K321 strains had nucleotide sequence identities ranging from 66.4 to 75.4% with the known PoAstV2 strains; U460 strain had nucleotide sequence identities of 57.0 to 65.1% regarding the known PoAstV3; and K062, K366, K451, and K456 strains had nucleotide sequence identities of 63.5 to 80% with the known PoAstV4 strains. The low sequence identities (<90%) indicate that novel genotypes of PoAstVs are circulating in the study area. Recombination analysis using whole genomes revealed evidence of multiple recombination events in PoAstV4, suggesting that recombination might have contributed to the observed genetic diversity. Linear antigen epitope prediction and a comparative analysis of capsid protein of our field strains identified potential candidate epitopes that could help in the design of immuno-diagnostic tools and a subunit vaccine. These findings provide new insights into the molecular epidemiology of porcine astroviruses in East Africa.

scholarly journals Complete Genome Sequence of a Lineage IV Peste des Petits Ruminants Virus from Turkey, 2018

2020 ◽  
Vol 9 (15) ◽  
Author(s):  
Sabri Hacıoğlu ◽  
Simon King ◽  
Şirin Gülsün Çizmeci ◽  
Öznur Yeşil ◽  
John Flannery ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Nucleotide Sequence Identity ◽  
Clinical Signs ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Peste Des Petits Ruminants ◽  
Sequence Identity ◽  
Lineage Iv

We report the whole-genome sequence of a peste des petits ruminants virus (PPRV) from a lamb exhibiting clinical signs in Turkey in September 2018. The genome of PPRV/Turkey/Central_Anatolia/2018 shows the highest nucleotide sequence identity (97.63%) to PPRV isolated in Turkey in 2000.

A genome-wide resource of intron spanning primers compatible for quantitative PCR and intron length polymorphism in rice

2019 ◽  
Vol 79 (02) ◽  
Author(s):  
Humira Sonah ◽  
Hasthi Ram ◽  
Bikram Pratap Singh ◽  
Jawaharlal Katara ◽  
Radha Chopra ◽  
...  
Keyword(s):  
Quantitative Pcr ◽  
Genome Sequence ◽  
Sequence Variation ◽  
Whole Genome Sequence ◽  
Pcr Analysis ◽  
Sequence Information ◽  
Whole Genome ◽  
Intron Length Polymorphism ◽  
Genome Wide ◽  
A Genome

Whole genome sequence availability in rice has provided several advantages for genomics as well as other omics assisted applications. Genome-wide molecular markers are one of such availability that has exceptional importance in modern plant breeding. In the present study, a resource of intron-spanning primers (ISPs) was developed using whole genome sequence information of two rice subspecies, japonica (cv. Nipponbare) and indica (cv. 93-11). The ISPs were designed in a way that the PCR using a cDNA template will yield 60 to 100 base pair size amplicon ideal for the quantitative PCR analysis. Whereas, PCR using genomic DNA will amplify the introns, which are more prone to sequence variation. The sequence variation in the intron serves as an excellent marker resource. The application of ISPs was demonstrated by characterizing 12 diverse rice cultivars. A total of eight out of ten ISPs were found to be polymorphic. The resource will be helpful for the rice molecular biologist and breeder community.

scholarly journals Zygotic Expression of the Double-Stranded RNA Binding Motif Protein Drb2p Is Required for DNA Elimination in the Ciliate Tetrahymena thermophila

2011 ◽  
Vol 10 (12) ◽  
pp. 1648-1659 ◽  
Author(s):  
Jason A. Motl ◽  
Douglas L. Chalker
Keyword(s):  
Rna Binding ◽  
Tetrahymena Thermophila ◽  
Germ Line ◽  
Rna Binding Proteins ◽  
Chromosome Breakage ◽  
Binding Motif ◽  
Double Stranded Rna ◽  
Content Type ◽  
Dna Elimination ◽  
Genes Encoding

ABSTRACTDouble-stranded RNA binding motif (DSRM)-containing proteins play many roles in the regulation of gene transcription and translation, including some with tandem DSRMs that act in small RNA biogenesis. We report the characterization of the genes for double-stranded RNA binding proteins 1 and 2 (DRB1andDRB2), two genes encoding nuclear proteins with tandem DSRMs in the ciliateTetrahymena thermophila.Both proteins are expressed throughout growth and development but exhibit distinct peaks of expression, suggesting different biological roles. In support of this, we show that expression ofDRB2is essential for vegetative growth whileDRB1expression is not. During conjugation, Drb1p and Drb2p localize to distinct nuclear foci. Cells lacking allDRB1copies are able to produce viable progeny, although at a reduced rate relative to wild-type cells. In contrast, cells lacking germ lineDRB2copies, which thus cannot express Drb2p zygotically, fail to produce progeny, arresting late into conjugation. This arrest phenotype is accompanied by a failure to organize the essential DNA rearrangement protein Pdd1p into DNA elimination bodies and execute DNA elimination and chromosome breakage. These results implicate zygotically expressed Drb2p in the maturation of these nuclear structures, which are necessary for reorganization of the somatic genome.

scholarly journals Whole-Genome Sequence Variation among Multiple Isolates of Pseudomonas aeruginosa

2003 ◽  
Vol 185 (4) ◽  
pp. 1316-1325 ◽  
Author(s):  
David H. Spencer ◽  
Arnold Kas ◽  
Eric E. Smith ◽  
Christopher K. Raymond ◽  
Elizabeth H. Sims ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Nucleotide Diversity ◽  
Sequence Variation ◽  
Genomic Sequence ◽  
Genetic Material ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Specific Sequence ◽  
O Antigen

ABSTRACT Whole-genome shotgun sequencing was used to study the sequence variation of three Pseudomonas aeruginosa isolates, two from clonal infections of cystic fibrosis patients and one from an aquatic environment, relative to the genomic sequence of reference strain PAO1. The majority of the PAO1 genome is represented in these strains; however, at least three prominent islands of PAO1-specific sequence are apparent. Conversely, ∼10% of the sequencing reads derived from each isolate fail to align with the PAO1 backbone. While average sequence variation among all strains is roughly 0.5%, regions of pronounced differences were evident in whole-genome scans of nucleotide diversity. We analyzed two such divergent loci, the pyoverdine and O-antigen biosynthesis regions, by complete resequencing. A thorough analysis of isolates collected over time from one of the cystic fibrosis patients revealed independent mutations resulting in the loss of O-antigen synthesis alternating with a mucoid phenotype. Overall, we conclude that most of the PAO1 genome represents a core P. aeruginosa backbone sequence while the strains addressed in this study possess additional genetic material that accounts for at least 10% of their genomes. Approximately half of these additional sequences are novel.

scholarly journals Draft Genome Sequence of Bacillus sp. Strain IITD106, Isolated from Oil-Contaminated Soil

2021 ◽  
Vol 10 (48) ◽  
Author(s):  
Arif Nissar Zargar ◽  
Saroj Mishra ◽  
Manoj Kumar ◽  
Preeti Srivastava
Keyword(s):  
Nucleotide Sequence ◽  
Genome Sequence ◽  
Contaminated Soil ◽  
Complete Nucleotide Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Bacillus Sp ◽  
Unique Ability

Here, we report the whole-genome sequence of Bacillus sp. strain IITD106. The bacterium has the unique ability to produce saponins. The complete nucleotide sequence will provide insights into the various genes and regulators involved in the biosynthesis of saponin.

scholarly journals Nucleotide sequence structure and consistency of a developmentally regulated DNA deletion in Tetrahymena thermophila.

1987 ◽  
Vol 7 (1) ◽  
pp. 435-443 ◽  
Author(s):  
C F Austerberry ◽  
M C Yao
Keyword(s):  
Tetrahymena Thermophila ◽  
Germ Line ◽  
Dna Recombination ◽  
Chromosome Breakage ◽  
Base Pairs ◽  
Developmentally Regulated ◽  
Junction Sequence ◽  
Macronuclear Development ◽  
Dna Deletion ◽  
Minor Degree

DNA deletion by site-specific chromosome breakage and rejoining occurs extensively during macronuclear development in the ciliate Tetrahymena thermophila. We have sequenced both the micronuclear (germ line) and rearranged macronuclear (somatic) forms of one region from which 1.1 kilobases of micronuclear DNA are reproducibly deleted during macronuclear development. The deletion junctions lie within a pair of 6-base-pair direct repeats. The termini of the deleted sequence are not inverted repeats. The precision of deletion at the nucleotide level was also characterized by hybridization with a synthetic oligonucleotide matching the determined macronuclear (rejoined) junction sequence. This deletion occurs in a remarkably sequence-specific manner. However, a very minor degree of variability in the macronuclear junction sequences was detected and was shown to be inherent in the mechanism of deletion itself. These results suggest that DNA deletion during macronuclear development in T. thermophila may constitute a novel type of DNA recombination and that it can create sequence heterogeneity on the order of a few base pairs at rejoining junctions.

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