Copies Of Repeat Research Articles

Complete chloroplast genome sequence of Bletilla striata (Thunb.) Reichb. f., a Chinese folk medicinal plant

Bletilla striata (Thunb.) Reichb. f. is one of the commonly used traditional Chinese medicine with tuber as medicine. We report herein the complete chloroplast genome sequence of Bletilla striata (Thunb.) Reichb. f. It has a length of 159,491 bp, which contained a small single-copy (SSC) region of 18,778 bp and a large single-copy (LSC) region of 87,139 bp, separated by two copies of an inverted repeat (IR) of 26,787 bp. The chloroplast genome contains 114 unique genes, including 80 PCG, 30 tRNA, and 4 rRNA genes. In addition, 18 genes contained one or two introns, which of those including 10 PCG genes possess a single intron, and 2 PCG genes harbor two introns; and 6 tRNA genes harbor a single intron. In this study, Bletilla stariata is sister to Bletilla formosana and clustered within the group consisting of the species that belong to Orchiidaceae.

The complete chloroplast genome sequence of Sorbus amabilis (Rosaceae)

Sorbus amabilis Cheng ex Yü, a small excellent ornamental tree species, is only distributed in Eastern China. In this study, we assembled and annotated the complete chloroplast (cp) genome of the species using the next-generation sequencing for the first time. The cp genome was 160,006 bp in size, consisting of two copies of invert repeat (IR) regions of 26,405 bp, one large single-copy (LSC) region of 87,870bp, and one small single-copy (SSC) region of 19,326 bp. The overall GC content of the genome was 36.55%. The genome was predicted to contain 128 genes, including 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis of 25 chloroplast genomes in Rosaceae indicated that S. amabilis is most closely related to S. commixta. These findings may provide useful information to the phylogeny of the genus Sorbus.

Aberrant Telomere Length in Circulating Cell-Free DNA as Possible Blood Biomarker with High Diagnostic Performance in Endometrial Cancer.

To investigate the diagnostic performance of relative telomere length (RTL) in cell-free DNA (cfDNA) for endometrioid endometrial cancer (EC). We measured RTL in cfDNA of 40 EC patients (65 ± 12years) and 31 healthy controls (HC) (63 ± 13years), excluding in both groups other oncologic and severenon-oncologic diseases to limit confounders. Circulating cfDNA was extracted from serum using the QIAamp DNA Blood Mini kit (Qiagen, Hilden, Germany). After the quantitative real-time polymerase chain reaction, telomere repeat copy number to single-gene copy number ratio was calculated. RTL in cfDNA was found to be significantly lower in EC patients than in HC (p < 0.0001). The diagnostic performance of cfDNA RTL was estimated with receiver operating characteristics (ROC) curve analysis, which showed a diagnostic accuracy for EC of 0.87 (95% CI: 0.79-0.95, p < 0.0001). The cutoff cfDNA RTL value of 2.505 (T/S copy ratio) reported a sensitivity of 80.0% (95% CI: 64.35-90.95) and a specificity of 80.65% (95% CI: 62.53-92.55). Significant differences of RTL among EC stages or grades (p = 0.85 and p = 0.89, respectively) were not observed. Our results suggest that cfDNA RTL analysis may be a diagnostic tool for EC detection since the early stage, whilst its diagnostic performance seems unsatisfactory for cancer progression, staging, and grading. However, further studies are needed to confirm these preliminary findings. In particular, future investigations should focus on high-risk patients (such as those with atypical endometrial hyperplasia) that may benefit from this tool, because TL shortening is not specific for EC and is influenced by other oncologic and non-oncologic diseases.

Complete chloroplast genome sequence of Pinellia ternata (Thunb.) Breit, a medicinal plants to China

Pinellia ternata (Thunb.) Breit is one of the commonly used traditional Chinese medicine with tuber as medicine. We report herein the complete chloroplast genome sequence of Pinellia ternata (Thunb.) Breit. It is length of 167,280 bp, which contained a small single-copy (SSC) region of 23,618 bp and a large single-copy (LSC) region of 92,450 bp, separated by two copies of an inverted repeat (IR) of 25,606 bp. The chloroplast genome contains 113 unique genes, including 79 PCG, 4 rRNA genes, and 30 tRNA genes. In addition, 19 genes contained one or two introns, which of those including 13 PCG genes possess a single intron and 2 PCG genes harbor two introns; and 6 tRNA genes harbor a single intron. In this study, Pinellia ternata is sister to Pinellia pedatisecta and clustered within the group consisting of the species that belong to Araceae.

Characterization of the complete plastid genome of Camellia amplexicaulis (Theaceae)

Camellia amplexicaulis (Pit.) Cohen-Stuart is a shrub or small tree that extensively cultivated throughout Vietnam and beyond, which is now considered to extinct in the wild. Here, the whole plastid genome of C. amplexicaulis was assembled using Illumina paired-end sequencing reads. The plastid genome is 157,203 bp in length with a typical quadripartite structure, containing two copies of inverted repeat (IR) regions (26,133 bp), a large-single copy (LSC) region (86,644 bp), and a small-single copy (SSC) region (18,293 bp). A total of 114 unique genes were encoded, of which 80 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. The phylogenetic result indicates C. amplexicaulis is closely related to Camellia szechuanensis C. W. Chi.

The Epithelial adhesin 1 tandem repeat region mediates protein display through multiple mechanisms.

ABSTRACTThe pathogenic yeast Candida glabrata is reliant on a suite of cell surface adhesins that play a variety of roles necessary for transmission, establishment and proliferation during infection. One particular adhesin, Epithelial Adhesin 1 [Epa1p], is responsible for binding to host tissue, a process which is essential for fungal propagation. Epa1p structure consists of three domains: an N-terminal intercellular binding domain responsible for epithelial cell binding, a C-terminal GPI anchor for cell wall linkage and a serine/threonine-rich linker domain connecting these terminal domains. The linker domain contains a 40-amino acid tandem repeat region, which we have found to be variable in repeat copy number between isolates from clinical sources. We hypothesized that natural variation in Epa1p repeat copy may modulate protein function. To test this, we recombinantly expressed Epa1p with various repeat copy numbers in S. cerevisiae to determine how differences in repeat copy number affect Epa1p expression, surface display and binding to human epithelial cells. Our data suggest that repeat copy number variation has pleiotropic effects, influencing gene expression, protein surface display and shedding from the cell surface of the Epa1p adhesin. This study serves to demonstrate repeat copy number variation can modulate protein function through a number of mechanisms in order to contribute to pathogenicity of C. glabrata.

The complete chloroplast genome sequence of Toxicodendron sylvestre (Anacardiaceae)

Toxicodendron sylvestre (Siebold & Zucc.) Kuntze is a deciduous tree species in the poison ivy genus of the sumac family. In this study, we sequenced and analyzed the complete chloroplast (cp) genome of T. sylvestre. The circular genome is 159,600 bp in length, including two copies of inverted repeat (IR) regions of 26,465 bp, one large single-copy (LSC) region of 87,630 bp, and one small single-copy (SSC) region of 19,040 bp. It encodes a total of 113 unique genes, including 80 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. Phylogenetic analysis based on 17 cp genome sequences revealed that T. sylvestre was more closely related to T. succedaneum.

The complete chloroplast genome of Clematis fruticosa Turcz. (Ranunculaceae)

Clematis fruticosa Turcz. is an erect shrubby plant with important ecological and economical value, which usually occurs in dry or desert areas. The complete chloroplast genome of C. fruticosa was assembled from Illumina pair-end sequence reads. The whole plastome is 159,684 bp in length and presents a quadripartite structure consisting of two copies of inverted repeat (IR) regions (31,045), a large single copy (LSC) region (79,461 bp) and a small single copy (SSC) region (18,133 bp). The plastome of C. fruticosa encodes a total of 137 genes, including 92 protein-coding genes, 1 pseudogene, 36 tRNA genes and 8 rRNA genes. The overall GC content of C. fruticosa plastome is 38.0%. A maximum likelihood (ML) phylogenetic analysis revealed that C. fruticosa was collectively sister to a clade of Clematis tangutica and Clematis aethusifolia with high support.

The complete chloroplast genome sequence of Quercus stewardiana (Fagaceae)

Quercus stewardiana A.Camus is an East Asian evergreen oak tree species belonging to Quercus section Cyclobalanopsis. In this study, we assembled and annotated the complete chloroplast (cp) genome of the species. The circular genome is 160,842 bp in size, presenting a typical quadripartite structure including two copies of inverted repeat (IR) regions (25,823 bp), one large single-copy (LSC) region (90,294 bp), and one small single-copy (SSC) region (18,902 bp). It encodes a total of 114 unique genes, including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis based on cp genome sequences of 35 Fagaceae species indicated that Q. stewardiana was more closely related to Q. myrsinifolia.

The complete plastid genome sequence of Quercus ciliaris (Fagaceae)

Quercus ciliaris C.C.Huang & Y.T.Chang is one of the dominant tree species in the subtropical evergreen broad-leaved forests of China. In this study, we sequenced and analyzed the complete chloroplast (cp) genome of the species. The circular genome is 160,842 bp in size, consisting of two copies of inverted repeat (IR) regions of 25,823 bp, one large single-copy (LSC) region of 90,294 bp, and one small single-copy (SSC) region of 18,902 bp. It encodes a total of 114 unique genes, including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis based on cp genome sequences of 35 Fagaceae species indicated that Q. ciliaris was among the members of section Cyclobalanopsis, and was most closely related to Q. myrsinifolia.

The complete chloroplast genome sequence of Toxicodendron succedaneum (Anacardiaceae)

Toxicodendron succedaneum (L.) Kuntze is a deciduous and dioecious tree species in the family Anacardiaceae with important economic values. In this study, we sequenced and analyzed the complete chloroplast (cp) genome of T. succedaneum. The circular genome is 159,710 bp in size, and presents a quadripartite structure including two copies of inverted repeat (IR) regions of 26,524 bp, one large single-copy (LSC) region of 87,622 bp, and one small single-copy (SSC) region of 19,040 bp. It encodes a total of 113 unique genes, including 80 protein-coding genes, 29 tRNA genes, and four rRNA genes. Phylogenetic analysis based on 16 cp genome sequences revealed that the genus Toxicodendron is closely related to Pistacia and Rhus, and T. succedaneum was most closely related to T. vernicifluum.

The complete chloroplast genome sequences of a wild diploid alfalfa Medicago edgeworthii (Leguminosae)

Medicago edgeworthii is a relatively unique species, which has the potential prospect to cross with M. sativa. In this study, we assembled the complete cp genome of M. edgeworthii using the Illumina sequencing data. The total genome is 122,442 bp in length and contains only one inverted repeat (IR) copy. The genome encodes 112 genes, including 76 protein-coding genes (PCGs), 32 tRNA genes, and 4 rRNA genes. Phylogenetic analysis using 11 cp genomes revealed the phylogenetic relationship of this species in Leguminosae.

The complete chloroplast genome of Elsholtzia densa var. ianthina (Lamiaceae)

Elsholtzia densa var. ianthina has important medicinal valve and is used as Tibetan medicine. The complete chloroplast genome of E. densa var. ianthina was assembled from Illumina pair-end sequence reads. The whole plastome is 149,118 bp in length and presents a quadripartite structure consisting of two copies of inverted repeat (IR) regions (25,167) separated by a large single copy (LSC) region (81,411 bp) and a small single copy (SSC) region (17,373 bp). The plastome of E. densa var. ianthina encodes a total of 130 genes, including 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes. The overall GC content of E. densa var. ianthina plastome is 37.9%. A maximum likelihood (ML) phylogenetic analysis revealed that E. densa var. ianthina was related to Elsholtziasplendens.

The Role of Variable Repetitive Protein Domainsin Azf1p Function and Prion Formation

Prions are naturally occurring, self‐propagating isoforms of proteins that represent a heritable mechanism for tuning protein function. The yeast transcription factor Azf1p was recently demonstrated to form a prion, [AZF1+], that confers resistance to the drug radicicol but reduces Azf1p target gene expression. Using the Prion‐Like Amino Acid Composition tool, we identified regions of Azf1p that are predicted to contribute to prion formation. Two notable candidates are the polyglutamine (polyQ) and polyasparagine (polyN) domains. Through a bioinformatic analysis of the genomes of 93 lab and wild isolates of S. cerevisiae, we determined that these domains vary in repeat copy number across strains of yeast. The polyQ domain has two alleles, while the polyN domain has six alleles ranging from 17 to 25 N residues. In this work, we are investigating the extent to which the variable polyQ and polyN domains of Azf1p play a role in its transcription factor activity and contribute to [AZF1+] prion formation. This research determines the effects of repeat‐length variation on protein localization and stability, prion activity, and target gene expression.Support or Funding InformationThis work is supported by the Army Research Office (W911NF‐19‐1‐0299)

Mitochondrial genomes and phylogenomic analysis of Ulva lactuca Linnaeus (Ulvophyceae, Chlorophyta)

Two mitogenomes of Ulva lactuca Linnaeus, one from Florida, USA and another nearly complete mtDNA from Chile, had previously been sequenced. Here, the complete mitogenome of U. lactuca from Shantou, China was sequenced and compared with them. The circular-mapping mitogenome of U. lactuca was 62,021 bp in size and 407 bases longer than that from the USA. The average sequence identity in gene sequence regions was 99.8% among these three U. lactuca mtDNAs. Differences in genome size were mainly caused by duplication mutations and insertion/deletion mutations of short DNA sequences. Two intergenic regions (nad6-trnS and trnF-trnG) contained long tandem repeats which displayed a high level of variation in repeat sequences and copy numbers, indicating fast mutation rates in these regions. The phylogenomic analysis revealed that these three samples of U. lactuca formed a strongly supported clade. The mitogenome can be used to understand the phylogeography and population genetics in Ulva on a global scale.

Molecular Characterization and Immuno-Reactivity Patterns of a Novel Plasmodium falciparum Armadillo-Type Repeat Protein, PfATRP.

Nearly half of the genes in the Plasmodium falciparum genome have not yet been functionally investigated. We used homology-based structural modeling to identify multiple copies of Armadillo repeats within one uncharacterized gene expressed during the intraerythrocytic stages, PF3D7_0410600, subsequently referred to as P. falciparum Armadillo-Type Repeat Protein (PfATRP). Soluble recombinant PfATRP was expressed in a bacterial expression system, purified to apparent homogeneity and the identity of the recombinant PfATRP was confirmed by mass spectrometry. Affinity-purified α-PfATRP rabbit antibodies specifically recognized the recombinant protein. Immunofluorescence assays revealed that α-PfATRP rabbit antibodies reacted with P. falciparum schizonts. Anti-PfATRP antibody exhibited peripheral staining patterns around the merozoites. Given the localization of PfATRP in merozoites, we tested for an egress phenotype during schizont arrest assays and demonstrated that native PfATRP is inaccessible on the surface of merozoites in intact schizonts. Dual immunofluorescence assays with markers for the inner membrane complex (IMC) and microtubules suggest partial colocalization in both asexual and sexual stage parasites. Using the soluble recombinant PfATRP in a screen of plasma samples revealed that malaria-infected children have naturally acquired PfATRP-specific antibodies.

Distribution patterns of microsatellites and development of its marker in different genomic regions of forest musk deer genome based on high throughput sequencing.

Forest musk deer (Moschus berezovskii, FMD) is an endangered artiodactyl species, male FMD produce musk. We have sequenced the whole genome of FMD, completed the genomic assembly and annotation, and performed bioinformatic analyses. Our results showed that microsatellites (SSRs) displayed nonrandomly distribution in genomic regions, and SSR abundances were much higher in the intronic and intergenic regions compared to other genomic regions. Tri- and hexanucleotide perfect (P) SSRs predominated in coding regions (CDSs), whereas, tetra- and pentanucleotide P-SSRs were less abundant. Trifold P-SSRs had more GC-contents in the 5′-untranslated regions (5'UTRs) and CDSs than other genomic regions, whereas mononucleotide P-SSRs had the least GC-contents. The repeat copy numbers (RCN) of the same mono- to hexanucleotide P-SSRs had different distributions in different genomic regions. The RCN of trinucleotide P-SSRs had increased significantly in the CDSs compared to the transposable elements (TEs), intronic and intergenic regions. The analysis of coefficient of variability (CV) of P-SSRs showed that the RCN of mononucleotide P-SSRs had relative higher variation in different genomic regions, followed by the CV pattern of RCN: dinucleotide P-SSRs > trinucleotide P-SSRs > tetranucleotide P-SSRs > pentanucleotide P-SSRs > hexanucleotide P-SSRs. The CV variations of RCN of the same mono- to hexanucleotide P-SSRs were relative higher in the intron and intergenic regions, followed by that in the TEs, and the relative lower was in the 5'UTR, CDSs and 3'UTRs. 58 novel polymorphic SSR loci were detected based on genotyping DNA from 36 captive FMD and 22 SSR markers finally showed polymorphism, stability, and repetition.

Determination of nuclear DNA content, ploidy, and FISH location of ribosomal DNA in Hibiscus hamabo

Hibiscus hamabo Sieb.et Zucc, a deciduous shrub or tree, is an important semi-mangrove plant with golden yellow flowers. The plant is also cultivated for its fiber and grown as an ornamental. It is halophytic and considered one of the best afforestation trees used in reclamation programs in urban and coastal areas high in salt content. However, very little work has been done on its genetics; therefore, this study was undertaken to determine the genome size, the chromosome numbers, and rDNA (18S rDNA and 5S rDNA) loci in H. hamabo using flow cytometry, protoplast spread technique, and oligonucleotide fluorescence in situ hybridization (FISH), respectively. H. hamabo was found to have a 2C-value of 4.06 + 0.08 pg (3973.08 + 78.90 Mbp) and a chromosome number of 2n = 92. We observed four 18S loci and one 5S rDNA locus on five different pairs of homologous chromosomes. The observed FISH signal intensities for the 18S rDNA varied from chromosome to chromosome, indicating that each locus had different rDNA repeat copy numbers. The pericentromeric regions of each chromosome observed were highly heterochromatic. The findings of this study will benefit future cytogenetics and genomic investigations as well as lay the groundwork for more efficient breeding programs aimed at developing improved H. hamabo hybrids.

Are Biological Consequences of Childhood Exposures Detectable in Telomere Length Decades Later?

Negative early-life exposures have been linked to a host of poor adult health outcomes, but are such early exposures associated with cellular senescence decades later? This study uses data from the Health and Retirement Study to examine the association between six childhood exposure domains (eg, socioeconomic disadvantage, risky parental behavior) and a biomarker of aging, telomere length, among 4,935 respondents. Telomere length is obtained from DNA of cells found in saliva and is measured as the telomere repeat copy number to single gene copy number ratio (T/S). Men who as children were exposed to risky parental behaviors or who reported risky adolescent behaviors have shorter telomeres (b = -0.031, p = .052; b = -0.041, p = .045, respectively); however, these relationships are attenuated after adjusting for adult risks and resources. Among women, parental substance abuse is associated with shorter telomeres even after adjusting for adult risks and resources (b = -0.041, p = .005). In addition, men and women whose mother lived at least until the age of 85 have longer telomeres than those without a long-lived mother (b = 0.021, p = .045; b = 0.032, p = .005, respectively). Taken together, the ways in which early-life exposures are associated with adult telomeres vary for men and women.

The association of telomere length and telomerase activity with adverse outcomes in older patients with non-ST-elevation acute coronary syndrome.

Non-ST elevation acute coronary syndrome (NSTEACS) occurs more frequently in older patients with an increased occurrence of recurrent cardiac events following the index presentation. Telomeres are structures consisting of repeated DNA sequences as associated shelterin proteins at the ends of chromosomes. We aim to determine whether telomere length (TL) and telomerase activity (TA) predicted poor outcomes in older patients presenting with NSTEACS undergoing invasive care. Older patients undergoing invasive management for NSTEACS were recruited to the ICON-1 biomarker study (NCT01933581). Peripheral blood mononuclear cells (PBMC) were recovered on 153 patients. DNA was isolated and mean TL was measured by quantitative PCR expressed as relative T (telomere repeat copy number) to S (single copy gene number) ratio (T/S ratio), and a telomere repeat amplification assay was used to assess TA during index presentation with NSTEACS. Primary clinical outcomes consisted of death, myocardial infarction (MI), unplanned revascularisation, stroke and significant bleeding recorded at 1 year. TL and TA were divided into tertile groups for analysis. Cox proportional hazards regression was performed. Ordinal regression was performed to evaluate the relationship between TL and TA and traditional cardiovascular risk factors at baseline. 298 patients were recruited in the ICON-1 study of which 153 had PBMC recovered. The mean age was 81.0 ± 4.0 years (64% male). Mean telomere length T/S ratio was 0.47 ± 0.25 and mean TA was 1.52 ± 0.61 units. The primary composite outcome occurred in 44 (28.8%) patients. There was no association between short TL or low TA and incidence of the primary composite outcome (Hazard Ratio [HR] 1.50, 95% Confidence Interval [CI] 0.68-3.34, p = 0.32 and HR 1.33, 95% CI 0.52-3.36, p = 0.51 respectively). TL and TA are not found to be associated with the incidence of adverse outcomes in older patients presenting with NSTEACS undergoing invasive care. URL: https://www.clinicaltrials.gov Unique identifier: NCT01933581.