Microsatellite density landscapes illustrate short tandem repeats aggregation in the complete reference human genome.

Background: Microsatellites are increasingly realized to have biological significance in human genome and health in past decades, the assembled complete reference sequence of human genome T2T-CHM13 brought great help for a comprehensive study of short tandem repeats in the human genome.

Results: Microsatellites density landscapes of all 24 chromosomes were built here for the first complete reference sequence of human genome T2T-CHM13. These landscapes showed that short tandem repeats (STRs) are prone to aggregate characteristically to form a large number of STRs density peaks.

The phylogeny of the Anderson's White-bellied Rat () based on complete mitochondrial genomes.

The phylogenetic structure of the genus has been studied based on several individual mitochondrial and nuclear genes, but the results seem to be inconsistent. In order to clarify the phylogeny of , we sequenced the complete mitochondrial genome of white-bellied rat ( of the family Muridae) by next-generation sequencing. The 16,291 bp mitochondrial genome consists of 22 transfer RNA genes, 13 protein-coding genes (PCGs), two ribosomal RNA genes, and one noncoding control region (D-Loop).

The only conserved microsatellite in coding regions of ebolavirus is the editing site.

Lots of viral genomes were found to contain microsatellites (SSRs) including Ebolavirus, and majority of Ebolavirus microsatellite sites are distributed in protein-coding regions of the genomes. Here, we totally identified 212 reserved microsatellite sites in the protein-coding regions of 213 genomic sequences from five Ebolavirus species. In these reserved microsatellite sites, there is only one significantly conserved microsatellite site among the sample Ebolavirus genomic sequences, and this microsatellite is located at RNA editing site of the GP gene, indicating the selective relevance with RNA editing there.

Genomic analysis of the brassica pathogen turnip mosaic potyvirus reveals its spread along the former trade routes of the Silk Road.

Plant pathogens have agricultural impacts on a global scale and resolving the timing and route of their spread can aid crop protection and inform control strategies. However, the evolutionary and phylogeographic history of plant pathogens in Eurasia remains largely unknown because of the difficulties in sampling across such a large landmass. Here, we show that turnip mosaic potyvirus (TuMV), a significant pathogen of brassica crops, spread from west to east across Eurasia from about the 17th century CE.

A comprehensive microsatellite landscape of human Y-DNA at kilobase resolution.

Background: Though interest in human simple sequence repeats (SSRs) is increasing, little is known about the exact distributional features of numerous SSRs in human Y-DNA at chromosomal level. Herein, totally 540 maps were established, which could clearly display SSR landscape in every bin of 1 k base pairs (Kbp) along the sequenced part of human reference Y-DNA (NC_000024.10), by our developed differential method for improving the existing method to reveal SSR distributional characteristics in large genomic sequences.

The complete mitochondrial genome of Uruguayan native cattle ().

Uruguayan beef is one of the most popular products in the export market. In this study, we report the complete mitochondrial genome sequence of Uruguayan native cattle for the first time. The total mitochondrial genome sequence is 16,339 bp in length with the base composition of 33.

Enhanced energy density of PVDF-based nanocomposites via a core-shell strategy.

In recent years, high energy density polymer capacitors have attracted a lot of scientific interest due to their potential applications in advanced power systems and electronic devices. Here, core-shell structured TiO@SrTiO@polydamine nanowires (TiO@SrTiO@PDA NWs) were synthesized via a combination of surface conversion reaction and in-situ polymerization method, and then incorporated into the poly(vinylidene fluoride) (PVDF) matrix. Our results showed that a small amount of TiO@SrTiO@PDA NWs can simultaneously enhance the breakdown strength and electric displacement of nanocomposite (NC) films, resulting in improved energy storage capability.

Relatively semi-conservative replication and a folded slippage model for short tandem repeats.

Background: The ubiquitous presence of short tandem repeats (STRs) in virtually all genomes implicates their functional relevance, while a widely-accepted definition of STR is yet to be established. Previous studies majorly focus on relatively longer STRs, while shorter repeats were generally excluded. Herein, we have adopted a more generous criteria to define shorter repeats, which has led to the definition of a much larger number of STRs that lack prior analysis.

Conserved microsatellites may contribute to stem-loop structures in 5', 3' terminals of Ebolavirus genomes.

Microsatellites (SSRs) are ubiquitous in coding and non-coding regions of the Ebolavirus genomes. We synthetically analyzed the microsatellites in whole-genome and terminal regions of 219 Ebolavirus genomes from five species. The Ebolavirus sequences were observed with small intraspecies variations and large interspecific variations, especially in the terminal non-coding regions.

RAEdb: a database of enhancers identified by high-throughput reporter assays.

High-throughput reporter assays have been recently developed to directly and quantitatively assess enhancer activity for thousands of regulatory elements. However, there is still no database to collect these enhancers. We developed RAEdb, the first database to collect enhancers identified by high-throughput reporter assays.

Cell membrane proteins with high N-glycosylation, high expression and multiple interaction partners are preferred by mammalian viruses as receptors.

Motivation: Receptor mediated entry is the first step for viral infection. However, the question of how viruses select receptors remains unanswered.

Results: Here, by manually curating a high-quality database of 268 pairs of mammalian virus-host receptor interaction, which included 128 unique viral species or sub-species and 119 virus receptors, we found the viral receptors are structurally and functionally diverse, yet they had several common features when compared to other cell membrane proteins: more protein domains, higher level of N-glycosylation, higher ratio of self-interaction and more interaction partners, and higher expression in most tissues of the host.

A universal computational model for predicting antigenic variants of influenza A virus based on conserved antigenic structures.

Rapid determination of the antigenicity of influenza A virus could help identify the antigenic variants in time. Currently, there is a lack of computational models for predicting antigenic variants of some common hemagglutinin (HA) subtypes of influenza A viruses. By means of sequence analysis, we demonstrate here that multiple HA subtypes of influenza A virus undergo similar mutation patterns of HA1 protein (the immunogenic part of HA).

Comparative analysis of microsatellites and compound microsatellites in T4-like viruses.

Microsatellites or simple sequence repeats (SSRs) are known to present ubiquitously in genomes of eukaryotes and prokaryotes, as well as viruses. A comprehensive analysis of microsatellites and compound microsatellites (CM) was performed for 67 T4-like bacteriophage genomes. We found that the number of repeats was generally proportional to the size of the genome.

The analysis of microsatellites and compound microsatellites in 56 complete genomes of Herpesvirales.

Simple sequence repeats (SSRs), or microsatellites, are special DNA/RNA sequences with repeated unit of 1-6 bp. The genomes of Herpesvirales have many repeating structures, which is an excellent system to study the evolution and roles of microsatellites and compound microsatellites in viruses. Therefore, 56 genomes of Herpesvirales were selected and the occurrence, composition and complexity of different repeats were investigated in the genomes.

Differential distributions of mononucleotide repeat sequences in 256 viral genomes and its potential implications.

Mononucleotide repeats (MNRs) have been systematically investigated in the genomes of eukaryotic and prokaryotic organisms. However, detailed information on the distribution of MNRs in viral genomes is limited. In this study, we examined the distributions of MNRs in 256 fully sequenced virus genomes which showed extensive variations across viral genomes, and is significantly influenced by both genome size and CG content.

Survey and analysis of simple sequence repeats (SSRs) present in the genomes of plant viroids.

Extensive simple sequence repeat (SSR) surveys have been performed for eukaryotic prokaryotic and viral genomes, but information regarding SSRs in viroids is limited. We undertook a survey to examine the presence of SSRs in viroid genomes. Our results show that the distribution of SSRs in viroids may influence secondary structure, and that SSRs could play a role in generating genetic diversity.

Coevolution between simple sequence repeats (SSRs) and virus genome size.

Background: Relationship between the level of repetitiveness in genomic sequence and genome size has been investigated by making use of complete prokaryotic and eukaryotic genomes, but relevant studies have been rarely made in virus genomes.

Results: In this study, a total of 257 viruses were examined, which cover 90% of genera. The results showed that simple sequence repeats (SSRs) is strongly, positively and significantly correlated with genome size.

Differential distribution of compound microsatellites in various Human Immunodeficiency Virus Type 1 complete genomes.

Compound microsatellites consist of two or more individual microsatellites, and may originate from dynamic mutations or imperfection of microsatellites. Previous studies have found microsatellites were present in 81 completed Human Immunodeficiency Virus Type 1 (HIV-1) genomes, suggesting compound microsatellites may exist in viral genomes. However, up to now, compound microsatellites have not been analyzed in any viral genomes.

High GC content of simple sequence repeats in Herpes simplex virus type 1 genome.

The presence, locations and composition of simple sequence repeats (SSRs) in Herpes simplex virus type 1 (HSV-1) genome were extracted and analyzed by using the software Imperfect Microsatellite Extractor (IMEx). There were 663 mon-, 502 di-, 184 tri-, 20 tetra-, 4 penta- and 4 hexanucleotide SSRs that were observed in different distribution between coding and noncoding regions in the HSV-1 genome. G/C, GC/CG, and (GGC)(n) were predominant in mononucleotide, dinucletide, trinucleotide repeats respectively.

Understanding lignin-degrading reactions of ligninolytic enzymes: binding affinity and interactional profile.

Previous works have demonstrated that ligninolytic enzymes mediated effective degradation of lignin wastes. The degrading ability greatly relied on the interactions of ligninolytic enzymes with lignin. Ligninolytic enzymes mainly contain laccase (Lac), lignin peroxidase (LiP) and manganese peroxidase (MnP).

Microsatellites in different Potyvirus genomes: survey and analysis.

Simple sequence repeats (SSRs) have been extensively used for various genetic and evolutionary studies in eukaryotic and prokaryotic organisms, while few relevant researches have been made in viruses. The Potyvirus is a fine system to study roles and evolution of SSRs in viruses. The densities, relative abundances, compositions and evolutionary inferences of SSRs in 45 different Potyvirus genomes have been analyzed in this study.

Microsatellite is an important component of complete hepatitis C virus genomes.

Microsatellites are common and play diverse roles in eukaryotic and prokaryotic genomes. However, to our knowledge, microsatellite distribution remains largely enigmatic in viruses yet is crucial for understanding instability of viral genomes. We have therefore, examined microsatellite distribution in 54 complete genomes of Hepatitis C virus (HCV) from six genotypes, showing microsatellites were an important component of HCV genomes.

MfSAT: Detect simple sequence repeats in viral genomes.

Simple sequence repeats (SSRs) are ubiquitous short tandem repeats, which are associated with various regulatory mechanisms and have been found in viral genomes. Herein, we develop MfSAT (Multi-functional SSRs Analytical Tool), a new powerful tool which can fast identify SSRs in multiple short viral genomes and then automatically calculate the numbers and proportions of various SSR types (mono-, di-, tri-, tetra-, penta- and hexanucleotide repeats). Furthermore, it also can detect codon repeats and report the corresponding amino acid.

Compound microsatellites in complete Escherichia coli genomes.

Compound microsatellites consisting of two or more repeats in close proximity have been found in eukaryotic genomes. So far such compound microsatellites have not been investigated in any prokaryotic genomes. We have therefore examined compound microsatellites in 22 complete genomes of Escherichia coli, which is one of the ideal model organisms to analyze the nature and evolution of prokaryotic compound microsatellites.

Comprehensive analysis of simple sequence repeats in pre-miRNAs.

Simple sequence repeats (SSRs) are tandem repeat units of 1-6 bp that are identified in various complete sequences. However, the distribution, nature, and origination of SSRs in pre-miRNAs, which are characteristic stem-loop sequences and are finally processed into ∼22 nt functional miRNAs contributing to regulate several biological processes, are still not well studied. The availability of large numbers of pre-miRNAs makes it possible to analyze and compare the occurrences of SSRs, the relative count of SSRs, or the longest SSRs in pre-miRNAs.