Comparison of microsatellite distribution in genomes of Centruroides exilicauda and Mesobuthus martensii

Comparison of microsatellite distribution in the genomes of Pteropus vampyrus and Miniopterus natalensis (Chiroptera)

BACKGROUND

Microsatellites are a ubiquitous occurrence in prokaryotic and eukaryotic genomes. Microsatellites have become one of the most popular classes of genetic markers due to their high reproducibility, multi-allelic nature, co-dominant mode of inheritance, abundance and wide genome coverage. We characterised microsatellites in the genomes and genes of two bat species, Pteropus vampyrus and Miniopterus natalensis. This characterisation was used for gene ontology analysis and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment of coding sequences (CDS).

RESULTS

Compared to M. natalensis, the genome size of P. vampyrus is larger and contains more microsatellites, but the total diversity of both species is similar. Mononucleotide and dinucleotide repeats were the most diverse in the genome of the two species. In each bat species, the microsatellite bias was obvious. The microsatellites with the largest number of repeat motifs in P. vampyrus from mononucleotide to hexanucleotide were (A)_n, (AC)_n, (CAA)_n, (AAAC)_n, (AACAA)_n and (AAACAA)_n, with frequencies of 97.94%, 58.75%, 30.53%, 22.82%, 54.68% and 22.87%, respectively, while in M. natalensis were (A)_n, (AC)_n, (TAT)_n, (TTTA)_n, (AACAA)_n and (GAGAGG)_n, with of 92.00%, 34.08%, 40.36%, 21.83%, 25.42% and 12.79%, respectively. In both species, the diversity of microsatellites was highest in intergenic regions, followed by intronic, untranslated and exonic regions and lowest in coding regions. Location analysis indicated that microsatellites were mainly concentrated at both ends of the genes. Microsatellites in the CDS are thus subject to higher selective pressure. In the GO analysis, two unique GO terms were found only in P. vampyrus and M. natalensis, respectively. In KEGG enriched pathway, the biosynthesis of other secondary metabolites and metabolism of other amino acids in metabolism pathways were present only in M. natalensis. The combined biological process, cellular components and molecular function ontology are reflected in the GO analysis and six functional enrichments in KEGG annotation, suggesting advantageous mutations during species evolution.

CONCLUSIONS

Our study gives a comparative characterization of the genomes of microsatellites composition in the two bat species. And also allow further study on the effect of microsatellites on gene function as well as provide an insight into the molecular basis for species adaptation to new and changing environments.

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. This analysis may help to further explore the biological significance of various microsatellites in Ebolavirus genomes.

PCAT18, as a novel differentially regulated long noncoding RNA in adult acute myeloid leukemia patients revealed by next-generation sequencing

INTRODUCTION

Long noncoding RNAs (lncRNAs) play significant roles in the carcinogenesis and progression of human tumors. The aim of this work was to evaluate the expression level of lncRNAs in adult acute myeloid leukemia (AML) patients and to explore the function of candidate lncRNA PCAT18 in clinical diagnosis and prognosis of AML.

METHODS

Noncoding RNA screening was performed by second-generation sequencing on adult newly diagnosed AML patients and healthy controls. GO and KEGG pathway analysis were performed for functional analysis of differentially regulated lncRNAs. The expression of candidate lncRNA PCAT18 was detected by real-time PCR. In K-562 and THP-1 cells, proliferation, and cell cycle analysis were performed using CCK-8 assay and Cell Cycle Assay Kit.

RESULTS

The lncRNA expression profile of AML patients and healthy controls showed that six upregulated (>5-fold) and eight downregulated (<0.2-fold) lncRNAs. The candidate lncRNA PCAT18 showed higher expression in AML patients with NPM1 mutation and favorable-risk. RT-PCR revealed a significant increase of PCAT18 expression comparing to control cells. PCAT18 overexpression obviously promoted cell proliferation and PCAT18 knockdown decreased cell proliferation. The fraction of the S phases was increased in the PCAT18 overexpression group and decreased in the PCAT18 knockdown group.

CONCLUSIONS

The candidate lncRNA PCAT18 in our study was firstly found upregulated in AML samples, that its overexpression promoted cell proliferation and G1/S transition. Further study of PCAT18 and its target mRNAs are needed to confirm the mechanism of PCAT18 in AML. PCAT18 may act as diagnostic and prognosis biomarker for AML.

Genome-wide mining of perfect microsatellites and tetranucleotide orthologous microsatellites estimates in six primate species

Advancement in genome sequencing and in silico mining tools have provided new opportunities for comparative primate genomics of microsatellites. The SSRs (simple sequence repeats) numbers were not correlated with the genome size (Pearson, r=0.310, p=0.550), and were positively correlated with the total length of SSRs (Pearson, r=0.992, p=0.00). A total of 224,289 tetranucleotide orthologous microsatellites families and 367 single-copy orthologous SSRs loci were found in six primate species by homologous alignment. The inner mutation types of single-copy orthologous SSRs loci included the copy number variance, point mutation, and chromosomal translocation. The accumulated repeat times and average length of tetranucleotide orthologous microsatellites in Rhinopithecus roxellana, Papio anubis and Macaca mulatta were longer than Homo sapiens and Pan troglodytes, which showed the tetranucleotide orthologous SSRs loci had more repeat times and longer average length on the branches with earlier divergence time, one exception may be Microcebus murinus as a primitive monkey with a smallest morphology in Malagasy. Our conclusion indicated that single-copy tetranucleotide orthologous SSRs sequences accumulated individual mutation more slowly through time in H. sapiens and P. troglodytes than in R. roxellanae, P. anubis and M. mulatta. However, such divergence wouldn't arise uniformly in all branches of the primate tree. A comparison of genomic sequence assemblages would offer remarkable insights about comparisons and contrasts, and the evolutionary processes of the microsatellites involved in human and nonhuman primate species.