#bioinformaticanalysis

[cytgen]

Abstract The ITS1-5.8S-ITS2 (ITS1-2) region of the 35S rDNA is widely used for molecular barcoding and in the phylogenetics of plants. It is believed that, due to concerted evolution, all copies of 35S rDNA in eukaryotic genomes should be effectively homogenized. However, the existence of intragenomic polymorphism of the ITS1-2 region in plant genomes has recently been demonstrated, which may be a consequence of hybridization within or between species. In this study, the intragenomic polymorphism of the ITS1-2 region was evaluated using Illumina amplicon sequencing in accessions of two invasive species of the genus Reynoutria, R. japonica and R. sachalinensis, from Ukraine and Romania. Hybridization between these species can lead to the emergence of more aggressive invasive forms. The ITS1-2 sequences of the species studied were found to be represented by some major and minor subclasses/variants, indicating their incomplete homogenization. The number of major variants range from two in R. japonica to six in R. sachalinensis. The ITS1-2 variants that are widespread in the genome of one species may be present at low levels in another species, indicating possible interspecies hybridization. The obtained results show that the ITS1-2 intragenomic polymorphism must be taken into account when performing barcoding, reconstructing the phylogeny of low-level taxa, and for the identification of hybrid forms.

[cytgen]

Abstract Phospholipase Cγ2 has the promotive effect on hepatic carcinoma development. Meanwhile, lncRNAs play a critical role in the pathology. Therefore, to make clear whether phospholipase Cγ2 could enhance HCC cell proliferation by regulating lncRNA transcription, hepatic carcinoma cells RH35 were infected with Ad-phospholipase Cγ2 constructed previously, followed by lncRNA sequencing by high-throughput technology. Differently expressed lncRNAs (DElncRNAs) and their target genes were identified according to strict criteria. GO and KEGG, Reactome pathway analyses were performed for analyzing biological processes and the related pathways of DElncRNAs. lncRNA/mRNA coexpression pairs were screened according to expression profiling combined with bioinformatics analysis. The results showed that 231 DElncRNAs were identified in Ad-phospholipase Cγ2-overexpressing cells compared to control, containing 60 up- and 171 down-regulated ones. Target genes prediction analysis showed that 61 cis- and 30 trans-acting DElncRNAs were matched to 55 and 26 targets, respectively. Co-expression analysis found 33 lncRNA/mRNA coexpression pairs including 24 pairs in cis. GO analysis showed that these cis-mode lncRNA/mRNA pairs were involved in cytoskeleton organization, cell adhesion, and multiple signaling pathways related to apoptosis, proliferation and metastasis. Collectively, phospholipase Cγ2 caused the significant alterations in expression of many lncRNAs in liver cancer cells, providing valuable insight into precise mechanism of phospholipase Cγ2-promoting liver cancer cell growth.