ALBERT

Description: Genes, Vol. 9, Pages 331: SEGF: A Novel Method for Gene Fusion Detection from Single-End Next-Generation Sequencing Data Genes doi: 10.3390/genes9070331 Authors: Hai Xu Xiaojin Wu Dawei Sun Shijun Li Siwen Zhang Miao Teng Jianlong Bu Xizhe Zhang Bo Meng Weitao Wang Geng Tian Huixin Lin Dawei Yuan Jidong Lang Shidong Xu With the development and application of next-generation sequencing (NGS) and target capture technology, the demand for an effective analysis method to accurately detect gene fusion from high-throughput data is growing. Hence, we developed a novel fusion gene analyzing method called single-end gene fusion (SEGF) by starting with single-end DNA-seq data. This approach takes raw sequencing data as input, and integrates the commonly used alignment approach basic local alignment search tool (BLAST) and short oligonucleotide analysis package (SOAP) with stringent passing filters to achieve successful fusion gene detection. To evaluate SEGF, we compared it with four other fusion gene discovery analysis methods by analyzing sequencing results of 23 standard DNA samples and DNA extracted from 286 lung cancer formalin fixed paraffin embedded (FFPE) samples. The results generated by SEGF indicated that it not only detected the fusion genes from standard samples and clinical samples, but also had the highest accuracy and sensitivity among the five compared methods. In addition, SEGF was capable of detecting complex gene fusion types from single-end NGS sequencing data compared with other methods. By using SEGF to acquire gene fusion information at DNA level, more useful information can be retrieved from the DNA panel or other DNA sequencing methods without generating RNA sequencing information to benefit clinical diagnosis or medication instruction. It was a timely and cost-effective measure with regard to research or diagnosis. Considering all the above, SEGF is a straightforward method without manipulating complicated arguments, providing a useful approach for the precise detection of gene fusion variation.

Description: Genes, Vol. 8, Pages 227: The Chloroplast Genome Sequence of Scutellaria baicalensis Provides Insight into Intraspecific and Interspecific Chloroplast Genome Diversity in Scutellaria Genes doi: 10.3390/genes8090227 Authors: Dan Jiang Zhenyu Zhao Teng Zhang Wenhao Zhong Chunsheng Liu Qingjun Yuan Luqi Huang Scutellaria baicalensis Georgi (Lamiaceae) is the source of the well-known traditional Chinese medicine “HuangQin” (Radix Scutellariae). Natural sources of S. baicalensis are rapidly declining due to high market demand and overexploitation. Moreover, the commercial products of Radix Scutellariae have often been found to contain adulterants in recent years, which may give rise to issues regarding drug efficacy and safety. In this study, we developed valuable chloroplast molecular resources by comparing intraspecific and interspecific chloroplast genome. The S. baicalensis chloroplast genome is a circular molecule consisting of two single-copy regions separated by a pair of inverted repeats. Comparative analyses of three Scutellaria chloroplast genomes revealed six variable regions (trnH-psbA, trnK-rps16, petN-psbM, trnT-trnL, petA-psbJ, and ycf1) that could be used as DNA barcodes. There were 25 single nucleotide polymorphisms(SNPs) and 29 indels between the two S. baicalensis genotypes. All of the indels occurred within non-coding regions. Phylogenetic analysis suggested that Scutellarioideae is a sister taxon to Lamioideae. These resources could be used to explore the variation present in Scutellaria populations and for further evolutionary, phylogenetic, barcoding and genetic engineering studies, in addition to effective exploration and conservation of S. baicalensis.

Description: Genes, Vol. 9, Pages 443: Global Long Noncoding RNA and mRNA Expression Changes between Prenatal and Neonatal Lung Tissue in Pigs Genes doi: 10.3390/genes9090443 Authors: Long Jin Silu Hu Teng Tu Zhiqing Huang Qianzi Tang Jideng Ma Xun Wang Xuewei Li Xuan Zhou Surong Shuai Mingzhou Li Lung tissue plays an important role in the respiratory system of mammals after birth. Early lung development includes six key stages, of which the saccular stage spans the pre- and neonatal periods and prepares the distal lung for alveolarization and gas-exchange. However, little is known about the changes in gene expression between fetal and neonatal lungs. In this study, we performed transcriptomic analysis of messenger RNA (mRNA) and long noncoding RNA (lncRNA) expressed in the lung tissue of fetal and neonatal piglets. A total of 19,310 lncRNAs and 14,579 mRNAs were identified and substantially expressed. Furthermore, 3248 mRNAs were significantly (FDR-adjusted p value ≤ 0.05, FDR: False Discovery Rate) differentially expressed and were mainly enriched in categories related to cell proliferation, immune response, hypoxia response, and mitochondrial activation. For example, CCNA2, an important gene involved in the cell cycle and DNA replication, was upregulated in neonatal lungs. We also identified 452 significantly (FDR-adjusted p value ≤ 0.05) differentially expressed lncRNAs, which might function in cell proliferation, mitochondrial activation, and immune response, similar to the differentially expressed mRNAs. These results suggest that differentially expressed mRNAs and lncRNAs might co-regulate lung development in early postnatal pigs. Notably, the TU64359 lncRNA might promote distal lung development by up-regulating the heparin-binding epidermal growth factor-like (HB-EGF) expression. Our research provides basic lung development datasets and will accelerate clinical researches of newborn lung diseases with pig models.