A tailing genome walking method suitable for genomes with high local GC content

The tailing genome walking strategies are simple and efficient. However, they sometimes can be restricted due to the low stringency of homo-oligomeric primers. Here we modified their conventional tailing step by adding polythymidine and polyguanine to the target single-stranded DNA (ssDNA). The tailed ssDNA was then amplified exponentially with a specific primer in the known region and a primer comprising 5′ polycytosine and 3′ polyadenosine. The successful application of this novel method for identifying integration sites mediated by φC31 integrase in goat genome indicates that the method is more suitable for genomes with high complexity and local GC content.     

UP-TORR: Online Tool for Accurate and Up-to-Date Annotation of RNAi Reagents

RNA interference (RNAi) is a widely adopted tool for loss-of-function studies but RNAi results only have biological relevance if the reagents are appropriately mapped to genes. Several groups have designed and generated RNAi reagent libraries for studies in cells or in vivo for Drosophila and other species. At first glance, matching RNAi reagents to genes appears to be a simple problem, as each reagent is typically designed to target a single gene. In practice, however, the reagent–gene relationship is complex. Although the sequences of oligonucleotides used to generate most types of RNAi reagents are static, the reference genome and gene annotations are regularly updated. Thus, at the time a researcher chooses an RNAi reagent or analyzes RNAi data, the most current interpretation of the RNAi reagent–gene relationship, as well as related information regarding specificity (e.g., predicted off-target effects), can be different from the original interpretation. Here, we describe a set of strategies and an accompanying online tool, UP-TORR (for Updated Targets of RNAi Reagents; www.flyrnai.org/up-torr), useful for accurate and up-to-date annotation of cell-based and in vivo RNAi reagents. Importantly, UP-TORR automatically synchronizes with gene annotations daily, retrieving the most current information available, and for Drosophila, also synchronizes with the major reagent collections. Thus, UP-TORR allows users to choose the most appropriate RNAi reagents at the onset of a study, as well as to perform the most appropriate analyses of results of RNAi-based studies.     

Development of a pharmacophore model for the catecholamine release-inhibitory peptide catestatin: Virtual screening and functional testing identify novel small molecule therapeutics of hypertension

The endogenous catecholamine release-inhibitory peptide catestatin (CST) regulates events leading to hypertension and cardiovascular disease. Earlier we studied the structure of CST by NMR, molecular modeling, and amino acid scanning mutagenesis. That structure has now been exploited for elucidation of interface pharmacophores that mediate binding of CST to its target, with consequent secretory inhibition. Designed pharmacophore models allowed screening of 3D structural domains. Selected compounds were tested on both cultured catecholaminergic cells and an in vivo model of hypertension; in each case, the candidates showed substantial mimicry of native CST actions, with preserved or enhanced potency and specificity. The approach and compounds have thus enabled rational design of novel drug candidates for treatment of hypertension or autonomic dysfunction.     

Proteogenomic Refinement of the Neomegalonema perideroedesT Genome Annotation

Neomegalonema perideroedes (formerly Meganema perideroedes) str. G1 is the type strain and only described isolate of the genus Neomegalonema (formerly Meganema) which belongs to the Alphaproteobacteria. N. perideroedes is distinguished by the ability to accumulate high amounts of polyhydroxyalkanoates and has been associated with bulking problems in wastewater treatment plants due to its filamentous morphology. In 2013, its genome was sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA), which aims to improve the sequencing coverage of the poorly represented regions of the bacterial and archaeal branches of the tree of life. As N. perideroedes str. G1 is relatively distantly related to well described species—being the only sequenced member of its proposed family—the in silico prediction of genes by nucleotide homology to reference genes might be less reliable. Here, a proteomic dataset for the refinement of the N. perideroedes genome annotations is generated which clearly indicates the shortcomings of high‐throughput in silico genome annotation.     

黄藤染色体核型及基因组大小分析

为探究黄藤(Daemonoropsjenkinsiana)染色体核型和基因组的大小,采用体细胞染色体常规制片法与显微摄影技术相结合的方法,对黄藤染色体进行了核型分析,同时以番茄(Lycopersicon esculentum)为内标,应用流式细胞术对黄藤叶片基因组大小、DNA含量和DNA倍性进行了测定。结果表明,黄藤茎尖是理想的染色体制片材料;黄藤的染色体数为2n=24,核型公式为K(2n)=1M+17m+5sm+1st,核型类型为2C;核型不对称系数61.20%;黄藤的DNA含量为1.57 pg,基因组大小为1 539.53 Mb,黄藤的DNA倍性为二倍体(2n)。这是首次报道黄藤的核型和基因组大小,为深入开展黄藤属及其近缘属植物的核型和基因组比较分析提供了参考依据。     

野生矮牡丹高通量转录组测序分析

为探究野生稷山矮牡丹(Paeonia jishanensis)花青素等抗氧化活性物质生物合成的遗传基础,本文采用高通量测序技术Illumina NextSeqTM500对其幼嫩叶片、嫩茎和花芽混合池样本进行转录组测序分析。共获得39450个unigene,其中3563个unigene中有4106个SSR位点。在Swiss Prot数据库中注释到29420个unigene,其中11个与花青素生物合成过程相关,22个与类黄酮生物合成过程相关,15个与异黄酮生物合成过程相关;NR数据库中注释高达100%,有12个与类黄酮生物合成相关,7个与花青素生物合成相关;GO数据库中注释到24291个unigene,分为生物学过程、细胞组分及分子功能等三大类53个功能组,有21个unigene与黄酮、黄酮醇及异黄酮生物合成有关,4个unigene与花青素合成有关;eggNOG数据库中注释到38238个unigene,涉及植物生长发育过程绝大多数生命活动过程;KEGG数据库注释到5709个unigene,分别定位到6大类别42个代谢途径,其中25个unigene与花青素生物合成相关。研究表明,在稷山矮牡丹转录组序列中,共鉴定和发掘出多个涉及类黄酮化合物生物合成、花青素生物合成过程的相关基因序列及SSR位点,为下一步开展相关代谢合成途径研究奠定了基础。     

Genomic analysis and lactose transporter expression in Kluyveromyces marxianus CCT 7735

Kluyveromyces marxianus CCT 7735 has been used to produce ethanol, aromatic compounds, enzymes and heterologous proteins besides assimilates lactose as carbon source. Its genome has 10.7 Mb and encodes 4787 genes distributed in 8 nuclear chromosomes and one mitochondrial. Contrary to Kluyveromyces lactis, which has a unique LAC12 gene (encodes lactose permease), K. marxianus possesses four. The presence of degenerated copies and Solo-LTRs related to retrotransposon TKM close to the LAC12 genes in K. marxianus indicates ectopic recombinations. The Lac12 permeases of K. marxianus and K. lactis are conserved, however the conservation is higher between the copy of the left side of the chromosome three and the unique copy of K. lactis, indicating that this copy is the ancestor. The expression of the four LAC12 genes occurred in aerobiosis and hypoxia. Notably, the high lactose consumption in hypoxia seems to be related to the high expression of the LAC12 genes.