Analysis of the Campylobacter jejuni Genome by SMRT DNA Sequencing Identifies Restriction-Modification Motifs

Campylobacter jejuni is a leading bacterial cause of human gastroenteritis. The goal of this study was to analyze the C. jejuni F38011 strain, recovered from an individual with severe enteritis, at a genomic and proteomic level to gain insight into microbial processes. The C. jejuni F38011 genome is comprised of 1,691,939 bp, with a mol.% (G+C) content of 30.5%. PacBio sequencing coupled with REBASE analysis was used to predict C. jejuni F38011 genomic sites and enzymes that may be involved in DNA restriction-modification. A total of five putative methylation motifs were identified as well as the C. jejuni enzymes that could be responsible for the modifications. Peptides corresponding to the deduced amino acid sequence of the C. jejuni enzymes were identified using proteomics. This work sets the stage for studies to dissect the precise functions of the C. jejuni putative restriction-modification enzymes. Taken together, the data generated in this study contributes to our knowledge of the genomic content, methylation profile, and encoding capacity of C. jejuni.     

De Novo Assembly and Functional Annotation of the Olive (Olea europaea) Transcriptome

Olive breeding programmes are focused on selecting for traits as short juvenile period, plant architecture suited for mechanical harvest, or oil characteristics, including fatty acid composition, phenolic, and volatile compounds to suit new markets. Understanding the molecular basis of these characteristics and improving the efficiency of such breeding programmes require the development of genomic information and tools. However, despite its economic relevance, genomic information on olive or closely related species is still scarce. We have applied Sanger and 454 pyrosequencing technologies to generate close to 2 million reads from 12 cDNA libraries obtained from the Picual, Arbequina, and Lechin de Sevilla cultivars and seedlings from a segregating progeny of a Picual × Arbequina cross. The libraries include fruit mesocarp and seeds at three relevant developmental stages, young stems and leaves, active juvenile and adult buds as well as dormant buds, and juvenile and adult roots. The reads were assembled by library or tissue and then assembled together into 81 020 unigenes with an average size of 496 bases. Here, we report their assembly and their functional annotation.     

Antioxidant Activity of Purified Protein Hydrolysates from Northern Whiting Fish (Sillago sihama) Muscle

In the present study, northern whiting fish (Sillago sihama) muscle was hydrolyzed with gastrointestinal enzymes (pepsin, trypsin and α-chymotrypsin) separately and the resulted protein hydrolysates were tested for antioxidant activities using DPPH radical scavenging activity and reducing power assays. The protein hydrolysate obtained from trypsin exhibited highest antioxidant activity. Further, it was fractionated by consecutive chromatography using anion exchange and gel filtration chromatography; the separated fractions were collected and evaluated for antioxidant activity. The results showed that fraction 2 exhibited high chelating activity (73.15 % at 0.5 mg/mL) and best radical scavenging activity for DPPH radical (55.16 % at 0.5 mg/mL), ABTS radical (57.98 % at 50 μg/mL), superoxide radical (39.55 % at 200 μg/mL) and hydroxyl radical (51.33 % at 100 μg/mL). In addition, the active fraction showed strong antioxidant activity in the inhibition of linoleic acid autooxidation (60 % at 0.5 mg/mL) and also it exhibited significant protective effect on DNA damage caused by hydroxyl radicals. The size of the active fraction was found to be <360.2 Da using mass spectroscopy. These results demonstrate that muscle protein hydrolysate from northern whiting fish could be a best alternative to produce natural antioxidant peptides.     

The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation

Background

The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while concomitantly creating a new set of challenges. The number of available assembled microbial genomes continues to grow rapidly and their quality reflects the quality of the sequencing technology used, but also of the analysis software employed for assembly and annotation.

Methodology/Principal Findings

In this work, we have explored the quality of the microbial draft genomes across various sequencing technologies. We have compared the draft and finished assemblies of 133 microbial genomes sequenced at the Department of Energy-Joint Genome Institute and finished at the Los Alamos National Laboratory using a variety of combinations of sequencing technologies, reflecting the transition of the institute from Sanger-based sequencing platforms to NGS platforms. The quality of the public assemblies and of the associated gene annotations was evaluated using various metrics. Results obtained with the different sequencing technologies, as well as their effects on downstream processes, were analyzed. Our results demonstrate that the Illumina HiSeq 2000 sequencing system, the primary sequencing technology currently used for de novo genome sequencing and assembly at JGI, has various advantages in terms of total sequence throughput and cost, but it also introduces challenges for the downstream analyses. In all cases assembly results although on average are of high quality, need to be viewed critically and consider sources of errors in them prior to analysis.

Conclusion

These data follow the evolution of microbial sequencing and downstream processing at the JGI from draft genome sequences with large gaps corresponding to missing genes of significant biological role to assemblies with multiple small gaps (Illumina) and finally to assemblies that generate almost complete genomes (Illumina+PacBio).     

辣椒脉斑驳病毒文昌分离物基因组测序及分析

辣椒脉斑驳病毒(Chilli veinal mottle virus,ChiVMV)近年来严重危害海南黄灯笼辣椒的产量,开展针对该病毒的研究以求达到对其有效防控迫在眉睫.本研究分7段克隆了ChiVMV文昌分离物(ChiVMV Wenchang isolate,ChiVMV-WC)的基因组.分段克隆的测序结果通过拼接,共获得ChiVMV-WC基因组9 717个核苷酸(nt)序列(GenBank登录号:GQ981316).在核苷酸序列的第164位~第9 270位存在一个大的开放阅读框(ORF),编码一个多聚蛋白(分子量为350.44 kD).近年来被证实的马铃薯Y病毒科的一个新的ORF (pretty interesting potyviridae ORF,PIPO)存在于ChiVMV-WC基因组核苷酸序列的第2 892位~第3 110位,编码一个由72个氨基酸聚合而成的多肽(分子量为8.26 kD).ChiVMV-WC与ChiVMV其它分离物的基因组核苷酸序列比较发现该病毒存在着较高的变异率.本研究通过与同属内病毒的同源性分析以及系统进化树分析,确定了ChiVMV-WC在生物进化史上的地位.