Classifying genomic sequences by sequence feature analysis

CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes

Background

Chloroplast is an essential organelle in plants which contains independent genome. Chloroplast genomes have been widely used for plant phylogenetic inference recently. The number of complete chloroplast genomes increases rapidly with the development of various genome sequencing projects. However, no comprehensive platform or tool has been developed for the comparative and phylogenetic analysis of chloroplast genomes. Thus, we constructed a comprehensive platform for the comparative and phylogenetic analysis of complete chloroplast genomes which was named as chloroplast genome analysis platform (CGAP).

Results

CGAP is an interactive web-based platform which was designed for the comparative analysis of complete chloroplast genomes. CGAP integrated genome collection, visualization, content comparison, phylogeny analysis and annotation functions together. CGAP implemented four web servers including creating complete and regional genome maps of high quality, comparing genome features, constructing phylogenetic trees using complete genome sequences, and annotating draft chloroplast genomes submitted by users.

Conclusions

Both CGAP and source code are available at http://www.herbbol.org:8000/chloroplast. CGAP will facilitate the collection, visualization, comparison and annotation of complete chloroplast genomes. Users can customize the comparative and phylogenetic analysis using their own unpublished chloroplast genomes.

Assessment of phylogenetic relationship of rare plant species collected from Saudi Arabia using internal transcribed spacer sequences of nuclear ribosomal DNA

The rare and endangered plants of any country are important genetic resources that often require urgent conservation measures. Assessment of phylogenetic relationships and evaluation of genetic diversity is very important prior to implementation of conservation strategies for saving rare and endangered plant species. We used internal transcribed spacer sequences of nuclear ribosomal DNA for the evaluation of sequence identity from the available taxa in the GenBank database by using the Basic Local Alignment Search Tool (BLAST). Two rare plant species viz, Heliotropium strigosum claded with H. pilosum (98% branch support) and Pancratium tortuosum claded with P. tenuifolium (61% branch support) clearly. However, some species, viz Scadoxus multiflorus, Commiphora myrrha and Senecio hadiensis showed close relationships with more than one species. We conclude that nuclear ribosomal internal transcribed spacer sequences are useful markers for phylogenetic study of these rare plant species in Saudi Arabia.

AGP: a multimethods web server for alignment-free genome phylogeny

Phylogenetic analysis based on alignment method meets huge challenges when dealing with whole-genome sequences, for example, recombination, shuffling, and rearrangement of sequences. Thus, various alignment-free methods for phylogeny construction have been proposed. However, most of these methods have not been implemented as tools or web servers. Researchers cannot use these methods easily with their data sets. To facilitate the usage of various alignment-free methods, we implemented most of the popular alignment-free methods and constructed a user-friendly web server for alignment-free genome phylogeny (AGP). AGP integrated the phylogenetic tree construction, visualization, and comparison functions together. Both AGP and all source code of the methods are available at http://www.herbbol.org:8000/agp (last accessed February 26, 2013). AGP will facilitate research in the field of whole-genome phylogeny and comparison.

HRAS: a webserver for early warning of human health risk brought by aflatoxin

Most people are aware that outdoor air pollution can damage their health, but many do not know that indoor air pollution can also exhibit significant negative health effects. Fungi parasitizing in air conditioning and ventilation systems can be one of indoor air pollution sources. Aflatoxin produced by Aspergillus flavus (A. flavus) became a central focus of indoor air pollution, especially in farmer markets. Therefore we developed an early warning system, Health Risk Assessment System, to estimate the growth rate of A. flavus, predict the amount of aflatoxin and provide early warning information. Firstly, the growth of A. flavus and the production of aflatoxin under different conditions were widely obtained through a comprehensive literature review. Secondly, three mathematical models were established to predict the A. flavus colony growth rate, lag phase duration and aflatoxin content, as functions of temperature and water activity based on present studies. Finally, all the results were evaluated by the user-supplied data using PHP programming language. We utilized the web page to show the results and display warning information. The JpGraph library was used to create a dynamic line chart, refreshing the warning information dynamically in real-time. The HARS provides accurate information for early warning purposes to let us take timely steps to protect ourselves.

Identification of medicinal vines by ITS2 using complementary discrimination methods

ETHNOPHARMACOLOGICAL RELEVANCE

Medicinal vines listed in Chinese pharmacopoeia possess important medicinal efficacy in traditional Chinese medicines.

AIM OF THE STUDY

The ITS2 region, which has several characteristics that make it a valuable DNA barcode, was studied to discriminate the stems of medicinal vines to confirm their identities and ensure their safe application in pharmaceuticals by using complementary discrimination methods.

MATERIALS AND METHODS

Complementary discrimination methods were performed on two datasets, including 393 samples of 170 species from 22 genera 13 families, which belonged to medicinal vines and their adulterants. Based on the primary ITS2 sequences, three main discrimination methods (phylogenetic tree, the nearest distance, and BLAST 1) were adopted to identify species. Moreover, we applied both two-dimensional (2-D) and three-dimensional (3-D) structures of ITS2 to differentiate species.

RESULTS

ITS2 performed well, with over 95.0% of species and 100% of genera being correctly differentiated for the two datasets. All results showed that the ITS2 region unveiled a remarkable ability to identify closely related species within different families and genera.

CONCLUSION

Our findings supported that the ITS2 region was an efficient marker for authentication of medicinal vines.

BRCA1: a new candidate gene for bovine mastitis and its association analysis between single nucleotide polymorphisms and milk somatic cell score

Bovine mastitis is a very complex and common disease of dairy cattle and a major source of economic losses to the dairy industry worldwide. In this study, the bovine breast cancer 1, early onset gene (BRCA1) was taken as a candidate gene for mastitis resistance. The main object of this study was to investigate whether the BRCA1 gene was associated with mastitis in cattle. Through DNA sequencing, Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) and Created Restriction Site PCR (CRS-PCR) methods, three SNPs (G22231T, T25025A, and C28300A) were detected and twenty-four combinations of these SNPs were observed. The single SNP and their genetic effects on somatic cell score (SCS) were evaluated and a significant association with SCS was found in C28300A. The mean of genotype EE was significantly lower than those of genotypes EF and FF. The results of combined genotypes analysis of three SNPs showed that BBDDFF genotype with the highest SCS were easily for the mastitis susceptibility, whereas AACCEE genotype with the lowest SCS were favorable for the mastitis resistance. The information provided in the present study will be very useful for improving mastitis resistance in dairy cattle by marker-assisted selection.

Phylogenetic study of Oryzoideae species and related taxa of the Poaceae based on atpB-rbcL and ndhF DNA sequences

Oryzoideae (Poaceae) plants have economic and ecological value. However, the phylogenetic position of some plants is not clear, such as Hygroryza aristata (Retz.) Nees. and Porteresia coarctata (Roxb.) Tateoka (syn. Oryza coarctata). Comprehensive molecular phylogenetic studies have been carried out on many genera in the Poaceae. The different DNA sequences, including nuclear and chloroplast sequences, had been extensively employed to determine relationships at both higher and lower taxonomic levels in the Poaceae. Chloroplast DNA ndhF gene and atpB-rbcL spacer were used to construct phylogenetic trees and estimate the divergence time of Oryzoideae, Bambusoideae, Panicoideae, Pooideae and so on. Complete sequences of atpB-rbcL and ndhF were generated for 17 species representing six species of the Oryzoideae and related subfamilies. Nicotiana tabacum L. was the outgroup species. The two DNA datasets were analyzed, using Maximum Parsimony and Bayesian analysis methods. The molecular phylogeny revealed that H. aristata (Retz.) Nees was the sister to Chikusichloa aquatica Koidz. Moreover, P. coarctata (Roxb.) Tateoka was in the genus Oryza. Furthermore, the result of evolution analysis, which based on the ndhF marker, indicated that the time of origin of Oryzoideae might be 31 million years ago.

Viral metagenomics

Characterisation of new viruses is often hindered by difficulties in amplifying them in cell culture, limited antigenic/serological cross-reactivity or the lack of nucleic acid hybridisation to known viral sequences. Numerous molecular methods have been used to genetically characterise new viruses without prior in vitro replication or the use of virus-specific reagents. In the recent metagenomic studies viral particles from uncultured environmental and clinical samples have been purified and their nucleic acids randomly amplified prior to subcloning and sequencing. Already known and novel viruses were then identified by comparing their translated sequence to those of viral proteins in public sequence databases. Metagenomic approaches to viral characterisation have been applied to seawater, near shore sediments, faeces, serum, plasma and respiratory secretions and have broadened the range of known viral diversity. Selection of samples with high viral loads, purification of viral particles, removal of cellular nucleic acids, efficient sequence-independent amplification of viral RNA and DNA, recognisable sequence similarities to known viral sequences and deep sampling of the nucleic acid populations through large scale sequencing can all improve the yield of new viruses. This review lists some of the animal viruses recently identified using sequence-independent methods, current laboratory and bioinformatics methods, together with their limitations and potential improvements. Viral metagenomic approaches provide novel opportunities to generate an unbiased characterisation of the viral populations in various organisms and environments.