Predicting RNA Secondary Structure Using Profile Stochastic Context-Free Grammars and Phylogenic Analysis

Stochastic context-free grammars （SCFGs） have been applied to predicting RNA secondary structure. The prediction of RNA secondary structure can be facilitated by incorporating with comparative sequence analysis. However, most of existing SCFG-based methods lack explicit phylogenic analysis of homologous RNA sequences, which is probably the reason why these methods are not ideal in practical application. Hence, we present a new SCFG-based method by integrating phylogenic analysis with the newly defined profile SCFG. The method can be summarized as： 1） we define a new profile SCFG, M, to depict consensus secondary structure of multiple RNA sequence alignment; 2） we introduce two distinct hidden Markov models, λ and λ＇, to perform phylogenic analysis of homologous RNA sequences. Here, λ＇ is for non-structural regions of the sequence and λ＇ is for structural regions of the sequence; 3） we merge λ and λ＇ into M to devise a combined model for prediction of RNA secondary structure. We tested our method on data sets constructed from the Rfam database. The sensitivity and specificity of our method are more accurate than those of the predictions by Pfold.

Small RNA deep sequencing reveals the presence of multiple viral infections in cucurbit crops in Guangdong,China

Viral diseases are among the most critical damaging factors that impose a global threat to the cucurbit industry.China is the world’s leading country for the production and consumption of cucurbits.Guangdong,a province in southern China dominated by the tropical and subtropical climate,favors the survival of different plant viruses and their vectors.Five main cucurbit crops showing various disease symptoms were surveyed and collected to identify viruses infecting cucurbits in Guangdong during 2018–2020.In the field,the incidence ranged from 5-30%,or even 60-100% in the case of severely infected cucurbits.A total of 357 symptomatic samples were collected and subsequently screened for cucurbit viruses by small RNA deep sequencing and assembly(sRSA).Seventeen virus species belonging to 10 genera were identified in the five main cucurbit crops.The most common viruses were papaya ringspot virus(PRSV;Potyvirus),zucchini tigre mosaic virus(ZTMV;Potyvirus),zucchini yellow mosaic virus(ZYMV;Potyvirus),and watermelon silver mottle virus(WSMoV;Orthotospovirus),with infection rates of 24.4,19.0,17.1,and 14.3%,respectively.Notably,the most prevalent viruses were melon yellow spot orthotospovirus(MYSV)in cucumber,PRSV in squash,cucumber green mottle mosaic virus(CGMMV;Tobamovirus)in bottle gourd,WSMoV in white gourd,and ZYMV in luffa.Mixed infections were prevalent,and the types of mixed infections varied substantially in different cucurbit crops.Moreover,the full-length nucleotide sequences of watermelon green mottle mosaic virus(WGMMV),CGMMV,and watermelon virus A(WVA;Wamavirus)identified in bottle gourd were cloned and analyzed.This study is the first reporting WGMMV infecting bottle gourd in China mainland.In summary,the results demonstrate that in Guangdong,the most prevalent viruses belong to potyviruses,orthotospoviruses,and tobamoviruses groups.The findings will facilitate agricultural researchers and farmers to plan and implement effective disease control strategies aiming at timely detection and management of cucurbit-infecting viral pathogens.

Analysis of Saccharina japonica transcriptome using the high-throughput DNA sequencing technique and its vanadium-dependent haloperoxidase gene

Saccharina is one of the most important cold-water living marine brown algal genera. In this study we ana-lyzed the transcriptome of S. japonica, which belongs to the 1 000 Plants （OneKP） Project, by using a next-generation high-throughput DNA sequencing technique. About 5.16 GB of raw data were generated, and 65 536 scaffolds with an average length of 454 bp were assembled with SOAP de novo assembly method. In total, 19 040 unigenes were identified by BLAST;25 734 scaffolds were clustered into 37 Gene ontology functional groups;6 760 scaffolds were classified into 25 COG categories, as well as 2 665 scaffolds that were assigned to 306 KEGG pathways. Majority of the unigenes exhibited more similarities to algae including brown algae and diatom than other cyanobacteria, marine diatom, and plant. Saccharina japonica has the outstanding capability to accumulate halogen such as Br and I via halogenation processes from seawater. We acquired 42 different vanadium-dependent haloperoxidases （vHPO） in S. japonica transcriptome data, including 5 segments of vanadium-dependent iodoperoxidase （vIPO） and 37 segments of vanadium-de-pendent bromoperoxidase （vBPO）. Complicated analyses of identified fulllength S. japonica vBPO1 and S. japonica vBPO2 revealed the importance of vBPO among species of brown algae and the strong relationship between marine algal vBPOs and vIPOs. This study will enhance our understanding of the biological charac-teristics and economic values of S. japonica species.

Effects of Salinity and Temperature on Bacterial Biodiversity in Hangu Solar Saltworks,China

1 Introduction The multi-pond solar saltworks inhabit diverse microbial groups in which a gradient of salinities range from seawater to Na Cl precipitation.Along the salinity gradient,the majority of microbial community changes

Genetic distances between Chinese populations calculated on gene frequencies of 38 loci

Genetic distances were calculated for Han subpopulations in different provinces, cities and au-tonomous regions and ethnic minorities in China by using gene frequency data of 38 loci, and genetic trees were con-structed. The results showed that, among both Han and ethnic minorities, there were two types, i.e. southern and northern Mongoloids, with Yangtze River as boundary. Therefore, both African origin theory and local origin theory about the modern man should answer the question; when did these two types separate and how did they develop. This paper also conclusively proved genetically that the Han subpopulations in different regions are genetically close to the lo-cal ethnic minorities, which indicates that much blood of ethnic minorities has mixed into Han, at the same time, some blood of Han also has mixed into the local ethnic minorities.

Wavelet Analysis of DNA Walks on the Human and Chimpanzee MAGE/CSAG-palindromes

The palindrome is one class of symmetrical duplications with reverse complementary characters, which is widely distributed in many organisms. Graphical representation of DNA sequence provides a simple way of viewing and comparing various genomic structures. Through 3-D DNA walk analysis, the similarity and differences in nucleotide composition, as well as the evolutionary relationship between human and chimpanzee MAGE]CSAG-palindromes, can be clearly revealed. Further wavelet analysis indicated that duplicated segments have irregular patterns compared to their surrounding sequences. However, sequence similarity analysis suggests that there is possible common ancestor between human and chimpanzee MAGE]CSAG-palindromes. Based on the specific distribution and orien- tation of the repeated sequences, a simple possible evolutionary model of the palindromes is suggested, which may help us to better understand the evolutionary course of the genes and the symmetrical sequences.

Molecular Epidemiology and Vaccine Compatibility Analysis of Seasonal Influenza Viruses in Wuhan, 2016–2019

Influenza viruses(FLUV)cause high morbidity and mortality annually in the world and pose a serious threat to the public health.Wuhan,as an important transportation hub in China,has a dense population and suitable climate,which also lays a major hidden danger for the outbreak of influenza.To survey and characterize the seasonal FLUV in Wuhan during 2016–2019,we collected 44,738 throat swabs,among which 15.5%were influenza A(FLUAV)positive,6.1%influenza B(FLUBV)and 0.3%co-infection.By monitoring FLUV in each month from June 2016 to May 2019,different with the previously seasonality pattern,only a single influenza peak was appeared in winter of 2017–2018 and 2018–2019,respectively.These data indicated that the complex circulation pattern of seasonal influenza in Wuhan.In addition,we found the age group was skewed towards 5–14 years group whose activity were mostly school based,which suggested school may be an important place for influenza outbreaks.Meanwhile,phylogenic analysis revealed that two subtypes(subclade 3C.2 a2 and 3C.2 a1b)of A(H3N2)were circulating in Wuhan and there was an obvious transition in 2018 because the two subclades were detected simultaneously.Furthermore,by estimating the vaccine effectiveness,we found that the vaccine strain of FLUAV didn’t seem to match very well the current epidemic strain,especially A(H3N2).Hence,more accurate prediction of seasonal outbreak is essential for vaccine design.Taken together,our results provided the current information about seasonal FLUV in Wuhan which form the basis for vaccine updating.