Analysis of the Relationship between Genome Diversity and Adult Survive Rate of Botryllus Schlosseri by AFLP

Objective: The self cross colonial prochordate, Botryllus schlosseri ( B.schlosseri ) occupy a key phylogenetic position in the evolution of vertebrates. To clarify the relationship of genome diversity and survive rate, five generations of B. schlosseri was investigated by amplified fragment length polymorphism (AFLP). Methods: AFLP markers are extremely sensitive to even small sequence variation, using PCR and high resolution electrophoresis to examine restriction fragments. Results: AFLP polymorphism was high in the parent and lower in its F1, F2, F3 and F4. Each primer combination generated from 80 to more than 120 bands, of which average 25.85% polymorphic loci in parent, 15.79% polymorphic among F1, 9.16% and 5.58% in F2, F3. The AFLP markers were transmitted from F1 to F2, F3 and F4 and inherited, segregated in expected Mendelian ratio. However, some of the markers were lost in F2, F3 and F4 while it disappeared in their mother. In addition, gene mutation new loci and lost loci among F1, F2, F3 and F4 were observed. These special fragments were cloned and sequenced. Then, the genomic DNA was analyzed by Southern hybridization with the probes from these specific fragments and the mechanism of gene mutation was clarified. Conclusion: These results suggest that there are high frequency of polymorphic loci and mutation in genome of B. schlosseri. Gene deletion or low diversity may be the reason for high rate of death of the offspring of inbred laboratory reared strains.

Large-scale genome-wide SNP analysis reveals the rugged(and ragged)landscape of global ancestry,phylogeny,and demographic history in chicken breeds

The worldwide chicken gene pool encompasses a remarkable,but shrinking,number of divergently selected breeds of diverse origin.This study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture,genetic variability,and detailed structure among 49 populations.These populations represent a significant sample of the world's chicken breeds from Europe(Russia,Czech Republic,France,Spain,UK,etc.),Asia(China),North America(USA),and Oceania(Australia).Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism(SNP)chip,a bioinformatic analysis was carried out.This included the calculation of heterozygosity/homozygosity statistics,inbreeding coefficients,and effective population size.It also included assessment of linkage disequilibrium and construction of phylogenetic trees.Using multidimensional scaling,principal component analysis,and ADMIXTURE-assisted global ancestry analysis,we explored the genetic structure of populations and subpopulations in each breed.An overall 49-population phylogeny analysis was also performed,and a refined evolutionary model of chicken breed formation was proposed,which included egg,meat,dual-purpose types,and ambiguous breeds.Such a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry breeding.In general,whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.

Genotypic,size and morphological diversity of virioplankton in a deep oligomesotrophic freshwater lake(Lac Pavin,France)

We examined changes in morphological and genomic diversities of viruses by means of transmission electronic microscopy and pulsed field gel electrophoresis （PFGE） over a nine-month period （April-December 2005） at four different depths in the oligomesotrophic Lac Pavin. We found that the majority of viruses in this lake belonged to the family of Siphouiridae or were untailed, with capsid sizes ranging from 30 to 60 nm, and exhibited genome sizes ranging from 15 to 45 kb. On average, 12 different genotypes dominated each of the PFGE fingerprints. The highest genomic viral richness was recorded in summer （mean = 14 bands per PFGE fingerprint） and in the epilimnion （mean = 13 bands per PFGE fingerprint）. Among the physico-chemical and biological variables considered, the availability of the hosts appeared to be the main factor regulating the variations in the viral diversity.

Rice Genomics: over the Past Two Decades and into the Future

Domestic rice(Oryza sativa L.) is one of the most important cereal crops, feeding a large number of worldwide populations. Along with various high-throughput genome sequencing projects, rice genomics has been making great headway toward direct ?eld applications of basic research advances in understanding the molecular mechanisms of agronomical traits and utilizing diverse germplasm resources. Here, we brie?y review its achievements over the past two decades and present the potential for its bright future.

Genetic technologies for extremely thermophilic microorganisms of Sulfolobus, the only genetically tractable genus of crenarchaea

Archaea represents the third domain of life, with the information-processing machineries more closely resembling those of eukaryotes than the machineries of the bacterial counterparts but sharing metabolic pathways with organisms of Bacteria, the sister prokaryotic phylum. Archaeal organisms also possess unique features as revealed by genomics and genome comparisons and by biochemical characterization of prominent enzymes. Nevertheless, diverse genetic tools are required for in vivo experiments to verify these interesting discoveries. Considerable efforts have been devoted to the development of genetic tools for archaea ever since their discovery, and great progress has been made in the creation of archaeal genetic tools in the past decade. Versatile genetic toolboxes are now available for several archaeal models, among which Sulfolobus microorganisms are the only genus representing Crenarchaeota because all the remaining genera are from Euryarchaeota. Nevertheless, genetic tools developed for Sulfolobus are probably the most versatile among all archaeal models, and these include viral and plasmid shuttle vectors, conventional and novel genetic manipulation methods, CRISPR-based gene deletion and mutagenesis, and gene silencing, among which CRISPR tools have been reported only for Sulfolobus thus far. In this review, we summarize recent developments in all these useful genetic tools and discuss their possible application to research into archaeal biology by means of Sulfolobus models.

Chevrier＇s Field Mouse(Apodemus chevrieri) and Père David＇s Vole(Eothenomys melanogaster) in China Carry Orthohepeviruses that form Two Putative Novel Genotypes Within the Species Orthohepevirus C

Hepatitis E virus(HEV)is the prototype of the family Hepeviridae and the causative agent of common acute viral hepatitis.Genetically diverse HEV-related viruses have been detected in a variety of mammals and some of them may have zoonotic potential.In this study,we tested 278 specimens collected from seven wild small mammal species in Yunnan province,China,for the presence and prevalence of orthohepevirus by broad-spectrum reverse transcription(RT)-PCR.HEV-related sequences were detected in two rodent species,including Chevrier’s field mouse(Apodemus chevrieri,family Muridae)and Père David’s vole(Eothenomys melanogaster,family Cricetidae),with the infection rates of 29.20%(59/202)and 7.27%(4/55),respectively.Further four representative full-length genomes were generated:two each from Chevrier’s field mouse(named Rd HEVAc14 and Rd HEVAc86)and Père David’s vole(Rd HEVEm40 and Rd HEVEm67).Phylogenetic analyses and pairwise distance comparisons of whole genome sequences and amino acid sequences of the gene coding regions showed that orthohepeviruses identified in Chinese Chevrier’s field mouse and Père David’s vole belonged to the species Orthohepevirus C but were highly divergent from the two assigned genotypes:HEV-C1 derived from rat and shrew,and HEV-C2 derived from ferret and possibly mink.Quantitative real-time RT-PCR demonstrated that these newly discovered orthohepeviruses had hepatic tropism.In summary,our work discovered two putative novel genotypes orthohepeviruses preliminarily named HEVC3 and HEV-C4 within the species Orthohepevirus C,which expands our understanding of orthohepevirus infection in the order Rodentia and gives new insights into the origin,evolution,and host range of orthohepevirus.