Clarification of relationship between single-nucleotide polymorphism panels of Shiga toxin-producing Escherichia coli O157:H7/H- strains

Eighty strains of enterohemorrhagic Escherichia coli O157:H7/H- were analyzed by three single-nucleotide polymorphism (SNP) panels using whole-genome sequencing data. The partial concordance of SNP types among the different SNP panels was observed on minimum spanning trees reconstructed with SNP data. As for lineage I/II strains, some of the clade 7 strains belonged to one unique SNP type as determined by three panels, suggesting that clade 7 should be divided into at least two genotypes, namely, the unique type and the rest. In addition, clade 8 contained two unique genotypes, which was consistent with the previous prediction. Similarly, for lineage II, clade 12 should be divided into three genotype strains. In contrast, many strains of several clades belonging to lineage I were clustered into the same node on each minimum spanning tree upon testing with the three SNP panels. Previous studies reported that lineage I diverged more recently than lineages I/II and II. Such low diversity in lineage I in this study may have arisen because this lineage has not accumulated SNPs because of its relatively recent divergence. Based on the concordance observed in this study, some of the previously published O157 genotype distribution data were successfully interpreted to clarify the clade distribution, which was well supported by previous literature.     

Geographical distribution and prevalence of tick‐borne encephalitis virus in questing Ixodes ricinus ticks and phylogeographic structure of the Ixodes ricinus vector in Norway

The tick‐borne encephalitis virus (TBEV), a zoonotic flaviviral infection, is endemic in large parts of Norway and Eurasia. Humans are mainly infected with TBEV via bites from infected ticks. In Norway, the main geographical distribution of ticks is along the Norwegian coastline from southeast (~59°N) and up to the southern parts of Nordland County (~65°N). In this study, we collected ticks by flagging along the coast from Østfold County to Nordland County. By whole‐genome sequencing of the mitochondrial genome of Ixodes ricinus, the phylogenetic tree suggests that there is limited phylogeographic structure both in Norway and in Europe. The overall TBEV prevalence is 0.3% for nymphs and 4.3% for adults. The highest estimated TBEV prevalence in adult ticks was detected in Rogaland and Vestfold County, while for nymphs it is highest in Vestfold, Vest‐Agder and Rogaland. The present work is one of the largest studies on distribution and prevalence of TBEV in ticks in Scandinavia, showing that the virus is wider distributed in Norway than previously anticipated.     

浅谈ArcGIS中坐标系统的转换

介绍ArcGIS软件中的坐标系和投影转换方法.利用MapGIS软件计算出布尔莎模型七参数的转换系数,在ArcGIS软件中实现了北京54高斯克吕格投影坐标系到WGS 84坐标系的转换.数据转换中需经历由北京54高斯克吕格投影坐标系转换到北京54坐标系,再由北京54坐标系转换到WGS 84坐标系.文中具体阐述了同一椭球体及不同椭球体的数据转换.     

全基因组测序(WGS)在畜禽群体进化和功能基因挖掘中的应用

全基因组测序(whole genome sequencing,WGS)是指通过高通量测序技术对物种个体或群体的基因组进行测序,并通过生物信息学技术对序列特征进行分析,以在全基因组水平探究物种的进化规律和筛选功能基因,主要包括从头测序(de novo)和重测序(re-sequencing).WGS具有信息全面、精确、高效等优点,尤其能对未知基因和未知结构变异进行高效探索,随着高通量测序技术的发展,WGS成本快速降低,使其迅速超越传统策略,成为当前群体进化分析和功能基因挖掘的最主要研究策略,并在畜禽中得到广泛应用.目前已经对鸡(Gallus gallus)、猪(Sus scrofa)、牛(Bos taurus)、绵羊(Ovis aries)、山羊(Caprahircus)、马(Equus caballus)、鸭(Anas platyrhynchos)和狗(Canis lupus)等畜禽进行了大量WGS研究,探究了畜禽进化规律,并挖掘出许多关键功能基因.此外,WGS在未来畜禽泛基因组的构建和全基因组选择育种中也将有广泛的应用.本文主要对WGS的特征和发展进行了介绍,概述和讨论了其在畜禽群体进化和功能基因挖掘中的应用,并简述了其关键要点和应用前景,以期为WGS在畜禽中得到进一步的应用提供理论参考.     

A de novo mutation in KRT5 in a crossbred calf with epidermolysis bullosa simplex

A 6-day-old Belgian Blue-Holstein calf was referred because of a syndrome resembling epidermolysis bullosa simplex (EBS). The clinical phenotype included irregular and differently sized erosions and ulcerations spread over the body, in particular on the limbs and over bone prominences, as well as in the nasal planum and oral mucosa. Blisters were easily induced by rubbing the skin. The skin lesions displayed a clear dermal-epidermal separation at the level of the basal cell layer. Post mortem examination revealed erosions in the pharynx, proximal esophagus, and rumen. Whole-genome sequencing revealed a heterozygous disruptive in-frame deletion variant in KRT5 (c.534_536delCAA). Genotyping of both parents confirmed the variant as de novo mutation. Clinicopathological and genetic findings were consistent with the diagnosis of KRT5-related EBS providing the second example of a spontaneous mutation causing epidermolysis bullosa in cattle.     

常用大地坐标系统及其转换

从应用角度阐述大地坐标系的构成,对椭球体、投影及其与大地坐标系之间关系进行了剖析。我国常用的高斯克吕格投影及三度带、六度带方面的知识作了介绍,对大地坐标的影响,特别是关键因子的影响进行了分析。结合实际应用中遇到的坐标问题进行了解释,使抽象难懂的投影简单化,易于理解。在大地坐标知识基础上介绍了坐标转换的方法,并总结了一些实际应用中遇到的大地坐标转换问题及解决方法。     

Translation of continuous artificial selection on phenotype into genotype during rice breeding programs

Understanding genetic diversity among local populations is a primary goal of modern crop breeding programs. Here, we demonstrated the genetic relationships of rice varieties in Hokkaido, Japan, one of the northern limits of rice cultivation around the world. Furthermore, artificial selection during rice breeding programs has been characterized using genome sequences. We utilized 8,565 single nucleotide polymorphisms and insertion/deletion markers distributed across the genome in genotype-by-sequencing for genetic diversity analyses. Phylogenetics, genetic population structure, and principal component analysis showed that a total of 110 varieties were classified into four distinct clusters according to different populations geographically and historically. Furthermore, the genome sequences of 19 rice varieties along with historic representations in Hokkaido, nucleotide diversity and F_ST values in each cluster revealed that artificial selection of elite phenotypes focused on chromosomal regions. These results clearly demonstrated the history of the selections on agronomic traits as genome sequences among current rice varieties from Hokkaido.