Quality control of next-generation sequencing data without a reference

Xiao

et al. 2018

Animal Genetics

Inbreeding, which has several causes including genetic drift, population bottlenecks, mating of close relatives and selection, can leave tracts of runs of homozygosity (ROH) along genomes. Recently, decreasing performance on reproductive traits, which might have resulted from inbreeding, has been observed in Chinese pigs. In this study, 830 individuals from Western and Chinese pig breeds were genotyped using the reducedrepresentation sequencing method. After imputation and quality control, 60 850 highconfidence SNPs were retained for ROH detection. A simulation was performed to explore the reliability of ROH detection with imputed data. Different ROH-related variables were compared between imputed and non-missing genotypes used in ROH detection. Furthermore, ROH islands were evaluated and annotated to find genes influenced by inbreeding in these pigs. The simulation results showed that imputed data with 0.7 as the average missing genotype rate and three heterozygotes allowed in a sliding window have comparable ROH detected compared with data with no missing genotypes. Compared with Western pig breeds, Chinese pigs had more autosomes covered by ROH longer than 5 Mb, indicating higher inbreeding in Chinese pigs in recent times. Genes related to reproduction, immunity, meat quality and adaptability in Chinese pigs and several genes related to growth speed and immunity in Western pigs were observed in short ROH islands. The reproduction-related gene PRM1 was found to be located in the most frequent long ROH island in Chinese pigs, which might explain the decreasing fertility in Chinese pig breeds.

“…Quality control of sequences was performed using the ngs qc toolkit v2.3 (Trivedi et al . ), and the parameters were set according to the original GGRS paper (Chen et al . ).…”

Section: Methodsmentioning

confidence: 99%

Distribution of runs of homozygosity in Chinese and Western pig breeds evaluated by reduced‐representation sequencing data

Xiao

et al. 2018

Animal Genetics

“…DNA libraries (fragment lengths ranging from 300 to 400 bp) were sequenced using an Illumina HiSeq4000 platform according to the manufacturer’s protocol. Quality control of sequences was performed using NGS QC Toolkit 28 v2.3, and the parameters were set according to the report from Chen et al . 27 .…”

Section: Methodsmentioning

confidence: 99%

Genomic analysis reveals genes affecting distinct phenotypes among different Chinese and western pig breeds

Xiao

et al. 2018

Sci Rep

The differences in artificial and natural selection have been some of the factors contributing to phenotypic diversity between Chinese and western pigs. Here, 830 individuals from western and Chinese pig breeds were genotyped using the reduced-representation genotyping method. First, we identified the selection signatures for different pig breeds. By comparing Chinese pigs and western pigs along the first principal component, the growth gene IGF1R; the immune genes IL1R1, IL1RL1, DUSP10, RAC3 and SWAP70; the meat quality-related gene SNORA50 and the olfactory gene OR1F1 were identified as candidate differentiated targets. Further, along a principal component separating Pudong White pigs from others, a potential causal gene for coat colour (EDNRB) was discovered. In addition, the divergent signatures evaluated by Fst within Chinese pig breeds found genes associated with the phenotypic features of coat colour, meat quality and feed efficiency among these indigenous pigs. Second, admixture and genomic introgression analysis were performed. Shan pigs have introgressed genes from Berkshire, Yorkshire and Hongdenglong pigs. The results of introgression mapping showed that this introgression conferred adaption to the local environment and coat colour of Chinese pigs and the superior productivity of western pigs.

“…FastQC was used to evaluate quality and trim the Illumina sequence reads if necessary [3]. Sequence-typing, identification of resistance genes and plasmid analysis was performed using ARIBA and its functions: MLST-calling, Resfinder and Plasmidfinder, respectively.…”

Section: Analysis Of Sequenced Datamentioning

confidence: 99%

Genetic features of Multi Drug Resistant (MDR) Klebsiella pneumoniae and its Plasmids

Fuster¹,

Tormo²,

Salvador³

et al. 2019

Preprint

Klebsiella pneumoniae, a major cause of both hospital and community-acquired infections, is listed by the World Health Organization as a critical priority antibiotic- resistant bacterial pathogen. With the appearance of sequencing techniques such as Next-generation Sequencing (NGS), there is the possibility to obtain the whole genome of the bacteria, getting to know all antimicrobial resistance determinants. The purpose of this study has been to apply this new technology to clinical microbiology, in order to characterize the resistome present in carbapenem-resistant K.pneumoniae strains isolated in a tertiary hospital in Valencia, Spain. A total of 234 isolates were prepared for whole-genome sequencing with Ilumina MiSeq, and sequences were later studied for antimicrobial resistance genes, sequence-typing and plasmids. Sequence-typing showed four major circulating clones in our hospital settings: ST11, ST307, ST101 and ST147, carrying different plasmids and different resistance determinants such as OXA-48 and NDM-1 carbapenemase. Application of new technologies such as whole-genome sequencing in clinical microbiology gives advantages when it comes to rapid therapy adjustment, consequently improving the patient’s clinical outcomes.