Rhipicephalus microplus, the cattle fever tick, is a global economic problem to the cattle industry due to direct infestation of cattle and pathogens transmitted during feeding. Cattle fever tick outbreaks continue to...
详细信息
Rhipicephalus microplus, the cattle fever tick, is a global economic problem to the cattle industry due to direct infestation of cattle and pathogens transmitted during feeding. Cattle fever tick outbreaks continue to occur along the Mexico-US border even though the tick has been eradicated from the USA. The organophosphate (OP) coumaphos targets acetylcholinesterase (AChE) and is the approved acaricide for eradicating cattle fever tick outbreaks. There is evidence for coumaphos resistance developing in cattle ticks in Mexico, and OP-resistant R. microplus ticks were discovered in outbreak populations of Texas in 2005. The molecular basis of coumaphos resistance is not known, and our study was established to gather further information on whether AChE1 is involved in the resistance mechanism. We also sought information on allele diversity in tick populations with different levels of coumaphos resistance. The overarching project goal was to define OP resistance-associated gene mutations such that a DNA-based diagnostic assay could be developed to assist the management of resistance. Three different AChE transcripts have been reported in R. microplus, and supporting genomic and transcriptomic data are available at CattleTickBase. Here, we report the complete R. microplus AChE1 gene ascertained by sequencing a bacterial artificial chromosome clone containing the entire coding region and the flanking 5' and 3' regions. We also report AChE1 sequences of larval ticks from R. microplus strains having different sensitivities to OP. To accomplish this, we sequenced a 669-bp region of the AChE1 gene corresponding to a 223 amino acid region of exon 2 to assess alleles in seven strains of R. microplus with varying OP resistance phenotypes. We identified 72 AChE1 sequence variants, 2 of which are strongly associated with OP-resistant phenotypes. Esterase-like sequences from the R. microplus transcriptome RmiTr Version 1.0 were compared to the available sequence databases to ident
作者：
Cao, DianjieAnhui Med Univ
Dept Pharmacol Clin Med Coll 789 Xiangshan Rd Hefei 230088 Anhui Peoples R China
The goal of this study was to find significant pathways associated with fruit color in Taxus chinensis var. mairei. Two Taxus chinensis var. mairei with fruits of different colors were sequenced using high-throughput ...
详细信息
The goal of this study was to find significant pathways associated with fruit color in Taxus chinensis var. mairei. Two Taxus chinensis var. mairei with fruits of different colors were sequenced using high-throughput sequencing. Then, unigene assembly, unigene annotation, and classification of Clusters of Orthologous Groups of proteins (COGs) were performed. Gene ontology (GO) classification and pathway enrichment analysis for unigenes were also conducted. protein coding sequences (CDS) were predicted. Subsequently, differentially expressed unigenes, functional enrichment pathways of differentially expressed unigenes, single nucleotide polymorphisms (SNPs), and simple sequence repeats (SSRs) were analyzed. The data of Taxus chinensis var. mairei were assembled into 45,112 unigenes with an average size of 1232 bp and an N50 of 1882 bp. The significantly enriched biological processes (BP) were metabolic processes, and cellular processes, followed by single-organism processes, and reproductive processes. Significantly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were metabolic pathways, pathways related to the biosynthesis of secondary metabolites, and RNA transport pathways. Transition had a higher number of SNP sites than transversion. Trinucleotide had the highest SSR motif numbers. Metabolic pathways and the biosynthesis of secondary metabolites may play significant roles in determining fruit color in Taxus chinensis var. mairei. In addition, the present dataset would provide a basis for future functional genomic research on Taxus chinensis var. mairei.
protein coding sequences are characterized by specific nucleotide composition in three codon positions as a result of mutational and selection pressures. To analyse the impact of mutations and different transi-tion/ t...
详细信息
ISBN:
(纸本)9789897580123
protein coding sequences are characterized by specific nucleotide composition in three codon positions as a result of mutational and selection pressures. To analyse the impact of mutations and different transi-tion/ transversion ratio on three codon position in protein coding sequences, we elaborated a model of genome evolution based Monte Carlo simulation. Selection was applied against stop translation codons and modified Metropolis-Hastings algorithm to maintain typical nucleotide composition of particular codon positions. The simulations were performed on genomes consisting of bacterial gene sequences. We used a series of nucleotide substitution matrices assuming different transition/ transversion ratio and nucleotide stationary distribution characteristic of the real mutational pressure. The simulations showed exponential decrease in the number of eliminated genomes with the growth of the transition/ transversion ratio. The same trend was also observed both for accepted and to lesser extent for rejected mutations. The third codon positions much more mutations accepted than rejected because of very similar composition to the mutational stationary distribution, whereas the first positions accumulated the smallest number of mutations and rejected the most as a result of strong selection on its nucleotide composition. The obtained results showed different response of three codon positions on mutational pressure related with their characteristic nucleotide composition.
暂无评论