Transposable element insertions(TEIs) are an important source of genomic innovation by contributing to plant adaptation, speciation, and the production of new varieties. The often large,complex plant genomes make iden...Transposable element insertions(TEIs) are an important source of genomic innovation by contributing to plant adaptation, speciation, and the production of new varieties. The often large,complex plant genomes make identifying TEIs from short reads difficult and expensive. Moreover, rare somatic insertions that refect mobilome dynamics are difficult to track using short reads.To address these challenges, we combined Cas9-targeted Nanopore sequencing(CANS) with the novel pipeline Nano Cas TE to trace both genetically inherited and somatic TEIs in plants. We performed CANS of the EVADé(EVD) retrotransposon in wild-type Arabidopsis thaliana and rapidly obtained up to 40× sequence coverage.Analysis of hemizygous T-DNA insertion sites and genetically inherited insertions of the EVD transposon in the ddm1(decrease in DNA methylation1) genome uncovered the crucial role of DNA methylation in shaping EVD insertion preference.We also investigated somatic transposition events of the ONSEN transposon family, finding that genes that are downregulated during heat stress are preferentially targeted by ONSENs. Finally, we detected hypomethylation of novel somatic insertions for two ONSENs. CANS and Nano Cas TE are effective tools for detecting TEIs and exploring mobilome organization in plants in response to stress and in different genetic backgrounds, as well as screening T-DNA insertion mutants and transgenic plants.展开更多
A dataset of 103 SARS-CoV isolates （101 human patients and 2 palm civets） was investigated on different aspects of genome polymorphism and isolate classification. The number and the distribution of single nucleotide...A dataset of 103 SARS-CoV isolates （101 human patients and 2 palm civets） was investigated on different aspects of genome polymorphism and isolate classification. The number and the distribution of single nucleotide variations （SNVs） and insertions and deletions, with respect to a “profile”, were determined and discussed （“profile” being a sequence containing the most represented letter per position）. Distribution of substitution categories per codon positions, as well as synonymous and non-synonymous substitutions in coding regions of annotated isolates, was determined, along with amino acid （a.a.） property changes. Similar analysis was performed for the spike （S） protein in all the isolates （55 of them being predicted for the first time）. The ratio Ka/Ks confirmed that the S gene was subjected to the Darwinian selection during virus transmission from animals to humans. Isolates from the dataset were classified according to genome polymorphism and genotypes. Genome polymorphism yields to two groups, one with a small number of SNVs and another with a large number of SNVs, with up to four subgroups with respect to insertions and deletions. We identified three basic nine-locus genotypes： TTTT/TTCGG, CGCC/TTCAT, and TGCC/TTCGT, with four subgenotypes. Both classifications proposed are in accordance with the new insights into possible epidemiological spread, both in space and time.展开更多
Insertion and deletion(indel) mutations, which can trigger single nucleotide substitutions on the flanking regions of genes, may generate abundant materials for disease defense, reproduction, species survival and evol...Insertion and deletion(indel) mutations, which can trigger single nucleotide substitutions on the flanking regions of genes, may generate abundant materials for disease defense, reproduction, species survival and evolution. However, genetic and evolutionary mechanisms of indels remain elusive. We establish a comparative genome-transcriptome-alignment approach for a large-scale identification of indels in Monopterus population. Over 2000 indels in 1738 indel genes, including 1-21 bp deletions and 1-15 bp insertions, were detected. Each indel gene had ～1.1 deletions/insertions, and 2-4 alleles in population. Frequencies of deletions were prominently higher than those of insertions on both genome and population levels. Most of the indels led to in frame mutations with multiples of three and majorly occurred in non-domain regions, indicating functional constraint or tolerance of the indels. All indel genes showed higher expression levels than non-indel genes during sex reversal. Slide window analysis of global expression levels in gonads showed a significant positive correlation with indel density in the genome. Moreover, indel genes were evolutionarily conserved and evolved slowly compared to nonindel genes. Notably, population genetic structure of indels revealed divergent evolution of Monopterus population, as bottleneck effect of biogeographic isolation by Taiwan Strait, China.展开更多
Let F be an algebraically closed field, A be a finite dimensional algebra over F, Г A be the Auslander Reiten quiver of A, Γ be a connected component of Γ A with oriented cycles and semi stable vertices and each no...Let F be an algebraically closed field, A be a finite dimensional algebra over F, Г A be the Auslander Reiten quiver of A, Γ be a connected component of Γ A with oriented cycles and semi stable vertices and each non stable vertex in Γ be a projective injective vertex. The structure of Γ is studied.展开更多
Global climate change and acquired resistance to insecticides are threats to world food security.Drosophila suzukii,a devastating invasive pest in many parts of the world,causes substantial economic losses to fruit pr...Global climate change and acquired resistance to insecticides are threats to world food security.Drosophila suzukii,a devastating invasive pest in many parts of the world,causes substantial economic losses to fruit production industries,forcing farmers to apply broad-spectrum insecticides frequently,This could lead to the development of insecticide resistance.We determined the Lethal Concentration 50 (median lethal concen- tration,LC50)values of zeta-cypermethrin,spinosad,and malathion insecticides against D.suzukii colonies established from Clarke and Pierce county Georgia,United States. The LC50 values were 3 fold higher in the Pierce county population for all insecticide treatments.We then used RNA sequencing to analyze the responses of Pierce and Clarke population flies surviving a LC50 treatment of the 3 insecticides.We identified a high num- ber of differentially expressed genes that are likely involved in detoxification and reduced cuticular penetration,especially in the Pierce population,with extensive overlap in differ- entially expressed genes between the 3 insecticide treatments.Finally,we predicted fewer nonsynonymous single nucleotide variants having deleterious effects on protein function among detoxification,insecticide target,and cuticular protein encoding genes in Pierce flies.Thus a combination of increased gene expression and fewer deleterious single nu- cleotide variants highlights molecular mechanisms underlying the higher LC50 values for Pierce population flies.展开更多
基金supported by the Russian Science Foundation (grant no. 20-74-10055RNA-seq and mobilome analyses of plants after heat stress)+1 种基金Kurchatov Genomic Center of All-Russia Research Institute of Agricultural Biotechnology (agreement no. 075-15-20191667CANS development)。
文摘Transposable element insertions(TEIs) are an important source of genomic innovation by contributing to plant adaptation, speciation, and the production of new varieties. The often large,complex plant genomes make identifying TEIs from short reads difficult and expensive. Moreover, rare somatic insertions that refect mobilome dynamics are difficult to track using short reads.To address these challenges, we combined Cas9-targeted Nanopore sequencing(CANS) with the novel pipeline Nano Cas TE to trace both genetically inherited and somatic TEIs in plants. We performed CANS of the EVADé(EVD) retrotransposon in wild-type Arabidopsis thaliana and rapidly obtained up to 40× sequence coverage.Analysis of hemizygous T-DNA insertion sites and genetically inherited insertions of the EVD transposon in the ddm1(decrease in DNA methylation1) genome uncovered the crucial role of DNA methylation in shaping EVD insertion preference.We also investigated somatic transposition events of the ONSEN transposon family, finding that genes that are downregulated during heat stress are preferentially targeted by ONSENs. Finally, we detected hypomethylation of novel somatic insertions for two ONSENs. CANS and Nano Cas TE are effective tools for detecting TEIs and exploring mobilome organization in plants in response to stress and in different genetic backgrounds, as well as screening T-DNA insertion mutants and transgenic plants.
基金This work was supported by the Ministry of Science and Technology,Republic of Serbia,Project No.1858
文摘A dataset of 103 SARS-CoV isolates （101 human patients and 2 palm civets） was investigated on different aspects of genome polymorphism and isolate classification. The number and the distribution of single nucleotide variations （SNVs） and insertions and deletions, with respect to a “profile”, were determined and discussed （“profile” being a sequence containing the most represented letter per position）. Distribution of substitution categories per codon positions, as well as synonymous and non-synonymous substitutions in coding regions of annotated isolates, was determined, along with amino acid （a.a.） property changes. Similar analysis was performed for the spike （S） protein in all the isolates （55 of them being predicted for the first time）. The ratio Ka/Ks confirmed that the S gene was subjected to the Darwinian selection during virus transmission from animals to humans. Isolates from the dataset were classified according to genome polymorphism and genotypes. Genome polymorphism yields to two groups, one with a small number of SNVs and another with a large number of SNVs, with up to four subgroups with respect to insertions and deletions. We identified three basic nine-locus genotypes： TTTT/TTCGG, CGCC/TTCAT, and TGCC/TTCGT, with four subgenotypes. Both classifications proposed are in accordance with the new insights into possible epidemiological spread, both in space and time.
基金supported by the National Natural Science Foundation of China (31571280 and 31771370)National Key Technologies R&D Program and Hubei Province Science and Technology project
文摘Insertion and deletion(indel) mutations, which can trigger single nucleotide substitutions on the flanking regions of genes, may generate abundant materials for disease defense, reproduction, species survival and evolution. However, genetic and evolutionary mechanisms of indels remain elusive. We establish a comparative genome-transcriptome-alignment approach for a large-scale identification of indels in Monopterus population. Over 2000 indels in 1738 indel genes, including 1-21 bp deletions and 1-15 bp insertions, were detected. Each indel gene had ～1.1 deletions/insertions, and 2-4 alleles in population. Frequencies of deletions were prominently higher than those of insertions on both genome and population levels. Most of the indels led to in frame mutations with multiples of three and majorly occurred in non-domain regions, indicating functional constraint or tolerance of the indels. All indel genes showed higher expression levels than non-indel genes during sex reversal. Slide window analysis of global expression levels in gonads showed a significant positive correlation with indel density in the genome. Moreover, indel genes were evolutionarily conserved and evolved slowly compared to nonindel genes. Notably, population genetic structure of indels revealed divergent evolution of Monopterus population, as bottleneck effect of biogeographic isolation by Taiwan Strait, China.
文摘Let F be an algebraically closed field, A be a finite dimensional algebra over F, Г A be the Auslander Reiten quiver of A, Γ be a connected component of Γ A with oriented cycles and semi stable vertices and each non stable vertex in Γ be a projective injective vertex. The structure of Γ is studied.
文摘Global climate change and acquired resistance to insecticides are threats to world food security.Drosophila suzukii,a devastating invasive pest in many parts of the world,causes substantial economic losses to fruit production industries,forcing farmers to apply broad-spectrum insecticides frequently,This could lead to the development of insecticide resistance.We determined the Lethal Concentration 50 (median lethal concen- tration,LC50)values of zeta-cypermethrin,spinosad,and malathion insecticides against D.suzukii colonies established from Clarke and Pierce county Georgia,United States. The LC50 values were 3 fold higher in the Pierce county population for all insecticide treatments.We then used RNA sequencing to analyze the responses of Pierce and Clarke population flies surviving a LC50 treatment of the 3 insecticides.We identified a high num- ber of differentially expressed genes that are likely involved in detoxification and reduced cuticular penetration,especially in the Pierce population,with extensive overlap in differ- entially expressed genes between the 3 insecticide treatments.Finally,we predicted fewer nonsynonymous single nucleotide variants having deleterious effects on protein function among detoxification,insecticide target,and cuticular protein encoding genes in Pierce flies.Thus a combination of increased gene expression and fewer deleterious single nu- cleotide variants highlights molecular mechanisms underlying the higher LC50 values for Pierce population flies.
