scholarly journals Genetic composition and evolution of the prevalent Mycobacterium tuberculosis lineages 2 and 4 in the Chinese and Zhejiang Province populations

2020 ◽  
Author(s):  
Beibei Wu ◽  
Wenlong Zhu ◽  
Yue Wang ◽  
Qi Wang ◽  
Lin Zhou ◽  
...  
Keyword(s):  
Zhejiang Province ◽  
Whole Genome Sequencing Data ◽  
Evolutionary Analysis ◽  
T Cell Epitopes ◽  
Sequencing Data ◽  
Maximum Likelihood Phylogenetic Tree ◽  
Human T Cell ◽  
Human Movements ◽  
Lineage 2 ◽  
Common Ancestors

AbstractThe causative agent of tuberculosis (TB) comprises seven human-adapted lineages. Human movements and host genetics are crucial to TB dissemination. We analyzed whole-genome sequencing data for a countrywide collection of 1154 isolates and a provincial collection of 1296 isolates, constructed the best-scoring maximum likelihood phylogenetic tree, conducted Bayesian evolutionary analysis to compute the most recent common ancestors of lineages 2 and 4, and assessed the antigenic diversity in human T cell epitopes by calculating pairwise dN/dS ratios. Of the 1296 Zhejiang isolates, 964 (74.38%) belonged to lineage 2 and 332 (25.62%) belonged to lineage 4. L2.2 is the most ancient sub-lineage in Zhejiang, first appearing approximately 6897 years ago (95% HDI: 6513-7298). L4.4 is the most modern sub-lineage, first appearing approximately 2217 years ago (95% HDI: 1864-2581). The dN/dS ratios revealed that the epitope and non-epitope regions of lineage 2 strains were significantly (P<0.001) more conserved than those of lineage 4. An increase in the frequency of lineage 4 may reflect its successful transmission over the last 20 years. The recent common ancestors and transmission routes of the sub-lineages are related to the entry of humans into China and Zhejiang Province.

scholarly journals Genetic Composition and Evolution of the Prevalent Mycobacterium Tuberculosis Lineages 2 and 4 in the Chinese and Zhejiang Province Populations

2020 ◽  
Author(s):  
Beibei Wu ◽  
Wenlong Zhu ◽  
Yue Wang ◽  
Qi Wang ◽  
Lin Zhou ◽  
...  
Keyword(s):  
T Cell ◽  
Zhejiang Province ◽  
Whole Genome Sequencing Data ◽  
Evolutionary Analysis ◽  
T Cell Epitopes ◽  
Sequencing Data ◽  
Human T Cell ◽  
Human Movements ◽  
Lineage 2 ◽  
Lineage Distribution

Abstract Background: There are seven human-adaptation lineages of Mycobacterium tuberculosis (Mtb). Tuberculosis (TB) dissemination is strongly influenced by human movements and host genetics. The detailed lineage distribution evolution of Mtb in Zhejiang Province is unknown. We aim to determine how different sub-lineages are transmitted and distributed within China and Zhejiang Province.Methods: We analyzed whole-genome sequencing data for a countrywide collection of 1154 isolates and a provincial collection of 1296 isolates, constructed the best-scoring maximum likelihood phylogenetic tree. Bayesian evolutionary analysis was used to calculate the latest common ancestor of lineages 2 and 4. The antigenic diversity of human T cell epitopes was evaluated by calculating the pairwise dN/dS ratios.Results: Of the Zhejiang isolates, 964 (74.38%) belonged to lineage 2 and 332 (25.62%) belonged to lineage 4. The distributions of the sub-lineages varied across the geographic regions of Zhejiang Province. L2.2 is the most ancient sub-lineage in Zhejiang, first appearing approximately 6897 years ago (95% HDI: 6513-7298). L4.4 is the most modern sub-lineage, first appearing approximately 2217 years ago (95% HDI: 1864-2581). The dN/dS ratios showed that the epitope and non-epitope regions of lineage 2 strains were significantly (P<0.001) more conserved than those of lineage 4.Conclusions: An increase in the frequency of lineage 4 may reflect its successful transmission over the last 20 years. The recent common ancestors of the sub-lineages and their transmission routes are relevant to the entry of humans into China and Zhejiang Province. Diversity in T cell epitopes may prevent Mycobacterium tuberculosis from being recognized by the immune system.

scholarly journals Genetic composition and evolution of the prevalent Mycobacterium tuberculosis lineages 2 and 4 in the Chinese and Zhejiang Province populations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Beibei Wu ◽  
Wenlong Zhu ◽  
Yue Wang ◽  
Qi Wang ◽  
Lin Zhou ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
T Cell ◽  
Zhejiang Province ◽  
Whole Genome Sequencing Data ◽  
Evolutionary Analysis ◽  
T Cell Epitopes ◽  
Sequencing Data ◽  
Human T Cell ◽  
Lineage 2 ◽  
Highest Posterior Density

Abstract Background There are seven human-adaptation lineages of Mycobacterium tuberculosis (Mtb). Tuberculosis (TB) dissemination is strongly influenced by human movements and host genetics. The detailed lineage distribution evolution of Mtb in Zhejiang Province is unknown. We aim to determine how different sub-lineages are transmitted and distributed within China and Zhejiang Province. Methods We analysed whole-genome sequencing data for a worldwide collection of 1154 isolates and a provincial collection of 1296 isolates, constructed the best-scoring maximum likelihood phylogenetic tree. Bayesian evolutionary analysis was used to calculate the latest common ancestor of lineages 2 and 4. The antigenic diversity of human T cell epitopes was evaluated by calculating the pairwise dN/dS ratios. Results Of the Zhejiang isolates, 964 (74.38%) belonged to lineage 2 and 332 (25.62%) belonged to lineage 4. The distributions of the sub-lineages varied across the geographic regions of Zhejiang Province. L2.2 is the most ancient sub-lineage in Zhejiang, first appearing approximately 6897 years ago (95% highest posterior density interval (HDI): 6513–7298). L4.4 is the most modern sub-lineage, first appearing approximately 2217 years ago (95% HDI: 1864–2581). The dN/dS ratios showed that the epitope and non-epitope regions of lineage 2 strains were significantly (P < 0.001) more conserved than those of lineage 4. Conclusions An increase in the frequency of lineage 4 may reflect its successful transmission over the last 20 years. The recent common ancestors of the sub-lineages and their transmission routes are relevant to the entry of humans into China and Zhejiang Province. Diversity in T cell epitopes may prevent Mycobacterium tuberculosis from being recognized by the immune system.

Genome-wide investigation of the AP2/ERF superfamily and their expression under salt stress in Chinese willow (Salix matsudana)

2020 ◽  
Author(s):  
Yanhong Chen ◽  
Yuna Jiang ◽  
Guoyuan Liu ◽  
Chunmei Yu ◽  
Bolin Lian ◽  
...  
Keyword(s):  
Salt Stress ◽  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Evolutionary Analysis ◽  
Sequencing Data ◽  
Genome Wide ◽  
Salix Matsudana

Abstract Background: AP2/ERF transcription factors (TFs) play indispensable roles in plant growth, development, and especially in various abiotic stresses responses. The AP2/ERF TF family has been discovered and classified in more than 50 species, including model plants, horticulture plants, crops, and trees. Many AP2/ERF TFs from various species have been functionally characterized. However, little is known about the AP2/ERF gene family of Chinese willow (Salix matsudana), which is a tetraploid ornamental tree species that is widely planted and is also considered a species that can improve the soil salinity of coastal beaches. The recently produced whole genome sequencing data of Salix matsudana allowed us to conduct an evolutionary analysis on the AP2/ERF genes during polyploidization and study the genome-wide expression profiles of AP2/ERF genes in Salix matsudana under salt stress. Results: In this study, 364 AP2/ERF genes of Salix matsudana (SmAP2/ERF) were identified and renamed according to the chromosomal location of the SmAP2/ERF genes. After phylogenetic analysis with known categories of genes from other species, the AP2/ERF genes were divided into three subfamilies: AP2 (55 members), ERF (301 members), and RAV (six members). Two Soloist genes were also identified. Gene structure and conserved motifs were analyzed in AP2/ERF genes, and introns were not found in most genes of the ERF subfamily, although some unique motifs were found to be important for the function of AP2/ERF genes. Syntenic relationships between the SmAP2/ERF genes and AP2/ERF genes from other species were also investigated to elucidate their evolutionary relationships during polyploidization. Moreover, analyses on the expression profiles under salt stress were also conducted.Conclusion: The progenitors of Salix matsudana underwent whole genome duplication not more than 10 Mya. Synteny analysis with other species showed macrosynteny between willow and poplar AP2/ERF genes and that Salix matsudana is genetically more closely related to Populus trichocarpa than to Salix purpurea. Further investigation of the AP2/ERF TFs demonstrated that differential expression patterns during salt stress and this information can help reveal the mechanism of salt tolerance regulation in Salix matsudana.

Identification of T-cell epitopes on E2 protein of rubella virus, as recognized by human T-cell lines and clones.

1992 ◽  
Vol 66 (11) ◽  
pp. 6788-6793 ◽  
Author(s):  
D Ou ◽  
P Chong ◽  
Y Choi ◽  
P McVeigh ◽  
W A Jefferies ◽  
...  
Keyword(s):  
T Cell ◽  
Cell Lines ◽  
Rubella Virus ◽  
T Cell Epitopes ◽  
E2 Protein ◽  
Human T Cell ◽  
T Cell Lines

scholarly journals SARS-CoV-2 Human T cell Epitopes: adaptive immune response against COVID-19.

2021 ◽  
Author(s):  
Alba Grifoni ◽  
John Sidney ◽  
Randi Vita ◽  
Bjoern Peters ◽  
Shane Crotty ◽  
...  
Keyword(s):  
Immune Response ◽  
T Cell ◽  
Adaptive Immune Response ◽  
T Cell Epitopes ◽  
Adaptive Immune ◽  
Human T Cell

scholarly journals Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes

2021 ◽  
Author(s):  
Eric S Tvedte ◽  
Mark Gasser ◽  
Benjamin C Sparklin ◽  
Jane Michalski ◽  
Carl E Hjelmen ◽  
...  
Keyword(s):  
Bacterial Genome ◽  
Hybrid Approach ◽  
Cost Effective ◽  
Fruit Fly ◽  
Drosophila Ananassae ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
E Coli ◽  
Hybrid Approaches ◽  
Long Read

Abstract The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. In both organisms tested, Sequel II assemblies had the highest consensus accuracy, even after accounting for differences in sequencing throughput. ONT and PacBio CLR had the longest reads sequenced compared to PacBio RS II and HiFi, and genome contiguity was highest when assembling these datasets. ONT Rapid Sequencing libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assembly or polishing eukaryotic genome assemblies, and an ONT-Illumina hybrid approach would be more cost-effective for many users. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs. The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.

scholarly journals A 127 kb truncating deletion of PGRMC1 is a novel cause of X-linked isolated paediatric cataract

2021 ◽  
Author(s):  
Johanna L. Jones ◽  
Mark A. Corbett ◽  
Elise Yeaman ◽  
Duran Zhao ◽  
Jozef Gecz ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Protein Interactions ◽  
Cholesterol Biosynthesis ◽  
Crystalline Lens ◽  
Whole Genome Sequencing Data ◽  
Mendelian Disease ◽  
Cataract Formation ◽  
Sequencing Data ◽  
Zebrafish Model ◽  
Paediatric Cataract

AbstractInherited paediatric cataract is a rare Mendelian disease that results in visual impairment or blindness due to a clouding of the eye’s crystalline lens. Here we report an Australian family with isolated paediatric cataract, which we had previously mapped to Xq24. Linkage at Xq24–25 (LOD = 2.53) was confirmed, and the region refined with a denser marker map. In addition, two autosomal regions with suggestive evidence of linkage were observed. A segregating 127 kb deletion (chrX:g.118373226_118500408del) in the Xq24–25 linkage region was identified from whole-genome sequencing data. This deletion completely removed a commonly deleted long non-coding RNA gene LOC101928336 and truncated the protein coding progesterone receptor membrane component 1 (PGRMC1) gene following exon 1. A literature search revealed a report of two unrelated males with non-syndromic intellectual disability, as well as congenital cataract, who had contiguous gene deletions that accounted for their intellectual disability but also disrupted the PGRMC1 gene. A morpholino-induced pgrmc1 knockdown in a zebrafish model produced significant cataract formation, supporting a role for PGRMC1 in lens development and cataract formation. We hypothesise that the loss of PGRMC1 causes cataract through disrupted PGRMC1-CYP51A1 protein–protein interactions and altered cholesterol biosynthesis. The cause of paediatric cataract in this family is the truncating deletion of PGRMC1, which we report as a novel cataract gene.

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