Molecular structure and phylogenetic analysis of complete chloroplast genomes of medicinal species Paeonia lactiflora from Zhejiang Province

Abstract Emergence of tigecycline-resistance tet(X) gene orthologues rendered tigecycline ineffective as last-resort antibiotic. To understand the potential origin and transmission mechanisms of these genes, we survey the prevalence of tet(X) and its orthologues in 2997 clinical E. coli and K. pneumoniae isolates collected nationwide in China with results showing very low prevalence on these two types of strains, 0.32% and 0%, respectively. Further surveillance of tet(X) orthologues in 3692 different clinical Gram-negative bacterial strains collected during 1994–2019 in hospitals in Zhejiang province, China reveals 106 (2.7%) tet(X)-bearing strains with Flavobacteriaceae being the dominant (97/376, 25.8%) bacteria. In addition, tet(X)s are found to be predominantly located on the chromosomes of Flavobacteriaceae and share similar GC-content as Flavobacteriaceae. It also further evolves into different orthologues and transmits among different species. Data from this work suggest that Flavobacteriaceae could be the potential ancestral source of the tigecycline resistance gene tet(X).

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Whole Chloroplast Genomes reveals the uniqueness of Bolivian native cacao (Theobroma cacao) from the northern part of Bolivia

10.1101/2021.04.16.440153 ◽

2021 ◽

Author(s):

Marcia Gumiel ◽

Oscar M Rollano-Penaloza ◽

Carmelo Peralta-Rivero ◽

Leslie Tejeda ◽

Valeria D. Palma Encinas ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Next Generation Sequencing ◽

Theobroma Cacao ◽

Phylogenetic Trees ◽

Plastid Genome ◽

Next Generation ◽

Center Of Origin ◽

Chloroplast Genomes ◽

Geographical Locations ◽

Generation Sequencing

We report the complete chloroplast sequences of two varieties of Theobroma cacao collected in the Bolivian Amazonia using Next-Generation Sequencing. Comparisons made between these two chloroplast genomes and the Belizean reference plastid genome identified 19 and 22 nucleotide variants. The phylogenetic analysis reported three main T. cacao clades belonging to the Forastero, Criollo and Trinitario groups. The Bolivian Native Cacao varieties were located inside the Trinitario group forming their unique branch. The Bolivian Native Cacao branch reveals a possible new subpopulation different from the well-characterized T. cacao subpopulations. The phylogenetic trees showed that the relationships among the T. cacao varieties were consistent with their geographical locations placing the Cacao Center of Origin in Western Amazon. The data presented here will contribute to the usage of ultrabarcoding to distinguish different T. cacao varieties and to identify native cacaos from introduced cacaos. Thus helping in the conservation of local native varieties of T. cacao.

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Peer Review #1 of "Comparative analysis of chloroplast genomes for five Dicliptera species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution (v0.1)"

10.7287/peerj.8450v0.1/reviews/1 ◽

2020 ◽

Keyword(s):

Molecular Structure ◽

Comparative Analysis ◽

Peer Review ◽

Adaptive Evolution ◽

Phylogenetic Relationships ◽

Chloroplast Genomes

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Comparative and Phylogenetic Analysis of the Complete Chloroplast Genomes of Three Paeonia Section Moutan Species (Paeoniaceae)

Frontiers in Genetics ◽

10.3389/fgene.2020.00980 ◽

2020 ◽

Vol 11 ◽

Author(s):

Liwei Wu ◽

Liping Nie ◽

Zhichao Xu ◽

Pei Li ◽

Yu Wang ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Chloroplast Genomes

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Molecular structure, phylogenetic analysis, tissue distribution, and function characterization of interferon-γ-inducible lysosomal thiol reductase (GILT) gene in sheep (Ovis aries)

Veterinary Immunology and Immunopathology ◽

10.1016/j.vetimm.2011.01.012 ◽

2011 ◽

Vol 140 (3-4) ◽

pp. 329-334 ◽

Cited By ~ 10

Author(s):

Hong-xin Ai ◽

Zhen-zhen Zhang ◽

Yue-fen Shen ◽

Jia-xin Zhang ◽

Xu-ming Zhou ◽

...

Keyword(s):

Molecular Structure ◽

Phylogenetic Analysis ◽

Tissue Distribution ◽

Interferon Γ ◽

Ovis Aries ◽

Function Characterization ◽

Thiol Reductase ◽

And Function

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Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes

Genes ◽

10.3390/genes11010115 ◽

2020 ◽

Vol 11 (1) ◽

pp. 115

Author(s):

Yuxin Hu ◽

Weiyue Xing ◽

Zhengyu Hu ◽

Guoxiang Liu

Keyword(s):

Phylogenetic Analysis ◽

Mitochondrial Genome ◽

Phylogenetic Relationship ◽

Phylogenetic Analyses ◽

Mitochondrial Protein ◽

Substitution Rates ◽

Protein Coding ◽

Protein Coding Genes ◽

Chloroplast Genomes ◽

Volvocine Algae

We sequenced the mitochondrial genome of six colonial volvocine algae, namely: Pandorina morum, Pandorina colemaniae, Volvulina compacta, Colemanosphaera angeleri, Colemanosphaera charkowiensi, and Yamagishiella unicocca. Previous studies have typically reconstructed the phylogenetic relationship between colonial volvocine algae based on chloroplast or nuclear genes. Here, we explore the validity of phylogenetic analysis based on mitochondrial protein-coding genes. We found phylogenetic incongruence of the genera Yamagishiella and Colemanosphaera. In Yamagishiella, the stochastic error and linkage group formed by the mitochondrial protein-coding genes prevent phylogenetic analyses from reflecting the true relationship. In Colemanosphaera, a different reconstruction approach revealed a different phylogenetic relationship. This incongruence may be because of the influence of biological factors, such as incomplete lineage sorting or horizontal gene transfer. We also analyzed the substitution rates in the mitochondrial and chloroplast genomes between colonial volvocine algae. Our results showed that all volvocine species showed significantly higher substitution rates for the mitochondrial genome compared with the chloroplast genome. The nonsynonymous substitution (dN)/synonymous substitution (dS) ratio is similar in the genomes of both organelles in most volvocine species, suggesting that the two counterparts are under a similar selection pressure. We also identified a few chloroplast protein-coding genes that showed high dN/dS ratios in some species, resulting in a significant dN/dS ratio difference between the mitochondrial and chloroplast genomes.

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