Characterization and Comparative Genomic Analyses of Pseudomonas aeruginosa Phage PaoP5: New Members Assigned to PAK_P1-like Viruses

AbstractDespite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first high-quality wild Cucurbita genome. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We found evidence of gene flow between the domesticated and wild subspecies, which likely alleviated the effects of the domestication bottleneck. We uncovered candidate domestication genes that are involved in the regulation of growth hormones, plant defense mechanisms, seed development, and germination. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.

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Complete chloroplast genomes of Leptodermis scabrida complex: comparative genomic analyses and phylogenetic relationships

Gene ◽

10.1016/j.gene.2021.145715 ◽

2021 ◽

pp. 145715

Author(s):

Ying Zhang ◽

Zhengfeng Wang ◽

Yanan Guo ◽

Sheng Chen ◽

Xianyi Xu ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Comparative Genomic ◽

Chloroplast Genomes ◽

Genomic Analyses

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Evidence from comparative genomic analyses indicating that Lactobacillus-mediated irritable bowel syndrome alleviation is mediated by the conjugated linoleic acid synthesis

Food & Function ◽

10.1039/d0fo02616f ◽

2021 ◽

Author(s):

Yang Liu ◽

Wei Xiao ◽

Leilei Yu ◽

Fengwei Tian ◽

Gang Wang ◽

...

Keyword(s):

Irritable Bowel Syndrome ◽

Linoleic Acid ◽

Gut Microbiota ◽

Acid Synthesis ◽

Comparative Genomic ◽

Low Grade ◽

Genomic Analyses ◽

Irritable Bowel ◽

Low Grade Inflammation ◽

Gut Microbiota Dysbiosis

Irritable bowel syndrome (IBS) is a chronic intestinal disorder accompanied by low-grade inflammation, visceral hypersensitivity, and gut microbiota dysbiosis. Several studies have indicated that Lactobacillus supplementation can help to alleviate...

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Phosphorus stress induces the synthesis of novel glycolipids in Pseudomonas aeruginosa that confer protection against a last-resort antibiotic

The ISME Journal ◽

10.1038/s41396-021-01008-7 ◽

2021 ◽

Author(s):

Rebekah A. Jones ◽

Holly Shropshire ◽

Caimeng Zhao ◽

Andrew Murphy ◽

Ian Lidbury ◽

...

Keyword(s):

Cystic Fibrosis ◽

Pseudomonas Aeruginosa ◽

Antibiotic Sensitivity ◽

Polymyxin B ◽

Growth Conditions ◽

Membrane Lipid ◽

Comparative Genomic ◽

P Limitation ◽

Lung Microbiome ◽

Glycolipid Synthesis

AbstractPseudomonas aeruginosa is a nosocomial pathogen with a prevalence in immunocompromised individuals and is particularly abundant in the lung microbiome of cystic fibrosis patients. A clinically important adaptation for bacterial pathogens during infection is their ability to survive and proliferate under phosphorus-limited growth conditions. Here, we demonstrate that P. aeruginosa adapts to P-limitation by substituting membrane glycerophospholipids with sugar-containing glycolipids through a lipid renovation pathway involving a phospholipase and two glycosyltransferases. Combining bacterial genetics and multi-omics (proteomics, lipidomics and metatranscriptomic analyses), we show that the surrogate glycolipids monoglucosyldiacylglycerol and glucuronic acid-diacylglycerol are synthesised through the action of a new phospholipase (PA3219) and two glycosyltransferases (PA3218 and PA0842). Comparative genomic analyses revealed that this pathway is strictly conserved in all P. aeruginosa strains isolated from a range of clinical and environmental settings and actively expressed in the metatranscriptome of cystic fibrosis patients. Importantly, this phospholipid-to-glycolipid transition comes with significant ecophysiological consequence in terms of antibiotic sensitivity. Mutants defective in glycolipid synthesis survive poorly when challenged with polymyxin B, a last-resort antibiotic for treating multi-drug resistant P. aeruginosa. Thus, we demonstrate an intriguing link between adaptation to environmental stress (nutrient availability) and antibiotic resistance, mediated through membrane lipid renovation that is an important new facet in our understanding of the ecophysiology of this bacterium in the lung microbiome of cystic fibrosis patients.

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Comparative genomic analyses of a virulent pseudorabies virus and a series of its in vitro passaged strains

Virology Journal ◽

10.1186/s12985-018-1102-8 ◽

2018 ◽

Vol 15 (1) ◽

Cited By ~ 1

Author(s):

Chao Ye ◽

Jiqiang Wu ◽

Wu Tong ◽

Tongling Shan ◽

Xuefei Cheng ◽

...

Keyword(s):

Pseudorabies Virus ◽

Comparative Genomic ◽

Genomic Analyses

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Rapid evolution and molecular convergence in cryptorchidism-related genes associated with inherently undescended testes in mammals

BMC Ecology and Evolution ◽

10.1186/s12862-021-01753-5 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Simin Chai ◽

Ran Tian ◽

Juanjuan Bi ◽

Shixia Xu ◽

Guang Yang ◽

...

Keyword(s):

Muscle Development ◽

Rapid Evolution ◽

Genetic Material ◽

Comparative Genomic ◽

Testicular Descent ◽

Ancestral State ◽

Undescended Testes ◽

Genomic Analyses ◽

Genetic Mechanisms ◽

Molecular Convergence

Abstract Background The mammalian testis is an important male exocrine gland and spermatozoa-producing organ that usually lies in extra-abdominal scrotums to provide a cooler environment for spermatogenesis and sperm storage. Testicles sometimes fail to descend, leading to cryptorchidism. However, certain groups of mammals possess inherently ascrotal testes (i.e. testes that do not descend completely or at all) that have the same physiological functions as completely descended scrotal testes. Although several anatomical and hormonal factors involved in testicular descent have been studied, there is still a paucity of comprehensive research on the genetic mechanisms underlying the evolution of testicular descent in mammals and how mammals with ascrotal testes maintain their reproductive health. Results We performed integrative phenotypic and comparative genomic analyses of 380 cryptorchidism-related genes and found that the mammalian ascrotal testes trait is derived from an ancestral scrotal state. Rapidly evolving genes in ascrotal mammals were enriched in the Hedgehog pathway—which regulates Leydig cell differentiation and testosterone secretion—and muscle development. Moreover, some cryptorchidism-related genes in ascrotal mammals had undergone positive selection and contained specific mutations and indels. Genes harboring convergent/parallel amino acid substitutions between ascrotal mammals were enriched in GTPase functions. Conclusions Our results suggest that the scrotal testis is an ancestral state in mammals, and the ascrotal phenotype was derived multiple times in independent lineages. In addition, the adaptive evolution of genes involved in testicular descent and the development of the gubernaculum contributed to the evolution of ascrotal testes. Accurate DNA replication, the proper segregation of genetic material, and appropriate autophagy are the potential mechanisms for maintaining physiological normality during spermatogenesis in ascrotal mammals. Furthermore, the molecular convergence of GTPases is probably a mechanism in the ascrotal testes of different mammals. This study provides novel insights into the evolution of the testis and scrotum in mammals and contributes to a better understanding of the pathogenesis of cryptorchidism in humans.

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The genomic sequence ofExiguobacterium chiriqhuchastr. N139 reveals a species that thrives in cold waters and extreme environmental conditions

PeerJ ◽

10.7717/peerj.3162 ◽

2017 ◽

Vol 5 ◽

pp. e3162 ◽

Cited By ~ 5

Author(s):

Ana Gutiérrez-Preciado ◽

Carlos Vargas-Chávez ◽

Mariana Reyes-Prieto ◽

Omar F. Ordoñez ◽

Diego Santos-García ◽

...

Keyword(s):

Acid Metabolism ◽

High Salinity ◽

Genomic Sequence ◽

Ultraviolet B ◽

Comparative Genomic ◽

Ultraviolet B Radiation ◽

Genomic Analyses ◽

High Concentrations ◽

And Coping ◽

Cold Lake

We report the genome sequence ofExiguobacterium chiriqhuchastr. N139, isolated from a high-altitude Andean lake. Comparative genomic analyses of theExiguobacteriumgenomes available suggest that our strain belongs to the same species as the previously reportedE. pavilionensisstr. RW-2 andExiguobacteriumstr. GIC 31. We describe this species and propose thechiriqhuchaname to group them. ‘Chiri qhucha’ in Quechua means ‘cold lake’, which is a common origin of these three cosmopolitan Exiguobacteria. The 2,952,588-bpE. chiriqhuchastr. N139 genome contains one chromosome and three megaplasmids. The genome analysis of the Andean strain suggests the presence of enzymes that conferE. chiriqhuchastr. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals, high ultraviolet B radiation, scavenging for phosphorous and coping with high salinity. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina.

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Draft Genome Sequence of Dermatophagoides pteronyssinus, the European House Dust Mite

Genome Announcements ◽

10.1128/genomea.00789-17 ◽

2017 ◽

Vol 5 (32) ◽

Cited By ~ 8

Author(s):

Rose Waldron ◽

Jamie McGowan ◽

Natasha Gordon ◽

Charley McCarthy ◽

E. Bruce Mitchell ◽

...

Keyword(s):

Genome Sequence ◽

Gene Prediction ◽

Draft Genome ◽

Dermatophagoides Pteronyssinus ◽

Mite Species ◽

Draft Genome Sequence ◽

Comparative Genomic ◽

Genomic Analyses ◽

Dust Mite ◽

Functional Analyses

ABSTRACT Dermatophagoides pteronyssinus is the European dust mite and a major source of human allergens. Here, we present the first draft genome sequence of the mite, as well as the ab initio gene prediction and functional analyses that will facilitate comparative genomic analyses with other mite species.

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