Comparative Genomic Analyses of Attenuated Strains of Mycoplasma gallisepticum

ABSTRACT Mycoplasma gallisepticum is a significant respiratory and reproductive pathogen of domestic poultry. While the complete genomic sequence of the virulent, low-passage M. gallisepticum strain R (Rlow) has been reported, genomic determinants responsible for differences in virulence and host range remain to be completely identified. Here, we utilize genome sequencing and microarray-based comparative genomic data to identify these genomic determinants of virulence and to elucidate genomic variability among strains of M. gallisepticum. Analysis of the high-passage, attenuated derivative of Rlow, Rhigh, indicated that relatively few total genomic changes (64 loci) occurred, yet they are potentially responsible for the observed attenuation of this strain. In addition to previously characterized mutations in cytadherence-related proteins, changes included those in coding sequences of genes involved in sugar metabolism. Analyses of the genome of the M. gallisepticum vaccine strain F revealed numerous differences relative to strain R, including a highly divergent complement of vlhA surface lipoprotein genes, and at least 16 genes absent or significantly fragmented relative to strain R. Notably, an Rlow isogenic mutant in one of these genes (MGA_1107) caused significantly fewer severe tracheal lesions in the natural host compared to virulent M. gallisepticum Rlow. Comparative genomic hybridizations indicated few genetic loci commonly affected in F and vaccine strains ts-11 and 6/85, which would correlate with proteins affecting strain R virulence. Together, these data provide novel insights into inter- and intrastrain M. gallisepticum genomic variability and the genetic basis of M. gallisepticum virulence.

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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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Decoding the Genomic Variability among Members of the Bifidobacterium dentium Species

Microorganisms ◽

10.3390/microorganisms8111720 ◽

2020 ◽

Vol 8 (11) ◽

pp. 1720

Author(s):

Gabriele Andrea Lugli ◽

Chiara Tarracchini ◽

Giulia Alessandri ◽

Christian Milani ◽

Leonardo Mancabelli ◽

...

Keyword(s):

Defense Mechanisms ◽

Ursus Arctos ◽

Primate Species ◽

Comparative Genomic ◽

Glycosyl Hydrolases ◽

Genomic Variability ◽

Fecal Samples ◽

Genomic Analyses ◽

Conserved Genes ◽

Genetic Features

Members of the Bifidobacterium dentium species are usually identified in the oral cavity of humans and associated with the development of plaque and dental caries. Nevertheless, they have also been detected from fecal samples, highlighting a widespread distribution among mammals. To explore the genetic variability of this species, we isolated and sequenced the genomes of 18 different B. dentium strains collected from fecal samples of several primate species and an Ursus arctos. Thus, we investigated the genomic variability and metabolic abilities of the new B. dentium isolates together with 20 public genome sequences. Comparative genomic analyses provided insights into the vast metabolic repertoire of the species, highlighting 19 glycosyl hydrolases families shared between each analyzed strain. Phylogenetic analysis of the B. dentium taxon, involving 1140 conserved genes, revealed a very close phylogenetic relatedness among members of this species. Furthermore, low genomic variability between strains was also confirmed by an average nucleotide identity analysis showing values higher than 98.2%. Investigating the genetic features of each strain, few putative functional mobile elements were identified. Besides, a consistent occurrence of defense mechanisms such as CRISPR–Cas and restriction–modification systems may be responsible for the high genome synteny identified among members of this taxon.

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The Genomes of Sheeppox and Goatpox Viruses

Journal of Virology ◽

10.1128/jvi.76.12.6054-6061.2002 ◽

2002 ◽

Vol 76 (12) ◽

pp. 6054-6061 ◽

Cited By ~ 163

Author(s):

E. R. Tulman ◽

C. L. Afonso ◽

Z. Lu ◽

L. Zsak ◽

J.-H. Sur ◽

...

Keyword(s):

Host Range ◽

Genomic Sequence ◽

Indian Subcontinent ◽

Interleukin 1 ◽

Central Africa ◽

Myxoma Virus ◽

Nucleotide Identity ◽

Comparative Genomic ◽

Genomic Changes ◽

Ankyrin Repeat Proteins

ABSTRACT Sheeppox virus (SPPV) and goatpox virus (GTPV), members of the Capripoxvirus genus of the Poxviridae, are etiologic agents of important diseases of sheep and goats in northern and central Africa, southwest and central Asia, and the Indian subcontinent. Here we report the genomic sequence and comparative analysis of five SPPV and GTPV isolates, including three pathogenic field isolates and two attenuated vaccine viruses. SPPV and GTPV genomes are approximately 150 kbp and are strikingly similar to each other, exhibiting 96% nucleotide identity over their entire length. Wild-type genomes share at least 147 putative genes, including conserved poxvirus replicative and structural genes and genes likely involved in virulence and host range. SPPV and GTPV genomes are very similar to that of lumpy skin disease virus (LSDV), sharing 97% nucleotide identity. All SPPV and GTPV genes are present in LSDV. Notably in both SPPV and GTPV genomes, nine LSDV genes with likely virulence and host range functions are disrupted, including a gene unique to LSDV (LSDV132) and genes similar to those coding for interleukin-1 receptor, myxoma virus M003.2 and M004.1 genes (two copies each), and vaccinia virus F11L, N2L, and K7L genes. The absence of these genes in SPPV and GTPV suggests a significant role for them in the bovine host range. SPPV and GTPV genomes contain specific nucleotide differences, suggesting they are phylogenetically distinct. Relatively few genomic changes in SPPV and GTPV vaccine viruses account for viral attenuation, because they contain 71 and 7 genomic changes compared to their respective field strains. Notable genetic changes include mutation or disruption of genes with predicted functions involving virulence and host range, including two ankyrin repeat proteins in SPPV and three kelch-like proteins in GTPV. These comparative genomic data indicate the close genetic relationship among capripoxviruses, and they suggest that SPPV and GTPV are distinct and likely derived from an LSDV-like ancestor.

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Comparative Genomics Analysis of Lactobacillus mucosae from Different Niches

Genes ◽

10.3390/genes11010095 ◽

2020 ◽

Vol 11 (1) ◽

pp. 95

Author(s):

Yan Jia ◽

Bo Yang ◽

Paul Ross ◽

Catherine Stanton ◽

Hao Zhang ◽

...

Keyword(s):

Genetic Diversity ◽

Sugar Metabolism ◽

Comparative Genomic ◽

Related Factors ◽

Genomic Analyses ◽

Human Vagina ◽

New Ideas ◽

Comparative Genomics Analysis ◽

Lactobacillus Mucosae ◽

First Time

The potential probiotic benefits of Lactobacillus mucosae have received increasing attention. To investigate the genetic diversity of L. mucosae, comparative genomic analyses of 93 strains isolated from different niches (human and animal gut, human vagina, etc.) and eight strains of published genomes were conducted. The results showed that the core genome of L. mucosae mainly encoded translation and transcription, amino acid biosynthesis, sugar metabolism, and defense function while the pan-genomic curve tended to be close. The genetic diversity of L. mucosae mainly reflected in carbohydrate metabolism and immune/competitive-related factors, such as exopolysaccharide (EPS), enterolysin A, and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas. It was worth noting that this research firstly predicted the complete EPS operon shared among L. mucosae. Additionally, the type IIIA CRISPR-Cas system was discovered in L. mucosae for the first time. This work provided new ideas for the study of this species.

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Molecular and comparative genomic analyses reveal evolutionarily conserved and unique features of the Schizosaccharomyces japonicus mycelial growth and the underlying genomic changes

Current Genetics ◽

10.1007/s00294-021-01206-y ◽

2021 ◽

Author(s):

László Attila Papp ◽

Lajos Ács-Szabó ◽

Gyula Batta ◽

Ida Miklós

Keyword(s):

Mycelial Growth ◽

Fungal Pathogens ◽

Hyphal Growth ◽

Phytopathogenic Fungus ◽

Comparative Genomic ◽

Human Pathogens ◽

Sequence Alignments ◽

Genomic Changes ◽

Expression Of Genes ◽

Genomic Analyses

AbstractFungal pathogens, from phytopathogenic fungus to human pathogens, are able to alternate between the yeast-like form and filamentous forms. This morphological transition (dimorphism) is in close connection with their pathogenic lifestyles and with their responses to changing environmental conditions. The mechanisms governing these morphogenetic conversions are still not fully understood. Therefore, we studied the filamentous growth of the less-known, non-pathogenic dimorphic fission yeast, S. japonicus, which belongs to an ancient and early evolved branch of the Ascomycota. Its RNA sequencing revealed that several hundred genes were up- or down-regulated in the hyphae compared to the yeast-phase cells. These genes belonged to different GO categories, confirming that mycelial growth is a rather complex process. The genes of transport- and metabolic processes appeared especially in high numbers among them. High expression of genes involved in glycolysis and ethanol production was found in the hyphae, while other results pointed to the regulatory role of the protein kinase A (PKA) pathway. The homologues of 49 S. japonicus filament-associated genes were found by sequence alignments also in seven distantly related dimorphic and filamentous species. The comparative genomic analyses between S. japonicus and the closely related but non-dimorphic S. pombe shed some light on the differences in their genomes. All these data can contribute to a better understanding of hyphal growth and those genomic rearrangements that underlie it.

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The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative

Horticulture Research ◽

10.1038/s41438-021-00544-9 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Josué Barrera-Redondo ◽

Guillermo Sánchez-de la Vega ◽

Jonás A. Aguirre-Liguori ◽

Gabriela Castellanos-Morales ◽

Yocelyn T. Gutiérrez-Guerrero ◽

...

Keyword(s):

Defense Mechanisms ◽

Population Level ◽

Growth Hormones ◽

Comparative Genomic ◽

Structural Variants ◽

Closely Related Species ◽

Level Data ◽

Genomic Analyses ◽

Genotype By Sequencing ◽

Regulation Of Growth

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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Special Issue: Genetic Basis of Phenotypic Variation in Drosophila and Other Insects

Genes ◽

10.3390/genes12081212 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1212

Author(s):

J. Spencer Johnston ◽

Carl E. Hjelmen

Keyword(s):

Next Generation Sequencing ◽

Genetic Basis ◽

Genomic Sequence ◽

Sequence Data ◽

Complete Genomic Sequence ◽

Special Issue ◽

Model Species ◽

Road Map ◽

Generation Sequencing ◽

Complete Genomic

Next-generation sequencing provides a nearly complete genomic sequence for model and non-model species alike; however, this wealth of sequence data includes no road map [...]

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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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