scholarly journals Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Jaewon Lim ◽  
Hong-Tae Park ◽  
Seyoung Ko ◽  
Hyun-Eui Park ◽  
Gyumin Lee ◽  
...  
Keyword(s):  
Mycobacterium Avium ◽  
Phenotypic Diversity ◽  
Control Strategies ◽  
Genomic Diversity ◽  
Phenotypic Traits ◽  
Whole Genome ◽  
Genomic Features ◽  
Phenotypic Differences ◽  
Mycobacterium Avium Subsp Paratuberculosis ◽  
Type Strains

AbstractMycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne’s disease, which is a chronic granulomatous enteropathy in ruminants. Determining the genetic diversity of MAP is necessary to understand the epidemiology and biology of MAP, as well as establishing disease control strategies. In the present study, whole genome-based alignment and comparative analysis were performed using 40 publicly available MAP genomes, including newly sequenced Korean isolates. First, whole genome-based alignment was employed to identify new genomic structures in MAP genomes. Second, the genomic diversity of the MAP population was described by pangenome analysis. A phylogenetic tree based on the core genome and pangenome showed that the MAP was differentiated into two major types (C- and S-type), which was in keeping with the findings of previous studies. However, B-type strains were discriminated from C-type strains. Finally, functional analysis of the pangenome was performed using three virulence factor databases (i.e., PATRIC, VFDB, and Victors) to predict the phenotypic diversity of MAP in terms of pathogenicity. Based on the results of the pangenome analysis, we developed a real-time PCR technique to distinguish among S-, B- and C-type strains. In conclusion, the results of our study suggest that the phenotypic differences between MAP strains can be explained by their genetic polymorphisms. These results may help to elucidate the diversity of MAP, extending from genomic features to phenotypic traits.

scholarly journals Brettanomyces bruxellensis: Overview of the hidden diversity and complexity of an anthropized yeast

2021 ◽  
Author(s):  
Jules Harrouard ◽  
Chris Eberlein ◽  
Patricia Ballestra ◽  
Marguerite Dols-Lafargue ◽  
Isabelle Masneuf-Pomarede ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Phenotypic Diversity ◽  
Nitrogen Sources ◽  
Genomic Diversity ◽  
Future Research ◽  
Phenotypic Traits ◽  
Bioethanol Production ◽  
Brettanomyces Bruxellensis ◽  
Ploidy Levels ◽  
The Impact

Human-associated microorganisms are ideal models to study the impact of environmental changes on species evolution and adaptation. The yeast Brettanomyces bruxellensis is a good example of organism facing anthropogenic-driven selective pressures. It is associated with fermentation processes in which it can be considered either as a spoiler (e.g. winemaking, bioethanol production) or as a beneficial microorganism (e.g. production of specific beers, kombucha). Besides its industrial interests, noteworthy parallels and dichotomies with Saccharomyces cerevisiae propelled B. bruxellensis as a valuable complementary yeast model. In this review, we emphasize that the broad genetic and phenotypic diversity of this species is only beginning to be revealed. Population genomic studies have revealed the co-existence of auto- and allotriploidization events with different evolutionary outcomes. The various diploid, autotriploid and allotriploid subpopulations are associated with specific fermented processes, suggesting independent adaptation phenomena to anthropized environments. Phenotypically, B. bruxellensis is renowned for its ability to metabolize a wide variety of carbon and nitrogen sources, which may explain its ability to colonize already fermented environments showing low-nutrient contents. Several traits of interest could be related to adaptation to human activities (e.g. nitrate metabolization in bioethanol production, resistance to sulphite treatments in winemaking). However, phenotypic traits are insufficiently studied in view of the great genomic diversity of the species. Future work will have to take into account strains of varied substrates, geographical origins as well as displaying different ploidy levels. Finally, we discuss the characteristics of B. bruxellensis which may prove to be of wider interest in future research.

scholarly journals Sorghum Association Panel Whole-Genome Sequencing Establishes Pivotal Resource for Dissecting Genomic Diversity

2021 ◽  
Author(s):  
Jon Lucas Boatwright ◽  
Sirjan Sapkota ◽  
Hongyu Jin ◽  
James Schnable ◽  
Zachary Brenton ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Phenotypic Diversity ◽  
Genotyping By Sequencing ◽  
Genomic Diversity ◽  
Evolutionary Divergence ◽  
Whole Genome ◽  
Linear Predictor ◽  
Association Panel ◽  
Genomic Marker

Association mapping panels represent foundational resources for understanding the genetic basis of phenotypic diversity and serve to advance plant breeding by exploring genetic variation across diverse accessions with distinct histories of evolutionary divergence and local adaptation. We report the whole-genome sequencing (WGS) of 400 sorghum [Sorghum bicolor (L.) Moench] accessions from the Sorghum Association Panel (SAP) at an average coverage of 38X (25X-72X), enabling the development of a high-density genomic-marker set of 43,983,694 variants including SNPs (~38 million), indels (~5 million), and CNVs (~170,000). We observe slightly more deletions among indels and a much higher prevalence of deletions among copy number variants compared to insertions. This new marker set enabled the identification of several putatively novel genomic associations for plant height and tannin content, which were not identified when using previous lower-density marker sets. WGS identified and scored variants in 5 kb bins where available genotyping-by-sequencing (GBS) data captured no variants, with half of all bins in the genome falling into this category. The predictive ability of genomic best unbiased linear predictor (GBLUP) models was increased by an average of 30% by using WGS markers rather than GBS markers. We identified 18 selection peaks across subpopulations that formed due to evolutionary divergence during domestication, and we found six Fst peaks resulting from comparisons between converted lines and breeding lines within the SAP that were distinct from the peaks associated with historic selection. This population has been and continues to serve as a significant public resource for sorghum research and demonstrates the value of improving upon existing genomic resources.

scholarly journals Effects of Age and Environment on Adaptive Immune Responses to Mycobacterium avium subsp. paratuberculosis (MAP) Vaccination in Dairy Goats in Relation to Paratuberculosis Control Strategies

2019 ◽  
Vol 6 (3) ◽  
pp. 62 ◽  
Author(s):  
Ad Koets ◽  
Lars Ravesloot ◽  
Robin Ruuls ◽  
Annemieke Dinkla ◽  
Susanne Eisenberg ◽  
...  
Keyword(s):  
Immune Responses ◽  
Mycobacterium Avium ◽  
Diagnostic Tests ◽  
Control Strategies ◽  
Mycobacterium Avium Subsp ◽  
Dairy Goats ◽  
Adaptive Immune Responses ◽  
Adaptive Immune ◽  
Mycobacterium Avium Subsp Paratuberculosis ◽  
Free Environment

Paratuberculosis infection is caused by Mycobacterium avium subsp. paratuberculosis (MAP). In the Netherlands, 75% herd level prevalence of caprine paratuberculosis has been estimated, and vaccination is the principal control strategy applied. Most goat dairy farms with endemic paratuberculosis systematically vaccinate goat kids in the first months of life with a commercially available whole cell MAP vaccine. We hypothesized that the development of adaptive immune responses in goats vaccinated at young age depends on the environment they are raised in, and this has implications for the application of immune diagnostic tests in vaccinated dairy goats. We evaluated the early immune response to vaccination in young goat kids sourced from a MAP unsuspected non-vaccinated herd and raised in a MAP-free environment. Subsequently we compared these with responses observed in birth year and vaccination matched adult goats raised on farms with endemic paratuberculosis. Results indicated that initial adaptive immune responses to vaccination are limited in a MAP-free environment. In addition, adult antibody positive vaccinated goats raised in a MAP endemic environment are less likely to be IS900 PCR-positive as compared to antibody negative herd mates. We conclude that test-and-cull strategies in a vaccinated herd are currently not feasible using available immune diagnostic tests.

scholarly journals Draft Genome Sequences of Two Bison-Type and Two Sheep-Type Strains of Mycobacterium avium subsp. paratuberculosis

2021 ◽  
Vol 10 (28) ◽  
Author(s):  
John P. Bannantine ◽  
Darrell O. Bayles
Keyword(s):  
United States ◽  
Mycobacterium Avium ◽  
Draft Genome ◽  
The United States ◽  
Mycobacterium Avium Subsp ◽  
Type B ◽  
Genome Sequences ◽  
Content Type ◽  
Mycobacterium Avium Subsp Paratuberculosis ◽  
Type Strains

Genome sequences of two type B and two type S strains of Mycobacterium avium subsp. paratuberculosis are presented. These strains were isolated in the United States from sheep, bison, and cattle suffering from Johne’s disease. These genomes will increase our understanding of the minor differences that exist among this genetically stable subspecies.

scholarly journals Multi-OMICS and Molecular Biology Perspective in Buffalo Genome

2021 ◽  
pp. 21-31
Author(s):  
Suranjana Sikdar ◽  
◽  
Tuhin Das ◽  
Emran Hossain Sajib ◽  
Kazi Mahbub Ur Rahman Rahman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Expression Profiling ◽  
Phenotypic Diversity ◽  
Genomic Research ◽  
Phenotypic Traits ◽  
Whole Genome ◽  
Single Nucleotide ◽  
Geographical Regions

The bovine species buffalo was domesticated from its wild strain Bubalus arnee and is widely used livestock in southern Asia. There are two distinct types of Buffalo- the swamp buffalo (B. bubalis kerebau) and the river buffalo (B. bubalis bubalis), which diverged from the wild Asian water buffalo and then evolved in separate geographical regions. Several research studies performed on buffalo, like- characterization of trait-specific Single Nucleotide Polymorphism (SNP), genetic and phenotypic diversity, gene prediction and function annotation, mapping of the draft genome, have helped our understanding of the buffalo genome. Some advanced discovery as identification of Single Nucleotide Variant (SNVs), Simple Sequence Repeats (SSR) marker and their association with various phenotypic traits, MicroRNA's expression profiling, whole-genome sequencing, etc. have also enabled us to track the chromosomal evolution, physiological processes, and gene expression of buffalo. Proper enhancement of these traits can lead us to apply multi-omics-based tools for better animal health and production. Recent advancement in genomic research on buffalo is being accelerated with the association of modern tools like- Genome-Wide Association Study (GWAS), genotyping by sequencing, epigenomic screening, microRNA's expression profiling, microarray technology, and whole-genome sequencing. All these tools bear great significance in breed up-gradation, identification of the phylogenetic relationship between species in proteome and genomic level, study gene expression level, diagnose diseases or developmental stages, phenotypic diversity, etc. All this knowledge paved the way for better optimization of production efficiency, product quality, and resistance to certain health hazards.

scholarly journals Complete Genome Sequence of JII-1961, a Bovine Mycobacterium avium subsp. paratuberculosis Field Isolate from Germany

2017 ◽  
Vol 5 (34) ◽  
Author(s):  
Petra Möbius ◽  
Gabriele Nordsiek ◽  
Martin Hölzer ◽  
Michael Jarek ◽  
Manja Marz ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Mycobacterium Avium ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Field Isolate ◽  
Human Beings ◽  
Content Type ◽  
Milk Products ◽  
Mycobacterium Avium Subsp Paratuberculosis ◽  
Type Strains

ABSTRACT Mycobacterium avium subsp. paratuberculosis causes Johne’s disease in ruminants and was also detected in nonruminant species, including human beings, and in milk products. We announce here the 4.829-Mb complete genome sequence of the cattle-type strain JII-1961 from Germany, which is very similar to cattle-type strains recovered from different continents.

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