Angiosperm genome comparisons reveal early polyploidy in the monocot lineage

The recent report of distinct Xanthomonas lineages of Xanthomonas arboricola pv. juglandis and Xanthomonas euroxanthea within the same walnut tree revealed that this consortium of walnut-associated Xanthomonas includes both pathogenic and nonpathogenic strains. As the implications of this co-colonization are still poorly understood, in order to unveil niche-specific adaptations, the genomes of three X. euroxanthea strains (CPBF 367, CPBF 424T, and CPBF 426) and of an X. arboricola pv. juglandis strain (CPBF 427) isolated from a single walnut tree in Loures (Portugal) were sequenced with two different technologies, Illumina and Nanopore, to provide consistent single scaffold chromosomal sequences. General genomic features showed that CPBF 427 has a genome similar to other X. arboricola pv. juglandis strains, regarding its size, number, and content of CDSs, while X. euroxanthea strains show a reduction regarding these features comparatively to X. arboricola pv. juglandis strains. Whole genome comparisons revealed remarkable genomic differences between X. arboricola pv. juglandis and X. euroxanthea strains, which translates into different pathogenicity and virulence features, namely regarding type 3 secretion system and its effectors and other secretory systems, chemotaxis-related proteins, and extracellular enzymes. Altogether, the distinct genomic repertoire of X. euroxanthea may be particularly useful to address pathogenicity emergence and evolution in walnut-associated Xanthomonas.

Download Full-text

Whole-Genome Relationships among Francisella Bacteria of Diverse Origins Define New Species and Provide Specific Regions for Detection

Applied and Environmental Microbiology ◽

10.1128/aem.02589-16 ◽

2016 ◽

Vol 83 (3) ◽

Cited By ~ 16

Author(s):

Jean F. Challacombe ◽

Jeannine M. Petersen ◽

La Verne Gallegos-Graves ◽

David Hodge ◽

Segaran Pillai ◽

...

Keyword(s):

New Species ◽

16S Rrna ◽

Response Times ◽

Amino Acid Sequences ◽

Clinical Samples ◽

Whole Genome ◽

Multiple Gene ◽

Content Type ◽

Environmental Surveys ◽

Genome Comparisons

ABSTRACT Francisella tularensis is a highly virulent zoonotic pathogen that causes tularemia and, because of weaponization efforts in past world wars, is considered a tier 1 biothreat agent. Detection and surveillance of F. tularensis may be confounded by the presence of uncharacterized, closely related organisms. Through DNA-based diagnostics and environmental surveys, novel clinical and environmental Francisella isolates have been obtained in recent years. Here we present 7 new Francisella genomes and a comparison of their characteristics to each other and to 24 publicly available genomes as well as a comparative analysis of 16S rRNA and sdhA genes from over 90 Francisella strains. Delineation of new species in bacteria is challenging, especially when isolates having very close genomic characteristics exhibit different physiological features—for example, when some are virulent pathogens in humans and animals while others are nonpathogenic or are opportunistic pathogens. Species resolution within Francisella varies with analyses of single genes, multiple gene or protein sets, or whole-genome comparisons of nucleic acid and amino acid sequences. Analyses focusing on single genes (16S rRNA, sdhA), multiple gene sets (virulence genes, lipopolysaccharide [LPS] biosynthesis genes, pathogenicity island), and whole-genome comparisons (nucleotide and protein) gave congruent results, but with different levels of discrimination confidence. We designate four new species within the genus; Francisella opportunistica sp. nov. (MA06-7296), Francisella salina sp. nov. (TX07-7308), Francisella uliginis sp. nov. (TX07-7310), and Francisella frigiditurris sp. nov. (CA97-1460). This study provides a robust comparative framework to discern species and virulence features of newly detected Francisella bacteria. IMPORTANCE DNA-based detection and sequencing methods have identified thousands of new bacteria in the human body and the environment. In most cases, there are no cultured isolates that correspond to these sequences. While DNA-based approaches are highly sensitive, accurately assigning species is difficult without known near relatives for comparison. This ambiguity poses challenges for clinical cases, disease epidemics, and environmental surveillance, for which response times must be short. Many new Francisella isolates have been identified globally. However, their species designations and potential for causing human disease remain ambiguous. Through detailed genome comparisons, we identified features that differentiate F. tularensis from clinical and environmental Francisella isolates and provide a knowledge base for future comparison of Francisella organisms identified in clinical samples or environmental surveys.

Download Full-text

Pseudomonas bijieensis sp. nov., isolated from cornfield soil

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004676 ◽

2019 ◽

Vol 71 (3) ◽

Cited By ~ 4

Author(s):

Jingling Liang ◽

Sai Wang ◽

Ayizekeranmu Yiming ◽

Luoyi Fu ◽

Iftikhar Ahmad ◽

...

Keyword(s):

16S Rrna ◽

Type Species ◽

Novel Species ◽

Guizhou Province ◽

Rrna Gene ◽

Gene Sequences ◽

Content Type ◽

Link Type ◽

Pr China ◽

Genome Comparisons

Strain L22-9T, a Gram-stain-negative and rod-shaped bacterium, motile by one polar flagellum, was isolated from cornfield soil in Bijie, Guizhou Province, PR China. Based on 16S rRNA gene sequences, it was identified as a Pseudomonas species. Multilocus sequence analysis of concatenated 16S rRNA, gyrB, rpoB and rpoD gene sequences showed that strain L22-9T formed a clearly separated branch, located in a cluster together with Pseudomonas brassicacearum LMG 21623T, Pseudomonas kilonensis DSM 13647T and Pseudomonas thivervalensis DSM 13194T. Whole-genome comparisons based on average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) confirmed that strain L22-9T should be classified as a novel species. It was most closely related to P. kilonensis DSM 13647T with ANI and dDDH values of 91.87 and 46.3 %, respectively. Phenotypic features that can distinguish strain L22-9T from P. kilonensis DSM 13647T are the assimilation ability of N-acetyl-d-glucosamine, poor activity of arginine dihydrolase and failure to ferment ribose and d-fucose. The predominant cellular fatty acids of strain L22-9T are C16 : 0, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The respiratory quinones consist of Q-9 and Q-8. The polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, two unidentified phosphoglycolipids, two unidentified aminophospholipids and an unidentified glycolipid. Based on the evidence, we conclude that strain L22-9T represents a novel species, for which the name Pseudomonas bijieensis sp. nov. is proposed. The type strain is L22-9T (=CGMCC 1.18528T=LMG 31948T), with a DNA G+C content of 60.85 mol%.

Download Full-text

Lysinibacillus antri sp. nov., isolated from cave soil

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004169 ◽

2020 ◽

Vol 70 (5) ◽

pp. 3295-3299 ◽

Cited By ~ 4

Author(s):

Manik Prabhu Narsing Rao ◽

Zhou-Yan Dong ◽

Xue-Ke Niu ◽

Kun Zhang ◽

Ying-Qian Kang ◽

...

Keyword(s):

Cell Wall ◽

Novel Species ◽

Guizhou Province ◽

Species Delineation ◽

Gram Stain ◽

West China ◽

Content Type ◽

South West ◽

Optimum Ph ◽

Genome Comparisons

A Gram-stain-positive, motile, rod-shaped and endospore-forming strain, SYSU K30002T, was isolated from a soil sample collected from a karst cave in Xingyi county, Guizhou province, south-west China. SYSU K30002T grew at 28–40 °C (optimum, 37 °C), at pH 5.0–8.0 (optimum, pH 7.0) and in the presence of 0–4 % (w/v) NaCl (optimum in the absence of NaCl). The cell-wall peptidoglycan type was A4α (Lys–Asp). The cell-wall sugars of SYSU K30002T were ribose, galactose and mannose, and MK-7 was the menaquinone. The major fatty acids were iso-C15 : 0, C16 : 1 ω7c alcohol and iso-C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and two unidentified phospholipids. The G+C content of the genomic DNA was 36.1 mol%. The average nucleotide identity values between SYSU K30002T and its closest relatives were below the cut-off level (95–96 %) for species delineation. Based on phenotypic, chemotaxonomic and genome comparisons, strain SYSU K30002T represents a novel species of the genus Lysinibacillus , for which the name Lysinibacillusantri sp. nov. is proposed. The type strain is SYSU K30002T (=KCTC 33955T=CGMCC 1.13504T).

Download Full-text

Whole genome comparisons of Staphylococcus agnetis isolates from cattle and chickens

10.1101/2020.01.06.896779 ◽

2020 ◽

Author(s):

Abdulkarim Shwani ◽

Pamela R. F. Adkins ◽

Nnamdi S. Ekesi ◽

Adnan Alrubaye ◽

Michael J. Calcutt ◽

...

Keyword(s):

Dairy Cattle ◽

Phylogenetic Trees ◽

University Of Missouri ◽

Commercial Broiler ◽

Chicken Isolate ◽

Broiler Farm ◽

Molecular Relationships ◽

The University ◽

The Relationship ◽

Genome Comparisons

AbstractS. agnetis has been previously associated with subclinical or clinically mild cases of mastitis in dairy cattle and is one of several Staphylococcal species that have been isolated from the bone and blood of lame broilers. We were the first to report that S. agnetis could be obtained frequently from bacterial chondronecrosis with osteomyelitis (BCO) lesions of lame broilers. Further, we showed that a particular isolate of S. agnetis, chicken isolate 908, can induce lameness in over 50% of exposed chickens, far exceeding normal BCO incidences in broiler operations. We have previously reported the assembly and annotation of the genome of isolate 908. To better understand the relationship between dairy cattle and broiler isolates, we assembled 11 additional genomes for S. agnetis isolates, including an additional chicken BCO strain, and ten isolates from milk, mammary gland secretions or udder skin, from the collection at the University of Missouri. To trace phylogenetic relationships, we constructed phylogenetic trees based on multi-locus sequence typing, and Genome-to-Genome Distance Comparisons. Chicken isolate 908 clustered with two of the cattle isolates along with three isolates from chickens in Denmark and an isolate of S. agnetis we isolated from a BCO lesion on a commercial broiler farm in Arkansas. We used a number of BLAST tools to compare the chicken isolates to those from cattle and identified 98 coding sequences distinguishing isolate 908 from the cattle isolates. None of the identified genes explain the differences in host or tissue tropism. These analyses are critical to understanding how Staphylococci colonize and infect different hosts and potentially how they can transition to alternative niches (bone vs dermis).ImportanceStaphylococcus agnetis has been recently recognized as associated with disease in dairy cattle and meat type chickens. The infections appear to be limited in cattle and systemic in broilers. This report details the molecular relationships between cattle and chicken isolates in order to understand how this recently recognized species infects different hosts with different disease manifestations. The data show the chicken and cattle isolates are very closely related but the chicken isolates all cluster together suggesting a single jump from cattle to chickens.

Download Full-text

Evolution of Traits Deduced from Genome Comparisons

Encyclopedia of Life Sciences ◽

10.1002/9780470015902.a0021746 ◽

2009 ◽

Author(s):

Jenny Tung ◽

Gregory A Wray

Keyword(s):

Genome Comparisons

Download Full-text

Whole-Genome k-mer Topic Modeling Associates Bacterial Families

Genes ◽

10.3390/genes11020197 ◽

2020 ◽

Vol 11 (2) ◽

pp. 197

Author(s):

Ernesto Borrayo ◽

Isaias May-Canche ◽

Omar Paredes ◽

J. Alejandro Morales ◽

Rebeca Romo-Vázquez ◽

...

Keyword(s):

Topic Modeling ◽

Latent Dirichlet Allocation ◽

Hierarchical Classification ◽

Whole Genome Sequence ◽

Whole Genome ◽

Sequence Comparisons ◽

Alignment Free ◽

Biological Phenomena ◽

Topic Distribution ◽

Genome Comparisons

Alignment-free k-mer-based algorithms in whole genome sequence comparisons remain an ongoing challenge. Here, we explore the possibility to use Topic Modeling for organism whole-genome comparisons. We analyzed 30 complete genomes from three bacterial families by topic modeling. For this, each genome was considered as a document and 13-mer nucleotide representations as words. Latent Dirichlet allocation was used as the probabilistic modeling of the corpus. We where able to identify the topic distribution among analyzed genomes, which is highly consistent with traditional hierarchical classification. It is possible that topic modeling may be applied to establish relationships between genome’s composition and biological phenomena.

Download Full-text