scholarly journals Genome assembly of the A-group Wolbachia in Nasonia oneida and phylogenomic analysis of Wolbachia strains reveals patterns of genome evolution and lateral gene transfer

2018 ◽  
Author(s):  
Xiaozhu Wang ◽  
Xiao Xiong ◽  
Wenqi Cao ◽  
Chao Zhang ◽  
John H. Werren ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Intracellular Bacteria ◽  
Whole Genome ◽  
Gene Duplications ◽  
Strain Variation ◽  
Wasp Species ◽  
Arthropod Species

AbstractWolbachia are obligate intracellular bacteria which commonly infect various nematode and arthropod species. Based on depth differences, we assembled the genome of Wolbachia in the parasitoid jewel wasp species Nasonia oneida (wOne), using 10X Genomics Chromium linked-read technology. The final draft assembly consists of 1,293,406 bp in 47 scaffolds with 1,114 coding genes and 97.01% genome completeness assessed by checkM. wOne is the A1 strain previously reported in N. oneida, and pyrosequencing confirms that the wasp strain lacks A2 and B types, which were likely lost during laboratory culturing. Polymorphisms identified in the wOneA1 genome have elevated read depths, indicating recent gene duplications rather that strain variation. These polymorphisms are enriched in nonsynonymous changes in 27 coding genes, including phase baseplate assembly proteins and transporter activity related genes. wOneA1 is more closely grouped with A-Wolbachia in the Drosophila simulans (wHa) than A-Wolbachia found in wasps. Genome variation was next evaluated in 34 published Wolbachia genomes for 211 single ortholog genes, and revealed six supergroup discordant trees, indicating recombination events not only between A and B supergroups, but also between A and E supergroups. Comparisons of strain divergence using the five genes of the Multi Locus Strain Typing (MLST) system show a high correlation (rho=0.98) between MLST and whole genome divergences, indicating that MLST is a reliable method for identifying related strains when whole genome data are not available. Assembling bacterial genomes from host genome projects can provide an effective method for sequencing Wolbachia genomes and characterizing their diversity.Author SummaryMore than half of the arthropod species are infected by the obligated intracellular bacteria Wolbachia. As one of the most widespread parasitic microbes, Wolbachia mediate important biological processes such as cytoplasmic incompatibility and lateral gene transfer in insects. Their evolutionary relationship has been characterize using five protein-coding and 16S rRNA genes. In this work, we identified 211 conserved single copies genes in 34 genome sequenced Wolbachia strains, and we discovered that they maintain the supergroup relationship classified previously based on selected genes. We constructed phylogenetic trees for individual genes and found only six genes display discordant tree structure between supergroups, due to lateral gene transfer and homologous recombination events. But these events are not common (3%) in Wolbachia genomes, at least in these conserved single copy genes. In addition to known lateral gene transfer events between A and B supergroups, we identified transfers between A and E supergroups for the first time. Selective maintenance of such transfers suggests possible roles in Wolbachia infection related functions. We also found enriched nonsynonymous polymorphisms in Nasonia oneida Wobachia genome, and their differences are more likely to result from gene duplications within the strain, rather than strain variation within the parasitoid.

scholarly journals Genome Assembly of the A-Group Wolbachia in Nasonia oneida Using Linked-Reads Technology

2019 ◽  
Vol 11 (10) ◽  
pp. 3008-3013 ◽  
Author(s):  
Xiaozhu Wang ◽  
Xiao Xiong ◽  
Wenqi Cao ◽  
Chao Zhang ◽  
John H Werren ◽  
...  
Keyword(s):  
Read Depth ◽  
Intracellular Bacteria ◽  
Bacterial Genomes ◽  
Wasp Species ◽  
Draft Assembly ◽  
Arthropod Species ◽  
Low Concentrations ◽  
Wolbachia Genome ◽  
Obligate Intracellular Bacteria ◽  
Laboratory Culturing

Abstract Wolbachia are obligate intracellular bacteria which commonly infect various nematode and arthropod species. Genome sequences have been generated from arthropod samples following enrichment for the intracellular bacteria, and genomes have also been assembled from arthropod whole-genome sequencing projects. However, these methods remain challenging for infections that occur at low titers in hosts. Here we report the first Wolbachia genome assembled from host sequences using 10× Genomics linked-reads technology. The high read depth attainable by this method allows for recovery of intracellular bacteria that are at low concentrations. Based on the depth differences (714× for the insect and 59× for the bacterium), we assembled the genome of a Wolbachia in the parasitoid jewel wasp species Nasonia oneida. The final draft assembly consists of 1,293, 06 bp in 47 scaffolds with 1,114 coding genes and 97.01% genome completeness assessed by checkM. Comparisons of the five Multi Locus Sequence Typing genes revealed that the sequenced Wolbachia genome is the A1 strain (henceforth wOneA1) previously reported in N. oneida. Pyrosequencing confirms that the wasp strain lacks A2 and B types previously detected in this insect, which were likely lost during laboratory culturing. Assembling bacterial genomes from host genome projects can provide an effective method for sequencing bacterial genomes, even when the infections occur at low density in sampled tissues.

scholarly journals Acinetobacter portensis sp. nov. and Acinetobacter guerrae sp. nov., isolated from raw meat

2020 ◽  
Vol 70 (8) ◽  
pp. 4544-4554 ◽  
Author(s):  
Ana Carvalheira ◽  
Lucia Gonzales-Siles ◽  
Francisco Salvà-Serra ◽  
Åsa Lindgren ◽  
Liselott Svensson-Stadler ◽  
...  
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Taxonomic Status ◽  
Cellular Fatty Acid ◽  
16S Rrna Genes ◽  
Whole Genome Sequence ◽  
Rrna Genes ◽  
Whole Genome ◽  
Content Type ◽  
Link Type

The taxonomic status of six strains of Acinetobacter obtained from meat samples, collected from supermarkets in Porto, Portugal, was investigated using polyphasic analysis. Partial rpoB sequence similarities lower than 95 % to other Acinetobacter species with validly published names led to the hypothesis that these strains represented novel species. This was confirmed based on comparative multilocus sequence analysis, which included the gyrB, recA and 16S rRNA genes, revealing that these strains represented two coherent lineages that were distinct from each other and from all known species. The names Acinetobacter portensis sp. nov. (comprising four strains) and Acinetobacter guerrae sp. nov. (comprising two strains) are proposed for these novel species. The species status of these two groups was confirmed by low (below 95 %) whole-genome sequence average nucleotide identity values and low (below 70 %) digital DNA–DNA hybridization similarities between the whole-genome sequences of the proposed type strains of each novel species and the representatives of the known Acinetobacter species. Phylogenomic treeing from core genome analysis supported these results. The coherence of each new species lineage was supported by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry differentiation of the species at the protein level, by cellular fatty acid profiles, and by unique and differential combinations of metabolic and physiological properties shared by each novel species. The type strain of A. portensis sp. nov. is AC 877T (=CCUG 68672T=CCM 8789T) and the type strain of A. guerrae sp. nov. is AC 1271T (=CCUG 68674T=CCM 8791T).

scholarly journals Intracellular Symbionts and Other Bacteria Associated with Deer Ticks (Ixodes scapularis) from Nantucket and Wellfleet, Cape Cod, Massachusetts

2004 ◽  
Vol 70 (1) ◽  
pp. 616-620 ◽  
Author(s):  
Micah J. Benson ◽  
Jeffrey D. Gawronski ◽  
Douglas E. Eveleigh ◽  
David R. Benson
Keyword(s):  
16S Rrna ◽  
Ixodes Scapularis ◽  
Pcr Amplification ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Cape Cod ◽  
Intracellular Bacteria ◽  
Cloning And Sequencing ◽  
Gram Negative ◽  
Insect Symbionts

ABSTRACT The diversity of bacteria associated with the deer tick (Ixodes scapularis) was assessed using PCR amplification, cloning, and sequencing of 16S rRNA genes originating from seven ticks collected from Nantucket Island and Wellfleet, Cape Cod, Mass. The majority of sequences obtained originated from gram-negative proteobacteria. Four intracellular bacteria were detected including strains of Ehrlichia, Rickettsia, and Wolbachia and an organism related to intracellular insect symbionts from the Cytophaga-Flavobacterium-Bacteroides group. Several strains of members of the Sphingomonadaceae were also detected in all but one tick. The results provide a view of the diversity of bacteria associated with I. scapularis ticks in the field.

scholarly journals Lateral gene transfer between obligate intracellular bacteria: Evidence from the Rickettsia massiliae genome

2007 ◽  
Vol 17 (11) ◽  
pp. 1657-1664 ◽  
Author(s):  
G. Blanc ◽  
H. Ogata ◽  
C. Robert ◽  
S. Audic ◽  
J.-M. Claverie ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Intracellular Bacteria ◽  
Obligate Intracellular ◽  
Rickettsia Massiliae ◽  
Obligate Intracellular Bacteria

scholarly journals Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes

Science ◽  
2007 ◽  
Vol 317 (5845) ◽  
pp. 1753-1756 ◽  
Author(s):  
J. C. D. Hotopp ◽  
M. E. Clark ◽  
D. C. S. G. Oliveira ◽  
J. M. Foster ◽  
P. Fischer ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Intracellular Bacteria

scholarly journals A dual endosymbiosis drives nutritional adaptation to hematophagy in the invasive tick Hyalomma marginatum

2021 ◽  
Author(s):  
Marie Buysse ◽  
Anna Maria Floriano ◽  
Yuval Gottlieb ◽  
Tiago Nardi ◽  
Francesco Comandatore ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Tick Species ◽  
Intracellular Bacteria ◽  
Bacterial Symbionts ◽  
Riboflavin Biosynthesis ◽  
Agricultural Pests ◽  
Symbiotic Interactions ◽  
Hyalomma Marginatum ◽  
Plant Sap

Many animals are dependent on microbial partners that provide essential nutrients lacking from their diet. Ticks, whose diet consists exclusively on vertebrate blood, rely on maternally inherited bacterial symbionts to supply B vitamins. While previously studied tick species consistently harbor a single lineage of those nutritional symbionts, we evidence here that the invasive tick Hyalomma marginatum harbors a unique dual-partner nutritional system between an ancestral symbiont, Francisella, and a more recently acquired symbiont, Midichloria. Using metagenomics, we show that Francisella exhibits extensive genome erosion that endangers the nutritional symbiotic interactions: Its genome includes folate and riboflavin biosynthesis pathways but deprived functional biotin biosynthesis on account of massive pseudogenization. Co-symbiosis compensates this deficiency since the Midichloria genome encompasses an intact biotin operon, which was primarily acquired via lateral gene transfer from unrelated intracellular bacteria commonly infecting arthropods. Thus, in H. marginatum, a mosaic of co-evolved symbionts incorporating gene combinations of distant phylogenetic origins emerged to prevent the collapse of an ancestral nutritional symbiosis. Such dual endosymbiosis was never reported in other blood feeders but was recently documented in agricultural pests feeding on plant sap, suggesting that it may be a key mechanism for advanced adaptation of arthropods to specialized diets.

scholarly journals Reclassification of Catabacter hongkongensis as Christensenella hongkongensis comb.nov. based on whole genome analysis

2020 ◽  
Author(s):  
Xiaoying Liu ◽  
Jessica L. Sutter ◽  
Jacobo de la Cuesta-Zuluaga ◽  
Jillian L. Waters ◽  
Nicholas D. Youngblut ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Genus ◽  
Evolutionary Relationship ◽  
Protein Sequences ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Strictly Anaerobic ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Close Relatives

AbstractThe genera Catabacter (family Catabacteraceae) and Christensenella (family Christensenellaceae) are close relatives within the phylum Firmicutes. Members of these genera are strictly anaerobic, non-spore forming, short straight rods with diverse phenotypes. Phylogenetic analysis of 16S rRNA genes suggest that Catabacter splits Christensenella into a polyphyletic clade. In an effort to ensure that family/genus names represent monophyletic clades, we performed a whole-genome based analysis of the genomes available for the cultured representatives of these genera: four species of Christensenella and two strains of Catabacter hongkongensis. A concatenated alignment of 135 shared protein sequences indicates that C. hongkongensis is indeed nested within the Christensenella clade. Based on their evolutionary relationship, we propose the transfer of Catabacter hongkongensis to the new genus as Christensenella hongkongensis comb.nov.

scholarly journals A Genome-Based Species Taxonomy of the Lactobacillus Genus Complex

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Stijn Wittouck ◽  
Sander Wuyts ◽  
Conor J. Meehan ◽  
Vera van Noort ◽  
Sarah Lebeer
Keyword(s):  
16S Rrna ◽  
Species Delimitation ◽  
De Novo ◽  
Species Level ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Whole Genome ◽  
Genome Sequences ◽  
Species Taxonomy ◽  
Type Strains

ABSTRACT There are more than 200 published species within the Lactobacillus genus complex (LGC), the majority of which have sequenced type strain genomes available. Although genome-based species delimitation cutoffs are accepted as the gold standard by the community, these are seldom actually checked for new or already published species. In addition, the availability of genome data is revealing inconsistencies in the species-level classification of many strains. We constructed a de novo species taxonomy for the LGC based on 2,459 publicly available genomes, using a 94% core nucleotide identity cutoff. We reconciled these de novo species with published species and subspecies names by (i) identifying genomes of type strains and (ii) comparing 16S rRNA genes of the genomes with 16S rRNA genes of type strains. We found that genomes within the LGC could be divided into 239 de novo species that were discontinuous and exclusive. Comparison of these de novo species to published species led to the identification of nine sets of published species that can be merged and one species that can be split. Further, we found at least eight de novo species that constitute new, unpublished species. Finally, we reclassified 74 genomes on the species level and identified for the first time the species of 98 genomes. Overall, the current state of LGC species taxonomy is largely consistent with genome-based species delimitation cutoffs. There are, however, exceptions that should be resolved to evolve toward a taxonomy where species share a consistent diversity in terms of sequence divergence. IMPORTANCE The Lactobacillus genus complex is a group of bacteria that constitutes an important source of strains with medical and food applications. The number of bacterial whole-genome sequences available for this taxon has been increasing rapidly in recent years. Despite this wealth of information, the species within this group are still largely defined by older techniques. Here, we constructed a completely new species-level taxonomy for the Lactobacillus genus complex based on ∼2,500 whole-genome sequences. As a result of this effort, we found that many genomes are not classified to their correct species, and we were able to correct these. In addition, we found that some published species are abnormally large, while others are too small. Finally, we discovered at least eight completely novel species that have not been published before. Our work will help the field to evolve toward a more meaningful and complete taxonomy, based on whole-genome sequences.

Classification of three corynebacterial strains isolated from a small paddock in North Rhine-Westphalia: proposal of Corynebacterium kalinowskii sp. nov., Corynebacterium comes sp. nov. and Corynebacterium occultum sp. nov.

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Lena Schaffert ◽  
Matthias Ruwe ◽  
Johanna Milse ◽  
Katharina Hanuschka ◽  
Vera Ortseifen ◽  
...  
Keyword(s):  
Genome Structure ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Phenotypic Characterization ◽  
Whole Genome ◽  
Content Type ◽  
Link Type ◽  
Yellow Orange

Three novel corynebacterial species were isolated from soil sampled at a paddock in Vilsendorf, North Rhine-Westphalia, Germany. The strains were coccoid or irregular rod-shaped, catalase-positive and pale white to yellow-orange in colour. By whole genome sequencing and comparison of the 16S rRNA genes as well as the whole genome structure, it was shown that all three strains represent novel species of the family Corynebacteriaceae , order Corynebacteriales , class Actinobacteria . This project describes the isolation, identification, sequencing, and phenotypic characterization of the three novel Corynebacterium species. We propose the names Corynebacterium kalinowskii sp. nov. (DSM 110639T=LMG 31801T), Corynebacterium comes sp. nov. (DSM 110640T=LMG 31802T), and Corynebacterium occultum sp. nov. (DSM 110642T=LMG 31803T).

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