Complete genomic sequence and phylogenomics analysis of Agrobacterium strain AB2/73: a new Rhizobium species with a unique mega-Ti plasmid

Abstract Background The Agrobacterium strain AB2/73 has a unique host range for the induction of crown gall tumors, and contains an exceptionally large, over 500 kbp mega Ti plasmid. We used whole genome sequencing to fully characterize and comparatively analyze the complex genome of strain AB2/73, including its Ti plasmid and virulence factors. Results We obtained a high-quality, full genomic sequence of AB2/73 by a combination of short-read Illumina sequencing and long-read Nanopore sequencing. The AB2/73 genome has a total size of 7,266,754 bp with 59.5% GC for which 7012 genes (6948 protein coding sequences) are predicted. Phylogenetic and comparative genomics analysis revealed that strain AB2/73 does not belong to the genus Agrobacterium, but to a new species in the genus Rhizobium, which is most related to Rhizobium tropici. In addition to the chromosome, the genome consists of 6 plasmids of which the largest two, of more than 1 Mbp, have chromid-like properties. The mega Ti plasmid is 605 kbp in size and contains two, one of which is incomplete, repABC replication units and thus appears to be a cointegrate consisting of about 175 kbp derived from an unknown Ti plasmid linked to 430 kbp from another large plasmid. In pTiAB2/73 we identified a complete set of virulence genes and two T-DNAs. Besides the previously described T-DNA we found a larger, second T-DNA containing a 6b-like onc gene and the acs gene for agrocinopine synthase. Also we identified two clusters of genes responsible for opine catabolism, including an acc-operon for agrocinopine degradation, and genes putatively involved in ridéopine catabolism. The plasmid also harbours tzs, iaaM and iaaH genes for the biosynthesis of the plant growth regulators cytokinin and auxin. Conclusions The comparative genomics analysis of the high quality genome of strain AB2/73 provided insight into the unusual phylogeny and genetic composition of the limited host range Agrobacterium strain AB2/73. The description of its unique genomic composition and of all the virulence determinants in pTiAB2/73 will be an invaluable tool for further studies into the special host range properties of this bacterium.

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Complete Genomic Sequence and Phylogenomics Analysis of Agrobacterium Strain AB2/73: A New Rhizobium Species with a Unique mega-Ti Plasmid

10.21203/rs.3.rs-635723/v1 ◽

2021 ◽

Author(s):

Marjolein J.G. Hooykaas ◽

Paul J.J. Hooykaas

Keyword(s):

Comparative Genomics ◽

Host Range ◽

Genomic Sequence ◽

Ti Plasmid ◽

Virulence Determinants ◽

High Quality ◽

Agrobacterium Strain ◽

Total Size ◽

Full Genomic Sequence ◽

Comparative Genomics Analysis

Abstract Background: The Agrobacterium strain AB2/73 has a unique host range for the induction of crown gall tumors, and contains an exceptionally large, over 500 kbp mega Ti plasmid. We used whole genome sequencing to fully characterize and comparatively analyze the complex genome of strain AB2/73, including its Ti plasmid and virulence factors. Results: We obtained a high-quality, full genomic sequence of AB2/73 by a combination of short-read Illumina sequencing and long-read Nanopore sequencing. The AB2/73 genome has a total size of 7,266,754 bp with 59.5% GC for which 7,012 genes (6,948 protein coding sequences) are predicted. Phylogenetic and comparative genomics analysis revealed that strain AB2/73 does not belong to the genus Agrobacterium, but to a new species in the genus Rhizobium, which is most related to Rhizobium tropici. In addition to the chromosome, the genome consists of 6 plasmids of which the largest two, of more than 1 Mbp, have chromid-like properties. The mega Ti plasmid is 605 kbp in size and contains two, one of which is incomplete, repABC replication units and thus appears to be a cointegrate consisting of about 175 kbp derived from an unknown Ti plasmid linked to 430 kbp from another large plasmid. In pTiAB2/73 we identified a complete set of virulence genes and two T-DNAs. Besides the previously described T-DNA we found a larger, second T-DNA containing a 6b-like onc gene and the acs gene for agrocinopine synthase. Also we identified two clusters of genes responsible for opine catabolism, including an acc-operon for agrocinopine degradation, and genes putatively involved in ridéopine catabolism. The plasmid also harbours tzs, iaaM and iaaH genes for the biosynthesis of the plant growth regulators cytokinin and auxin. Conclusions: The comparative genomics analysis of the high quality genome of strain AB2/73 provided insight into the unusual phylogeny and genetic composition of the limited host range Agrobacterium strain AB2/73. The description of its unique genomic composition and of all the virulence determinants in pTiAB2/73 will be an invaluable tool for further studies into the special host range properties of this bacterium.

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Fine mapping of the wheat powdery mildew resistance gene Pm52 using comparative genomics analysis and the Chinese Spring reference genomic sequence

Theoretical and Applied Genetics ◽

10.1007/s00122-019-03291-7 ◽

2019 ◽

Vol 132 (5) ◽

pp. 1451-1461 ◽

Cited By ~ 8

Author(s):

Peipei Wu ◽

Jinghuang Hu ◽

Jingwei Zou ◽

Dan Qiu ◽

Yunfeng Qu ◽

...

Keyword(s):

Comparative Genomics ◽

Powdery Mildew ◽

Resistance Gene ◽

Fine Mapping ◽

Chinese Spring ◽

Powdery Mildew Resistance ◽

Genomic Sequence ◽

Powdery Mildew Resistance Gene ◽

Mildew Resistance ◽

Comparative Genomics Analysis

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Faculty Opinions recommendation of New classes of self-cleaving ribozymes revealed by comparative genomics analysis.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.725633870.793508844 ◽

2015 ◽

Author(s):

Robert Batey

Keyword(s):

Comparative Genomics ◽

Comparative Genomics Analysis

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Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity

Journal of Fungi ◽

10.3390/jof7050337 ◽

2021 ◽

Vol 7 (5) ◽

pp. 337

Author(s):

Daniel Peterson ◽

Tang Li ◽

Ana M. Calvo ◽

Yanbin Yin

Keyword(s):

Comparative Genomics ◽

Orthologous Gene ◽

Gene Clusters ◽

Phytopathogenic Fungi ◽

Secreted Proteins ◽

Economic Losses ◽

Comparative Genomic ◽

Signal Peptides ◽

Comparative Genomics Analysis

Phytopathogenic Ascomycota are responsible for substantial economic losses each year, destroying valuable crops. The present study aims to provide new insights into phytopathogenicity in Ascomycota from a comparative genomic perspective. This has been achieved by categorizing orthologous gene groups (orthogroups) from 68 phytopathogenic and 24 non-phytopathogenic Ascomycota genomes into three classes: Core, (pathogen or non-pathogen) group-specific, and genome-specific accessory orthogroups. We found that (i) ~20% orthogroups are group-specific and accessory in the 92 Ascomycota genomes, (ii) phytopathogenicity is not phylogenetically determined, (iii) group-specific orthogroups have more enriched functional terms than accessory orthogroups and this trend is particularly evident in phytopathogenic fungi, (iv) secreted proteins with signal peptides and horizontal gene transfers (HGTs) are the two functional terms that show the highest occurrence and significance in group-specific orthogroups, (v) a number of other functional terms are also identified to have higher significance and occurrence in group-specific orthogroups. Overall, our comparative genomics analysis determined positive enrichment existing between orthogroup classes and revealed a prediction of what genomic characteristics make an Ascomycete phytopathogenic. We conclude that genes shared by multiple phytopathogenic genomes are more important for phytopathogenicity than those that are unique in each genome.

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Comparative genomics suggests a taxonomic revision of the Staphylococcus cohnii species complex

Genome Biology and Evolution ◽

10.1093/gbe/evab020 ◽

2021 ◽

Author(s):

Anna Lavecchia ◽

Matteo Chiara ◽

Caterina De Virgilio ◽

Caterina Manzari ◽

Carlo Pazzani ◽

...

Keyword(s):

Comparative Genomics ◽

Species Complex ◽

Large Scale ◽

Genomic Sequence ◽

Bacterial Species ◽

Taxonomic Revision ◽

Distinct Species ◽

The Novel ◽

Staphylococcus Cohnii ◽

Taxonomic Assignments

Abstract Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.

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Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level

Frontiers in Microbiology ◽

10.3389/fmicb.2016.00998 ◽

2016 ◽

Vol 7 ◽

Cited By ~ 19

Author(s):

Xinpeng Tian ◽

Zhewen Zhang ◽

Tingting Yang ◽

Meili Chen ◽

Jie Li ◽

...

Keyword(s):

Comparative Genomics ◽

Marine Environment ◽

Streptomyces Species ◽

Genomic Level ◽

Comparative Genomics Analysis

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Genome of Deerpox Virus

Journal of Virology ◽

10.1128/jvi.79.2.966-977.2005 ◽

2005 ◽

Vol 79 (2) ◽

pp. 966-977 ◽

Cited By ~ 42

Author(s):

C. L. Afonso ◽

G. Delhon ◽

E. R. Tulman ◽

Z. Lu ◽

A. Zsak ◽

...

Keyword(s):

Host Range ◽

Chemokine Receptors ◽

Transforming Growth Factor ◽

Genomic Sequence ◽

Core Protein ◽

Interleukin 1 ◽

Transforming Growth Factor Β1 ◽

Open Reading Frames ◽

Host Responses ◽

Tgf Β1

ABSTRACT Deerpox virus (DPV), an uncharacterized and unclassified member of the Poxviridae, has been isolated from North American free-ranging mule deer (Odocoileus hemionus) exhibiting mucocutaneous disease. Here we report the genomic sequence and comparative analysis of two pathogenic DPV isolates, W-848-83 (W83) and W-1170-84 (W84). The W83 and W84 genomes are 166 and 170 kbp, containing 169 and 170 putative genes, respectively. Nucleotide identity between DPVs is 95% over the central 157 kbp. W83 and W84 share similar gene orders and code for similar replicative, structural, virulence, and host range functions. DPV open reading frames (ORFs) with putative virulence and host range functions include those similar to cytokine receptors (R), including gamma interferon receptor (IFN-γR), interleukin 1 receptor (IL-1R), and type 8 CC-chemokine receptors; cytokine binding proteins (BP), including IL-18BP, IFN-α/βBP, and tumor necrosis factor binding protein (TNFBP); serpins; and homologues of vaccinia virus (VACV) E3L, K3L, and A52R proteins. DPVs also encode distinct forms of major histocompatibility complex class I, C-type lectin-like protein, and transforming growth factor β1 (TGF-β1), a protein not previously described in a mammalian chordopoxvirus. Notably, DPV encodes homologues of cellular endothelin 2 and IL-1R antagonist, novel poxviral genes also likely involved in the manipulation of host responses. W83 and W84 differ from each other by the presence or absence of five ORFs. Specifically, homologues of a CD30 TNFR family protein, swinepox virus SPV019, and VACV E11L core protein are absent in W83, and homologues of TGF-β1 and lumpy skin disease virus LSDV023 are absent in W84. Phylogenetic analysis indicates that DPVs are genetically distinct from viruses of other characterized poxviral genera and that they likely comprise a new genus within the subfamily Chordopoxvirinae.

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