Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria

Understanding the population structure and genetic diversity of plant pathogens, as well as the effect of agricultural practices on pathogen evolution, is important for disease management. Developments in molecular methods have contributed to increase the resolution for accurate pathogen identification, but those based on analysis of DNA sequences can be less straightforward to use. To address this, we developed Gall-ID, a web-based platform that uses DNA sequence information from 16S rDNA, multilocus sequence analysis and whole genome sequences to group disease-associated bacteria to their taxonomic units. Gall-ID was developed with a particular focus on gall-forming bacteria belonging toAgrobacterium,Pseudomonas savastanoi,Pantoea agglomerans, andRhodococcus. Members of these groups of bacteria cause growth deformation of plants, and some are capable of infecting many species of field, orchard, and nursery crops. Gall-ID also enables the use of high-throughput sequencing reads to search for evidence for homologs of characterized virulence genes, and provides downloadable software pipelines for automating multilocus sequence analysis, analyzing genome sequences for average nucleotide identity, and constructing core genome phylogenies. Lastly, additional databases were included in Gall-ID to help determine the identity of other plant pathogenic bacteria that may be in microbial communities associated with galls or causative agents in other diseased tissues of plants. The URL for Gall-ID ishttp://gall-id.cgrb.oregonstate.edu/.

Download Full-text

Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria

10.7287/peerj.preprints.1998v3 ◽

2016 ◽

Author(s):

Edward W Davis II ◽

Alexandra J Weisberg ◽

Javier F Tabima ◽

Niklaus J. Grunwald ◽

Jeff Chang

Keyword(s):

Sequence Analysis ◽

Dna Sequences ◽

Pathogenic Bacteria ◽

Plant Pathogens ◽

High Throughput Sequencing ◽

Agricultural Practices ◽

Multilocus Sequence Analysis ◽

Sequence Information ◽

Genome Sequences ◽

Causative Agents

Understanding the population structure and genetic diversity of plant pathogens, as well as the effect of agricultural practices on pathogen evolution, are important for disease management. Developments in molecular methods have contributed to increasing the resolution for accurate pathogen identification but those based on analysis of DNA sequences can be less straightforward to use. To address this, we developed Gall-ID, a web-based platform that uses DNA sequence information from 16S rDNA, multilocus sequence analysis and whole genome sequences to group disease-associated bacteria to their taxonomic units. Gall-ID was developed with a particular focus on gall-forming bacteria belonging to Agrobacterium, Pseudomonas savastanoi, Pantoea agglomerans, and Rhodococcus. Members of these groups of bacteria cause growth deformation of plants, and some are capable of infecting many species of field, orchard, and nursery crops. Gall-ID also enables the use of high-throughput sequencing reads to search for evidence for homologs of characterized virulence genes, and provides downloadable software pipelines for automating multilocus sequence analysis, analyzing genome sequences for average nucleotide identity, and constructing core genome phylogenies. Lastly, additional databases were included in Gall-ID to help determine the identity of other plant pathogenic bacteria that may be in microbial communities associated with galls or causative agents in other diseased tissues of plants. The URL for Gall-ID is http://gall-id.cgrb.oregonstate.edu/.

Download Full-text

Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria

10.7287/peerj.preprints.1998v2 ◽

2016 ◽

Author(s):

Edward W Davis II ◽

Alexandra J Weisberg ◽

Javier F Tabima ◽

Niklaus J. Grunwald ◽

Jeff Chang

Keyword(s):

Sequence Analysis ◽

Dna Sequences ◽

Pathogenic Bacteria ◽

Plant Pathogens ◽

High Throughput Sequencing ◽

Agricultural Practices ◽

Multilocus Sequence Analysis ◽

Sequence Information ◽

Genome Sequences ◽

Causative Agents

Understanding the population structure and genetic diversity of plant pathogens, as well as the effect of agricultural practices on pathogen evolution, are important for disease management. Developments in molecular methods have contributed to increasing the resolution for accurate pathogen identification but those based on analysis of DNA sequences can be less straightforward to use. To address this, we developed Gall-ID, a web-based platform that uses DNA sequence information from 16S rDNA, multilocus sequence analysis and whole genome sequences to group disease-associated bacteria to their taxonomic units. Gall-ID was developed with a particular focus on gall-forming bacteria belonging to Agrobacterium, Pseudomonas savastanoi, Pantoea agglomerans, and Rhodococcus. Members of these groups of bacteria cause growth deformation of plants, and some are capable of infecting many species of field, orchard, and nursery crops. Gall-ID also enables the use of high-throughput sequencing reads to search for evidence for homologs of characterized virulence genes, and provides downloadable software pipelines for automating multilocus sequence analysis, analyzing genome sequences for average nucleotide identity, and constructing core genome phylogenies. Lastly, additional databases were included in Gall-ID to help determine the identity of other plant pathogenic bacteria that may be in microbial communities associated with galls or causative agents in other diseased tissues of plants. The URL for Gall-ID is http://gall-id.cgrb.oregonstate.edu/.

Download Full-text

Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria

10.7287/peerj.preprints.1998v1 ◽

2016 ◽

Author(s):

Edward W Davis ◽

Alexandra J Weisberg ◽

Javier F Tabima ◽

Niklaus J. Grunwald ◽

Jeff Chang

Keyword(s):

Sequence Analysis ◽

Dna Sequences ◽

Pathogenic Bacteria ◽

Plant Pathogens ◽

High Throughput Sequencing ◽

Agricultural Practices ◽

Multilocus Sequence Analysis ◽

Sequence Information ◽

Genome Sequences ◽

Causative Agents

Understanding the population structure and genetic diversity of plant pathogens, as well as the effect of agricultural practices on pathogen evolution, are important for disease management. Developments in molecular methods have contributed to increasing the resolution for accurate pathogen identification but those based on analysis of DNA sequences can be less straightforward to use. To address this, we developed Gall-ID, a web-based platform that uses DNA sequence information from 16S rDNA, multilocus sequence analysis and whole genome sequences to group disease-associated bacteria to their taxonomic units. Gall-ID was developed with a particular focus on gall-forming bacteria belonging to Agrobacterium, Pseudomonas savastanoi, Pantoea agglomerans, and Rhodococcus. Members of these groups of bacteria cause growth deformation of plants, and some are capable of infecting many species of field, orchard, and nursery crops. Gall-ID also enables the use of high-throughput sequencing reads to search for evidence for homologs of characterized virulence genes, and provides downloadable software pipelines for automating multilocus sequence analysis, analyzing genome sequences for average nucleotide identity, and constructing core genome phylogenies. Lastly, additional databases were included in Gall-ID to help determine the identity of other plant pathogenic bacteria that may be in microbial communities associated with galls or causative agents in other diseased tissues of plants. The URL for Gall-ID is http://gall-id.cgrb.oregonstate.edu/.

Download Full-text

The Diversity of Bacteria Associated with the Invasive Gall Wasp Dryocosmus kuriphilus, Its Galls and a Specialist Parasitoid on Chestnuts

Insects ◽

10.3390/insects13010086 ◽

2022 ◽

Vol 13 (1) ◽

pp. 86

Author(s):

Xiaohui Yang ◽

Yu Hui ◽

Daohong Zhu ◽

Yang Zeng ◽

Lvquan Zhao ◽

...

Keyword(s):

Pathogenic Bacteria ◽

Plant Pathogens ◽

High Throughput Sequencing ◽

Bacterial Species ◽

Gall Wasp ◽

Potential Vector ◽

Dryocosmus Kuriphilus ◽

Torymus Sinensis ◽

Galling Insects ◽

First Time

Dryocosmus kuriphilus (Hymenoptera: Cynipidae) induces galls on chestnut trees, which results in massive yield losses worldwide. Torymus sinensis (Hymenoptera: Torymidae) is a host-specific parasitoid that phenologically synchronizes with D. kuriphilus. Bacteria play important roles in the life cycle of galling insects. The aim of this research is to investigate the bacterial communities and predominant bacteria of D. kuriphilus, T. sinensis, D. kuriphilus galls and the galled twigs of Castanea mollissima. We sequenced the V5–V7 region of the bacterial 16S ribosomal RNA in D. kuriphilus, T. sinensis, D. kuriphilus galls and galled twigs using high-throughput sequencing for the first time. We provide the first evidence that D. kuriphilus shares most bacterial species with T. sinensis, D. kuriphilus galls and galled twigs. The predominant bacteria of D. kuriphilus are Serratia sp. and Pseudomonas sp. Furthermore, the bacterial community structures of D. kuriphilus and T. sinensis clearly differ from those of the other groups. Many species of the Serratia and Pseudomonas genera are plant pathogenic bacteria, and we suggest that D. kuriphilus may be a potential vector of plant pathogens. Furthermore, a total of 111 bacteria are common to D. kuriphilus adults, T. sinensis, D. kuriphilus galls and galled twigs, and we suggest that the bacteria may transmit horizontally among D. kuriphilus, T. sinensis, D. kuriphilus galls and galled twigs on the basis of their ecological associations.

Download Full-text

An integrated pipeline for NGS and annotation of the complete mitochondrial genome of the giant intestinal fluke, Fasciolopsis buski (Lankester,1857) Loss, 1899 (Digenea: Fasciolidae)

10.7287/peerj.preprints.58v1 ◽

2013 ◽

Author(s):

Devendra Kumar Biswal ◽

Sudeep Ghatani ◽

Jollin A Shylla ◽

Ranjana Sahu ◽

Nandita Mullapudi ◽

...

Keyword(s):

Mitochondrial Genome ◽

High Throughput ◽

Dna Sequences ◽

High Throughput Sequencing ◽

Fasciola Hepatica ◽

Whole Genome Sequence ◽

Genome Sequences ◽

Fasciolopsis Buski ◽

Mt Genome ◽

Control Regions

Helminths include both parasitic nematodes (roundworms) and platyhelminths (trematode and cestode flatworms) that are abundant, and are of clinical importance. The genetic characterization of parasitic flatworms using advanced molecular tools is central to the diagnosis and control of infections. Although the nuclear genome houses suitable genetic markers (e.g., in ribosomal (r) DNA) for species identification and molecular characterization, the mitochondrial (mt) genome consistently provides a rich source of novel markers for informative systematics and epidemiological studies. In the last decade, there have been some important advances in mtDNA genomics of helminths, especially lung flukes, liver flukes and intestinal flukes. Fasciolopsis buski, often called the giant intestinal fluke, is one of the largest digenean trematodes infecting humans and found primarily in Asia, in particular the Indian subcontinent. Next-generation sequencing (NGS) technologies now provide opportunities for high throughput sequencing, assembly and annotation within a short span of time. Herein, we describe a high-throughput sequencing and bioinformatics pipeline for mt genomics for F. buski that emphasizes the utility of short read NGS platforms such as Ion Torrent and Illumina in successfully sequencing and assembling the mt genome using innovative approaches for PCR primer design as well as assembly. We took advantage of our NGS whole genome sequence data (unpublished so far) for F. buski and its comparison with available data for the Fasciola hepatica mtDNA as the reference genome for design of precise and specific primers for amplification of mt genome sequences from F. buski. A long-range PCR was carried out to create a NGS library enriched in mt DNA sequences. Two different NGS platforms were employed for complete sequencing, assembly and annotation of the F. buski mt genome. The complete mt genome sequences of the intestinal fluke comprise 14,118 bp and is thus the shortest trematode mitochondrial genome sequenced to date. The noncoding control regions are separated into two parts by the tRNA-Gly gene and donot contain either tandem repeats or secondary structures, which are typical for trematode control regions. The gene content and arrangement are identical to that of F. hepatica. The F. buski mtDNA genome has a close resemblance with F. hepatica and has a similar gene order tallying with that of other trematodes. The mtDNA for the intestinal fluke is reported herein for the first time by our group that would help invesigate Fasciolidae taxonomy and systematics with the aid of mtDNA NGS data. More so, it would serve as a resource for comparative mitochondrial genomics and systematic studies of trematode parasites.

Download Full-text

Phylogenetic analysis of the pathogenic bacteria Spiroplasma penaei based on multilocus sequence analysis

Journal of Invertebrate Pathology ◽

10.1016/j.jip.2009.10.004 ◽

2010 ◽

Vol 103 (1) ◽

pp. 30-35 ◽

Cited By ~ 10

Author(s):

Allan Heres ◽

Donald V. Lightner

Keyword(s):

Phylogenetic Analysis ◽

Sequence Analysis ◽

Pathogenic Bacteria ◽

Multilocus Sequence Analysis

Download Full-text

Prophage Genomics

Microbiology and Molecular Biology Reviews ◽

10.1128/mmbr.67.2.238-276.2003 ◽

2003 ◽

Vol 67 (2) ◽

pp. 238-276 ◽

Cited By ~ 441

Author(s):

Carlos Canchaya ◽

Caroline Proux ◽

Ghislain Fournous ◽

Anne Bruttin ◽

Harald Brüssow

Keyword(s):

Pathogenic Bacteria ◽

Plant Pathogens ◽

Bacterial Genome ◽

Ecological Niches ◽

Host Bacterium ◽

Mobile Dna ◽

Genome Sequences ◽

Bacterial Genomes ◽

Gram Positive ◽

Gram Positive Bacteria

SUMMARY The majority of the bacterial genome sequences deposited in the National Center for Biotechnology Information database contain prophage sequences. Analysis of the prophages suggested that after being integrated into bacterial genomes, they undergo a complex decay process consisting of inactivating point mutations, genome rearrangements, modular exchanges, invasion by further mobile DNA elements, and massive DNA deletion. We review the technical difficulties in defining such altered prophage sequences in bacterial genomes and discuss theoretical frameworks for the phage-bacterium interaction at the genomic level. The published genome sequences from three groups of eubacteria (low- and high-G+C gram-positive bacteria and γ-proteobacteria) were screened for prophage sequences. The prophages from Streptococcus pyogenes served as test case for theoretical predictions of the role of prophages in the evolution of pathogenic bacteria. The genomes from further human, animal, and plant pathogens, as well as commensal and free-living bacteria, were included in the analysis to see whether the same principles of prophage genomics apply for bacteria living in different ecological niches and coming from distinct phylogenetical affinities. The effect of selection pressure on the host bacterium is apparently an important force shaping the prophage genomes in low-G+C gram-positive bacteria and γ-proteobacteria.

Download Full-text

Data mining of DNA sequences submitted by Peruvian institutions to public genetic databases

Revista Peruana de Biología ◽

10.15381/rpb.v28i1.17867 ◽

2021 ◽

Vol 28 (1) ◽

pp. e17867

Author(s):

Pedro Eduardo Romero ◽

Camila Castillo-Vilcahuaman

Keyword(s):

Genetic Diversity ◽

Dna Sequences ◽

Genetic Information ◽

Vibrio Parahaemolyticus ◽

Pathogenic Bacteria ◽

Pasteurella Multocida ◽

Genetic Research ◽

Sequence Information ◽

Taxonomic Groups ◽

Pathogenic Agents

Genetic diversity is an important component of biodiversity, and it is crucial for current efforts to protect and sustainably manage several organisms and habitats. As far as we know, there is only one work describing Peruvian genetic information stored in public databases. We aimed to update this previous work searching in four public databases that stored digital sequence information: Nucleotide, BioProject, PATRIC, BOLD. With this information, we comment on the contribution of Peruvian institutions during recent years. In Nucleotide, the largest database, Bacteria are the most sequenced organisms by Peruvian institutions (70.60%), pathogenic bacteria such as Pasteurella multocida, Neisseria meningitidis, and Vibrio parahaemolyticus were the most abundant. We found no sequence records from the Archaea domain. In BioProject, the most common sequence belongs to Salmonella enterica subsp. enterica serovar Infantis. In PATRIC, a database of pathogenic agents, Mycobacterium tuberculosis and Yersinia pestis had the highest number of entries. Finally, in BOLD, an exclusively Eukaryotic database, Chordata (Aves and Actinopterygii), Angiospermae, and Arthropoda (Insecta, and Arachnida) were the most frequent records. Our results would indicate research preferences of Peruvian institutions, focusing on infectious diseases and some Eukaryotic phyla. Although there has been a significant increase of DNA information submitted by Peruvian institutions since the last report, the genetic diversity reflected in these databases remains inconsistent with the diversity in the country. More efforts must be made to obtain genetic information from more underestimated taxonomic groups and to promote more genetic research in regional Peruvian institutions.

Download Full-text

Earthworms drastically change fungal and bacterial communities during vermicomposting of sewage sludge

Scientific Reports ◽

10.1038/s41598-021-95099-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jorge Domínguez ◽

Manuel Aira ◽

Keith A. Crandall ◽

Marcos Pérez-Losada

Keyword(s):

Sewage Sludge ◽

Community Composition ◽

Fungal Community ◽

High Throughput Sequencing ◽

Wastewater Treatment Plants ◽

Agricultural Practices ◽

Fungal Community Composition ◽

Earthworm Casts ◽

Composition And Structure ◽

Sustainable Agricultural Practices

AbstractWastewater treatment plants produce hundreds of million tons of sewage sludge every year all over the world. Vermicomposting is well established worldwide and has been successful at processing sewage sludge, which can contribute to alleviate the severe environmental problems caused by its disposal. Here, we utilized 16S and ITS rRNA high-throughput sequencing to characterize bacterial and fungal community composition and structure during the gut- and cast-associated processes (GAP and CAP, respectively) of vermicomposting of sewage sludge. Bacterial and fungal communities of earthworm casts were mainly composed of microbial taxa not found in the sewage sludge; thus most of the bacterial (96%) and fungal (91%) taxa in the sewage sludge were eliminated during vermicomposting, mainly through the GAP. Upon completion of GAP and during CAP, modified microbial communities undergo a succession process leading to more diverse microbiotas than those found in sewage sludge. Consequently, bacterial and fungal community composition changed significantly during vermicomposting. Vermicomposting of sewage resulted in a stable and rich microbial community with potential biostimulant properties that may aid plant growth. Our results support the use of vermicompost derived from sewage sludge for sustainable agricultural practices, if heavy metals or other pollutants are under legislation limits or adequately treated.

Download Full-text