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Paraburkholderia kururiensis M130

ABSTRACT: Genome Sequencing of the rice endophyte Burkholderia kururiensis M130

PROVIDER: PRJNA183622 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR1523200.fastq.gz	Fastqsanger.gz
	SRR1523201.fastq.gz	Fastqsanger.gz
	SRR1523196.fastq.gz	Fastqsanger.gz
	SRR1523197.fastq.gz	Fastqsanger.gz

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Paraburkholderia kururiensis

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Tn-Seq analysis of Paraburkholderia kururiensis M130 and Burkholderia vietnamiensis LMG10929 during rice root colonization

Project description:Tn-Seq analyses of Paraburkholderia kururiensis M130 and Burkholderia vietnamiensis LMG10929 during rice root colonization (cv japonica Nipponbare and cv indica IR64)

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Comparative genomics of Paraburkholderia kururiensis and its potential in bioremediation, biofertilization, and biocontrol of plant pathogens.

Project description:Burkholderia harbors versatile Gram-negative species and is β-Proteobacteria. Recently, it was proposed to split the genus in two main branches: one of animal and plant pathogens and another, Paraburkholderia, harboring environmental and plant-beneficial species. Currently, Paraburkholderia comprises more than 70 species with ability to occupy very diverse environmental niches. Herein, we sequenced and analyzed the genome of Paraburkholderia kururiensis type strain KP23T , and compared to P. kururiensis M130, isolated in Brazil, and P. kururiensis susbp. thiooxydans, from Korea. This study focused on the gene content of the three genomes with special emphasis on their potential of plant-association, biocontrol, and bioremediation. The comparative analyses revealed several genes related to plant benefits, including biosynthesis of IAA, ACC deaminase, multiple efflux pumps, dioxygenases, and degradation of aromatic compounds. Importantly, a range of genes for protein secretion systems (type III, IV, V, and VI) were characterized, potentially involved in P. kururiensis well documented ability to establish endophytic association with plants. These findings shed light onto bacteria-plant interaction mechanisms at molecular level, adding novel information that supports their potential application in bioremediation, biofertilization, and biocontrol of plant pathogens. P. kururiensis emerges as a promising model to investigate adaptation mechanisms in different ecological niches.

| S-EPMC6692535 | biostudies-literature

Paraburkholderia

Project description:Burkholderia species Genome sequencing and assembly

| PRJNA417370 | ENA

Paraburkholderia tuberum STM678

Project description:Burkholderia tuberum STM678 genome sequencing project

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The RNA-seq analysis of rice roots colonized by the endophytic bacterium Azoarcus olearius BH72 after one-, three- and seven-days post inoculation and after three days of boosted colonization.

Project description:Purpose: Transcriptional profiling of Oryza sativa japonica Nipponbare roots after one, three and seven days post inoculation with Azoarcus olearius BH72 (vs. non-inoculated controls) to understand the changes in transcriptomic response of rice roots to colonization by bacterial endophyte at initial stages of interaction; Additional set-up was included in which bacterial growth was boosted (through increasing 20-times carbon source - malic acid in the plant's hydroponic medium) to study rice roots transcriptome during enhanced colonization by the endophyte after three days post inoculation. Methods: Rice root mRNA profiles after one day, three days (including additional set-ups for boosted colonization), and seven days post inoculation with Azoarcus olearius BH72 and corresponding non-inoculated controls were generated by RNA sequencing, in triplicates, using Illumina NextSeq 500. Raw reads were then filtered, trimmed (PHRED > 33) and mapped onto IRGSP-1 version of Oryza sativa ssp. japonica cv. Nipponbare genome using CLC Genomics Workbench 8.5.1 (Qiagen, Germany). Expression of 17 selected genes was confirmed via RT-qPCR. Results: Using the RNA-Seq technology we obtained transcriptomic data from 24 sequencing libraries, with an average 46,181,160 clean reads per library, of which 87% or more were mapped onto the Oryza sativa ssp. japonica cv. Nipponbare IRGSP-1.0 genome (Fig. S3). We considered genes as differentially regulated (DEG) that exhibited at least 1.5-fold-change in expression level between Azo-colonized and non-colonized roots and FDR<0.05. Conclusions: Bacteria appeared to short-circuit the initial root defense responses for a compatible interaction during endophytic establishment, involving previously unknown putative rice candidate genes.

2021-09-01 | GSE174616 | GEO

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