Genomic Resource of Rice Seed Associated Bacteria

Midha, Samriti; Bansal, Kanika; Sharma, Shikha; Kumar, N. Vinod; Patil, Prabhu B.; Chaudhry, Vasvi

doi:10.3389/fmicb.2015.01551

Cited by 56 publications

(34 citation statements)

References 7 publications

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“…The appearance of the full GA biosynthetic operon in Xanthomonas bromi noted here (Figure 2) falls neatly within this paradigm, as X. bromi also nominally enters via stomata and causes leaf streak disease in grasses from the Poaceae BEP clade (Hersemann et al, 2016). Although little is known about the lifestyle of the Pseudomonas psychrotolerans strain that was also found here to contain the full GA biosynthetic operon, this genus contains many phytopathogens, and this strain was isolated from rice (Midha et al, 2015), consistent with the overall scenario presented above.…”

Section: Discussionsupporting

confidence: 73%

Investigating the Phylogenetic Range of Gibberellin Biosynthesis in Bacteria

Nagel

Peters

2017

MPMI

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Summary Certain plant-associated microbes can produce gibberellin (GA) phytohormones, as first described for the rice fungal pathogen Gibberella fujikuroi and more recently for bacteria, including several rhizobia and the rice bacterial pathogen Xanthomonas oryzae pv. oryzicola. The relevant enzymes are encoded by a biosynthetic operon that exhibits both a greater phylogenetic range and scattered distribution among plant-associated bacteria. Here the phylogenetic distribution of this operon was investigated. To demonstrate conserved functionality, the enzymes encoded by the disparate operon from Xanthomonas translucens pv. translucens, along with those from the most divergent example, found in Erwinia tracheiphila, were biochemically characterized. In both of these phytopathogens the operon leads to production of the bioactive GA4. Based on these results, it seems that this operon is widely dedicated to GA biosynthesis. However, there is intriguing variation in exact product. In particular, although all plant pathogens seem to produce bioactive GA4, rhizobia generally only produce the penultimate hormonal precursor GA9. This is suggested to reflect their distinct interactions with plants, as production of GA4 counteracts the jasmonic acid-mediated defense response, reflecting the importance of wounds as the entry point for these phytopathogens, while such suppression presumably is detrimental in the rhizobial symbiotic relationship.

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Section: Discussionsupporting

confidence: 73%

Investigating the Phylogenetic Range of Gibberellin Biosynthesis in Bacteria

Nagel

Peters

2017

MPMI

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“…While large core genomes were observed for combinations of strains in the Pnan1, Pnan2 and Pnst clusters, lower intraspecific variability (average unique CDSs = 247; range 14–682 CDSs) exists among Pnan2 strains. This may be linked to the fact that four of the five Pnan2 strains analyzed were isolated from rice seeds in the same study ( Midha et al, 2016 ). Many more unique CDSs could be observed when comparing Pnan1 strains (average unique CDSs = 589; range 298–1601 CDSs).…”

Section: Resultsmentioning

confidence: 99%

Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii

et al. 2017

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Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart’s wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes, has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis. While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range.

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“…The main focus of these genome sequencing projects has been on phytopathogenic isolates, including strains from pineapple, rice, Eucalyptus , cotton, maize and onion (Adam et al ., ; Choi et al ., ; De Maayer et al ., ; Medrano and Bell, ; Weller‐Stuart et al ., ). However, a variety of endophytic isolates (Midha et al ., ; Sheibani‐Tezerji et al ., ), plant growth‐promoting strains, isolates with potential biotechnological and biological control applications (Gasser et al ., ; Gkorezis et al ., ; Hara et al ., ; Kim et al ., ; Megías et al ., ; Shi et al ., ; Smith et al ., ; Wu et al ., ) and a clinical isolate (De Maayer et al ., ) have also been sequenced.…”

Section: Pantoea Ananatis In the Genome Sequencing Eramentioning

confidence: 99%