Genome comparison and transcriptome analysis of the invasive brown root rot pathogen, Phellinus noxius, from different geographic regions reveals potential enzymes associated with degradation of different wood substrates

Caballero, Jorge Ibarra; Ata, Jessa P.; Leddy, K.A.; Glenn, Travis C.; Kieran, Troy J.; Klopfenstein, Ned B.; Kim, Mee‐Sook; Stewart, Jane E.

doi:10.1016/j.funbio.2019.12.007

Cited by 11 publications

(14 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Several institutions have conducted genomic sequencing of P. noxius (Ibarra Caballero et al 2020). These efforts have improved our understanding of why P. noxius can attack such a wide range of tree species and cause rapid tree death and decomposition.…”

Section: Genomic and Transcriptomic Studies Can Provide Insights Into...mentioning

confidence: 99%

“…These efforts have improved our understanding of why P. noxius can attack such a wide range of tree species and cause rapid tree death and decomposition. Collaborative work among institutions and comparisons of P. noxius genomes have provided insights into its ecology, pathogenicity, and ability to cause bark and wood decomposition on living trees (Ibarra Caballero et al 2020).…”

Section: Genomic and Transcriptomic Studies Can Provide Insights Into...mentioning

confidence: 99%

“…Researchers discovered that some isolates were more aggressive than others in Taiwan, and then identified enzyme-encoding genes associated with increased tree mortality and wood decomposition (Chung et al 2017, Ibarra Caballero et al 2020. Chung et al (2017) also determined that 74 percent of the predicted genes of P. noxius are the same as at least one other basidiomycete.…”

Section: Genomic and Transcriptomic Studies Can Provide Insights Into...mentioning

confidence: 99%

See 2 more Smart Citations

Brown root rot disease caused by Phellinus noxius in U.S.-Affiliated Pacific Islands

Cannon

Klopfenstein

Kim

et al. 2022

Self Cite

View full text Add to dashboard Cite

Phellinus noxius is a fungus that causes brown root rot disease in tree and shrub species of subtropical and tropical regions. It has infected and rapidly killed hundreds of important tree and shrub species in these regions. It is widespread in the Pacific Region including all the island states of American Samoa, the Federated States of Micronesia (Chuuk, Kosrae, Pohnpei, and Yap), the Republic of Palau, the Commonwealth of the Northern Mariana Islands (Islands of Rota and Saipan), and Guam. This report explains how to detect brown root rot disease and its causal pathogen (P. noxius) by recognizing the signs and symptoms of the disease as well as using molecular techniques. It discusses several characteristics of P. noxius that make it such a destructive pathogen in the areas where it occurs and explains how the hot, humid, and sometimes stormy conditions that occur on these islands contribute significantly to disease spread and development. This publication also describes multiple approaches that have been attempted to control this fungus along with science-based information for consideration when trying to manage the pathogen.

show abstract

Section: Genomic and Transcriptomic Studies Can Provide Insights Into...mentioning

confidence: 99%

Section: Genomic and Transcriptomic Studies Can Provide Insights Into...mentioning

confidence: 99%

Section: Genomic and Transcriptomic Studies Can Provide Insights Into...mentioning

confidence: 99%

See 1 more Smart Citation

Brown root rot disease caused by Phellinus noxius in U.S.-Affiliated Pacific Islands

Cannon

Klopfenstein

Kim

et al. 2022

Self Cite

View full text Add to dashboard Cite

show abstract

“…The process_radtag program from stacks version 2.55 (Catchen et al, 2011(Catchen et al, , 2013 was used to ensure cut-sites remained intact and perform quality trimming with parameters -r (rescue barcodes and RAD-tags), -c (clean data, remove any read with an uncalled base) and -q (discard reads with low-quality scores). The reads were aligned to a reference genome of isolate P919-02W.7 (Ibarra Caballero et al, 2020; GCA_010367325.1) using bowtie2 version 2.3.2 (Langmead & Salzberg, 2012) with default settings. SAM files were sorted and converted to BAM files with samtools version 1.7 (Li et al, 2009).…”

Section: Dna Extraction Radseq and Bioinformatics Analysesmentioning

confidence: 99%

“…For example, the genetic groups of P. noxius determined inStewart et al (2020) have different suitable climate space, and potential hybridization among these groups may favour their adaptation to wider range of climatic/environmental conditions. Also, IbarraCaballero et al (2020) showed that the P. noxius genome encodes a large arsenal of wood-degrading enzymes, and exchange and accumulation of such genetic regions among different genetic groups could contribute to its virulence and wide host range.…”

mentioning

confidence: 99%

Long evolutionary history of an emerging fungal pathogen of diverse tree species in eastern Asia, Australia and the Pacific Islands

et al. 2022

Self Cite

View full text Add to dashboard Cite

Emerging plant pathogens have been increasing exponentially over the last century. To address this issue, it is critical to determine whether these pathogens are native to ecosystems or have been recently introduced. Understanding the ecological and evolutionary processes fostering emergence can help to manage their spread and predict epidemics/epiphytotics. Using restriction site‐associated DNA sequencing data, we studied genetic relationships, pathways of spread and the evolutionary history of Phellinus noxius, an emerging root‐rotting fungus of unknown origin, in eastern Asia, Australia and the Pacific Islands. We analysed patterns of genetic variation using Bayesian inference, maximum‐likelihood phylogeny, population splits and mixtures measuring correlations in allele frequencies and genetic drift, and finally applied coalescent‐based theory using Approximate Bayesian computation (ABC) with supervised machine learning. Population structure analyses revealed five genetic groups with signatures of complex recent and ancient migration histories. The most probable scenario of ancient pathogen spread is movement from an unsampled population to Malaysia and the Pacific Islands, with subsequent spread to Taiwan and Australia. Furthermore, ABC analyses indicate P. noxius spread occurred thousands of generations ago, contradicting previous assumptions that this pathogen was recently introduced to multiple geographical regions. Our results suggest that recent emergence of P. noxius in eastern Asia, Australia and the Pacific Islands has probably been driven by anthropogenic and natural disturbances, such as deforestation, land‐use change, severe weather events and/or introduction of exotic plants. This study provides a novel example of applying genome‐wide allele frequency data to unravel the dynamics of pathogen emergence under changing ecosystem conditions.

show abstract

Ligninolytic Microbes and Their Role in Effluent Management of Pulp and Paper Industry

Yadav¹,

Patil²,

Kumaraswamy

et al. 2020

Waste to Energy: Prospects and Applications

View full text Add to dashboard Cite

Genome comparison and transcriptome analysis of the invasive brown root rot pathogen, Phellinus noxius, from different geographic regions reveals potential enzymes associated with degradation of different wood substrates

Cited by 11 publications

References 57 publications

Brown root rot disease caused by Phellinus noxius in U.S.-Affiliated Pacific Islands

Brown root rot disease caused by Phellinus noxius in U.S.-Affiliated Pacific Islands

Long evolutionary history of an emerging fungal pathogen of diverse tree species in eastern Asia, Australia and the Pacific Islands

Ligninolytic Microbes and Their Role in Effluent Management of Pulp and Paper Industry

Contact Info

Product

Resources

About