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The Genomics of the Tree Pathogen Fungus Phellinus noxius and Microbiota Analysis of the Rhizosphere of Infected Trees.

Record Type:	Language materials, manuscript : Monograph/item
Title/Author:	The Genomics of the Tree Pathogen Fungus Phellinus noxius and Microbiota Analysis of the Rhizosphere of Infected Trees./
Author:	Tsang, Karen Sze Wing.
Description:	1 online resource (160 pages)
Notes:	Source: Dissertations Abstracts International, Volume: 83-05, Section: B.
Contained By:	Dissertations Abstracts International83-05B.
Subject:	Microbiology. -
Online resource:	click for full text (PQDT)
ISBN:	9798492724368

The Genomics of the Tree Pathogen Fungus Phellinus noxius and Microbiota Analysis of the Rhizosphere of Infected Trees.
Tsang, Karen Sze Wing.

The Genomics of the Tree Pathogen Fungus Phellinus noxius and Microbiota Analysis of the Rhizosphere of Infected Trees. - 1 online resource (160 pages)

Source: Dissertations Abstracts International, Volume: 83-05, Section: B.

Thesis (Ph.D.)--The Chinese University of Hong Kong (Hong Kong), 2020.

Includes bibliographical references

Phellinus noxius is a highly infectious and destructive fungal pathogen that causes brown root rot disease. This pathogen causes fatal damage to plant hosts through targeting the water-transport system, effectively rotting away the roots of the host plant, and has become a cause for concern in Hong Kong. It is difficult to eradicate due to its ability to survive in soil and wood debris for over 10 years and there is currently no cure. Little is known about this pathogen, including its virulence, pathogenicity, outbreak patterns and genomic sequences, which are vital in the battle to understand and control this disease.This study presents the assembled first high-quality reference genome of a Hong Kong P. noxius isolate YTM97 using sequences from Ion Torrent PGM, Illumina MiSeq and PacBio RSII. Three more Hong Kong P. noxius strains were sequenced with Illumina MiSeq and assembled as draft genomes for comparison. The Japanese isolate KPN57 was assembled using available raw reads. The assembled high-quality Hong Kong P. noxius YTM97 reference genome has a genome size of 31.2 Mb over 28 contigs, and a genome completeness of 93.8% . Genomic and transcriptomic analyses revealed 22 effector proteins, and many CAZymes were significantly upregulated. It was also revealed the presence of AA4 CAZymes in all P. noxius isolates, however AA4 was not present in the other pathogenic and non-pathogenic white-rot fungi used in the analysis.Phylogenetic analyses supported the recent reclassification of the species and revealed a lack of intra-species genetic diversity. Mating type analysis discovered a different mating type to the only other published assembled P. noxius KPN91 Japanese isolate, and revealed high similarities between the mating type genes of the YTM97 isolate and the geographically distant Japanese KPN57 isolate located in the Amami Islands.This study also presents the composition and diversity of the bacterial, archaeal and fungal rhizosphere microbiome among four species of healthy and P. noxius infected trees belonging to Mallotus paniculatus, Celtis sinensis, Cinnamomum camphora and Ficus microcarpa using Ion Torrent amplicon sequencing. Rhizosphere microbiome results revealed that overall, there was dominance of Proteobacteria and Actinobacteria in bacteria, Crenarchaeota and Euryarchaeota in archaea, and Ascomycota and Basidiomycota in fungi. P. noxius infection did not affect the alpha diversity of the bacterial rhizosphere microbiome in all four tree species but affected that of archaea and fungi in a tree species-dependent manner. Infection with P. noxius only affected the bacterial rhizosphere composition in M. paniculatus but not the other three tree species. By contrast, P. noxius infection affected the composition of the archaeal and fungal rhizosphere microbiome in all four tree species. Collectively, these results suggest that potential diagnostic biomarkers for brown root rot disease are tree species-specific and should be developed based on different taxonomic groups.In conclusion, this study has produced the first high-quality reference genome sequence for a Hong Kong P. noxius isolate, and facilitated further understanding of the pathogenicity and wood-degrading capability of P. noxius, as well as provided new information to compare isolates to understand the spread, evolution and infection mechanisms. It has provided insights into the rhizosphere microbiome in healthy and P. noxius infected trees and laid a solid foundation for future comprehensive studies.

Electronic reproduction.
Ann Arbor, Mich. :
ProQuest,
2024

Mode of access: World Wide Web

ISBN: 9798492724368Subjects--Topical Terms:

591510
Microbiology.
Subjects--Index Terms:

GenomicsIndex Terms--Genre/Form:

554714
Electronic books.

The Genomics of the Tree Pathogen Fungus Phellinus noxius and Microbiota Analysis of the Rhizosphere of Infected Trees.
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520 $a Phellinus noxius is a highly infectious and destructive fungal pathogen that causes brown root rot disease. This pathogen causes fatal damage to plant hosts through targeting the water-transport system, effectively rotting away the roots of the host plant, and has become a cause for concern in Hong Kong. It is difficult to eradicate due to its ability to survive in soil and wood debris for over 10 years and there is currently no cure. Little is known about this pathogen, including its virulence, pathogenicity, outbreak patterns and genomic sequences, which are vital in the battle to understand and control this disease.This study presents the assembled first high-quality reference genome of a Hong Kong P. noxius isolate YTM97 using sequences from Ion Torrent PGM, Illumina MiSeq and PacBio RSII. Three more Hong Kong P. noxius strains were sequenced with Illumina MiSeq and assembled as draft genomes for comparison. The Japanese isolate KPN57 was assembled using available raw reads. The assembled high-quality Hong Kong P. noxius YTM97 reference genome has a genome size of 31.2 Mb over 28 contigs, and a genome completeness of 93.8% . Genomic and transcriptomic analyses revealed 22 effector proteins, and many CAZymes were significantly upregulated. It was also revealed the presence of AA4 CAZymes in all P. noxius isolates, however AA4 was not present in the other pathogenic and non-pathogenic white-rot fungi used in the analysis.Phylogenetic analyses supported the recent reclassification of the species and revealed a lack of intra-species genetic diversity. Mating type analysis discovered a different mating type to the only other published assembled P. noxius KPN91 Japanese isolate, and revealed high similarities between the mating type genes of the YTM97 isolate and the geographically distant Japanese KPN57 isolate located in the Amami Islands.This study also presents the composition and diversity of the bacterial, archaeal and fungal rhizosphere microbiome among four species of healthy and P. noxius infected trees belonging to Mallotus paniculatus, Celtis sinensis, Cinnamomum camphora and Ficus microcarpa using Ion Torrent amplicon sequencing. Rhizosphere microbiome results revealed that overall, there was dominance of Proteobacteria and Actinobacteria in bacteria, Crenarchaeota and Euryarchaeota in archaea, and Ascomycota and Basidiomycota in fungi. P. noxius infection did not affect the alpha diversity of the bacterial rhizosphere microbiome in all four tree species but affected that of archaea and fungi in a tree species-dependent manner. Infection with P. noxius only affected the bacterial rhizosphere composition in M. paniculatus but not the other three tree species. By contrast, P. noxius infection affected the composition of the archaeal and fungal rhizosphere microbiome in all four tree species. Collectively, these results suggest that potential diagnostic biomarkers for brown root rot disease are tree species-specific and should be developed based on different taxonomic groups.In conclusion, this study has produced the first high-quality reference genome sequence for a Hong Kong P. noxius isolate, and facilitated further understanding of the pathogenicity and wood-degrading capability of P. noxius, as well as provided new information to compare isolates to understand the spread, evolution and infection mechanisms. It has provided insights into the rhizosphere microbiome in healthy and P. noxius infected trees and laid a solid foundation for future comprehensive studies.
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