ORCID Profile
0000-0002-9169-9245
Current Organisation
University of Tokyo
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Publisher: Wiley
Date: 24-11-2021
DOI: 10.1111/NPH.17842
Abstract: Chromosome folding links genome structure with gene function by generating distinct nuclear compartments and topologically associating domains. In mammals, these undergo preferential interactions and regulate gene expression. However, their role in fungal genome biology is unclear. Here, we combine Nanopore (ONT) sequencing with chromatin conformation capture sequencing (Hi‐C) to reveal chromosome and epigenetic ersity in a group of obligate plant symbionts: the arbuscular mycorrhizal fungi (AMF). We find that five phylogenetically distinct strains of the model AMF Rhizophagus irregularis carry 33 chromosomes with substantial within‐species variability in size, as well as in gene and repeat content. Strain‐specific Hi‐C contact maps reveal a ‘checkerboard’ pattern that underline two dominant euchromatin (A) and heterochromatin (B) compartments. Each compartment differs in the level of gene transcription, regulation of candidate effectors and methylation frequencies. The A‐compartment is more gene‐dense and contains most core genes, while the B‐compartment is more repeat‐rich and has higher rates of chromosomal rearrangement. While the B‐compartment is transcriptionally repressed, it has significantly more secreted proteins and in planta upregulated candidate effectors, suggesting a possible host‐induced change in chromosome conformation. Overall, this study provides a fine‐scale view into the genome biology and evolution of model plant symbionts, and opens avenues to study the epigenetic mechanisms that modify chromosome folding during host–microbe interactions.
Publisher: Cold Spring Harbor Laboratory
Date: 07-10-2022
DOI: 10.1101/2022.10.06.511072
Abstract: Bio ersity has typically been quantified using species richness, but this ignores evolutionary history. Due to the increasing availability of robust phylogenies, methods have been developed that incorporate phylogenetic relationships into quantification of bio ersity. CANAPE (categorical analysis of neo- and paleo-endemism) is one such method that can provide insight into the evolutionary processes generating bio ersity. The only currently available software implementing CANAPE is Bio erse, which is written in Perl and can be used either through a graphical user interface (GUI) or user-developed scripts. However, many researchers, particularly in the fields of ecology and evolutionary biology, use the R programming language to conduct their analyses. Here, we present canaper , a new R package that provides functions to conduct CANAPE in R. canaper implements methods for efficient computation, including parallelization and encoding of community data as sparse matrices. The interface is designed for maximum simplicity and reproducibility CANAPE can be conducted with two functions, and parallel computing can be enabled with one line of code. Our case study shows that canaper produces equivalent results to Bio erse and can complete computations on moderately sized datasets quickly ( 10 min to reproduce a canonical study). canaper allows researchers to conduct all analyses from data import and cleaning through CANAPE within R, thereby averting the need to manually import and export data and analysis results between programs. We anticipate canaper will become a part of the toolkit for analyzing bio ersity in R.
Publisher: Springer Science and Business Media LLC
Date: 12-04-2017
Publisher: Wiley
Date: 18-07-2023
DOI: 10.1111/ECOG.06638
Abstract: Bio ersity has typically been quantified using species richness, but this ignores evolutionary history. Due to the increasing availability of robust phylogenies, methods have been developed that incorporate phylogenetic relationships into quantification of bio ersity. CANAPE (categorical analysis of neo‐ and paleo‐endemism) is one such method that can provide insight into the evolutionary processes generating bio ersity. The only currently available software implementing CANAPE is Bio erse, which is written in Perl and can be used either through a graphical user interface (GUI) or user‐developed scripts. However, many researchers, particularly in the fields of ecology and evolutionary biology, use the R programming language to conduct their analyses. Here, we present canaper, a new R package ( www.r‐project.org ) that provides functions to conduct CANAPE in R. canaper implements methods for efficient computation, including parallelization and encoding of community data as sparse matrices. The interface is designed for maximum simplicity and reproducibility CANAPE can be conducted with two functions, and parallel computing can be enabled with one line of code. Our case study shows that canaper produces equivalent results to Bio erse and can complete computations on moderately sized datasets quickly ( min to reproduce a canonical study). canaper allows researchers to conduct all analyses from data import and cleaning through CANAPE within R, thereby obviating the need to manually import and export data and analysis results between programs. We anticipate canaper will become a part of the toolkit for analyzing bio ersity in R.
Publisher: Cold Spring Harbor Laboratory
Date: 12-08-2021
DOI: 10.1101/2021.08.12.456011
Abstract: Chromosome folding links genome structure with gene function by generating distinct nuclear compartments and topologically associating domains (TADs). In mammals, these undergo preferential interactions and regulate gene expression. However, their role in fungal genome biology is unclear. Here, we combine Nanopore (ONT) sequencing with chromatin conformation capture sequencing (Hi-C) to reveal chromosome and epigenetic ersity in a group of obligate plant symbionts the arbuscular mycorrhizal fungi (AMF). We find that five phylogenetically distinct strains of the model AMF Rhizophagus irregularis carry 33 chromosomes with substantial within species variability in size, as well as in gene and repeat content. Strain-specific Hi-C contact maps all reveal a ‘checkerboard’ pattern that underline two dominant euchromatin (A) and heterochromatin (B) compartments. Each compartment differs in the level of gene transcription, regulation of candidate effectors and methylation frequencies. The A-compartment is more gene-dense and contains most core genes, while the B-compartment is more repeat-rich and has higher rates of chromosomal rearrangement. While the B-compartment is transcriptionally repressed, it has significantly more secreted proteins and in planta up-regulated candidate effectors, suggesting a possible host-induced change in chromosome conformation. Overall, this study provides a fine-scale view into the genome biology and evolution of prominent plant symbionts, and opens avenues to study the epigenetic mechanisms that modify chromosome folding during host-microbe interactions.
Publisher: Cold Spring Harbor Laboratory
Date: 18-01-2023
DOI: 10.1101/2023.01.15.524138
Abstract: Arbuscular mycorrhizal fungi (AMF) are prominent root symbionts with a multinucleate cytoplasm that can carry thousands of nuclei deriving from two parental strains and varying in relative abundance in a large syncytium. Here, we set out to improve our understanding of such remarkable genetics by resolving the nuclear genomes of all publicly available AMF heterokaryons using PacBio HiFi and Hi-C sequencing. We find that all AMF heterokaryons carry two sets of homologous chromosomes, where genes associated with plant colonization reside in gene-sparse, repeat-rich compartments. The co-existing nuclear genomes are phylogenetically related but differ significantly in content and epigenetics, resulting in nucleus-specific regulatory programs during mycorrhizal interactions. AMF heterokaryons carry signatures of past genetic exchange indicative of sexual reproduction, followed by clonal haplotype evolution. This work uncovers the contribution and origin of nuclear genomes present in AMF heterokaryons and opens avenues for improvement and environmental application of these strains.
No related grants have been discovered for Wataru Iwasaki.