Draft genome sequences of five Calonectria species from Eucalyptus plantations in China, Celoporthe dispersa, Sporothrix phasma and Alectoria sarmentosa

Liu, Feifei; Chen, ShuaiFei; Ferreira, M. A.; Chang, Runlei; Sayari, Mohammad; Kanzi, Aquillah M.; Wingfield, Brenda D.; Wingfield, Michael J.; Pizarro, David; Crespo, Ana; Divakar, Pradeep K.; Beer, Z. Wilhelm de; Duong, Tuan A.

doi:10.1186/s43008-019-0023-5

Cited by 17 publications

(7 citation statements)

References 82 publications

(99 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Genome assemblies for the isolates chosen as representatives for each taxon collected in this study resulted in the addition of 12 draft genomes to the Ophiostomatales, and the release of the first draft genome publicly available for an isolate residing in the Graphiaceae (Microascales). The genome assembly statistics of the Ophiostomatales isolates collected during this study mirror those available for species residing in Ophiostoma, Sporothrix, Graphilbum, Leptographium s.l., Ceratocystiopsis and Raffaelea (DiGuistini et al 2011;Forgetta et al 2013;Haridas et al 2013;Teixeira et al 2014;van der Nest et al 2014;Wingfield et al 2015aWingfield et al , b, 2016Wingfield et al , 2017aWingfield et al , 2018D' Alessandro et al 2016;Huang et al 2016;Shang et al 2016;Jeon et al 2017;Vanderpool et al 2018;Liu et al 2019). Comparisons of genome statistics, specifically estimated size, GC content and number of predicted genes, generally correlate with the taxonomic placement of each species (Additional file 3: Table S3).…”

Section: Discussionmentioning

confidence: 99%

Ophiostomatoid fungi associated with pine bark beetles and infested pines in south-eastern Australia, including Graphilbum ipis-grandicollis sp. nov.

et al. 2021

View full text Add to dashboard Cite

The ophiostomatoid fungi are an assemblage of ascomycetes which are arguably best-known for their associations with bark and ambrosia beetles (Curculonidae) and blue stain (sap stain) of many economically important tree species. These fungi are considered a significant threat to coniferous forests, which has resulted in numerous studies characterising the diversity of bark beetles and their ophiostomatoid associates globally. The diversity of ophiostomatoid fungi present in Australian pine plantations, however, remains largely undetermined. The aims of this study were therefore to reconsider the diversity of ophiostomatoid fungi associated with Pinus in Australia, and to establish the baseline of expected taxa found within these plantation ecosystems. To achieve this, we reviewed Australian plant pathogen reference collections, and analysed samples collected during forest health surveillance programs from the major pine growing regions in south-eastern Australia. In total, 135 ophiostomatoid isolates (15 from reference collections and 120 collected during the current study) were assessed using morphological identification and ITS screening which putatively distinguished 15 taxonomic groups. Whole genome sequencing (WGS) of representative isolates from each taxon was performed to obtain high-quality sequence data for multi-locus phylogenetic analysis. Our results revealed a greater than expected diversity, expanding the status of ophiostomatoid fungi associated with Pinus in Australia to include 14 species from six genera in the Ophiostomatales and a single species residing in the Microascales. While most of these were already known to science, our study includes seven first records for Australia and the description of one new species, Graphilbum ipis-grandicollis sp. nov.. This study also provides an early example of whole genome sequencing (WGS) approaches replacing traditional PCR-based methods for taxonomic surveys. This not only allowed for robust multi-locus sequence extraction during taxonomic assessment, but also permitted the rapid establishment of a curated genomic database for ophiostomatoid fungi which will continue to aid in the development of improved diagnostic resources and capabilities for Australian biosecurity.

show abstract

Section: Discussionmentioning

confidence: 99%

Ophiostomatoid fungi associated with pine bark beetles and infested pines in south-eastern Australia, including Graphilbum ipis-grandicollis sp. nov.

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Metagenome skimming was thus suggested to be a promising technique to facilitate genome mining of lichen-forming fungi by circumventing the time-consuming, sometimes unfeasible, step of aposymbiotic cultivation. Up to 2019 only two publicly available lichen genomes have been assembled from metagenomic data (i.e., that of Cetradonia linearis and Alectoria sarmentosa , [ 116 , 141 ]), and these are far from being complete, still indicating how challenging is genomeassembling from metagenomic data. However, just recently Greshake Tzovaras et al [ 140 ] have successfully reconstructed the hologenome of the mycobiont Umbilicaria postulata combining short Illumina with long PacBio reads with a comprehensive assembly scheme.…”

Section: Genomic Advances In Ascomycotamentioning

confidence: 99%

An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

Muggia

Ametrano

Sterflinger

et al. 2020

Life

View full text Add to dashboard Cite

Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.

show abstract

“…The estimated genome size and gene number for I. knoxdaviesiana is similar to those of other species in Cryphonectriaceae , such as Chrysoporthe austroafricana (44.6 Mb, 13,484 genes, Wingfield et al 2015b ), C. cubensis (42.6 Mb, 13,121 genes, Wingfield et al 2015a ), C deuterocubensis (43.9 Mb, 13,772 genes, Wingfield et al 2015a ), C. puriensis (44.7 Mb, 13,166 genes, van der Nest et al 2021 ) , Celoporthe dispersa (40 Mb, 12,078 genes, Liu et al 2019 ), and Cryphonectria parasitica (43.9 Mb, 11 184 genes, http://genome.jgi.doe.gov/Crypa2/Crypa2.home.html ).…”

Section: Resultsmentioning

confidence: 99%

“…Twelve genome sequences are currently available for species of Cryphonectriaceae . These include, Chrysoporthe austroafricana (Wingfield et al 2015b ), C. cubensis , C. deuterocubensis (Wingfield et al 2015a ), C. puriensis (van der Nest et al 2021 ), Celoporthe dispersa (Liu et al 2019 ), as well as seven species of Cryphonectria ( https://www.ncbi.nlm.nih.gov/genome/ ). The aim of this study was to provide genome sequence data for I. knoxdaviesiana , a fourth genus of Cryphonectriaceae .…”

Section: Introductionmentioning

confidence: 99%