Genomic and genetic insights into a cosmopolitan fungus, Paecilomyces variotii (Eurotiales)

Andrew Urquhart, Stephen Mondo, Miia Riitta Mäkelä, James Hane, Ad Wiebenga, Guifen He, Sirma Mihaltcheva, Jasmyn Pangilinan, Anna Lipzen, Kerrie Barry, Ronald de Vries, Igor V. Grigoriev, Alexander Idnurm

Research output: Contribution to journalArticleScientificpeer-review

Abstract

Species in the genus Paecilomyces, a member of the fungal order Eurotiales, are ubiquitous in nature and impact a variety of human endeavors. Here, the biology of one common species, Paecilomyces variotii, was explored using genomics and functional genetics. Sequencing the genome of two isolates revealed key genome and gene features in this species. A striking feature of the genome was the two-part nature, featuring large stretches of DNA with normal GC content separated by AT-rich regions, a hallmark of many plant-pathogenic fungal genomes. These AT-rich regions appeared to have been mutated by repeat-induced point (RIP) mutations. We developed methods for genetic transformation of P. variotii, including forward and reverse genetics as well as crossing techniques. Using transformation and crossing, RIP activity was identified, demonstrating for the first time that RIP is an active process within the order Eurotiales. A consequence of RIP is likely reflected by a reduction in numbers of genes within gene families, such as in cell wall degradation, and reflected by growth limitations on P. variotii on diverse carbon sources. Furthermore, using these transformation tools we characterized a conserved protein containing a domain of unknown function (DUF1212) and discovered it is involved in pigmentation.

Original languageEnglish
Article number3058
JournalFrontiers in Microbiology
Volume9
Number of pages21
ISSN1664-302X
DOIs
Publication statusPublished - 13 Dec 2018
MoE publication typeA1 Journal article-refereed

Fields of Science

  • Agrobacterium tumefaciens-mediated transformation
  • Byssochlamys spectabilis
  • DUF1212
  • Eurotiales
  • genome defense
  • leuA
  • mitochondrial membrane carrier
  • INDUCED POINT MUTATION
  • MULTIPLE SEQUENCE ALIGNMENT
  • ASPERGILLUS-NIDULANS
  • BIOCHEMICAL-CHARACTERIZATION
  • MEDIATED TRANSFORMATION
  • TRANSPOSABLE ELEMENTS
  • HEAT-RESISTANCE
  • PURIFICATION
  • PROTEIN
  • BYSSOCHLAMYS
  • 1183 Plant biology, microbiology, virology

Cite this

Urquhart, Andrew ; Mondo, Stephen ; Mäkelä, Miia Riitta ; Hane, James ; Wiebenga, Ad ; He, Guifen ; Mihaltcheva, Sirma ; Pangilinan, Jasmyn ; Lipzen, Anna ; Barry, Kerrie ; de Vries, Ronald ; Grigoriev, Igor V. ; Idnurm, Alexander . / Genomic and genetic insights into a cosmopolitan fungus, Paecilomyces variotii (Eurotiales). In: Frontiers in Microbiology. 2018 ; Vol. 9.
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abstract = "Species in the genus Paecilomyces, a member of the fungal order Eurotiales, are ubiquitous in nature and impact a variety of human endeavors. Here, the biology of one common species, Paecilomyces variotii, was explored using genomics and functional genetics. Sequencing the genome of two isolates revealed key genome and gene features in this species. A striking feature of the genome was the two-part nature, featuring large stretches of DNA with normal GC content separated by AT-rich regions, a hallmark of many plant-pathogenic fungal genomes. These AT-rich regions appeared to have been mutated by repeat-induced point (RIP) mutations. We developed methods for genetic transformation of P. variotii, including forward and reverse genetics as well as crossing techniques. Using transformation and crossing, RIP activity was identified, demonstrating for the first time that RIP is an active process within the order Eurotiales. A consequence of RIP is likely reflected by a reduction in numbers of genes within gene families, such as in cell wall degradation, and reflected by growth limitations on P. variotii on diverse carbon sources. Furthermore, using these transformation tools we characterized a conserved protein containing a domain of unknown function (DUF1212) and discovered it is involved in pigmentation.",
keywords = "Agrobacterium tumefaciens-mediated transformation, Byssochlamys spectabilis, DUF1212, Eurotiales, genome defense, leuA, mitochondrial membrane carrier, INDUCED POINT MUTATION, MULTIPLE SEQUENCE ALIGNMENT, ASPERGILLUS-NIDULANS, BIOCHEMICAL-CHARACTERIZATION, MEDIATED TRANSFORMATION, TRANSPOSABLE ELEMENTS, HEAT-RESISTANCE, PURIFICATION, PROTEIN, BYSSOCHLAMYS, 1183 Plant biology, microbiology, virology",
author = "Andrew Urquhart and Stephen Mondo and M{\"a}kel{\"a}, {Miia Riitta} and James Hane and Ad Wiebenga and Guifen He and Sirma Mihaltcheva and Jasmyn Pangilinan and Anna Lipzen and Kerrie Barry and {de Vries}, Ronald and Grigoriev, {Igor V.} and Alexander Idnurm",
year = "2018",
month = "12",
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Urquhart, A, Mondo, S, Mäkelä, MR, Hane, J, Wiebenga, A, He, G, Mihaltcheva, S, Pangilinan, J, Lipzen, A, Barry, K, de Vries, R, Grigoriev, IV & Idnurm, A 2018, 'Genomic and genetic insights into a cosmopolitan fungus, Paecilomyces variotii (Eurotiales)', Frontiers in Microbiology, vol. 9, 3058. https://doi.org/10.3389/fmicb.2018.03058

Genomic and genetic insights into a cosmopolitan fungus, Paecilomyces variotii (Eurotiales). / Urquhart, Andrew; Mondo, Stephen ; Mäkelä, Miia Riitta; Hane, James ; Wiebenga, Ad ; He, Guifen ; Mihaltcheva, Sirma ; Pangilinan, Jasmyn; Lipzen, Anna ; Barry, Kerrie ; de Vries, Ronald ; Grigoriev, Igor V. ; Idnurm, Alexander .

In: Frontiers in Microbiology, Vol. 9, 3058, 13.12.2018.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Genomic and genetic insights into a cosmopolitan fungus, Paecilomyces variotii (Eurotiales)

AU - Urquhart, Andrew

AU - Mondo, Stephen

AU - Mäkelä, Miia Riitta

AU - Hane, James

AU - Wiebenga, Ad

AU - He, Guifen

AU - Mihaltcheva, Sirma

AU - Pangilinan, Jasmyn

AU - Lipzen, Anna

AU - Barry, Kerrie

AU - de Vries, Ronald

AU - Grigoriev, Igor V.

AU - Idnurm, Alexander

PY - 2018/12/13

Y1 - 2018/12/13

N2 - Species in the genus Paecilomyces, a member of the fungal order Eurotiales, are ubiquitous in nature and impact a variety of human endeavors. Here, the biology of one common species, Paecilomyces variotii, was explored using genomics and functional genetics. Sequencing the genome of two isolates revealed key genome and gene features in this species. A striking feature of the genome was the two-part nature, featuring large stretches of DNA with normal GC content separated by AT-rich regions, a hallmark of many plant-pathogenic fungal genomes. These AT-rich regions appeared to have been mutated by repeat-induced point (RIP) mutations. We developed methods for genetic transformation of P. variotii, including forward and reverse genetics as well as crossing techniques. Using transformation and crossing, RIP activity was identified, demonstrating for the first time that RIP is an active process within the order Eurotiales. A consequence of RIP is likely reflected by a reduction in numbers of genes within gene families, such as in cell wall degradation, and reflected by growth limitations on P. variotii on diverse carbon sources. Furthermore, using these transformation tools we characterized a conserved protein containing a domain of unknown function (DUF1212) and discovered it is involved in pigmentation.

AB - Species in the genus Paecilomyces, a member of the fungal order Eurotiales, are ubiquitous in nature and impact a variety of human endeavors. Here, the biology of one common species, Paecilomyces variotii, was explored using genomics and functional genetics. Sequencing the genome of two isolates revealed key genome and gene features in this species. A striking feature of the genome was the two-part nature, featuring large stretches of DNA with normal GC content separated by AT-rich regions, a hallmark of many plant-pathogenic fungal genomes. These AT-rich regions appeared to have been mutated by repeat-induced point (RIP) mutations. We developed methods for genetic transformation of P. variotii, including forward and reverse genetics as well as crossing techniques. Using transformation and crossing, RIP activity was identified, demonstrating for the first time that RIP is an active process within the order Eurotiales. A consequence of RIP is likely reflected by a reduction in numbers of genes within gene families, such as in cell wall degradation, and reflected by growth limitations on P. variotii on diverse carbon sources. Furthermore, using these transformation tools we characterized a conserved protein containing a domain of unknown function (DUF1212) and discovered it is involved in pigmentation.

KW - Agrobacterium tumefaciens-mediated transformation

KW - Byssochlamys spectabilis

KW - DUF1212

KW - Eurotiales

KW - genome defense

KW - leuA

KW - mitochondrial membrane carrier

KW - INDUCED POINT MUTATION

KW - MULTIPLE SEQUENCE ALIGNMENT

KW - ASPERGILLUS-NIDULANS

KW - BIOCHEMICAL-CHARACTERIZATION

KW - MEDIATED TRANSFORMATION

KW - TRANSPOSABLE ELEMENTS

KW - HEAT-RESISTANCE

KW - PURIFICATION

KW - PROTEIN

KW - BYSSOCHLAMYS

KW - 1183 Plant biology, microbiology, virology

U2 - 10.3389/fmicb.2018.03058

DO - 10.3389/fmicb.2018.03058

M3 - Article

VL - 9

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

SN - 1664-302X

M1 - 3058

ER -