De novo assembly and genome analyses of the marine-derived Scopulariopsis brevicaulis strain LF580 unravels life-style traits and anticancerous scopularide biosynthetic gene cluster

Abhishek Kumar, Bernard Henrissat, Mikko Arvas, Muhammad Fahad Syed, Nils Thieme, J. Philipp Benz, Jens Laurids Sørensen, Eric Record, Stefanie Pöggeler, Frank Kempken

Research output: Contribution to journalArticleScientificpeer-review

15 Citations (Scopus)

Abstract

The marine-derived Scopulariopsis brevicaulis strain LF580 produces scopularides A and B, which have anticancerous properties. We carried out genome sequencing using three next-generation DNA sequencing methods. De novo hybrid assembly yielded 621 scaffolds with a total size of 32.2 Mb and 16298 putative gene models. We identified a large non-ribosomal peptide synthetase gene (nrps1) and supporting pks2 gene in the same biosynthetic gene cluster. This cluster and the genes within the cluster are functionally active as confirmed by RNA-Seq. Characterization of carbohydrate-active enzymes and major facilitator superfamily (MFS)-type transporters lead to postulate S. brevicaulis originated from a soil fungus, which came into contact with the marine sponge Tethya aurantium. This marine sponge seems to provide shelter to this fungus and micro-environment suitable for its survival in the ocean. This study also builds the platform for further investigations of the role of life-style and secondary metabolites from S. brevicaulis.
Original languageEnglish
Article numbere0140398
JournalPLoS ONE
Volume10
Issue number10
DOIs
Publication statusPublished - 2015
MoE publication typeA1 Journal article-refereed

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Scopulariopsis
Multigene Family
multigene family
lifestyle
Life Style
Genes
Porifera
Genome
genome
Fungi
Peptide Synthases
genes
DNA Sequence Analysis
Oceans and Seas
soil fungi
Soil
ligases
Carbohydrates
RNA
secondary metabolites

Cite this

Kumar, Abhishek ; Henrissat, Bernard ; Arvas, Mikko ; Syed, Muhammad Fahad ; Thieme, Nils ; Benz, J. Philipp ; Sørensen, Jens Laurids ; Record, Eric ; Pöggeler, Stefanie ; Kempken, Frank. / De novo assembly and genome analyses of the marine-derived Scopulariopsis brevicaulis strain LF580 unravels life-style traits and anticancerous scopularide biosynthetic gene cluster. In: PLoS ONE. 2015 ; Vol. 10, No. 10.
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title = "De novo assembly and genome analyses of the marine-derived Scopulariopsis brevicaulis strain LF580 unravels life-style traits and anticancerous scopularide biosynthetic gene cluster",
abstract = "The marine-derived Scopulariopsis brevicaulis strain LF580 produces scopularides A and B, which have anticancerous properties. We carried out genome sequencing using three next-generation DNA sequencing methods. De novo hybrid assembly yielded 621 scaffolds with a total size of 32.2 Mb and 16298 putative gene models. We identified a large non-ribosomal peptide synthetase gene (nrps1) and supporting pks2 gene in the same biosynthetic gene cluster. This cluster and the genes within the cluster are functionally active as confirmed by RNA-Seq. Characterization of carbohydrate-active enzymes and major facilitator superfamily (MFS)-type transporters lead to postulate S. brevicaulis originated from a soil fungus, which came into contact with the marine sponge Tethya aurantium. This marine sponge seems to provide shelter to this fungus and micro-environment suitable for its survival in the ocean. This study also builds the platform for further investigations of the role of life-style and secondary metabolites from S. brevicaulis.",
author = "Abhishek Kumar and Bernard Henrissat and Mikko Arvas and Syed, {Muhammad Fahad} and Nils Thieme and Benz, {J. Philipp} and S{\o}rensen, {Jens Laurids} and Eric Record and Stefanie P{\"o}ggeler and Frank Kempken",
year = "2015",
doi = "10.1371/journal.pone.0140398",
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Kumar, A, Henrissat, B, Arvas, M, Syed, MF, Thieme, N, Benz, JP, Sørensen, JL, Record, E, Pöggeler, S & Kempken, F 2015, 'De novo assembly and genome analyses of the marine-derived Scopulariopsis brevicaulis strain LF580 unravels life-style traits and anticancerous scopularide biosynthetic gene cluster', PLoS ONE, vol. 10, no. 10, e0140398. https://doi.org/10.1371/journal.pone.0140398

De novo assembly and genome analyses of the marine-derived Scopulariopsis brevicaulis strain LF580 unravels life-style traits and anticancerous scopularide biosynthetic gene cluster. / Kumar, Abhishek; Henrissat, Bernard; Arvas, Mikko; Syed, Muhammad Fahad; Thieme, Nils; Benz, J. Philipp; Sørensen, Jens Laurids; Record, Eric; Pöggeler, Stefanie; Kempken, Frank.

In: PLoS ONE, Vol. 10, No. 10, e0140398, 2015.

Research output: Contribution to journalArticleScientificpeer-review

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AU - Henrissat, Bernard

AU - Arvas, Mikko

AU - Syed, Muhammad Fahad

AU - Thieme, Nils

AU - Benz, J. Philipp

AU - Sørensen, Jens Laurids

AU - Record, Eric

AU - Pöggeler, Stefanie

AU - Kempken, Frank

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AB - The marine-derived Scopulariopsis brevicaulis strain LF580 produces scopularides A and B, which have anticancerous properties. We carried out genome sequencing using three next-generation DNA sequencing methods. De novo hybrid assembly yielded 621 scaffolds with a total size of 32.2 Mb and 16298 putative gene models. We identified a large non-ribosomal peptide synthetase gene (nrps1) and supporting pks2 gene in the same biosynthetic gene cluster. This cluster and the genes within the cluster are functionally active as confirmed by RNA-Seq. Characterization of carbohydrate-active enzymes and major facilitator superfamily (MFS)-type transporters lead to postulate S. brevicaulis originated from a soil fungus, which came into contact with the marine sponge Tethya aurantium. This marine sponge seems to provide shelter to this fungus and micro-environment suitable for its survival in the ocean. This study also builds the platform for further investigations of the role of life-style and secondary metabolites from S. brevicaulis.

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