Telomere-to-telomere genome assembly of asparaginase-producing Trichoderma simmonsii

Abstract Background Trichoderma is a genus of fungi in the family Hypocreaceae and includes species known to produce enzymes with commercial use. They are largely found in soil and terrestrial plants. Recently, Trichoderma simmonsii isolated from decaying bark and decorticated wood was newly identif...

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Autores principales:	Dawoon Chung, Yong Min Kwon, Youngik Yang
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Trichoderma simmonsii Telomere-to-telomere assembly Comparative genome analysis Asparaginase Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/fb46db46f825464180a7950b41c24d64
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spelling	oai:doaj.org-article:fb46db46f825464180a7950b41c24d642021-11-21T12:26:37ZTelomere-to-telomere genome assembly of asparaginase-producing Trichoderma simmonsii10.1186/s12864-021-08162-41471-2164https://doaj.org/article/fb46db46f825464180a7950b41c24d642021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08162-4https://doaj.org/toc/1471-2164Abstract Background Trichoderma is a genus of fungi in the family Hypocreaceae and includes species known to produce enzymes with commercial use. They are largely found in soil and terrestrial plants. Recently, Trichoderma simmonsii isolated from decaying bark and decorticated wood was newly identified in the Harzianum clade of Trichoderma. Due to a wide range of applications in agriculture and other industries, genomes of at least 12 Trichoderma spp. have been studied. Moreover, antifungal and enzymatic activities have been extensively characterized in Trichoderma spp. However, the genomic information and bioactivities of T. simmonsii from a particular marine-derived isolate remain largely unknown. While we screened for asparaginase-producing fungi, we observed that T. simmonsii GH-Sj1 strain isolated from edible kelp produced asparaginase. In this study, we report a draft genome of T. simmonsii GH-Sj1 using Illumina and Oxford Nanopore technologies. Furthermore, to facilitate biotechnological applications of this species, RNA-sequencing was performed to elucidate the transcriptional profile of T. simmonsii GH-Sj1 in response to asparaginase-rich conditions. Results We generated ~ 14 Gb of sequencing data assembled in a ~ 40 Mb genome. The T. simmonsii GH-Sj1 genome consisted of seven telomere-to-telomere scaffolds with no sequencing gaps, where the N50 length was 6.4 Mb. The total number of protein-coding genes was 13,120, constituting ~ 99% of the genome. The genome harbored 176 tRNAs, which encode a full set of 20 amino acids. In addition, it had an rRNA repeat region consisting of seven repeats of the 18S-ITS1–5.8S-ITS2–26S cluster. The T. simmonsii genome also harbored 7 putative asparaginase-encoding genes with potential medical applications. Using RNA-sequencing analysis, we found that 3 genes among the 7 putative genes were significantly upregulated under asparaginase-rich conditions. Conclusions The genome and transcriptome of T. simmonsii GH-Sj1 established in the current work represent valuable resources for future comparative studies on fungal genomes and asparaginase production.Dawoon ChungYong Min KwonYoungik YangBMCarticleTrichoderma simmonsiiTelomere-to-telomere assemblyComparative genome analysisAsparaginaseBiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss 1, Pp 1-18 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Trichoderma simmonsii Telomere-to-telomere assembly Comparative genome analysis Asparaginase Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	Trichoderma simmonsii Telomere-to-telomere assembly Comparative genome analysis Asparaginase Biotechnology TP248.13-248.65 Genetics QH426-470 Dawoon Chung Yong Min Kwon Youngik Yang Telomere-to-telomere genome assembly of asparaginase-producing Trichoderma simmonsii
description	Abstract Background Trichoderma is a genus of fungi in the family Hypocreaceae and includes species known to produce enzymes with commercial use. They are largely found in soil and terrestrial plants. Recently, Trichoderma simmonsii isolated from decaying bark and decorticated wood was newly identified in the Harzianum clade of Trichoderma. Due to a wide range of applications in agriculture and other industries, genomes of at least 12 Trichoderma spp. have been studied. Moreover, antifungal and enzymatic activities have been extensively characterized in Trichoderma spp. However, the genomic information and bioactivities of T. simmonsii from a particular marine-derived isolate remain largely unknown. While we screened for asparaginase-producing fungi, we observed that T. simmonsii GH-Sj1 strain isolated from edible kelp produced asparaginase. In this study, we report a draft genome of T. simmonsii GH-Sj1 using Illumina and Oxford Nanopore technologies. Furthermore, to facilitate biotechnological applications of this species, RNA-sequencing was performed to elucidate the transcriptional profile of T. simmonsii GH-Sj1 in response to asparaginase-rich conditions. Results We generated ~ 14 Gb of sequencing data assembled in a ~ 40 Mb genome. The T. simmonsii GH-Sj1 genome consisted of seven telomere-to-telomere scaffolds with no sequencing gaps, where the N50 length was 6.4 Mb. The total number of protein-coding genes was 13,120, constituting ~ 99% of the genome. The genome harbored 176 tRNAs, which encode a full set of 20 amino acids. In addition, it had an rRNA repeat region consisting of seven repeats of the 18S-ITS1–5.8S-ITS2–26S cluster. The T. simmonsii genome also harbored 7 putative asparaginase-encoding genes with potential medical applications. Using RNA-sequencing analysis, we found that 3 genes among the 7 putative genes were significantly upregulated under asparaginase-rich conditions. Conclusions The genome and transcriptome of T. simmonsii GH-Sj1 established in the current work represent valuable resources for future comparative studies on fungal genomes and asparaginase production.
format	article
author	Dawoon Chung Yong Min Kwon Youngik Yang
author_facet	Dawoon Chung Yong Min Kwon Youngik Yang
author_sort	Dawoon Chung
title	Telomere-to-telomere genome assembly of asparaginase-producing Trichoderma simmonsii
title_short	Telomere-to-telomere genome assembly of asparaginase-producing Trichoderma simmonsii
title_full	Telomere-to-telomere genome assembly of asparaginase-producing Trichoderma simmonsii
title_fullStr	Telomere-to-telomere genome assembly of asparaginase-producing Trichoderma simmonsii
title_full_unstemmed	Telomere-to-telomere genome assembly of asparaginase-producing Trichoderma simmonsii
title_sort	telomere-to-telomere genome assembly of asparaginase-producing trichoderma simmonsii
publisher	BMC
publishDate	2021
url	https://doaj.org/article/fb46db46f825464180a7950b41c24d64
work_keys_str_mv	AT dawoonchung telomeretotelomeregenomeassemblyofasparaginaseproducingtrichodermasimmonsii AT yongminkwon telomeretotelomeregenomeassemblyofasparaginaseproducingtrichodermasimmonsii AT youngikyang telomeretotelomeregenomeassemblyofasparaginaseproducingtrichodermasimmonsii
_version_	1718419042083012608

Telomere-to-telomere genome assembly of asparaginase-producing Trichoderma simmonsii

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