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

Chung, Dawoon ; Kwon, Yong Min ; Yang, Youngik

BMC genomics, 2021-11, Vol.22 (1), p.830-830, Article 830 [Periódico revisado por pares]

England: BioMed Central Ltd

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Título:
Telomere-to-telomere genome assembly of asparaginase-producing Trichoderma simmonsii
Autor: Chung, Dawoon ; Kwon, Yong Min ; Yang, Youngik
Assuntos: Amino acids ; Analysis ; Ascomycota ; Asparaginase ; Bark ; Comparative genome analysis ; Comparative studies ; Enzymatic activity ; Enzymes ; Fungi ; Fungicides ; Gene sequencing ; Genes ; Genetic aspects ; Genetic research ; Genetic transcription ; Genome ; Genomes ; Genomics ; Growth hormone ; Hypocreales ; Microbial enzymes ; Morphology ; Physiological aspects ; Ribonucleic acid ; RNA ; rRNA ; Sequence analysis ; Structure ; Telomere ; Telomere-to-telomere assembly ; Telomeres ; Terrestrial environments ; Transcription ; Transcriptomes ; Transfer RNA ; Trichoderma ; Trichoderma - genetics ; Trichoderma simmonsii
É parte de: BMC genomics, 2021-11, Vol.22 (1), p.830-830, Article 830
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Descrição: 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. 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. 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.
Editor: England: BioMed Central Ltd
Idioma: Inglês

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

Chung, Dawoon ; Kwon, Yong Min ; Yang, Youngik

England: BioMed Central Ltd

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