Telomere-to-telomere genome assembly of matsutake (<i>Tricholoma matsutake</i>)

Kurokochi, Hiroyuki; Tajima, Naoyuki; Sato, Mitsuhiko; Yoshitake, Kazutoshi; Asakawa, Shuichi; Isobe, Sachiko; Shirasawa, Kenta

doi:10.1093/dnares/dsad006

Cited by 11 publications

(7 citation statements)

References 25 publications

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“…In the case of Drechmeria coniospora [82], the centromere region demonstrates heightened repeat content, diminished gene density, and lowered GC content. A different pattern emerges in the centromere region of Tricholoma matsutake [83], which were characterized by GC-rich, LINEs-rich, and devoid of LTRs. These findings suggested substantial differences in genome structure between centromeric regions and other sections of the chromosomes, and great variation among different species.…”

Section: Discussionmentioning

confidence: 92%

Telomere-to-Telomere Genome Assembly of Tibetan Medicinal Mushroom Ganoderma leucocontextum and the First Copia Centromeric Retrotransposon in Macro-Fungi Genome

Wang,

Meng,

Yang

et al. 2023

JoF

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A complete telomere-to-telomere (T2T) genome has been a longstanding goal in the field of genomic research. By integrating high-coverage and precise long-read sequencing data using multiple assembly strategies, we present here the first T2T gap-free genome assembly of Ganoderma leucocontextum strain GL72, a Tibetan medicinal mushroom. The T2T genome, with a size of 46.69 Mb, consists 13 complete nuclear chromosomes and typical telomeric repeats (CCCTAA)n were detected at both ends of 13 chromosomes. The high mapping rate, uniform genome coverage, a complete BUSCOs of 99.7%, and base accuracy exceeding 99.999% indicate that this assembly represents the highest level of completeness and quality. Regions characterized by distinct structural attributes, including highest Hi-C interaction intensity, high repeat content, decreased gene density, low GC content, and minimal or no transcription levels across all chromosomes may represent potential centromeres. Sequence analysis revealed the first Copia centromeric retrotransposon in macro-fungi genome. Phylogenomic analysis identified that G. leucocontextum and G. tsugae diverged from the other Ganoderma species approximately 9.8–17.9 MYA. The prediction of secondary metabolic clusters confirmed the capability of this fungus to produce a substantial quantity of metabolites. This T2T gap-free genome will contribute to the genomic ‘dark matter’ elucidation and server as a great reference for genetics, genomics, and evolutionary studies of G. leucocontextum.

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Section: Discussionmentioning

confidence: 92%

Telomere-to-Telomere Genome Assembly of Tibetan Medicinal Mushroom Ganoderma leucocontextum and the First Copia Centromeric Retrotransposon in Macro-Fungi Genome

Wang,

Meng,

Yang

et al. 2023

JoF

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“…These observations suggest that marY2N and its derivatives are enriched in centromeric regions. Another well-studied retroelement in T. matsutake , marY1 ( Murata and Yamada 2000 ; Kurokochi et al . 2023 ), was distributed across all 13 chromosomes in Tbkm_v1 ( Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Genes within nonrepetitive regions were extracted using the “intersect” tool in BEDTools ( Quinlan and Hall 2010 ) and the Tbkm_v1 repeat library created with RepeatModeler. The corresponding gene regions between Tbkm_v1 and TMA_r1.0 ( Kurokochi et al . 2023 ) were determined using TBLASTN, with an E -value cutoff of 1.0e −10 .…”

Section: Methodsmentioning

confidence: 99%

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Near-complete de novo assembly of Tricholoma bakamatsutake chromosomes revealed the structural divergence and differentiation of Tricholoma genomes

Ichida,

Murata,

Hatakeyama

et al. 2023

G3: Genes, Genomes, Genetics

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Tricholoma bakamatsutake, which is an edible ectomycorrhizal fungus associated with Fagaceae trees, may have diverged before the other species in Tricholoma section Caligata. We generated a highly contiguous whole-genome sequence for T. bakamatsutake SF-Tf05 isolated in an Oak (Quercus salicina) forest in Japan. The assembly of high-fidelity long reads, with a median read length of 12.3 kb, resulted in 13 chromosome-sized contigs comprising 142,068,211 bases with an average GC content of 43.94%. The 13 chromosomes were predicted to encode 11,060 genes. A contig (122,566 bases) presumably containing the whole circular mitochondrial genome was also recovered. The chromosome-wide comparison of T. bakamatsutake and T. matsutake (TMA_r1.0) indicated that the basic number of chromosomes (13) was conserved, but the structures of the corresponding chromosomes diverged, with multiple inversions and translocations. Gene conservation and cluster analyses revealed at least three phylogenetic clades in Tricholoma section Caligata. Specifically, all T. bakamatsutake strains belonged to the “bakamatsutake” clade, which is most proximal to the “caligatum” clade consisting of T. caligatum and T. fulvocastaneum. The constructed highly contiguous nearly telomere-to-telomere genome sequence of a T. bakamatsutake isolate will serve as a fundamental resource for future research on the evolution and differentiation of Tricholoma species.

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“…These three assemblies were generated using short-read (Illumina, San Diego, CA, USA), long-read (PacBio, Menlo Park, CA, USA; Oxford Nanopore Technologies, Oxford, UK), linked-read (10X Genomics, Pleasanton, CA, USA), and/or optical mapping technologies (Bionano Genomics, San Diego, CA, USA). The currently available high-fidelity (HiFi) long-read sequencing technology of PacBio could be used to establish telomere-to-telomere genome assemblies (Kurokochi et al 2023; Sato et al 2023), which are continuous assemblies ranging from one end of a chromosome to the other end without gaps.…”

Section: Introductionmentioning

confidence: 99%

Near-complete genome assembly of tomato (Solanum lycopersicum) cultivar Micro-Tom

Shirasawa,

Ariizumi

2023

Preprint

Self Cite

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We present a near-complete genome assembly of tomato (Solanum lycopersicum) cultivar Micro-Tom, which has been recognized as a model cultivar for fruit research. The genome DNA of Micro-Tom, provided by the National BioResource Project (NBRP) Tomato of Japan, was sequenced to obtain 72 Gb of high-fidelity long reads. These reads were assembled into 140 contigs, spanning 832.8 Mb, with an N50 length of 39.6 Mb. The contigs were aligned against the tomato reference genome sequence SL4.0 to establish a chromosome-level assembly. The genome assembly of Micro-Tom contained 98.5% complete BUSCOs and a total of 31,429 genes. Comparative genome structure analysis revealed that Micro-Tom possesses a cluster of rDNA genes spanning a 15 Mb stretch at the short arm of chromosome 2. This region was not found in the genome assemblies of previously sequenced tomato cultivars, possibly because of the inability of previous technologies to sequence such repetitive DNA. In conclusion, the near-complete genome assembly of Micro-Tom reported in this study would advance the genomics and genetics research on tomato and facilitate the breeding of improved tomato cultivars.

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Telomere-to-telomere genome assembly of matsutake (Tricholoma matsutake)

Cited by 11 publications

References 25 publications

Telomere-to-Telomere Genome Assembly of Tibetan Medicinal Mushroom Ganoderma leucocontextum and the First Copia Centromeric Retrotransposon in Macro-Fungi Genome

Telomere-to-Telomere Genome Assembly of Tibetan Medicinal Mushroom Ganoderma leucocontextum and the First Copia Centromeric Retrotransposon in Macro-Fungi Genome

Near-complete de novo assembly of Tricholoma bakamatsutake chromosomes revealed the structural divergence and differentiation of Tricholoma genomes

Near-complete genome assembly of tomato (Solanum lycopersicum) cultivar Micro-Tom

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