High quality genome sequence reveals the 12 pseudo-chromosomes of <i>Ganoderma boninense</i>

Utomo, Condro; Za, Tanjung; Aditama, Redi; Rf, Nurani Buana; Ad, Madu Pratomo; Tryono, Reno; Liwang, Tony

doi:10.1101/817510

Cited by 6 publications

(6 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…After Hi-C read mapping onto the assembly, generating a draft contact map, and applying automatic reordering of scaffolds in the genome assembly followed by manual correction, more than 85% of the initial genome assembly's scaffolds were successfully grouped into 12 super scaffolds, which are presumed to correspond to the 12 chromosomes of the fungus (Figure 2). This observation aligns with previous findings on the number of chromosomes (12)(13) in other Ganoderma species [40,58,59]. The contact map obtained after reordering, its corresponding labeling, and a table containing the coordinates and sizes of the super scaffolds can be found in Supplementary Files S4-S6, respectively.…”

Section: Improving G Lucidum Genome Assembly Using the Chromosome Con...supporting

confidence: 88%

“…Chromosome conformation capture techniques such as Hi-C have been extensively utilized to significantly enhance the quality of assembled eukaryotic genomes [37], as well as of the microbial genomes from metagenomes [38,39]. However, their utilization in fungal genome research has been relatively scarce, with only one Hi-C-aided Ganoderma genome assembly (G. boninense) published to date [40]. In this study, we obtained a genome assembly for the strain G. lucidum 5.1 by employing a combination of high-throughput shotgun sequencing and the Hi-C method and explored its potential for xylomannan and fucogalactan synthesis.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Unraveling the Polysaccharide Biosynthesis Potential of Ganoderma lucidum: A Chromosome-Level Assembly Using Hi-C Sequencing

Sonets,

Dovidchenko,

Ulianov

et al. 2023

JoF

View full text Add to dashboard Cite

Ganoderma lucidum exhibits the ability to synthesize a diverse range of biologically active molecules with significant pharmaceutical potential, including xylomannan and fucogalactan, which have demonstrated antitumor activity. However, there exists considerable intra-species variability in the capacity to produce these metabolites at high concentrations, likely reflecting the high genomic diversity observed from a limited number of strains sequenced to date. We employed high-throughput shotgun sequencing to obtain the complete genome sequence of G. lucidum strain 5.1, which is distinguished by its remarkable xylomannan synthesis capabilities. Through the utilization of semi-automatic reordering based on conformation capture (Hi-C) data, we substantially enhanced the assembly process, resulting in the generation of 12 chromosome-level scaffolds with a cumulative length of 39 Mbp. By employing both de novo and homology-based approaches, we performed comprehensive annotation of the genome, thereby identifying a diverse repertoire of genes likely involved in polysaccharide biosynthesis. The genome sequence generated in this study serves as a valuable resource for elucidating the molecular mechanisms underlying the medicinal potential of Ganoderma species, discovering novel pharmaceutically valuable compounds, and elucidating the ecological mechanisms of the species. Furthermore, the chromosome contact map obtained for the first time for this species extends our understanding of 3D fungal genomics and provides insights into the functional and structural organization within the fungal kingdom.

show abstract

Section: Improving G Lucidum Genome Assembly Using the Chromosome Con...supporting

confidence: 88%

Section: Introductionmentioning

confidence: 99%

Unraveling the Polysaccharide Biosynthesis Potential of Ganoderma lucidum: A Chromosome-Level Assembly Using Hi-C Sequencing

Sonets,

Dovidchenko,

Ulianov

et al. 2023

JoF

View full text Add to dashboard Cite

show abstract

“…The 19,851 gene models predicted from PER71 assembly are comparable to G3 with 21,074 coding sequences [27] and G. lucidum with 16,113 genes [28]. Although the number of gene models is higher compared to G. lucidum, 71.30% of PER71 predicted genes are similar to RefSeq proteins.…”

Section: Discussionmentioning

confidence: 99%

Transcriptional effects of carbon and nitrogen starvation on Ganoderma boninense, an oil palm phytopathogen

Nagappan

Ooi

Chan

et al. 2023

Preprint

View full text Add to dashboard Cite

Background Ganoderma boninense is a phytopathogen of oil palm, causing basal and upper stem rot diseases. Methods The genome sequence was used as a reference to study gene expression during growth in a starved carbon (C) and nitrogen (N) environment with minimal sugar and sawdust as initial energy sources. This study was conducted to mimic possible limitations of the C-N nutrient sources during the growth of G. boninense in oil palm plantations. Results Genome sequencing of an isolate collected from a palm tree in West Malaysia generated an assembly of 67.12 Mb encoding 19,851 predicted genes. Transcriptomic analysis from a time course during growth in this starvation media identified differential expressed genes (DEGs) that were found to be associated with 30 metabolic pathways. During the active growth phase (Day2), 27 DEGs related to four pathways, including secondary metabolite biosynthesis, carbohydrate metabolism, glycan metabolism and mycotoxin biosynthesis. G. boninense genes involved in the carbohydrate metabolism pathway that contribute to the degradation of plant cell walls were up-regulated. Interestingly, several genes associated with the mycotoxin biosynthesis pathway were identified as playing a possible role in pathogen-host interaction. Several genes associated with mycotoxin biosynthesis were associated with pathogen-host interactions. In addition, metabolomics analysis revealed six metabolites, maltose, xylobiose, glucooligosaccharide, glycylproline, dimethylfumaric acid and arabitol that were up-regulated on Day2 of the time course. Conclusions This study provides information on genes expressed by G. boninense in metabolic pathways that may play a role in the initial infection of the host.

show abstract

“…The genome sequence of the Gb strain G3 was used in this study 32,33 . A fine draft genome sequence was constructed by the hybrid assembly of short reads on the Illumina HiSeq 4000 platform combined with long reads on the PacBio RS II platform to generate a draft genome of this fungus.…”

Section: Global Genome Assembly and Characteristicsmentioning

confidence: 99%

Whole-genome sequencing of Ganoderma boninense, the causal agent of basal stem rot disease in oil palm, via combined short- and long-read sequencing

Utomo,

Tanjung,

Aditama

et al. 2024

Sci Rep

Self Cite

View full text Add to dashboard Cite

The hemibiotrophic Basidiomycete pathogen Ganoderma boninense (Gb) is the dominant causal agent of oil palm basal stem rot disease. Here, we report a complete chromosomal genome map of Gb using a combination of short-read Illumina and long-read Pacific Biosciences (PacBio) sequencing platforms combined with chromatin conformation capture data from the Chicago and Hi-C platforms. The genome was 55.87 Mb in length and assembled to a high contiguity (N50: 304.34 kb) of 12 chromosomes built from 112 scaffolds, with a total of only 4.34 Mb (~ 7.77%) remaining unplaced. The final assemblies were evaluated for completeness of the genome by using Benchmarking Universal Single Copy Orthologs (BUSCO) v4.1.4, and based on 4464 total BUSCO polyporales group searches, the assemblies yielded 4264 (95.52%) of the conserved orthologs as complete and only a few fragmented BUSCO of 42 (0.94%) as well as a missing BUSCO of 158 (3.53%). Genome annotation predicted a total of 21,074 coding genes, with a GC content ratio of 59.2%. The genome features were analyzed with different databases, which revealed 2471 Gene Ontology/GO (11.72%), 5418 KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthologous/KO (25.71%), 13,913 Cluster of Orthologous Groups of proteins/COG (66.02%), 60 ABC transporter (0.28%), 1049 Carbohydrate-Active Enzymes/CAZy (4.98%), 4005 pathogen–host interactions/PHI (19%), and 515 fungal transcription factor/FTFD (2.44%) genes. The results obtained in this study provide deep insight for further studies in the future.

show abstract

High quality genome sequence reveals the 12 pseudo-chromosomes of Ganoderma boninense

Cited by 6 publications

References 27 publications

Unraveling the Polysaccharide Biosynthesis Potential of Ganoderma lucidum: A Chromosome-Level Assembly Using Hi-C Sequencing

Unraveling the Polysaccharide Biosynthesis Potential of Ganoderma lucidum: A Chromosome-Level Assembly Using Hi-C Sequencing

Transcriptional effects of carbon and nitrogen starvation on Ganoderma boninense, an oil palm phytopathogen

Whole-genome sequencing of Ganoderma boninense, the causal agent of basal stem rot disease in oil palm, via combined short- and long-read sequencing

Contact Info

Product

Resources

About