Near-gapless genome and transcriptome analyses provide insights into fruiting body development in Lentinula edodes

Shen, Nan; Xie, Haoyu; Liu, Kefang; Li, Xinru; Wang, Lu; Deng, Youjin; Chen, Lianfu; Bian, Yinbing; Xiao, Yang

doi:10.1016/j.ijbiomac.2024.130610

Cited by 2 publications

(1 citation statement)

References 107 publications

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“…The growth rate is an important index for breeding new strains, and the rapid growth of strains can reduce microbial contamination and shorten the production cycle [41]. We found that there was little correlation between the growth rate of monokaryotic strains and the growth rate of the mycelia of hybrids, and the growth rate of hybrids was greater than that of the monokaryotic strains, which was also reported in macrofungi [42], possibly due to the complementary coordination mechanism between the two cell nucleus in somatic cells [34,43]. Transcriptome analysis of the hybrid dikaryon and the two parental monokaryotic strains of Pleurotus ostreatus showed that 7953 and 7787 genes were upregulated more than 3 times, and that 8421 and 7425 genes were downregulated, respectively, compared to their parental monokaryotic strains.…”

Section: Discussionmentioning

confidence: 72%

ISSR-Assisted Breeding of Excellent New Strains of Ganoderma lingzhi through Single-Spore Selfing

Li,

Wang,

Fan

et al. 2024

Agriculture

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To improve our understanding of the selfing of G. lingzhi basidiospore monokaryons and increase the efficiency of breeding excellent strains, 52 basidiospore monokaryons were isolated from a commercial G. lingzhi strain (laboratory number P). A severe partial segregation was observed using the chi-square test, the growth rate of the monokaryotic strains was normally distributed, and colonies exhibited 5 forms. The genetic diversity of the monokaryotic strains was further demonstrated by intersimple sequence repeat (ISSR) analysis, and the similarity coefficient was in the range of 0.49–1, which was consistent with the genotype classification results. In total, 14 AxBx monokaryotic strains were randomly selected for selfing with the 1 AyBy strain when the similarity coefficient was 0.76, and a total of 14 offspring were obtained via selfing, all of which were incompatible with their parents. The traits of the selfing progenies were diverse. The mycelial growth rate, fruiting body yield, and polysaccharide, triterpene, and sterol contents were the main indices. According to the membership function value, 71.43% of the selfing progeny were super parent, and the A88 strain with the best comprehensive traits was selected. These findings prove that ISSR molecular marker-assisted breeding reduces blindness, greatly reduces workload, and improves work efficiency.

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Section: Discussionmentioning

confidence: 72%

ISSR-Assisted Breeding of Excellent New Strains of Ganoderma lingzhi through Single-Spore Selfing

Li,

Wang,

Fan

et al. 2024

Agriculture

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Telomere-to-Telomere Haplotype-Resolved Genomes of Agrocybe chaxingu Reveals Unique Genetic Features and Developmental Insights

Chen,

Wei,

Meng

et al. 2024

JoF

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Agrocybe chaxingu is a widely cultivated edible fungus in China, which is rich in nutrients and medicinal compounds. However, the lack of a high-quality genome hinders further research. In this study, we assembled the telomere-to-telomere genomes of two sexually compatible monokaryons (CchA and CchB) derived from a primarily cultivated strain AS-5. The genomes of CchA and CchB were 50.60 Mb and 51.66 Mb with contig N50 values of 3.95 Mb and 3.97 Mb, respectively. Each contained 13 complete chromosomes with telomeres at both ends. The high mapping rate, uniform genome coverage, high LAI score, all BUSCOs with 98.5%, and all base accuracy exceeding 99.999% indicated the high level of integrity and quality of these two assembled genomes. Comparison of the two genomes revealed that approximately 30% of the nucleotide sequences between homologous chromosomes were non-syntenic, including 19 translocations, 36 inversions, and 15 duplications. An additional gene CchA_000467 was identified at the Mat A locus of CchA, which was observed exclusively in the Cyclocybe cylindracea species complex. A total of 613 (4.26%) and 483 (3.4%) unique genes were identified in CchA and CchB, respectively, with over 80% of these being hypothetical proteins. Transcriptomic analysis revealed that the expression levels of unique genes in CchB were significantly higher than those in CchA, and both CchA and CchB had unique genes specifically expressed at stages of mycelium and fruiting body. It was indicated that the growth and development of the A. chaxingu strain AS-5 required the coordinated action of two different nuclei, with CchB potentially playing a more significant role. These findings contributed to a more profound comprehension of the growth and developmental processes of basidiomycetes.

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Near-gapless genome and transcriptome analyses provide insights into fruiting body development in Lentinula edodes

Cited by 2 publications

References 107 publications

ISSR-Assisted Breeding of Excellent New Strains of Ganoderma lingzhi through Single-Spore Selfing

ISSR-Assisted Breeding of Excellent New Strains of Ganoderma lingzhi through Single-Spore Selfing

Telomere-to-Telomere Haplotype-Resolved Genomes of Agrocybe chaxingu Reveals Unique Genetic Features and Developmental Insights

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