Gastrodia elata, an obligate mycoheterotrophic orchid, requires complete carbon and mineral nutrient supplementation from mycorrhizal fungi during its entire life cycle. Although full mycoheterotrophy occurs most often in the Orchidaceae family, no chromosome-level reference genome from this group has been assembled to date. Here, we report a high-quality chromosome-level genome assembly of G. elata, using Illumina and PacBio sequencing methods with Hi-C technique. The assembled genome size was found to be 1045 Mb, with an N50 of 50.6 Mb and 488 scaffolds. A total of 935 complete (64.9%) matches to the 1440 embryophyte Benchmarking Universal Single-Copy Orthologs were identified in this genome assembly. Hi-C scaffolding of the assembled genome resulted in 18 pseudochromosomes, 1008 Mb in size and containing 96.5% of the scaffolds. A total of 18,844 protein-coding sequences (CDSs) were predicted in the G. elata genome, of which 15,619 CDSs (82.89%) were functionally annotated. In addition, 74.92% of the assembled genome was found to be composed of transposable elements. Phylogenetic analysis indicated a significant contraction of genes involved in various biosynthetic processes and cellular components and an expansion of genes for novel metabolic processes and mycorrhizal association. This result suggests an evolutionary adaptation of G. elata to a mycoheterotrophic lifestyle. In summary, the genomic resources generated in this study will provide a valuable reference genome for investigating the molecular mechanisms of G. elata biological functions. Furthermore, the complete G. elata genome will greatly improve our understanding of the genetics of Orchidaceae and its mycoheterotrophic evolution.

Gastrodia elata is an obligate mycoheterotrophic orchid that is symbiotically associated with at least two fungal partners: a broad range of Mycena spp. for seed germination and Armillaria mellea f...

Tricholoma matsutake, a highly valued ectomycorrhizal fungus, requires a symbiotic relationship with pine trees for growth, complicating its cultivation. This study presents a comprehensive comparative genomic analysis of Tricholoma species, with a focus on T. matsutake. Genomic data from 19 assemblies representing 13 species were analyzed to identify genus-, species-, and strain-specific genes, revealing significant evolutionary adaptations. Notably, T. matsutake exhibits a higher proportion of repetitive elements compared to other species, with retrotransposons like LTR Gypsy dominating its genome. Phylogenomic analyses showed that T. matsutake forms a monophyletic group closely related to T. bakamatsutake. Gene family expansion and contraction analyses highlighted the unique evolutionary pressures on T. matsutake, particularly the loss of tryptophan-related metabolic pathways and the gain of genes related to iron ion homeostasis, which may be crucial for its adaptation to nutrient-limited environments. Additionally, the reduction in secreted proteins and carbohydrate-active enzymes reflects the host-dependent lifestyle of T. matsutake and related species. These findings enhance our understanding of the genetic and evolutionary mechanisms underlying the complex symbiotic relationships of T. matsutake, offering potential avenues for optimizing its cultivation and commercial value.

We report the high-quality genome sequence of Tricholoma matsutake strain 2001, which was isolated from a mushroom fruiting body in South Korea. The genome has 80 contigs, a size of 162.6 Mb, and an N ₅₀ value of 5,103,859 bp and will provide insight into the symbiotic association between T. matsutake and Pinus densiflora .

<!----> <!----> Over the course of 10 000 years, selective breeding converted a Mesoamerican grass with little agricultural value, known as teosinte, into the important commercial crop maize (Zea mays) (Gewin, 2003; Doebley, 2004). Historically, breeding efforts have concentrated on increasing the yield, aesthetics, harvestability, and robustness of maize (Tuxill et al., 2010; Andorf et al., 2019). Modern breeders continue to seek improvements to maize, but traditional breeding programs are constrained by long generation times, linkage drag, and the loss of genetic diversity during domestication (Nannas and Dawe, 2015; Andorf et al., 2019). Whole genome sequencing analysis, detailed genetic mapping studies, and the ability to transform maize have led to new methods to overcome some of these constraints inherent to traditional selective breeding (Gordon-Kamm et al., 1990; Schnable et al., 2009; Eichten et al., 2011; for a review see Andorf et al., 2019). More recently, precision genome editing methods have been successfully used in many major commercial crops that are important for supporting the world’s growing population (Ji et al., 2013; Luo et al., 2016; Jaganathan et al., 2018). In this chapter, we will review recent advancements in maize genome editing technologies, the current state of the art breeding technology in maize and other systems. <!----> <!---->