Weak population spatial genetic structure and low infraspecific specificity for fungal partners in the rare mycoheterotrophic orchid Epipogium aphyllum

Organellar phylogenomics at the epidendroid orchid base, with a focus on the mycoheterotrophic Wullschlaegelia

BACKGROUND AND AIMS

Heterotrophic plants have long been a challenge for systematists, exemplified by the base of the orchid subfamily Epidendroideae, which contains numerous mycoheterotrophic species.

METHODS

Here we address the utility of organellar genomes in resolving relationships at the epidendroid base, specifically employing models of heterotachy, or lineage-specific rate variation over time. We further conduct comparative analyses of plastid genome evolution in heterotrophs and structural variation in matK.

KEY RESULTS

We present the first complete plastid genomes (plastomes) of Wullschlaegelia, the sole genus of the tribe Wullschlaegelieae, revealing a highly reduced genome of 37 kb, which retains a fraction of the genes present in related autotrophs. Plastid phylogenomic analyses recovered a strongly supported clade composed exclusively of mycoheterotrophic species with long branches. We further analysed mitochondrial gene sets, which recovered similar relationships to those in other studies using nuclear data, but the placement of Wullschlaegelia remains uncertain. We conducted comparative plastome analyses among Wullschlaegelia and other heterotrophic orchids, revealing a suite of correlated substitutional and structural changes relative to autotrophic species. Lastly, we investigated evolutionary and structural variation in matK, which is retained in Wullschlaegelia and a few other 'late stage' heterotrophs and found evidence for structural conservation despite rapid substitution rates in both Wullschlaegelia and the leafless Gastrodia.

CONCLUSIONS

Our analyses reveal the limits of what the plastid genome can tell us on orchid relationships in this part of the tree, even when applying parameter-rich heterotachy models. Our study underscores the need for increased taxon sampling across all three genomes at the epidendroid base, and illustrates the need for further research on addressing heterotachy in phylogenomic analyses.

Contributions to the Inocybe umbratica-paludinella (Agaricales) Group in China: Taxonomy, Species Diversity, and Molecular Phylogeny

Inocybe is the largest genus in the family Inocybaceae, with approximately 1000 species worldwide. Basic data on the species diversity, geographic distribution, and the infrageneric framework of Inocybe are still incomplete because of the intricate nature of this genus, which includes numerous unrecognized taxa that exist around the world. A multigene phylogeny of the I. umbratica-paludinella group, initially designated as the "I. angustifolia subgroup", was conducted using the ITS-28S-rpb2 nucleotide datasets. The seven species, I. alabamensis, I. angustifolia, I. argenteolutea, I. olivaceonigra, I. paludinella, I. subangustifolia, and I. umbratica, were confirmed as members of this species group. At the genus level, the I. umbratica-paludinella group is a sister to the lineage of the unifying I. castanea and an undescribed species. Inocybe sect. Umbraticae sect. nov. was proposed to accommodate species in the I. umbratica-paludinella group and the I. castanea lineage. This section now comprises eight documented species and nine new species from China, as described in this paper. Additionally, new geographical distributions of I. angustifolia and I. castanea in China are reported. The nine new species and I. angustifolia, I. castanea, I. olivaceonigra, and I. umbratica are described in detail and illustrated herein with color plates based on Chinese materials. A global key to 17 species in the section Umbraticae is provided. The results of the current study provide a more detailed basis for the accurate identification of species in the I. umbratica-paludinella group and a better understanding of their phylogenetic placement.

In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing

High-throughput sequencing technology has been facilitated the development of new methodologies and approaches for studying the origin and evolution of plant genomes and subgenomes, population domestication, and functional genomics. Orchids have tens of thousands of members in nature. Many of them have promising application potential in the extension and conservation of the ecological chain, the horticultural use of ornamental blossoms, and the utilization of botanical medicines. However, a large-scale gene knockout mutant library and a sophisticated genetic transformation system are still lacking in the improvement of orchid germplasm resources. New gene editing tools, such as the favored CRISPR-Cas9 or some base editors, have not yet been widely applied in orchids. In addition to a large variety of orchid cultivars, the high-precision, high-throughput genome sequencing technology is also required for the mining of trait-related functional genes. Nowadays, the focus of orchid genomics research has been directed to the origin and classification of species, genome evolution and deletion, gene duplication and chromosomal polyploidy, and flower morphogenesis-related regulation. Here, the progressing achieved in orchid molecular biology and genomics over the past few decades have been discussed, including the evolution of genome size and polyploidization. The frequent incorporation of LTR retrotransposons play important role in the expansion and structural variation of the orchid genome. The large-scale gene duplication event of the nuclear genome generated plenty of recently tandem duplicated genes, which drove the evolution and functional divergency of new genes. The evolution and loss of the plastid genome, which mostly affected genes related to photosynthesis and autotrophy, demonstrated that orchids have experienced more separate transitions to heterotrophy than any other terrestrial plant. Moreover, large-scale resequencing provide useful SNP markers for constructing genetic maps, which will facilitate the breeding of novel orchid varieties. The significance of high-throughput sequencing and gene editing technologies in the identification and molecular breeding of the trait-related genes in orchids provides us with a representative trait-improving gene as well as some mechanisms worthy of further investigation. In addition, gene editing has promise for the improvement of orchid genetic transformation and the investigation of gene function. This knowledge may provide a scientific reference and theoretical basis for orchid genome studies.