Cryptic Species Diversity and Phylogenetic Relationship in the Rust Genus Chrysomyxa from China

Abstract

Chrysomyxa rusts are fungal pathogens widely distributed in the Northern hemisphere, causing spruce needle and cone rust diseases, and they are responsible for significant economic losses in China. Taxonomic delimitation and precise species identification are difficult within this genus because some characters often overlap in several species. Adequate species delimitation, enhanced by the use of DNA-based methodologies, will help to establish well-supported species boundaries and enable the identification of cryptic species. Here, we explore the cryptic species diversity in the rust genus Chrysomyxa from China. Species delimitation analyses are conducted using a distance-based method (ABGD) and three tree-based methods (GMYC, bPTP, and mPTP) based on combined LSU and ITS sequences of over 60 specimens. Although there is some incongruence among species delimitation methods, two new species and three putative cryptic species are identified. The key to 20 Chrysomyxa species distributed in China is presented. These results suggest that a significant level of undiscovered cryptic diversity is likely to be found in Chrysomyxa from China. Future studies should consider multiple analytical methods when dealing with multi-locus datasets.

Detection of oat crown rust disease in Taiwan (2019-2021)

“…ITS sequences amplified from four Taiwanese rust isolates and published sequences from Puccinia graminis and P. coronata f. sp. avenae were used to generate a phylogenetic tree, with the ITS from Chrysomyxa contibuerculata used as a Pucciniomycete outgroup (Szabo 2006; Wang et al 2022). The four ITS sequences from Taiwanese Pca isolates were nearly identical to P. coronata ITS collected on oat, Lolium , and Rhamnus cathartica , which correspond to previously described Clade V (representing Pca ) in P. coronata subspecies trees (Liu and Hambleton 2013; Szabo 2006).…”

“…The sequencing data were curated using CodonCode Aligner (CodonCode Corporation, Centerville, Ohio, USA) prior to phylogenetic analysis. Seventeen Puccinia coronata ITS sequences and two Puccinia graminis ITS sequences (Szabo 2006) in addition to one ITS from Chrysomyxa conituberculata (Wang et al 2022) were downloaded from NCBI and were included in the phylogenetic analysis. Phylogenetic analysis was performed using the maximum likelihood method implemented in software Mega X (Kumar et al 2018) with 5,000 bootstrap.…”

Characterization of Fomes fomentarius s.s. and F. inzengae in Belgian Beech Forests

“…There was no correlation between the density of the wood samples used and the mass loss measured (r = −0.06), indicating that the nature of the wood is not involved. Cryptic fungal species are common among forest pathogens [21,39,40]. These species are difficult to distinguish based on macroscopic morphological characteristics.…”

Morphospecies and molecular diversity of ‘lace corals’: the genus Reteporella (Bryozoa: Cheilostomatida) in the central North Atlantic Azores Archipelago

“…3 from Croatia). Incongruent performance of these tree-based species delimitation methods has been previously linked to higher substitution rates, unevenness of sampling, different population sizes among species, ongoing gene flow, or unresolved nodes, leading to over-splitting or over-lumping of the taxa [46].…”