ITS2 sequence–structure phylogeny reveals diverse endophytic Pseudocercospora fungi on poplars

Abstract

For matching the new fungal nomenclature to abolish pleomorphic names for a fungus, a genus Pseudocercospora s. str. was suggested to host holomorphic Pseudocercosproa fungi. But the Pseudocercosproa fungi need extra phylogenetic loci to clarify their taxonomy and diversity for their existing and coming species. Internal transcribed spacer 2 (ITS2) secondary structures have been promising in charactering species phylogeny in plants, animals and fungi. In present study, a conserved model of ITS2 secondary structures was confirmed on fungi in Pseudocercospora s. str. genus using RNAshape program. The model has a typical eukaryotic four-helix ITS2 secondary structure. But a single U base occurred in conserved motif of U-U mismatch in Helix 2, and a UG emerged in UGGU motif in Helix 3 to Pseudocercospora fungi. The phylogeny analyses based on the ITS2 sequence-secondary structures with compensatory base change characterizations are able to delimit more species for Pseudocercospora s. str. than phylogenic inferences of traditional multi-loci alignments do. The model was employed to explore the diversity of endophytic Pseudocercospora fungi in poplar trees. The analysis results also showed that endophytic Pseudocercospora fungi were diverse in species and evolved a specific lineage in poplar trees. This work suggested that ITS2 sequence-structures could become as additionally significant loci for species phylogenetic and taxonomic studies on Pseudocerospora fungi, and that Pseudocercospora endophytes could be important roles to Pseudocercospora fungi's evolution and function in ecology.

Rapid and reliable distinguish of Morinda officinalis How by loop-mediated isothermal amplification (LAMP) assay

“…DNA barcodes is an e cacious molecular tool that can provide species-level resolution to distinguish various creatures differentiation, currently has been widely used in plant identi cation 23 . The ITS2 sequence has been recommended as an effective core molecular marker of the DNA barcode 24 , which can be used to verify a wider range of herbal species groups with high variability and species discrimination 25 . These advantages make ITS2 sequence becomes a prospective barcode gene target to increase the success rate of LAMP assay.…”

Internal transcribed spacer 2 (ITS2) molecular morphometric analysis based species delimitation of foliar endophytic fungi from Aglaia elaeagnoidea, Flacourtia inermis and Premna serratifolia

“…In recent years, a substantial number of studies have demonstrated the ITS2 molecular morphometrics approach to produce significant vital phylogenetic information for delimiting the eukaryotes at different taxonomic levels, especially at genus and species ranks [31–35]. ITS2, a sub-region of ITS genetic marker, lies between the 5.8S and 28S genes of tandemly repeated rRNA genes.…”