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Phylogenetic relationships of Puccinia species infecting Lycieae based on BI analysis of combined ITS2 and CO3 sequences. This cladogram resulted from a 50% majority rule consensus of 87 500 trees sampled with Bayesian MCMCMC. Branches in boldface indicate a support of PP >0.95 and ML BS >70%. Support values are ordered as PP/ML BS. Drawings indicate teliospore morphology within a clade or lineage.
Source publication
We present a taxonomic and phylogenetic study of Puccinia species (rust fungi) infecting tribe Lycieae (Solanaceae), with focus on the New World taxa. Phylogenetic analyses using nuclear (nuc) rDNA 5.8S-ITS2 (ITS2) and mitochondrial (mt) cytochrome oxidase subunit 3 (CO3) show that Puccinia species occurring on Lyciae are grouped in two major linea...
Citations
... A few were included in the early attempts at a phylogenetic reconstruction for Pucciniales (Wingfield et al. 2004) and Pucciniaceae (Maier et al. 2007). In addition, a few studies on specific taxa have been undertaken: a species complex of Endophyllum (Wood and Crous 2005), Macuropyxis fulva (Martin et al. 2017), Phakopsora myrtacearum (Maier et al. 2016), Puccinia on Lycieae (Ireland et al. 2019;Otálora and Berndt 2018), Solanaceae (Boshoff et al. 2022), and indigenous rye grass (Pretorius et al. 2015), Puccorchidium (Beenken and Wood 2015), Stomatisora (Wood et al. 2014), and Ravenelia (Ebinghaus et al. 2018(Ebinghaus et al. , 2020. ...
... For phylogenetic analyses only the ITS2 and CO3 regions were included. DNA sequences (ITS2 and CO3 gene regions) of Puccinia species known to infect plant species from the Lycieae (Ot alora and Berndt, 2018) were downloaded from NCBI and aligned with those of the rust fungus samples collected from L. ferocissimum in MAFFT (Katoh and Standley, 2013). Alignments were manually adjusted in Mesquite (Maddison and Maddison, 2018) and ambiguously aligned regions were excluded. ...
... For this bootstrap analysis, GTRGAMMA was used as the substitution model and 1000 bootstrap iterations were implemented. Bayesian and RAxML support values, as well as the New and Old World lineage designations of Ot alora and Berndt (2018), were added to the Bayesian consensus tree by editing the output in Adobe Illustrator (Adobe Inc., USA). All trees were rooted with Puccinia hemerocallidis, Puccinia pampeana and Puccinia dichondrae. ...
... aecia ¼ aecia from the site where the Western Cape isolate of P. rapipes was collected (Table A.4). Support values are shown above each branch, ordered as Bayesian posterior probabilities followed by RAxML bootstrap values (PP/BS). New and Old World lineages indicated as per Ot alora and Berndt (2018). in exp. 7 (86e93 %). ...
Fungal plant pathogens are increasingly recognised as being among the most effective and safe agents in classical weed biological control programs worldwide. Suitability of the rust fungus P. rapipes as a classical biological control agent for Lycium ferocissimum (African boxthorn) in Australia was assessed using a streamlined agent selection framework. Studies with P. rapipes were undertaken to elucidate its life cycle, confirm its taxonomic placement and determine its pathogenicity to L. ferocissimum and seven closely-related Solanaceae species that occur in Australia. Field surveys in the native range of South Africa, experiments in a containment facility in Australia and DNA sequencing confirmed that P. rapipes is macrocyclic and autoecious, producing all five spore stages on L. ferocissimum. The stages not previously encountered, spermogonia and aecia, are described. Sequencing also confirmed that P. rapipes is sister to Puccinia afra, in the 'Old World Lineage' of Puccinia species on Lycieae. Two purified isolates of the fungus, representing the Eastern and Western Cape distributions of P. rapipes in South Africa, were cultured in the containment facility for use in pathogenicity testing. L. ferocissimum and all of the Lycium species of Eurasian origin tested ‒ Lycium barbarum (goji berry), Lycium chinense (goji berry 'chinense') and Lycium ruthenicum (black goji berry) - were susceptible to both isolates of P. rapipes. The Australian native L. australe and three more distantly related species in different genera tested were resistant to both isolates. The isolate from the Western Cape was significantly more pathogenic on L. ferocissimum from Australia, than the Eastern Cape isolate. Our results indicate that P. rapipes may be sufficiently host specific to pursue as a biological control agent in an Australian context, should regulators be willing to accept damage to the Eurasian goji berries being grown, albeit to a limited extent, in Australia.
Lycium chinense Mill is a deciduous broad-leaved shrub belonging to the Solanaceae family and, is widely distributed throughout Korea. This plant is native to, or cultivated for various oriental medicinal purposes in, multiple regions of Asia, including Korea, China, and Japan (Lee 1982; Kim et al. 1994). Eleven Puccinia species have been reported to infect Lycium species (Otálora et al. 2018). In May and October 2022, symptoms of rust disease caused by Puccinia sp. were observed on almost all the leaves of about 60 sprawling stems of L. chinense plants on the seashore of Jeju island, Korea (33°14′15.0835″N, 126°30′53.40E). Brownish red (uredinium) or blackish brown (telium) pustules were observed on upper and lower surfaces of infected leaves. These symptoms were observed on about 40 L. chinense plants, barely growing between rocks on the seashore of Ulsan Metropolitan City, and on the about 20 L. chinense plants on a small home garden of Jindo-gun, Korea, in June and October 2023, respectively. Uredinia were amphigenous, individually scattered, but sometimes formed groups of two or three on leaves and sepals, ferruginous, pulverulent, and surrounded by a ruptured epidermis, often developing into blackish telia. Urediniospores were either ellipsoid or ovoid, approximately 29.3–34.9 × 17–24.3 μm, with yellowish walls, 1–2 μm thick. The germ pores were bizonate, and each band contained four pores covered by low papillae. Blackish-brown telia were observed on both leaf surfaces. Teliospores were broadly ellipsoidal, and rounded at the apex and towards the base. They were measured approximately 37.1–53.4 × 25–34.5 μm. The walls were light chestnut-brown and 2–3.7 μm thick, apically up to 5–9 μm thick. The swollen pedicel was persistent, basal, hyaline, smooth, and similar in length to the spores (Fig. 1). These morphological characteristics were similar to those of P. tumidipes, as described by Otálora et al. (2018). The representative specimens were preserved at the Animal and Plant Quarantine Agency Herbarium (PQK220531, -230605, and -231026). The fungal internal transcribed spacer (ITS2) and cytochrome oxidase subunit 3(CO3) regions were amplified from the total DNA of the isolates, using the primer pairs ITS5, ITS4, CO3F1, and CO3R1 for phylogenetic analysis (White et al. 1990; Vialle et al. 2009). PCR products were sequenced (Celemics, Seoul, Korea), and deposited in GenBank (Accession numbers are shown in Fig. 2.). The combined ITS2 and CO3 sequences were grouped with those of other isolates of P. tumidipes in the phylogenetic tree (Fig. 2). In November 2022, three pathogenicity tests were conducted using a urediniospore suspension made with the PQK220531 isolate in sterile distilled water. The suspension was smeared onto the upper surface of healthy L. chinense leaves. The three inoculated plants were kept in the dark at saturated moisture levels for 24 hours and placed in an isolated glasshouse together with the three control plants. After two weeks, uredinia of P. tumidipes were observed on the leaves of the inoculated plants, but not on the control plants. Although no spermogonial or aecial stage has been observed in Korea, our study has proven that P. tumidipes is the causal fungus of rust disease in L. chinense. This result is also the first discovery of the New-World P. tumidipes in Asia, showing this fungus is not limitedly distributed in America and suggesting further surveys be done on its exact geographical distribution.
Rust fungi are important plant pathogens and have been extensively studied on crops and other host plants worldwide. This study describes the heterecious life cycle of a rust fungus on Digitaria eriantha (finger grass) and the Solanum species S. lichtensteinii (large yellow bitter apple), S. campylacanthum (bitter apple), and S. melongena (eggplant) in South Africa. Following field observations, inoculation studies involving telial isolates collected from Digitaria plants produced spermogonia and aecia on S. lichtensteinii, S. campylacanthum, and S. melongena. Likewise, inoculation of finger grass with aeciospores collected from the aforementioned Solanum species produced uredinia on D. eriantha. Pennisetum glaucum (pearl millet varieties Milkstar and Okashana, as well as 17 experimental lines) and S. elaeagnifolium (silverleaf nightshade or bitter apple) were resistant to the rust isolates. Morphological descriptions and molecular phylogenetic data confirmed the identity of the rust on Digitaria as P. digitariae, herein reinstated as a species and closely related to P. penicillariae the pearl millet rust, also reinstated. Puccinia digitariae has a macrocyclic, heterecious life cycle in which teliospores overwinter on dormant D. eriantha plants. Aecia sporulate on species of Solanum during spring and early summer to provide inocula that infect new growth of Digitaria.
Background
Anisodus acutangulus (Solanaceae), an important folk medicinal herb in China, produces up to 1.2% alkaloids more than that in other Solanaceae plants such as Hyoscyamus niger, while its evolutionary position in Hyoscyameae is not very clear.
Objective
To explain the evolutionary position of A. acutangulus in the Solanaceae via complete chloroplast genome(cp) sequence.
Methods
Complete chloroplast genome of A. acutangulus was obtained and characterized using the Illumina PE150 pair-end sequencing data. Structure of the genome, codon usage, nucleotide variability (Pi) value, distribution of repeats and SSRs between A. acutangulus and other seven Solanaceae species were analyzed. Previously published 22 Solanaceae cp genomes were used to construct phylogenetic tree.
Results
The complete cp genome of A. acutangulus is 156082 bp in length, showed the typical quadripartite structure. The complete cp genome of A. acutangulus was highly conserved. A total of 112 unique genes were found in cp genome of A. acutangulus, among which 17 were duplicated. Further, we found eight hotspot regions for genome divergence could be explored as new DNA barcodes for the identification of the Solanaceae species. Phylogenetic analysis showed that A. acutangulus formed a clade with H. niger.
Conclusion
A. acutangulus belongs to Hyoscyameae subfamily and the complete cp genome provides valuable information for phylogenetic reconstruction or comparative genomics of A. acutangulus.
Rusts constitute a major group of the Kingdom Fungi and they are distributed all over the world on a wide range of wild and cultivated plants. It is the largest natural group of plant pathogens including 95% of the subphylum Pucciniomycotina and about 8% of all described Fungi. This article provides an overview and outline of rust fungi of India with important descriptive notes. After compilation of available literature on Indian rust fungi from various sources, it was observed that these fungi are distributed in 16 families, 69 genera and 640 species. They belong to Coleosporiaceae, Crossopsoraceae, Gymnosporangiaceae, Melampsoraceae, Milesinaceae, Ochropsoraceae, Phakopsoraceae, Phragmidiaceae, Pileolariaceae, Pucciniaceae, Pucciniastraceae, Raveneliaceae, Skierkaceae, Sphaerophragmiaceae, Tranzscheliaceae and Zaghouaniaceae. There are still many rust fungi with uncertain taxonomic position, and they have been referred to incertae sedis. The placement of all fungal genera is provided at the class, order and family-level along with number of species in a genus. Notes for each rust family along with total Indian records and other taxonomic information on transferred genera and species are also presented. A phylogenetic analysis from a combined LSU and ITS dataset for 25 rust genera is presented to provide a better understanding of their phylogeny and evolution.
Rusts constitute a major group of the Kingdom Fungi and they are distributed all over the world on a wide range of wild and cultivated plants. It is the largest natural group of plant pathogens including 95% of the subphylum Pucciniomycotina and about 8% of all described Fungi. This article provides an overview and outline of rust fungi of India with important descriptive notes. After compilation of available literature on Indian rust fungi from various sources, it was observed that these fungi are distributed in 16 families, 69 genera and 640 species. They belong to Coleosporiaceae, Crossopsoraceae, Gymnosporangiaceae, Melampsoraceae, Milesinaceae, Ochropsoraceae, Phakopsoraceae, Phragmidiaceae, Pileolariaceae, Pucciniaceae, Pucciniastraceae, Raveneliaceae, Skierkaceae, Sphaerophragmiaceae, Tranzscheliaceae and Zaghouaniaceae. There are still many rust fungi with uncertain taxonomic position, and they have been referred to incertae sedis. The placement of all fungal genera is provided at the class, order and family-level along with number of species in a genus. Notes for each rust family along with total Indian records and other taxonomic information on transferred genera and species are also presented. A phylogenetic analysis from a combined LSU and ITS dataset for 25 rust genera is presented to provide a better understanding of their phylogeny and evolution.
