Article
Plant Sciences
Joanna Sokolowska, Hanna Fuchs, Konrad Celinski
Summary: In this study, we conducted a comprehensive study for the first time to summarize the legitimacy of using the ITS2 region for taxa discrimination among Pinaceae. The obtained results clearly show that its usefulness for this purpose is limited.
Article
Microbiology
Wael A. Fathy, Natascha Techen, Khaled N. M. Elsayed, Ehab A. Essawy, Eman Tawfik, Khairiah Mubarak Alwutayd, Mohamed S. Abdelhameed, Ola Hammouda, Samir A. Ross
Summary: The absence of proper identification and documentation of microalgae is a common concern in the field of applied phycology, algal physiology, and biochemistry publications. A promising solution lies in employing DNA barcoding techniques and establishing comprehensive databases of reference sequences. This study focuses on the molecular characterization and strain identification of Tetraselmis and Chlorella species using the internal transcribed spacer (ITS) barcode approach.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Mycology
Junichiro Hiruma, Honoka Nojo, Hitoshi Tsuchihashi, Hiromitsu Noguchi, Masataro Hiruma, Kazutoshi Harada, Rui Kano
Summary: In this study, T. interdigitale isolates were obtained from Japanese patients and their ITS types were investigated. The results showed that all 29 isolates belong to ITS type II, while one clinical isolate of T. mentagrophytes was similar to ITS type II*. Additionally, a terbinafine-resistant strain of T. interdigitale also belonged to ITS type II.
Article
Immunology
Gobena Ameni, Alebachew Messele Kebede, Aboma Zewude, Musse Girma Abdulla, Rahel Asfaw, Mesfin Mamo Gobena, Martina Kyalo, Francesca Stomeo, Balako Gumi, Teshale Sori
Summary: This study conducted a phylogenetic analysis of Histoplasma capsulatum isolated from cases of epizootic lymphangitis (EL) in horses in central Ethiopia and evaluated their relationship with isolates from other countries and clades. By analyzing the internal transcribed spacer (ITS) region of rRNA genes, the study identified different clades of H. capsulatum and revealed that the Ethiopian isolates were closely related to isolates from Latin America and Eurasia, but distantly related to isolates from North America.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Microbiology
Vinciane Monod, Valerie Hofstetter, Vivian Zufferey, Olivier Viret, Katia Gindro, Daniel Croll
Summary: The evolution of sequencing technology and multiplexing has expanded our ability to characterize fungal diversity. However, obtaining an unbiased assessment of the fungal community remains challenging. This study found that shorter amplicons had higher sequencing depths and overall diversity, with no significant bias in phylogenetic composition. Despite the increased resolution of longer amplicons, the shorter amplicons provided clearer resolution of the fungal community. The choice of ribosomal amplicons should be carefully evaluated and adjusted according to specific goals.
MICROBIOLOGY SPECTRUM
(2022)
Article
Plant Sciences
Dong-Pil Jin, Sunhee Sim, Jong-Won Park, Ji-Eun Choi, Jiwon Yoon, Chae Eun Lim, Min-Ha Kim
Summary: This study used DNA barcoding to accurately identify Korean Caryophyllaceae and found that ITS sequences were more accurate for identification than chloroplast sequences. Among the genera, five genera (Eremogone, Minuartia, Pseudostellaria, Sagina, and Stellaria) were successfully identified, while the identification of species in Cerastium, Gypsophila, Dianthus, Silene, and Spergularia showed relatively low resolutions.
Article
Microbiology
Nadia Stoppani, Silvia Colussi, Paolo Pastorino, Marino Prearo, Simona Sciuto, Ilhan Altinok, Rafet Cagri Ozturk, Mustafa Ture, Ana Isabel Vela, Maria del Mar Blanco, Charalampos Kotzamanidis, Konstantina Bitchava, Andigoni Malousi, Lucio Fariano, Donatella Volpatti, Pier Luigi Acutis, Jose Francisco Fernandez-Garayzabal
Summary: The aim of this study was to use the transcribed spacer (ITS) region between 16S rRNA and 23S rRNA as a potential useful molecular target to differentiate L. garvieae from L. petauri for accurate discrimination between these two species. Seven SNPs were identified that separate L. garvieae from L. petauri based on the ITS region sequence. The 16S-23S rRNA ITS region can be used as a diagnostic marker to quickly identify the pathogens in a lactococcosis outbreak.
Article
Biochemistry & Molecular Biology
Zhehui Jiang, Meiqi Zhang, Lingyang Kong, Yihong Bao, Weichao Ren, Hongyuan Li, Xiubo Liu, Zhen Wang, Wei Ma
Summary: This study systematically documented and identified Apiaceae plants in the grassland ecosystem of Heilongjiang Province using nuclear and chloroplast sequences. The results can enrich the reference Apiaceae DNA barcode database.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Microbiology
Fernando Martinez-Hernandez, Fabiola Sanchez-Aguillon, Joel Martinez-Ocana, Nelly Raquel Gonzalez-Arenas, Mirza Romero-Valdovinos, Eduardo Lopez-Escamilla, Pablo Maravilla, Guiehdani Villalobos
Summary: This study evaluated the genetic variability of the ITS region and pfor A gene of Trichomonas vaginalis from female patients and explored its implications in the host-parasite relationship. Results showed two main clusters in the ITS haplotypes and suggested that pfor A could be used as a marker for confirming trichomonads genus and species.
Review
Ecology
Havard Kauserud
Summary: This text discusses the inherent limitations of using the rDNA Internal Transcribed Spacer (ITS) region as a DNA barcode marker in fungal ecology studies. It highlights the challenges in species delimitation, the lack of significant interspecific divergence, and the uncertainty in species-level taxonomy. It also emphasizes the complexity and variation introduced by PCR and sequencing errors in DNA metabarcoding data. The importance of the ITS region as a general DNA (meta)barcoding marker for fungi is acknowledged but caution against naïve or simplistic use is stressed.
Article
Multidisciplinary Sciences
Jessica M. Velez, Reese M. Morris, Rytas Vilgalys, Jessy Labbe, Christopher W. Schadt
Summary: The ectomycorrhizal fungal symbiont Cenococcum geophilum is globally distributed and shows resistance to multiple environmental stressors. It is considered a cryptic species complex, with significant phylogenetic divergence observed within morphologically identical strains. The data suggest divergence within multiple cryptic species, with significant genetic variation among isolates from different geographic locations.
Article
Food Science & Technology
Alice Giusti, Enrica Ricci, Laura Gasperetti, Marta Galgani, Luca Polidori, Francesco Verdigi, Roberto Narducci, Andrea Armani
Summary: This study aimed to build an ITS gene dataset to aid the Italian Health Service in mushroom identification. By retrieving and filtering ITS sequences from GenBank and BOLD databases, as well as collecting wild specimens, a dataset of 5977 sequences was successfully established to support regional poisoning cases.
Article
Ecology
Steven L. Miller, Abbie Gongloff
Summary: This study conducted intensive research on fairy rings in the Laramie Basin of southeastern Wyoming, identifying multiple fungal species responsible for forming fairy rings. Most fairy rings were found in drier mixed-grass prairie vegetation, while only a small percentage occurred in mesic shrub dominated riparian vegetation. Fungal species exhibited preferences for elevation and slope aspect, with rings scarce on east facing slopes.
Article
Biotechnology & Applied Microbiology
Yakelin Rodriguez-Yon, Camila Maistro-Patreze, Orivaldo Jose Saggin-Junior, Ramon Antonio Rivera, Madelaine Quinones, Geert Haesaert, Diederik van Tuinen
Summary: Inoculation with Glomus cubense isolate can improve yield in crops such as banana, cassava, forages, etc. Methods using taxon-discriminating primer set and molecular approaches have successfully traced and quantified the G. cubense isolate in roots and soil, demonstrating potential for quality control of mycorrhizal inoculants in agroecosystems.
FOLIA MICROBIOLOGICA
(2021)
Article
Microbiology
Shuqian Hu, Xiang Li, Xin Yin, Runmeng Li, Ruiyang Zhang, Junhao Zang, Yin Liu
Summary: This study developed a species-specific method for identification and classification of Pseudomonas based on ITS sequences combined with next-generation sequencing (NGS).
Article
Plant Sciences
Nicolas J. Rawlence, Benjamin C. M. Potter, Nic Dussex, Lachie Scarsbrook, David A. Orlovich, Jonathan M. Waters, Matt McGlone, Michael Knapp
Summary: This study uses chloroplast genetic markers to elucidate the Pleistocene history and present-day distribution of southern beech species in New Zealand, showing broadly concordant phylogeographic patterns. The genetic diversity of silver beech is centered in the northern South Island, with unique haplotypes in various regions separated by known 'beech gaps'. In contrast, the subgenus Fuscospora shows significantly less genetic diversity.
NEW ZEALAND JOURNAL OF BOTANY
(2021)
Article
Plant Sciences
Julia Bohorquez, Andy R. Nilsen, Matthew J. Larcombe, David A. Orlovich, Janice M. Lord
Summary: This study investigated the viability and germination of ectomycorrhizal fungi (EMF) spores associated with southern beech forest in New Zealand. Different spore taxa showed varying germination rates and responses to different temperature and light conditions. For storing EMF material as inoculum, it is recommended to dry fruiting bodies at 30 degrees C and prepare fresh spore suspensions in water when needed.
NEW ZEALAND JOURNAL OF BOTANY
(2021)
Article
Ecology
Laura G. van Galen, Janice M. Lord, David A. Orlovich, Matthew J. Larcombe
Summary: Nothofagus (southern beech) restoration projects are becoming increasingly important in the southern hemisphere, but current techniques yield mixed results. Providing shelter, controlling weeds, and protecting from herbivores have positive effects on seedling survival and growth, while fertilizer application and other techniques show inconsistent results. Researchers suggest that future research should focus on unexplored techniques such as ectomycorrhizal fungal inoculum to enhance restoration efforts.
RESTORATION ECOLOGY
(2021)
Article
Plant Sciences
Andy R. Nilsen, Olivia C. Macrae, Kane M. Andrew, Xin Yue Wang, Mia C. Te Tana, Karl Soop, Chris M. Brown, Tina C. Summerfield, David A. Orlovich
Summary: Cortinarius is a diverse genus of mycorrhizal fungi, with some species like C. epiphaeus and C. taylorianus proving difficult to identify. In species where genetic information is lacking from type specimens, accurate identification may be challenging.
NEW ZEALAND JOURNAL OF BOTANY
(2021)
Review
Biodiversity Conservation
P. L. Guy, C. Delmiglio, M. N. Pearson
Summary: Over the past two centuries, more than 200 plant viruses and their invertebrate vectors have invaded New Zealand, with at least 16 viruses affecting native flora, including rare and endangered species. Different viruses have different host ranges, with some even spreading from crops to native plants and impacting the vegetation ecosystem negatively.
BIOLOGICAL INVASIONS
(2022)
Article
Plant Sciences
Patricio Saldivia, Steven J. Wagstaff, Ilse Breitwieser, David A. Orlovich, Janice M. Lord
Summary: Pleurophyllum lade is a major clade within the subtribe Celmisiinae (tribe Asteraceae), primarily found in New Zealand and surrounding islands. This clade is characterized by its purple to dark red disc corollas, distinguishing it from other members of Celmisiinae. The paper presents a new generic taxonomy for this clade, discussing the morphological differences and providing taxonomic keys for genera and species.
Article
Plant Sciences
Karl Soop, Jerry A. Cooper, Andy R. Nilsen, David A. Orlovich
Summary: Cortinarius is the largest genus of mushrooms in the world with a cosmopolitan distribution. This article reviews the diversity of the subgenus Leprocybe in the Southern Hemisphere and proposes three new species. The classification of some species found in New Zealand needs further study to determine their position within the phylogeny of the family.
NEW ZEALAND JOURNAL OF BOTANY
(2022)
Article
Plant Sciences
P. L. Guy
Summary: The presence of Clover yellow mosaic virus (ClYMV) in two cultivars of ornamental verbena in New Zealand has been reported. The NZ isolates were found to be closely related to ClYMV from verbena in the UK and Poland, and less closely related to isolates from clover in Australia and Japan. This suggests a separate incursion of ClYMV into New Zealand, as it has been intercepted in quarantine in tulips and detected in white clover in Auckland.
AUSTRALASIAN PLANT DISEASE NOTES
(2022)
Article
Biodiversity Conservation
Laura G. G. van Galen, Janice M. M. Lord, David A. A. Orlovich, Tim Jowett, Matthew J. J. Larcombe
Summary: This study reveals how various factors interact to limit tree seedling establishment in grasslands and provides new insights into forest expansion into neighboring ecosystems. The study also assists restoration practitioners in selecting techniques to enhance seedling establishment and highlights the challenges of high seedling establishment rates through direct seeding approaches in open grasslands.
JOURNAL OF APPLIED ECOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Laura G. van Galen, David A. Orlovich, Janice M. Lord, Julia Bohorquez, Andy R. Nilsen, Tina C. Summerfield, Matthew J. Larcombe
Summary: This study examined the factors affecting ectomycorrhizal fungal communities in Nothofagus forests in New Zealand's South Island using metabarcoding analysis. The results showed that community assembly is primarily determined by deterministic processes, and different factors influence the turnover of rare and common species.
Article
Plant Sciences
Laura G. van Galen, Janice M. Lord, David A. Orlovich, Matthew J. Larcombe
Summary: Seed stratification is important for improving germination rate. Moist cold stratification significantly increases germination rate compared to dry cold stratification, with most germination occurring within 30 days.
NEW ZEALAND JOURNAL OF BOTANY
(2022)
Article
Plant Sciences
Laura G. van Galen, David A. Orlovich, Janice M. Lord, Andy R. Nilsen, Ludovic Dutoit, Matthew J. Larcombe
Summary: The mechanisms of diversification in fungi are not well understood. Ectomycorrhizal symbionts often prefer specific host genera or families, suggesting that host-symbiont selection may drive fungal diversification. However, it is unknown if there are correlated evolutionary patterns between ectomycorrhizal hosts and symbionts, especially in systems dominated by hosts from the same genus.
Article
Plant Sciences
Karl Soop, Andy R. Nilsen, David A. Orlovich, Joseph F. Ammirati, Balint Dima
Summary: A major fungal lineage centered around Cortinarius vibratilis is identified through morphological and molecular phylogenetic analyses, forming a well-supported clade referred to as the new subgenus C. subg. Vibratiles. This subgenus includes four sections and various small clades. Additionally, two new myxacioid sections, C. sect. Microspermi and C. sect. Turcopedes, are proposed.
Review
Plant Sciences
Karl Soop, Jerry A. Cooper, Andy R. Nilsen, Noah Siegel, David A. Orlovich
Summary: This paper reviews the diversity of phlegmacioid taxa in New Zealand and other parts of the Southern Hemisphere. Using molecular phylogeny, it is found that these taxa are represented in six out of the ten recognized genera of Cortinariaceae. The paper proposes eight new species and two new sections.
NEW ZEALAND JOURNAL OF BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Anne K. Beulke, Alicia Abadia-Cardoso, Devon E. Pearse, Laura C. Goetz, Neil F. Thompson, Eric C. Anderson, John Carlos Garza
Summary: This study used genetic pedigree reconstruction to investigate the sex-specific patterns of life history traits and their genetic and environmental underpinnings in anadromous steelhead trout. The results showed that spawn date was highly heritable and had a high genetic correlation across sexes, while age at maturity was also highly heritable with a lower genetic correlation across sexes. Additionally, a migration-associated inversion polymorphism was found to have sex-specific correlations with age at maturity.