| 2 | Improving ITS sequence data for identification of plant pathogenic fungi显示文摘Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours.These taxa often have complex and poorly understood life cycles,lack observable,discriminatory morphological characters,and may not be amenable to in vitro culturing.As a result,species identification is frequently difficult.Molecular(DNA sequence)data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi,with the nuclear ribosomal internal transcribed spacer(ITS)region being the most popular marker.However,international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality,making their use in the molecular identification of plant pathogenic fungi problematic.Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages.A third objective was to enrich the sequences with geographical and ecological metadata.The results-a total of 31,954 changes-are incorporated in and made available through the UNITE database for molecular identification of fungi(http://gffzz7cc2bea597fa4d6chv5xkw66fwcbk6fcq.ffgz.tsg.suse.edu.cn),including standalone FASTA files of sequence data for local BLAST searches,use in the next-generation sequencing analysis platforms QIIME and mothur,and related applications.The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi,and we invite all researchers with pertinent expertise to join the annotation effort. | R.Henrik Nilsson Kevin D.Hyde Julia Pawlowska Martin Ryberg Leho Tedersoo Anders Bjornsgard Aas Siti A.Alias Artur Alves Cajsa Lisa Anderson Alexandre Antonelli A.Elizabeth Arnold Barbara Bahnmann Mohammad Bahram Johan Bengtsson-Palme Anna Berlin Sara Branco Putarak Chomnunti Asha Dissanayake Rein Drenkhan Hanna Friberg Tobias Guldberg Froslev Bettina Halwachs Martin Hartmann Beatrice Henricot Ruvishika Jayawardena Ari Jumpponen Havard Kauserud Sonja Koskela Tomasz Kulik Kare Liimatainen Bjorn D.Lindahl Daniel Lindner Jian-Kui Liu Sajeewa Maharachchikumbura Dimuthu Manamgoda Svante Martinsson Maria Alice Neves Tuula Niskanen Stephan Nylinder Olinto Liparini Pereira Danilo Batista Pinho Teresita M.Porter Valentin Queloz Taavi Riit Marisol Sánchez-García Filipe de Sousa Emil Stefańczyk Mariusz Tadych Susumu Takamatsu Qing Tian Dhanushka Udayanga Martin Unterseher Zheng Wang Saowanee Wikee Jiye Yan Ellen Larsson Karl-Henrik Larsson Urmas Koljalg Kessy Abarenkov | 2014 | Fungal Diversity2014，，4： | 1 |
| 3 | Revisiting taxonomy,morphological evolution,and fossil calibration strategies in Chloranthaceae显示文摘Chloranthaceae is one of the earliest diverging angiosperm families and is comprised of approximately 75 species in four genera (Chloranthus,Sarcandra,Ascarina,and Hedyosmum).This family has received considerable attention because of its seemingly primitive morphology,disjunct tropical distribution in Asia and America,and extensive fossil record from the Early Cretaceous.In the present study,we reconstructed the phylogeny of Chloran- thaceae based on a combined dataset of three plastid DNA regions and 56 species.We then estimated divergence times in the family using two relaxed molecular clock methods (BEAST and penalized likelihood).We focused on testing the influence of fossil taxa in calibrating the molecular phylogeny,and on assessing the current taxonomy of the family in light of the phylogenetic results.Our results indicate that most intrageneric divisions within Asca-rina and Hedyosmum are not monophyletic.The results from the dating analysis suggest that the Hedyosmum-like fossil Asteropollis represents a stem lineage of Hedyosmum,as has been suggested previously from morphological analyses.In contrast,our results indicate that the Chloranthus-like fossil Chloranthistemon,previously suggested on morphological grounds to be a stem relative of Chloranthus,may,instead,belong to the branch leading to the clade Chloranthus + Sarcandra.The median crown ages of Chloranthus,Sarcandra,Ascarina,and Hedyosmum estimated in the BEAST analysis were 26.3,9.5,31.0 and 45.8 million years ago (Ma),respectively,whereas the divergence between Chloranthus and Sarcandra,the splitting of Ascarina with the former two genera,and Hedyos- mum separating from the three genera were estimated to 63.8,95.7 and 111.1 Ma.The present study sheds further light on the temporal evolution of Chloranthaceae and exemplifies how molecular dating analyses may be used to explore alternative phylogenetic placements of fossil taxa. | Qiang ZHANG Alexandre ANTONELLI Taylor S. FEILD Hong-Zhi KONG | 2011 | Journal of Systematics and Evolution2011，49，4： | 1 |
您所在的机构暂未开通此部分的功能，请联系管理员