Genome assemblies for two Neotropical trees: Jacaranda copaia and Handroanthus guayacan

The lack of genomic resources for tropical canopy trees is impeding several research avenues in tropical forest biology. We present genome assemblies for two Neotropical hardwood species, Jacaranda copaia and Handroanthus (formerly Tabebuia) guayacan, that are model systems for research on tropical tree demography and flowering phenology. For each species, we combined Illumina short-read data with in vitro proximity-ligation (Chicago) libraries to generate an assembly. For J. copaia, we obtained 104X physical coverage and produced an assembly with N50/N90 scaffold lengths of 1.020 Mbp/0.277 Mbp. For H. guayacan, we obtained 129X coverage and produced an assembly with N50/N90 scaffold lengths of 0.795 Mbp/0.165 Mbp. J. copaia and H. guayacan assemblies contained 95.8% and 87.9% of benchmarking orthologs, although they constituted only 77.1% and 66.7% of the estimated genome sizes of 799 Mbp and 512 Mbp, respectively. These differences were potentially due to high repetitive sequence content (> 59.31% and 45.59%) and high heterozygosity (0.5% and 0.8%) in each species. Finally, we compared each new assembly to a previously sequenced genome for H. impetiginosus using whole-genome alignment. This analysis indicated extensive gene duplication in H. impetiginosus since its divergence from H. guayacan.

Research in Forest Biology in the Era of Climate Change and Rapid Urbanization

Green plants provide the foundation for the structure, function, and interactions among organisms in both tropical and temperate zones. To date, many investigations have revealed patterns and mechanisms that generate plant diversity at various scales and from diverse ecological perspectives. However, in the era of climate change, anthropogenic disturbance, and rapid urbanization, new insights are needed to understand how plant species in these forest habitats are changing and adapting. Here, we recognize four themes that link studies from Asia and Europe presented in this Special Issue: (1) genetic analyses of diverse plant species; (2) above- and below-ground forest biodiversity; (3) trait expression and biological mechanisms; and (4) interactions of woody plants within a changing environment. These investigations enlarge our understanding of the origins of diversity, trait variation and heritability, and plant–environment interactions from diverse perspectives.

Experimental evidence that fungal symbionts of beetles suppress wood decay by competing with decay fungi

Throughout forests worldwide, bark and ambrosia beetles inoculate dead and dying trees with symbiotic fungi. We experimentally determined the effects of three common and widely distributed ascomycete symbionts, and one introduced Asian basidiomycete symbiont on the decay of pine sapwood. Ascomycetes caused less than 5% mass loss and no structural degradation, whereas the basidiomycete Flavodon ambrosius caused nearly 15% mass loss and visible degradation of wood structure. In co-inoculation experiments, the beetle symbionts Ophiostoma ips and Raffaelea fusca reduced white and brown rot decay through competition with Ganoderma curtisii and Phaeolus schweinitzii, respectively. The inhibitory effects of O. ips and R. fusca on decay were negated when co-inoculated with F. ambrosius, suggesting that widespread introduction of this beetle symbiont could alter forest carbon fluxes. In contrast to the predominant forest biology narrative, most bark and ambrosia beetles introduce fungi that delay rather than facilitate tree biomass recycling.

Experimental evidence that fungal symbionts of beetles suppress wood decay by competing with decay fungi

Throughout forests worldwide, bark and ambrosia beetles inoculate dead and dying trees with symbiotic fungi. We experimentally determined the effects of three common and widely distributed ascomycete symbionts, and one introduced Asian basidiomycete symbiont on the decay of pine sapwood. Ascomycetes caused less than 5% mass loss and no structural degradation, whereas the basidiomycete Flavodon ambrosius caused nearly 15% mass loss and visible degradation of wood structure. In co-inoculation experiments, the beetle symbionts Ophiostoma ips and Raffaelea fusca reduced white and brown rot decay through competition with Ganoderma curtisii and Phaeolus schweinitzii, respectively. The inhibitory effects of O. ips and R. fusca on decay were negated when co-inoculated with F. ambrosius, suggesting that widespread introduction of this beetle symbiont could alter forest carbon fluxes. In contrast to the predominant forest biology narrative, most bark and ambrosia beetles introduce fungi that delay rather than facilitate tree biomass recycling.

Reviewer Acknowledgements for Journal of Plant Studies, Vol. 7, No. 1

Journal of Plant Studies wishes to acknowledge the following individuals for their assistance with peer review of manuscripts for this issue. Their help and contributions in maintaining the quality of the journal are greatly appreciated.Journal of Plant Studies is recruiting reviewers for the journal. If you are interested in becoming a reviewer, we welcome you to join us. Please find the application form and details at http://www.ccsenet.org/reviewer and e-mail the completed application form to [email protected] for Volume 7, Number 1Adriana F. Sestras, University of Agricultural Sciences and Veterinary Medicine, RomaniaAlireza Valdiani, University of Copenhagen, DenmarkAmi Lokhandwala, University of Mississippi, Department of Biology, USAIsabel Desgagné-Penix, Université du Québec à Trois-Rivières, CanadaKirandeep Kaur Mani, California seed and Plant Labs, Pleasant Grove, CA, USAMartina Pollastrini, University of Florence, ItalyMassimo Zacchini, Institute of Agroenvironmental and Forest Biology, ItalyMatteo Busconi, Università Cattolica del Sacro Cuore, ItalyMelekber Sulusoglu, Arslanbey Vocational School Kocaeli University, TurkeyMilana Trifunovic-Momcilov, Institute for Biological Research “Sinisa Stankovic”, SerbiaMohamed Trigui, Sfax Preparatory Engineering Institute and CBS, TunisiaMohammad Nurul Amin, Noakhali Science and Technology University, BangladeshMontaser Fawzy Abdel-Monaim, Plant Pathology Res. Instatute, Agric. Res. Center, EgyptNina Ivanovska, Institute of Microbiology, BulgariaPanagiotis Madesis, Centre for Research and Technology Hellas/Institiute of Applied Biosciences, GreeceRajiv Ranjan, T. P. Varma College, IndiaRaksha Singh, University of Arkansas, USASlawomir Borek, Adam Mickiewicz University, PolandSuheb Mohammed, University of Virginia, USA

Metadata provide insights on patterns of epiparasitism in mistletoes (Santalales), an overlooked topic in forest biology

Mistletoes are aerial-branch parasites belonging to one of five families in the Santalales. Usually, mistletoe hosts are autotrophic, but if the hosts themselves are parasitic, the plant parasitizing the host is an epiparasite. Three categories of epiparasites are recognized, chance-, obligate-, and auto-epiparasites. Loranthaceae and Viscaceae comprise about 97% of mistletoe species and also the largest number of epiparasites. We report frequencies and biogeographical distributions of epiparasite – parasite host combinations for Loranthaceae and Viscaceae, and we summarize epiparasitism in other mistletoe families. Parasitic hosts are primarily recruited from Loranthaceae, whereas most epiparasites are members of Viscaceae. Twenty-seven species are considered likely to be obligate epiparasites. Data suggest species abundance influences whether mistletoes serve as host to other mistletoes. We found no reports of epiparasitism in Misodendraceae and only a few reports for Santalaceae, although Santalaceae are often root-parasitic hosts. In Phacellaria (Amphorogynaceae) all species are obligate epiparasites, mainly on Loranthaceae. Epiparasitism occurs worldwide and is most common in the tropics and subtropics. The greatest number of reports is from Oceania, the smallest from Africa. Epiparasitism in mistletoes has received little research attention, yet our research shows that this life form contributes to species and structural diversity in forest ecosystems across the globe.

From the experience of LIFE+ ManFor C.BD to the Manual of Best Practices in Sustainable Forest Management

This volume should be interpreted as a manual of best practices for sustainable forest management deriving from the experience of the project LIFE09ENV/IT/000078 ManFor C.BD coordinated by the National Research Council through the Institute of Agro-environmental and Forest Biology (CNR-IBAF). The other Project partners are: the Council for Agricultural Research and Economics (CREA), the University of Molise (UNIMOL), the Slovenian Forestry Institute (SFI) and the regions of Veneto and Molise. In addition, the National Centre for Forest Biodiversity of Verona and the Regional Office to biodiversity of Castel di Sangro of the Italian National Forest Service (CFS), as well as the Slovenian Forest Service (SFS) collaborated to the project. This manual consists of several individual articles dealing with specific issues related to the project. These articles are conceptually organized into five categories that from the description of the project and of its activities arrive at providing operative indications for forestry operators.

First Report of Melampsora larici-populina on Populus spp. in Eastern North America

In September 2002, yellow spots were observed on the leaf surface of a hybrid poplar (Populus maximowiczii Henry × P. balsamifera L.) grown at the Berthier forest nursery (46°2′N, 73°11′W) in the St. Lawrence Valley (Lanaudière Region, Québec, Canada). Disease severity was low, but the pathogen was present on a hybrid that was previously thought to be resistant to Melampsora medusae Thuem, the only reported poplar rust in eastern North America. Uredinia typical of a Melampsora sp. were observed on the abaxial leaf surface. The observed urediniospores were longer (32 to 48 μm) than the expected range for M. medusae (23 to 35 μm) and possessed an apical bald spot; thick paraphyses were also observed. These characteristics are diagnostic of M. larici-populina Kleb (2). Samples were deposited in the National Mycological Herbarium of Canada (DAOM 232107 and 232108) and in the Quebec Forest Biology Herbarium (QFB14703 and 14704). DNA was extracted from uredinia, and the internal transcribed spacer (ITS) of the ribosomal RNA gene was amplified and sequenced (GenBank Accession Nos. AY429656 and AY429657). There was a 100% match between the two sequences obtained and that of M. larici-populina (GenBank Accession No. AY375267), but there was approximately 12% divergence with the ITS sequence of M. medusae (GenBank Accession No. AY375273-5). This is the first report of M. larici-populina in eastern North America. This fungus was reported on P. trichocarpa × P. deltoides hybrids in the western United States in the early 1990s (1). It appears that M. larici-populina can overwinter in Québec because it was observed again at the nursery in September 2003. The occurrence of M. larici-populina in eastern North America has direct implications for the poplar industry since the host specificities of M. medusae and M. larici-populina differ; P. balsamifera and P. maximowiczii are sensitive to M. larici-populina (3). Hybrids with P. balsamifera or P. trichocarpa components may be particularly at risk. References: (1) G. Newcombe and G. A. Chastagner. Plant Dis. 77:532, 1993. (2) J. Pinon. Eur. J. For. Pathol. 3:221, 1973. (3) J. Pinon. Silvae Genet. 41:25, 1992.