EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

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Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

With a pace of about twice the observed rate of global warming, the temperature on the Qinghai-Tibetan Plateau (Earth's third pole') has increased by 0.2 degrees C per decade over the past 50years, which results in significant permafrost thawing and glacier retreat. Our review suggested that warming enhanced net primary production and soil respiration, decreased methane (CH4) emissions from wetlands and increased CH4 consumption of meadows, but might increase CH4 emissions from lakes. Warming-induced permafrost thawing and glaciers melting would also result in substantial emission of old carbon dioxide (CO2) and CH4. Nitrous oxide (N2O) emission was not stimulated by warming itself, but might be slightly enhanced by wetting. However, there are many uncertainties in such biogeochemical cycles under climate change. Human activities (e.g. grazing, land cover changes) further modified the biogeochemical cycles and amplified such uncertainties on the plateau. If the projected warming and wetting continues, the future biogeochemical cycles will be more complicated. So facing research in this field is an ongoing challenge of integrating field observations with process-based ecosystem models to predict the impacts of future climate change and human activities at various temporal and spatial scales. To reduce the uncertainties and to improve the precision of the predictions of the impacts of climate change and human activities on biogeochemical cycles, efforts should focus on conducting more field observation studies, integrating data within improved models, and developing new knowledge about coupling among carbon, nitrogen, and phosphorus biogeochemical cycles as well as about the role of microbes in these cycles.

The impacts of climate change and human activities on biogeochemical cycles on the Qinghai-Tibetan Plateau

The Colletotrichum acutatum species complex

Fungal endophytes residing in the internal tissues of living plants occur in almost every plant on earth from the arctic to the tropics. The endophyte–host relationship is described as a balanced symbiotic continuum ranging from mutualism through commensalism to parasitism. This overview will highlight selected aspects of endophyte diversity, host specificity, endophyte–host interaction and communication as well as regulation of secondary metabolite production with emphasis on advanced genomic methods and their role in improving our current knowledge of endophytic associations. Furthermore, the chemical potential of endophytic fungi for drug discovery will be discussed with focus on the detection of pharmaceutically valuable plant constituents as products of fungal biosynthesis. In addition, selected examples of bioactive metabolites reported in recent years (2008–2010) from fungal endophytes residing in terrestrial plants are presented grouped according to their reported biological activities.

Fungal endophytes: unique plant inhabitants with great promises

Notes on 113 fungal taxa are compiled in this paper, including 11 new genera, 89 new species, one new subspecies, three new combinations and seven reference specimens. A wide geographic and taxonomic range of fungal taxa are detailed. In the Ascomycota the new genera Angustospora (Testudinaceae), Camporesia (Xylariaceae), Clematidis, Crassiparies (Pleosporales genera incertae sedis), Farasanispora, Longiostiolum (Pleosporales genera incertae sedis), Multilocularia (Parabambusicolaceae), Neophaeocryptopus (Dothideaceae), Parameliola (Pleosporales genera incertae sedis), and Towyspora (Lentitheciaceae) are introduced. Newly introduced species are Angustospora nilensis, Aniptodera aquibella, Annulohypoxylon albidiscum, Astrocystis thailandica, Camporesia sambuci, Clematidis italica, Colletotrichum menispermi, C. quinquefoliae, Comoclathris pimpinellae, Crassiparies quadrisporus, Cytospora salicicola, Diatrype thailandica, Dothiorella rhamni, Durotheca macrostroma, Farasanispora avicenniae, Halorosellinia rhizophorae, Humicola koreana, Hypoxylon lilloi, Kirschsteiniothelia tectonae, Lindgomyces okinawaensis, Longiostiolum tectonae, Lophiostoma pseudoarmatisporum, Moelleriella phukhiaoensis, M. pongdueatensis, Mucoharknessia anthoxanthi, Multilocularia bambusae, Multiseptospora thysanolaenae, Neophaeocryptopus cytisi, Ocellularia arachchigei, O. ratnapurensis, Ochronectria thailandica, Ophiocordyceps karstii, Parameliola acaciae, P. dimocarpi, Parastagonospora cumpignensis, Pseudodidymosphaeria phlei, Polyplosphaeria thailandica, Pseudolachnella brevifusiformis, Psiloglonium macrosporum, Rhabdodiscus albodenticulatus, Rosellinia chiangmaiensis, Saccothecium rubi, Seimatosporium pseudocornii, S. pseudorosae, Sigarispora ononidis and Towyspora aestuari. New combinations are provided for Eutiarosporella dactylidis (sexual morph described and illustrated) and Pseudocamarosporium pini. Descriptions, illustrations and / or reference specimens are designated for Aposphaeria corallinolutea, Cryptovalsa ampelina, Dothiorella vidmadera, Ophiocordyceps formosana, Petrakia echinata, Phragmoporthe conformis and Pseudocamarosporium pini. The new species of Basidiomycota are Agaricus coccyginus, A. luteofibrillosus, Amanita atrobrunnea, A. digitosa, A. gleocystidiosa, A. pyriformis, A. strobilipes, Bondarzewia tibetica, Cortinarius albosericeus, C. badioflavidus, C. dentigratus, C. duboisensis, C. fragrantissimus, C. roseobasilis, C. vinaceobrunneus, C. vinaceogrisescens, C. wahkiacus, Cyanoboletus hymenoglutinosus, Fomitiporia atlantica, F. subtilissima, Ganoderma wuzhishanensis, Inonotus shoreicola, Lactifluus armeniacus, L. ramipilosus, Leccinum indoaurantiacum, Musumecia alpina, M. sardoa, Russula amethystina subp. tengii and R. wangii are introduced. Descriptions, illustrations, notes and / or reference specimens are designated for Clarkeinda trachodes, Dentocorticium ussuricum, Galzinia longibasidia, Lentinus stuppeus and Leptocorticium tenellum. The other new genera, species new combinations are Anaeromyces robustus, Neocallimastix californiae and Piromyces finnis from Neocallimastigomycota, Phytophthora estuarina, P. rhizophorae, Salispina, S. intermedia, S. lobata and S. spinosa from Oomycota, and Absidia stercoraria, Gongronella orasabula, Mortierella calciphila, Mucor caatinguensis, M. koreanus, M. merdicola and Rhizopus koreanus in Zygomycota.

Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa

The mycota and decomposing potential of endophytic fungi associated with Acer truncatum, a common tree in northern China, were investigated. The colonization rate of endophytic fungi was significantly higher in twigs (77%) than in leaves (11%). However, there was no significant difference in the colonization rates of endophytic fungi between lamina (9%) and midrib (14%) tissues. A total of 58 endophytic taxa were recovered using two isolation methods and these were identified based on morphology and ITS sequence data. High numbers of leaf endophytes were obtained in the method to determine decomposition of leaves by the natural endophyte community (35 taxa) as compared to disk fragment methodology (9 taxa). The weight loss in A. truncatum leaves decomposed by endophyte communities increased with incubation time; the weight loss was significantly higher at 20 weeks than at 3 and 8 weeks. Both common and rare endophytic taxa produced extracellular enzymes in vitro and showed different leaf decay abilities. Our results indicated that the composition and diversity of endophytic fungi obtained differed using two isolation methods. This study suggests that endophytic fungi play an important role in recycling of nutrients in natural ecosystems.

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Community composition of endophytic fungi in Acer truncatum and their role in decomposition

Pestalotiopsis is a taxonomically confused, pathogenic and chemically creative genus requiring a critical re-examination using a multi-gene phylogeny based on ex-type and ex-epitype cultures. In this study 40 isolates of Pestalotiopsis, comprised of 28 strains collected from living and dead plant material of various host plants from China were studied by means of morphology and analysis of ITS, β–tubulin and tef1 gene sequence data. Based on molecular and morphological data we describe 14 new species (Pestalotiopsis asiatica, P. chinensis, P. chrysea, P. clavata, P. diversiseta, P. ellipsospora, P. inflexa, P. intermedia, P. linearis, P. rosea, P. saprophyta, P. umberspora, P. unicolor and P. verruculosa) and three species are epitypified (P. adusta, P. clavispora and P. foedans). Of the 10 gene regions (ACT, β-tubulin, CAL, GPDH, GS, ITS, LSU, RPB 1, SSU and tef1) utilized to resolve cryptic Pestalotiopsis species, ITS, β–tubulin and tef1 proved to be the better markers. The other gene regions were less useful due to poor success in PCR amplification and/or in their ability to resolve species boundaries. As a single gene tef1 met the requirements for an ideal candidate and functions well for species delimitation due to its better species resolution and PCR success. Although β-tubulin showed fairly good differences among species, a combination of ITS, β-tubulin and tef1 gene data gave the best resolution as compared to single gene analysis. This work provides a backbone tree for 22 ex-type/epitypified species of Pestalotiopsis and can be used in future studies of the genus.

http://www.im.ac.cn/UserFiles/File/2012/2012-12/2012_A%20multi-locus%20backbone%20tree%20for%20Pestalotiopsis,%20with%20a%20polyphasic%20characterization%20of%2014%20new%20species.pdf

A multi-locus backbone tree for Pestalotiopsis, with a polyphasic characterization of 14 new species

Endophytic fungi are an important component, are ubiquitous and occur within all know plants, including a broad range of hosts in various ecosystems, and therefore play an important role in the natural environment. More than 1 million species of endophytic fungi are estimated to exist based on a ratio of vascular plants to fungal species of 1:4 or 1:5. Nevertheless, our recognition of endophyte diversity is limited at present. In surveys of endophyte diversity, traditional techniques, such as cultivation-dependent methods, have been routinely used in previous studies. The discovery of endophytic fungi in natural environments, however, has been limited by traditional methodology due to some non-sporulating and non-culturable fungi. Molecular techniques, such as DNA fingerprinting and sequencing methods, have been successfully employed in the detection and identification of endophytic fungi, and different endophyte diversity and community composition have been documented by cultivation-dependent and molecul...

Endophytic fungal diversity: review of traditional and molecular techniques

Revealing the relationship between plants and fungi is very important in understanding biodiversity maintenance, community stability, and ecosystem functioning. However, differences in the community and network structures of phyllosphere epiphytic and endophytic fungi are currently poorly documented. In this study, we examined epiphytic and endophytic fungal communities associated with the leaves of six mangrove species using Illumina MiSeq sequencing of internal transcribed spacer 2 (ITS2) sequences. A total of 635 operational taxonomic units (OTUs) of endophytic and epiphytic fungi were obtained at a 97% sequence similarity level; they were dominated by Dothideomycetes and Tremellomycetes. Plant identity had a significant effect on the OTU richness of endophytic fungi, but not on epiphytic fungi. The community composition of epiphytic and endophytic fungi was significantly different, and plant identity had a greater effect on endophytic fungi than on epiphytic fungi. Network analysis showed that both epiphytic and endophytic network structures were characterized by significantly highly specialized and modular but lowly connected and anti-nested properties. Furthermore, the endophytic network had higher levels of specialization and modularity but lower connectance and stronger anti-nestedness than the epiphytic network. This study reveals that the phyllosphere epiphytic and endophytic fungal communities differ, and plant identity has a greater effect on the endophytic fungi than on epiphytic fungi. These findings demonstrate the role of host plant identity in driving phyllosphere epiphytic and endophytic community structure.

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Phyllosphere epiphytic and endophytic fungal community and network structures differ in a tropical mangrove ecosystem

http://www.im.ac.cn/UserFiles/File/2012/2012-12/2012_Community%20structure%20and%20preference%20of%20endophytic%20fungi%20of%20three%20woody%20plants%20in%20a%20mixed%20forest.pdf

Xiang Sun

Papers

Community composition of endophytic fungi in Acer truncatum and their role in decomposition

A multi-locus backbone tree for Pestalotiopsis, with a polyphasic characterization of 14 new species

Endophytic fungal diversity: review of traditional and molecular techniques

Phyllosphere epiphytic and endophytic fungal community and network structures differ in a tropical mangrove ecosystem

Community structure and preference of endophytic fungi of three woody plants in a mixed forest