JGI Fungal Genomics Program

Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented her

Shallow Genome Sequencing for Phylogenomics of Mycorrhizal Fungi from Endangered Orchids

ABSTRACT Most plant species form symbioses with mycorrhizal fungi and this relationship is especially important for orchids. Fungi in the genera Tulasnella, Ceratobasidium, and Serendipita are critically important for orchid germination, growth and development. The goals of this study are to understand the phylogenetic relationships of mycorrhizal fungi and to improve the taxonomic resources for these groups. We identified 32 fungal isolates with the internal transcribed spacer region and used shallow genome sequencing to functionally annotate these isolates. We constructed phylogenetic trees from 408 orthologous nuclear genes for 50 taxa representing 14 genera, 11 families, and five orders in Agaricomycotina. While confirming relationships among the orders Cantharellales, Sebacinales, and Auriculariales, our results suggest novel relationships between families in the Cantharellales. Consistent with previous studies, we found the genera Ceratobasidium and Thanatephorus of Cerabotasidiaceae to not be monophyletic. Within the monophyletic genus Tulasnella , we found strong phylogenetic signals that suggest a potentially new species and a revision of current species boundaries (e.g. Tulasnella calospora ); however it is premature to make taxonomic revisions without further sampling and morphological descriptions. There is low resolution of Serendipita isolates collected. More sampling is needed from areas around the world before making evolutionary-informed changes in taxonomy. Our study adds value to an important living collection of fungi isolated from endangered orchid species, but also informs future investigations of the evolution of orchid mycorrhizal fungi

Inorganic nitrogen availability alters Eucalyptus grandis receptivity to the ectomycorrhizal fungus Pisolithus albus but not symbiotic nitrogen transfer.

Forest trees are able to thrive in nutrient-poor soils in part because they obtain growth-limiting nutrients, especially nitrogen (N), through mutualistic symbiosis with ectomycorrhizal (ECM) fungi. Addition of inorganic N into these soils is known to disrupt this mutualism and reduce the diversity of ECM fungi. Despite its ecological impact, the mechanisms governing the observed effects of elevated inorganic N on mycorrhizal communities remain unknown. We address this by using a compartmentalized in vitro system to independently alter nutrients to each symbiont. Using stable isotopes, we traced the nutrient flux under different nutrient regimes between Eucalyptus grandis and its ectomycorrhizal symbiont, Pisolithus albus. We demonstrate that giving E. grandis independent access to N causes a significant reduction in root colonization by P. albus. Transcriptional analysis suggests that the observed reduction in colonization may be caused, in part, by altered transcription of microbe perception genes and defence genes. We show that delivery of N to host leaves is not increased by host nutrient deficiency but by fungal nutrient availability instead. Overall, this advances our understanding of the effects of N fertilization on ECM fungi and the factors governing nutrient transfer in the E. grandis-P. microcarpus interaction

СОВЛАДАНИЕ СО СТРЕССОВЫМИ И ПРОБЛЕМНЫМИ ДЛЯ ЛИЧНОСТИ СИТУАЦИЯМИ И СЛАБОВЫРАЖЕННЫЕ ДЕПРЕССИВНЫЕ РАССТРОЙСТВА У ЛИЦ МОЛОДОГО ВОЗРАСТА В ПЕРИОДЕ АДАПТАЦИИ

Background: To investigate the relationship of coping with stressful and problematic for the individual situations and weakly expressed depressive disorders in young people.Materials and methods: A total of almost 100 first-year students (groups “M” and “F”, in proportion 1/1) of Pedagogical University in the period of adaptation to the educational process were examined. For psychological diagnosis of coping with stress behavior the “Methodology for psychological diagnosis methods of coping with stressful and problematic situations for the individual” [Wasserman L.I., et al., 2009] was used. We investigated the coping strategies such as “Confrontation”, “Distancing”, “ Self-control “, “Search for social support”, “Taking responsibility”, “Escape-avoidance”, “Planning to solve the problem,” “Positive reappraisal”. Determination of the background of depressive mood in clinically low severity or uncertainty, and evaluation of a syndrome belonging to a certain class of depression conducted by the “Scale for rapid psychological diagnosis semistructured depressive disorders” [Bespal’ko I.G., 2004].Results: The gender structure of coping strategies and their relationship are revealed and analyzed.Conclusion: Thus, it’s need for successful adaptation of students to the educational process to create in training groups a favorable psycho-pedagogical climate in order to create self-organizing skills and individualization according to the personal characteristics of students; to interact with students to overcome the difficulties in their studies; it’s need an early identification of students at risk and preventing their possible disadaptation of violations during the socialization of means (if necessary) a psycho-diagnostics and counseling; to solve personal problems in the adaptation period by providing advice or other assistance for the warning of deviant behavior.Цель. Изучить взаимосвязь совладания со стрессовыми и проблемными для личности ситуациями и слабовыраженных депрессивных расстройств у лиц молодого возраста.Материалы и методы. Обследовано 100 практически студентов первого курса (группы «М» и «Ж», в соотношении 1/1) педагогического университета в периоде адаптации к учебному процессу. Для психологической диагностики совладающего со стрессом поведения использована «Методика для психологической диагностики способов совладания со стрессовыми и проблемными для личности ситуациями» [Вассерман Л.И., и др., 2009]. Исследовались такие копинг-стратегии, как «Конфронтация», «Дистанцирование», «Самоконтроль», «Поиск социальной поддержки», «Принятие ответственности», «Бегство-избегание», «Планирование решения проблемы», «Положительная переоценка». Определение депрессивного фона настроения в клинически малой степени выраженности или неопределённости, и оценивание принадлежности синдрома к определённому классу депрессий проведено по «Шкале для экспресс-психологической диагностики слабоструктурированных депрессивных расстройств» [Беспалько И.Г., 2004]. Каждый участник подписывал форму информированного согласия на обследование. Статистическая обработка данных осуществлялась с помощью пакета прикладных программ Statistica 7.0.Результаты. Выявлены и проанализированы гендерная структура копинг-стратегий и их связь со слабовыраженными депрессивными расстройствами.Заключение. Показано, что для успешной адаптации студентов к учебному процессу необходимы создание в обучающих группах благоприятного психолого-педагогического микроклимата с целью формирования и индивидуализации умений самоорганизации в соответствии с личностными особенностями студентов; взаимодействие со студентами для преодоления трудностей в учебе; раннее выявление студентов группы риска и предупреждение у них возможных нарушений адаптации в период социализации посредством (при необходимости) психодиагностики и консультирования; решения личностных проблем в адаптационный период посредством оказания консультативной или иной другой помощи для предупреждений отклоняющегося поведения

Phylogenomic analyses of non-Dikarya fungi supports horizontal gene transfer driving diversification of secondary metabolism in the amphibian gastrointestinal symbiont, Basidiobolus

Research into secondary metabolism (SM) production by fungi has resulted in the discovery of diverse, biologically active compounds with significant medicinal applications. However, the fungi rich in SM production are taxonomically restricted to Dikarya, two phyla of Kingdom Fungi, Ascomycota and Basidiomycota. Here, we explore the potential for SM production in Mucoromycota and Zoopagomycota, two phyla of nonflagellated fungi that are not members of Dikarya, by predicting and identifying core genes and gene clusters involved in SM. The majority of non-Dikarya have few genes and gene clusters involved in SM production except for the amphibian gut symbionts in the genus Basidiobolus . Basidiobolus genomes exhibit an enrichment of SM genes involved in siderophore, surfactin-like, and terpene cyclase production, all these with evidence of constitutive gene expression. Gene expression and chemical assays confirm that Basidiobolus has significant siderophore activity. The expansion of SMs in Basidiobolus are partially due to horizontal gene transfer from bacteria, likely as a consequence of its ecology as an amphibian gut endosymbiont

Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi.

Fungi that decay wood have characteristic associations with certain tree species, but the mechanistic bases for these associations are poorly understood. We studied substrate-specific gene expression and RNA editing in six species of wood-decaying fungi from the 'Antrodia clade' (Polyporales, Agaricomycetes) on three different wood substrates (pine, spruce, and aspen) in submerged cultures. We identified dozens to hundreds of substrate-biased genes (i.e., genes that are significantly upregulated in one substrate relative to the other two substrates) in each species, and these biased genes are correlated with their host ranges. Evolution of substrate-biased genes is associated with gene family expansion, gain and loss of genes, and variation in cis- and trans- regulatory elements, rather than changes in protein coding sequences. We also demonstrated widespread RNA editing events in the Antrodia clade, which differ from those observed in the Ascomycota in their distribution, substitution types, and the genomic environment. Moreover, we found that substrates could affect editing positions and frequency, including editing events occurring in mRNA transcribed from wood-decay-related genes. This work shows the extent to which gene expression and RNA editing differ among species and substrates, and provides clues into mechanisms by which wood-decaying fungi may adapt to different hosts

Fungal Endophytes of Populus trichocarpa Alter Host Phenotype, Gene Expression, and Rhizobiome Composition.

Mortierella and Ilyonectria genera include common species of soil fungi that are frequently detected as root endophytes in many plants, including Populus spp. However, the ecological roles of these and other endophytic fungi with respect to plant growth and function are still not well understood. The functional ecology of two key taxa from the P. trichocarpa rhizobiome, M. elongata PMI93 and I. europaea PMI82, was studied by coupling forest soil bioassays with environmental metatranscriptomics. Using soil bioassay experiments amended with fungal inoculants, M. elongata was observed to promote the growth of P. trichocarpa. This response was cultivar independent. In contrast, I. europaea had no visible effect on P. trichocarpa growth. Metatranscriptomic studies revealed that these fungi impacted rhizophytic and endophytic activities in P. trichocarpa and induced shifts in soil and root microbial communities. Differential expression of core genes in P. trichocarpa roots was observed in response to both fungal species. Expression of P. trichocarpa genes for lipid signaling and nutrient uptake were upregulated, and expression of genes associated with gibberellin signaling were altered in plants inoculated with M. elongata, but not I. europaea. Upregulation of genes for growth promotion, downregulation of genes for several leucine-rich repeat receptor kinases, and alteration of expression of genes associated with plant defense responses (e.g., jasmonic acid, salicylic acid, and ethylene signal pathways) also suggest that M. elongata manipulates plant defenses while promoting plant growth