Phylogenetic Relationships, Pathogenic Traits, and Wood-Destroying Properties of Porodaedalea niemelaei M. Fischer Isolated in the Northern Forest Limit of Larix gmelinii Open Woodlands in the Permafrost Area

The phytopathogenic and wood destroying traits were studied in a basidiomycete fungus, Porodaedalea niemelaei M. Fischer, widespread in Siberian permafrost woodlands of Gmelinii larch, Larix gmelinii (Rupr.) Rupr. Numerous stands of dying out and fallen larch trees with white-rot („corrosion rot“) were found in the study area. Butt rot incidence varied from 63 to 100 % depending on the stand age and raised up to 0.5-1.5 m above root collar on average or up to 9 m maximum. Root rot was also widespread, including larch undergrowth. The biodiversity of xylotrophic fungi was low, with a pronounced dominance of P. niemelaei. The main factors of dying out of L. gmelinii were infection by P. niemelaei promoted by mechanical damage of roots by reindeers during migration and climate anomalies. The cultures isolated from the fruiting bodies were identified as Porodaedalea niemelaei M. Fischer based on the combination of morphological, culture, and molecular genetic methods. Under laboratory conditions, the strains were characterized as psychrotolerant (temperature limit from 6 to 22 °C) and preferred cultural media based mostly on natural and plant substrates. The most active biodegradation occurred on the broadleaf wood substrates causing up to 50 % of the biomass loss accompanied by active decomposing of the lignocellulosic complex and increasing the amount of water-soluble substances. The phylogenetic analysis demonstrated that P. niemelaei is clearly different from other well-studied Porodaedalea species, such as P. chrysoloma, P. pini, and P. cancriformans, and is very close to a group of unclassified fungi isolated in Norway and Finland. The phylogenetic analysis included 43 isolates and was based on four genetic markers – ITS, nLSU, rpb2, and tef1, commonly used in fungal phylogenetic

Патогенные и дереворазрушающие свойства Porodaedalea niemelaei M. Fischer в редколесьях Larix gmelinii в районах вечной мерзлоты

The phytopathogenic and wood destroying traits were studied in a basidiomycete fungus, Porodaedalea niemelaei M. Fischer, widespread in Siberian permafrost woodlands of Gmelinii larch, Larix gmelinii (Rupr.) Rupr. Numerous stands of dying out and fallen larch trees with white-rot („corrosion rot“) were found in the study area. Butt rot incidence varied from 63 to 100 % depending on the stand age and raised up to 0.5-1.5 m above root collar on average or up to 9 m maximum. Root rot was also widespread, including larch undergrowth. The biodiversity of xylotrophic fungi was low, with a pronounced dominance of P. niemelaei. The main factors of dying out of L. gmelinii were infection by P. niemelaei promoted by mechanical damage of roots by reindeers during migration and climate anomalies. The cultures isolated from the fruiting bodies were identified as Porodaedalea niemelaei M. Fischer based on the combination of morphological, culture, and molecular genetic methods. Under laboratory conditions, the strains were characterized as psychrotolerant (temperature limit from 6 to 22 °C) and preferred cultural media based mostly on natural and plant substrates. The most active biodegradation occurred on the broadleaf wood substrates causing up to 50 % of the biomass loss accompanied by active decomposing of the lignocellulosic complex and increasing the amount of water-soluble substances. The phylogenetic analysis demonstrated that P. niemelaei is clearly different from other well-studied Porodaedalea species, such as P. chrysoloma, P. pini, and P. cancriformans, and is very close to a group of unclassified fungi isolated in Norway and Finland. The phylogenetic analysis included 43 isolates and was based on four genetic markers – ITS, nLSU, rpb2, and tef1, commonly used in fungal phylogeneticsИзучены фитопатогенные и дереворазрушающие свойства базидиального гриба Porodaedalea niemelaei M. Fischer, широко распространённого на территории Сибири в районе вечной мерзлоты в редколесьях Larix gmelinii (Rupr.) Rupr. В районе исследования обнаружены многочисленные куртины усыхающих деревьев и ветровальные лиственницы с наличием коррозионной гнили. Встречаемость напенной гнили варьирует в пределах 63-100 % в зависимости от возраста древостоя; средняя высота подъема 0,5-1,5 м, максимально до 9 м. Корневая гниль распространена повсеместно, включая подрост лиственницы. Биоразнообразие ксилотрофных грибов скудное с выраженным доминированием P. niemelaei. Основным фактором усыхания Larix gmelinii является наличие грибной инфекции, способствующими – механическое повреждение корней и климатические аномалии. Культура гриба, изолированная из плодового тела, по совокупности морфолого-культуральных и молекулярно-генетических методов идентифицирована как Porodaedalea niemelaei M. Fischer. В лабораторных условиях штамм характеризуется как психротолерантный (температурный предел 6-22 °С), предпочитающий питательные среды на основе натуральных растительных компонентов. Биодеструкция растительных субстратов активнее протекает на лиственной древесине – убыль массы до 50 % на фоне активной биодеградации компонентов лигноцеллюлозного комплекса и увеличения количества водорастворимых веществ. Филогенетический анализ выявил значительные отличия P. niemelaei от других хорошо изученных видов Porodaedalea, таких как P. chrysoloma, P. pini и P. cancriformans, и близость к группе неклассифицированных грибов, выделенных в Норвегии и Финляндии. Филогенетический анализ включал 43 изолята и базировался на четырех маркерах (ITS, nLSU, rpb2 и tef1), широко применяемых в филогении грибов. Нуклеотидные последовательности всех маркеров были проверены в недавно полностью секвенированном геноме P. niemelaei, у изолята, использованного в этом исследовании (http://genome.jgi.doe.gov/PornieStandDraft_FD/PornieStandDraft_FD.info.html)

Патогенные и дереворазрушающие свойства Porodaedalea niemelaei M. Fischer в редколесьях Larix gmelinii в районах вечной мерзлоты

The phytopathogenic and wood destroying traits were studied in a basidiomycete fungus, Porodaedalea niemelaei M. Fischer, widespread in Siberian permafrost woodlands of Gmelinii larch, Larix gmelinii (Rupr.) Rupr. Numerous stands of dying out and fallen larch trees with white-rot („corrosion rot“) were found in the study area. Butt rot incidence varied from 63 to 100 % depending on the stand age and raised up to 0.5-1.5 m above root collar on average or up to 9 m maximum. Root rot was also widespread, including larch undergrowth. The biodiversity of xylotrophic fungi was low, with a pronounced dominance of P. niemelaei. The main factors of dying out of L. gmelinii were infection by P. niemelaei promoted by mechanical damage of roots by reindeers during migration and climate anomalies. The cultures isolated from the fruiting bodies were identified as Porodaedalea niemelaei M. Fischer based on the combination of morphological, culture, and molecular genetic methods. Under laboratory conditions, the strains were characterized as psychrotolerant (temperature limit from 6 to 22 °C) and preferred cultural media based mostly on natural and plant substrates. The most active biodegradation occurred on the broadleaf wood substrates causing up to 50 % of the biomass loss accompanied by active decomposing of the lignocellulosic complex and increasing the amount of water-soluble substances. The phylogenetic analysis demonstrated that P. niemelaei is clearly different from other well-studied Porodaedalea species, such as P. chrysoloma, P. pini, and P. cancriformans, and is very close to a group of unclassified fungi isolated in Norway and Finland. The phylogenetic analysis included 43 isolates and was based on four genetic markers – ITS, nLSU, rpb2, and tef1, commonly used in fungal phylogeneticsИзучены фитопатогенные и дереворазрушающие свойства базидиального гриба Porodaedalea niemelaei M. Fischer, широко распространённого на территории Сибири в районе вечной мерзлоты в редколесьях Larix gmelinii (Rupr.) Rupr. В районе исследования обнаружены многочисленные куртины усыхающих деревьев и ветровальные лиственницы с наличием коррозионной гнили. Встречаемость напенной гнили варьирует в пределах 63-100 % в зависимости от возраста древостоя; средняя высота подъема 0,5-1,5 м, максимально до 9 м. Корневая гниль распространена повсеместно, включая подрост лиственницы. Биоразнообразие ксилотрофных грибов скудное с выраженным доминированием P. niemelaei. Основным фактором усыхания Larix gmelinii является наличие грибной инфекции, способствующими – механическое повреждение корней и климатические аномалии. Культура гриба, изолированная из плодового тела, по совокупности морфолого-культуральных и молекулярно-генетических методов идентифицирована как Porodaedalea niemelaei M. Fischer. В лабораторных условиях штамм характеризуется как психротолерантный (температурный предел 6-22 °С), предпочитающий питательные среды на основе натуральных растительных компонентов. Биодеструкция растительных субстратов активнее протекает на лиственной древесине – убыль массы до 50 % на фоне активной биодеградации компонентов лигноцеллюлозного комплекса и увеличения количества водорастворимых веществ. Филогенетический анализ выявил значительные отличия P. niemelaei от других хорошо изученных видов Porodaedalea, таких как P. chrysoloma, P. pini и P. cancriformans, и близость к группе неклассифицированных грибов, выделенных в Норвегии и Финляндии. Филогенетический анализ включал 43 изолята и базировался на четырех маркерах (ITS, nLSU, rpb2 и tef1), широко применяемых в филогении грибов. Нуклеотидные последовательности всех маркеров были проверены в недавно полностью секвенированном геноме P. niemelaei, у изолята, использованного в этом исследовании (http://genome.jgi.doe.gov/PornieStandDraft_FD/PornieStandDraft_FD.info.html)

De novo sequencing, assembly and functional annotation of Armillaria borealis genome

Статья из журнала.BACKGROUND: Massive forest decline has been observed almost everywhere as a result of negative anthropogenic and climatic effects, which can interact with pests, fungi and other phytopathogens and aggravate their effects. Climatic changes can weaken trees and make fungi, such as Armillaria more destructive. Armillaria borealis (Marxm. & Korhonen) is a fungus from the Physalacriaceae family (Basidiomycota) widely distributed in Eurasia, including Siberia and the Far East. Species from this genus cause the root white rot disease that weakens and often kills woody plants. However, little is known about ecological behavior and genetics of A. borealis. According to field research data, A. borealis is less pathogenic than A. ostoyae, and its aggressive behavior is quite rare. Mainly A. borealis behaves as a secondary pathogen killing trees already weakened by other factors. However, changing environment might cause unpredictable effects in fungus behavior. RESULTS: The de novo genome assembly and annotation were performed for the A. borealis species for the first time and presented in this study. The A. borealis genome assembly contained ~ 68 Mbp and was comparable with ~ 60 and ~ 79.5 Mbp for the A. ostoyae and A. mellea genomes, respectively. The N50 for contigs equaled 50,544 bp. Functional annotation analysis revealed 21,969 protein coding genes and provided data for further comparative analysis. Repetitive sequences were also identified. The main focus for further study and comparative analysis will be on the enzymes and regulatory factors associated with pathogenicity. CONCLUSIONS: Pathogenic fungi such as Armillaria are currently one of the main problems in forest conservation. A comprehensive study of these species and their pathogenicity is of great importance and needs good genomic resources. The assembled genome of A. borealis presented in this study is of sufficiently good quality for further detailed comparative study on the composition of enzymes in other Armillaria species. There is also a fundamental problem with the identification and classification of species of the Armillaria genus, where the study of repetitive sequences in the genomes of basidiomycetes and their comparative analysis will help us identify more accurately taxonomy of these species and reveal their evolutionary relationships