دورية أكاديمية
De novo sequencing, assembly and functional annotation of Armillaria borealis genome.
| العنوان: | De novo sequencing, assembly and functional annotation of Armillaria borealis genome. |
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| المؤلفون: | Akulova VS; Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036, Krasnoyarsk, Russia.; Laboratory of Genomic Research and Biotechnology, Federal Research Center 'Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences', 660036, Krasnoyarsk, Russia., Sharov VV; Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036, Krasnoyarsk, Russia.; Laboratory of Genomic Research and Biotechnology, Federal Research Center 'Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences', 660036, Krasnoyarsk, Russia.; Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, 660074, Krasnoyarsk, Russia., Aksyonova AI; Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036, Krasnoyarsk, Russia., Putintseva YA; Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036, Krasnoyarsk, Russia., Oreshkova NV; Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036, Krasnoyarsk, Russia.; Laboratory of Genomic Research and Biotechnology, Federal Research Center 'Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences', 660036, Krasnoyarsk, Russia.; Laboratory of Forest Genetics and Selection, V. N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, 660036, Krasnoyarsk, Russia., Feranchuk SI; Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036, Krasnoyarsk, Russia.; Department of Informatics, National Research Technical University, 664074, Irkutsk, Russia.; Limnological Institute, Siberian Branch of Russian Academy of Sciences, 664033, Irkutsk, Russia., Kuzmin DA; Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036, Krasnoyarsk, Russia.; Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, 660074, Krasnoyarsk, Russia., Pavlov IN; Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036, Krasnoyarsk, Russia.; Laboratory of Reforestation, Mycology and Plant Pathology, V. N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, 660036, Krasnoyarsk, Russia.; Department of Chemical Technology of Wood and Biotechnology, Reshetnev Siberian State University of Science and Technology, Krasnoyarsk, 660049, Russia., Litovka YA; Laboratory of Reforestation, Mycology and Plant Pathology, V. N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, 660036, Krasnoyarsk, Russia.; Department of Chemical Technology of Wood and Biotechnology, Reshetnev Siberian State University of Science and Technology, Krasnoyarsk, 660049, Russia., Krutovsky KV; Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036, Krasnoyarsk, Russia. kkrutov@gwdg.de.; Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, 37077, Göttingen, Germany. kkrutov@gwdg.de.; Center for Integrated Breeding Research, George-August University of Göttingen, 37075, Göttingen, Germany. kkrutov@gwdg.de.; Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333, Moscow, Russia. kkrutov@gwdg.de.; Department of Ecosystem Science and Management, Texas A&M University, College Station, TX, 77843-2138, USA. kkrutov@gwdg.de. |
| المصدر: | BMC genomics [BMC Genomics] 2020 Sep 10; Vol. 21 (Suppl 7), pp. 534. Date of Electronic Publication: 2020 Sep 10. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: London : BioMed Central, [2000- |
| مواضيع طبية MeSH: | Armillaria*/genetics , Basidiomycota*, Plants ; Siberia |
| مستخلص: | 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. |
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| معلومات مُعتمدة: | 14.Y26.31.0004 Government of Russian Federation; 0287-2019-0002 Federal Research Center "Krasnoyarsk Scientific Center"; 0356-2016-0704 Federal Research Center "Krasnoyarsk Scientific Center"; 0356-2019-0024 Federal Research Center "Krasnoyarsk Scientific Center" |
| فهرسة مساهمة: | Keywords: Annotation; Armillaria; De novo sequencing; Fungal forest pathogen; Genome |
| SCR Organism: | Armillaria borealis |
| تواريخ الأحداث: | Date Created: 20200911 Date Completed: 20210514 Latest Revision: 20240801 |
| رمز التحديث: | 20240801 |
| مُعرف محوري في PubMed: | PMC7487993 |
| DOI: | 10.1186/s12864-020-06964-6 |
| PMID: | 32912216 |
| قاعدة البيانات: | MEDLINE |
Find this article in full text from Springer Verlag. 
Full Text Finder | تدمد: | 1471-2164 |
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| DOI: | 10.1186/s12864-020-06964-6 |