Perspectives of using Illumina MiSeq for identification of arbuscular mycorrhizal fungi
Arbuscular mycorrhiza fungi (AMF) form one of the most common symbiosis with the majority of land plants. AMF supply the plant with various mineral elements, primarily phosphorus, and improve the water supply. The search for the most effective AMF strains for symbiosis and the creation of microbial...
Saved in:
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2020-04-01
|
| Series: | Вавиловский журнал генетики и селекции |
| Subjects: | |
| Online Access: | https://vavilov.elpub.ru/jour/article/view/2383 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832575104696975360 |
|---|---|
| author | A. A. Kryukov A. O. Gorbunova E. M. Machs Y. V. Mikhaylova A. V. Rodionov P. M. Zhurbenko A. P. Yurkov |
| author_facet | A. A. Kryukov A. O. Gorbunova E. M. Machs Y. V. Mikhaylova A. V. Rodionov P. M. Zhurbenko A. P. Yurkov |
| author_sort | A. A. Kryukov |
| collection | DOAJ |
| description | Arbuscular mycorrhiza fungi (AMF) form one of the most common symbiosis with the majority of land plants. AMF supply the plant with various mineral elements, primarily phosphorus, and improve the water supply. The search for the most effective AMF strains for symbiosis and the creation of microbial preparations on that basis is an important task for modern biology. Owing to the difficulties of cultivation without a host plant and their high genetic polymorphism, identifying AMF is very difficult. The high number of cryptic species often also makes morphological identification unreliable. Recent years have seen growth in the number of AMF biodiversity studies performed by modern NGS-based methods, Illumina MiSeq in particular. Currently, there are still many questions that remain for the identification of AМF. The most important are whether conservative or variable sequences should be used to select a marker for barcoding and whether universal primers or those specific to AMF should be used. In our work, we have successfully used universal primers ITS3 and ITS4 for the sequencing in Illumina MiSeq of the 5.8S rDNA – ITS2 region of the 35S rRNA genes, which contain both a conservative and variable regions. The molecular genetic approach for AMF identification was quite effective and allowed us to reliably identify eight of nine isolates to the species level: five isolates of Rhizophagus irregularis, and one isolate of R. invermaius, Paraglomus laccatum, and Claroideoglomus etunicatum, respectively. For all five R. irregularis isolates high variability in the ITS region and the absence of ecotopic-related molecular characters in the ITS2 region were demonstrated. The NCBI data is still insufficient for accurate AMF identification of Acaulospora sp. isolates from the genus to the species level. |
| format | Article |
| id | doaj-art-99371c6992f3478a81fea1347d6b07b5 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2020-04-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-99371c6992f3478a81fea1347d6b07b52025-02-01T09:58:08ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592020-04-0124215816710.18699/VJ19.38-o995Perspectives of using Illumina MiSeq for identification of arbuscular mycorrhizal fungiA. A. Kryukov0A. O. Gorbunova1E. M. Machs2Y. V. Mikhaylova3A. V. Rodionov4P. M. Zhurbenko5A. P. Yurkov6All-Russian Research Institute for Agricultural MicrobiologyAll-Russian Research Institute for Agricultural Microbiology; Saint Petersburg State UniversityKomarov Botanical Institute of the Russian Academy of SciencesKomarov Botanical Institute of the Russian Academy of SciencesSaint Petersburg State University Komarov Botanical Institute of the Russian Academy of SciencesKomarov Botanical Institute of the Russian Academy of SciencesAll-Russian Research Institute for Agricultural MicrobiologyArbuscular mycorrhiza fungi (AMF) form one of the most common symbiosis with the majority of land plants. AMF supply the plant with various mineral elements, primarily phosphorus, and improve the water supply. The search for the most effective AMF strains for symbiosis and the creation of microbial preparations on that basis is an important task for modern biology. Owing to the difficulties of cultivation without a host plant and their high genetic polymorphism, identifying AMF is very difficult. The high number of cryptic species often also makes morphological identification unreliable. Recent years have seen growth in the number of AMF biodiversity studies performed by modern NGS-based methods, Illumina MiSeq in particular. Currently, there are still many questions that remain for the identification of AМF. The most important are whether conservative or variable sequences should be used to select a marker for barcoding and whether universal primers or those specific to AMF should be used. In our work, we have successfully used universal primers ITS3 and ITS4 for the sequencing in Illumina MiSeq of the 5.8S rDNA – ITS2 region of the 35S rRNA genes, which contain both a conservative and variable regions. The molecular genetic approach for AMF identification was quite effective and allowed us to reliably identify eight of nine isolates to the species level: five isolates of Rhizophagus irregularis, and one isolate of R. invermaius, Paraglomus laccatum, and Claroideoglomus etunicatum, respectively. For all five R. irregularis isolates high variability in the ITS region and the absence of ecotopic-related molecular characters in the ITS2 region were demonstrated. The NCBI data is still insufficient for accurate AMF identification of Acaulospora sp. isolates from the genus to the species level.https://vavilov.elpub.ru/jour/article/view/2383glomeromycotinaarbuscular mycorrhizaillumina miseqrhizophagus irregularisr. invermaiusparaglomus laccatumclaroideoglomus etunicatumacaulospora |
| spellingShingle | A. A. Kryukov A. O. Gorbunova E. M. Machs Y. V. Mikhaylova A. V. Rodionov P. M. Zhurbenko A. P. Yurkov Perspectives of using Illumina MiSeq for identification of arbuscular mycorrhizal fungi Вавиловский журнал генетики и селекции glomeromycotina arbuscular mycorrhiza illumina miseq rhizophagus irregularis r. invermaius paraglomus laccatum claroideoglomus etunicatum acaulospora |
| title | Perspectives of using Illumina MiSeq for identification of arbuscular mycorrhizal fungi |
| title_full | Perspectives of using Illumina MiSeq for identification of arbuscular mycorrhizal fungi |
| title_fullStr | Perspectives of using Illumina MiSeq for identification of arbuscular mycorrhizal fungi |
| title_full_unstemmed | Perspectives of using Illumina MiSeq for identification of arbuscular mycorrhizal fungi |
| title_short | Perspectives of using Illumina MiSeq for identification of arbuscular mycorrhizal fungi |
| title_sort | perspectives of using illumina miseq for identification of arbuscular mycorrhizal fungi |
| topic | glomeromycotina arbuscular mycorrhiza illumina miseq rhizophagus irregularis r. invermaius paraglomus laccatum claroideoglomus etunicatum acaulospora |
| url | https://vavilov.elpub.ru/jour/article/view/2383 |
| work_keys_str_mv | AT aakryukov perspectivesofusingilluminamiseqforidentificationofarbuscularmycorrhizalfungi AT aogorbunova perspectivesofusingilluminamiseqforidentificationofarbuscularmycorrhizalfungi AT emmachs perspectivesofusingilluminamiseqforidentificationofarbuscularmycorrhizalfungi AT yvmikhaylova perspectivesofusingilluminamiseqforidentificationofarbuscularmycorrhizalfungi AT avrodionov perspectivesofusingilluminamiseqforidentificationofarbuscularmycorrhizalfungi AT pmzhurbenko perspectivesofusingilluminamiseqforidentificationofarbuscularmycorrhizalfungi AT apyurkov perspectivesofusingilluminamiseqforidentificationofarbuscularmycorrhizalfungi |