Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (<i>Rhizophagus irregularis</i>) in Pea (<i>Pisum sativum</i> L.) Roots
Alternative splicing (AS), a process that enables formation of different mRNA isoforms due to alternative ways of pre-mRNA processing, is one of the mechanisms for fine-tuning gene expression. Currently, the role of AS in symbioses formed by plants with soil microorganisms is not fully understood. I...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2020-12-01
|
| Series: | Plants |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2223-7747/9/12/1700 |
| _version_ | 1797545833079504896 |
|---|---|
| author | Evgeny A. Zorin Alexey M. Afonin Olga A. Kulaeva Emma S. Gribchenko Oksana Y. Shtark Vladimir A. Zhukov |
| author_facet | Evgeny A. Zorin Alexey M. Afonin Olga A. Kulaeva Emma S. Gribchenko Oksana Y. Shtark Vladimir A. Zhukov |
| author_sort | Evgeny A. Zorin |
| collection | DOAJ |
| description | Alternative splicing (AS), a process that enables formation of different mRNA isoforms due to alternative ways of pre-mRNA processing, is one of the mechanisms for fine-tuning gene expression. Currently, the role of AS in symbioses formed by plants with soil microorganisms is not fully understood. In this work, a comprehensive analysis of the transcriptome of garden pea (<i>Pisum sativum</i> L.) roots in symbiosis with arbuscular mycorrhiza was performed using RNAseq and following bioinformatic analysis. AS profiles of mycorrhizal and control roots were highly similar, intron retention accounting for a large proportion of the observed AS types (67%). Using three different tools (SUPPA2, DRIMSeq and IsoformSwitchAnalyzeR), eight genes with AS events specific for mycorrhizal roots of pea were identified, among which four were annotated as encoding an apoptosis inhibitor protein, a serine/threonine-protein kinase, a dehydrodolichyl diphosphate synthase, and a pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH1. In pea mycorrhizal roots, the isoforms of these four genes with preliminary stop codons leading to a truncated ORFs were up-regulated. Interestingly, two of these four genes demonstrating mycorrhiza-specific AS are related to the process of splicing, thus forming parts of the feedback loops involved in fine-tuning of gene expression during mycorrhization. |
| first_indexed | 2024-03-10T14:21:37Z |
| format | Article |
| id | doaj.art-a5f2033926174daaad746be842b6eb96 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-10T14:21:37Z |
| publishDate | 2020-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-a5f2033926174daaad746be842b6eb962023-11-20T23:22:13ZengMDPI AGPlants2223-77472020-12-01912170010.3390/plants9121700Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (<i>Rhizophagus irregularis</i>) in Pea (<i>Pisum sativum</i> L.) RootsEvgeny A. Zorin0Alexey M. Afonin1Olga A. Kulaeva2Emma S. Gribchenko3Oksana Y. Shtark4Vladimir A. Zhukov5All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, RussiaAll-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, RussiaAll-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, RussiaAll-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, RussiaAll-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, RussiaAll-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, RussiaAlternative splicing (AS), a process that enables formation of different mRNA isoforms due to alternative ways of pre-mRNA processing, is one of the mechanisms for fine-tuning gene expression. Currently, the role of AS in symbioses formed by plants with soil microorganisms is not fully understood. In this work, a comprehensive analysis of the transcriptome of garden pea (<i>Pisum sativum</i> L.) roots in symbiosis with arbuscular mycorrhiza was performed using RNAseq and following bioinformatic analysis. AS profiles of mycorrhizal and control roots were highly similar, intron retention accounting for a large proportion of the observed AS types (67%). Using three different tools (SUPPA2, DRIMSeq and IsoformSwitchAnalyzeR), eight genes with AS events specific for mycorrhizal roots of pea were identified, among which four were annotated as encoding an apoptosis inhibitor protein, a serine/threonine-protein kinase, a dehydrodolichyl diphosphate synthase, and a pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH1. In pea mycorrhizal roots, the isoforms of these four genes with preliminary stop codons leading to a truncated ORFs were up-regulated. Interestingly, two of these four genes demonstrating mycorrhiza-specific AS are related to the process of splicing, thus forming parts of the feedback loops involved in fine-tuning of gene expression during mycorrhization.https://www.mdpi.com/2223-7747/9/12/1700transcriptomicsRNAseqalternative splicingarbuscular mycorrhiza<i>P. sativum</i> |
| spellingShingle | Evgeny A. Zorin Alexey M. Afonin Olga A. Kulaeva Emma S. Gribchenko Oksana Y. Shtark Vladimir A. Zhukov Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (<i>Rhizophagus irregularis</i>) in Pea (<i>Pisum sativum</i> L.) Roots Plants transcriptomics RNAseq alternative splicing arbuscular mycorrhiza <i>P. sativum</i> |
| title | Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (<i>Rhizophagus irregularis</i>) in Pea (<i>Pisum sativum</i> L.) Roots |
| title_full | Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (<i>Rhizophagus irregularis</i>) in Pea (<i>Pisum sativum</i> L.) Roots |
| title_fullStr | Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (<i>Rhizophagus irregularis</i>) in Pea (<i>Pisum sativum</i> L.) Roots |
| title_full_unstemmed | Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (<i>Rhizophagus irregularis</i>) in Pea (<i>Pisum sativum</i> L.) Roots |
| title_short | Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (<i>Rhizophagus irregularis</i>) in Pea (<i>Pisum sativum</i> L.) Roots |
| title_sort | transcriptome analysis of alternative splicing events induced by arbuscular mycorrhizal fungi i rhizophagus irregularis i in pea i pisum sativum i l roots |
| topic | transcriptomics RNAseq alternative splicing arbuscular mycorrhiza <i>P. sativum</i> |
| url | https://www.mdpi.com/2223-7747/9/12/1700 |
| work_keys_str_mv | AT evgenyazorin transcriptomeanalysisofalternativesplicingeventsinducedbyarbuscularmycorrhizalfungiirhizophagusirregularisiinpeaipisumsativumilroots AT alexeymafonin transcriptomeanalysisofalternativesplicingeventsinducedbyarbuscularmycorrhizalfungiirhizophagusirregularisiinpeaipisumsativumilroots AT olgaakulaeva transcriptomeanalysisofalternativesplicingeventsinducedbyarbuscularmycorrhizalfungiirhizophagusirregularisiinpeaipisumsativumilroots AT emmasgribchenko transcriptomeanalysisofalternativesplicingeventsinducedbyarbuscularmycorrhizalfungiirhizophagusirregularisiinpeaipisumsativumilroots AT oksanayshtark transcriptomeanalysisofalternativesplicingeventsinducedbyarbuscularmycorrhizalfungiirhizophagusirregularisiinpeaipisumsativumilroots AT vladimirazhukov transcriptomeanalysisofalternativesplicingeventsinducedbyarbuscularmycorrhizalfungiirhizophagusirregularisiinpeaipisumsativumilroots |