Transcriptomic and genomic identification of spliceosomal genes from Euglena gracilis
Diverse splicing types in nuclear and chloroplast genes of protist Euglena gracilis have been recognized for decades. However, the splicing machinery responsible for processing nuclear precursor messenger RNA introns, including trans-splicing of the 5′ termi...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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China Science Publishing & Media Ltd.
2023-09-01
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| Series: | Acta Biochimica et Biophysica Sinica |
| Subjects: | |
| Online Access: | https://www.sciengine.com/doi/10.3724/abbs.2023143 |
| _version_ | 1827698429470441472 |
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| author | Gao Pingwei Zhong Yujie Sun Chengfu |
| author_facet | Gao Pingwei Zhong Yujie Sun Chengfu |
| author_sort | Gao Pingwei |
| collection | DOAJ |
| description | Diverse splicing types in nuclear and chloroplast genes of protist Euglena gracilis have been recognized for decades. However, the splicing machinery responsible for processing nuclear precursor messenger RNA introns, including trans-splicing of the 5′ terminal outron and spliced leader (SL) RNA, remains elusive. Here, we identify 166 spliceosomal protein genes and two snRNA genes from E. gracilis by performing bioinformatics analysis from a combination of next-generation and full-length transcriptomic RNA sequencing (RNAseq) data as well as draft genomic data. With the spliceosomal proteins we identified in hand, the insensitivity of E. gracilis to some splicing modulators is revealed at the sequence level. The prevalence of SL RNA-mediated trans-splicing is estimated to be more than 70% from our full-length RNAseq data. Finally, the splicing proteomes between E. gracilis and its three evolutionary cousins within the same Excavata group are compared. In conclusion, our study characterizes the spliceosomal components in E. gracilis and provides the molecular basis for further exploration of underlying splicing mechanisms. |
| first_indexed | 2024-03-10T13:30:12Z |
| format | Article |
| id | doaj.art-9b9a93db4ee245f78a31886eb9e20e89 |
| institution | Directory Open Access Journal |
| issn | 1672-9145 |
| language | English |
| last_indexed | 2024-03-10T13:30:12Z |
| publishDate | 2023-09-01 |
| publisher | China Science Publishing & Media Ltd. |
| record_format | Article |
| series | Acta Biochimica et Biophysica Sinica |
| spelling | doaj.art-9b9a93db4ee245f78a31886eb9e20e892023-11-21T08:12:34ZengChina Science Publishing & Media Ltd.Acta Biochimica et Biophysica Sinica1672-91452023-09-01551740174810.3724/abbs.202314320d259ccTranscriptomic and genomic identification of spliceosomal genes from Euglena gracilisGao Pingwei0Zhong Yujie1Sun Chengfu2[][][]Diverse splicing types in nuclear and chloroplast genes of protist Euglena gracilis have been recognized for decades. However, the splicing machinery responsible for processing nuclear precursor messenger RNA introns, including trans-splicing of the 5′ terminal outron and spliced leader (SL) RNA, remains elusive. Here, we identify 166 spliceosomal protein genes and two snRNA genes from E. gracilis by performing bioinformatics analysis from a combination of next-generation and full-length transcriptomic RNA sequencing (RNAseq) data as well as draft genomic data. With the spliceosomal proteins we identified in hand, the insensitivity of E. gracilis to some splicing modulators is revealed at the sequence level. The prevalence of SL RNA-mediated trans-splicing is estimated to be more than 70% from our full-length RNAseq data. Finally, the splicing proteomes between E. gracilis and its three evolutionary cousins within the same Excavata group are compared. In conclusion, our study characterizes the spliceosomal components in E. gracilis and provides the molecular basis for further exploration of underlying splicing mechanisms. https://www.sciengine.com/doi/10.3724/abbs.2023143txcavataspliceosomeintrontranscriptome<italic>trans</italic>-splicingSF3B |
| spellingShingle | Gao Pingwei Zhong Yujie Sun Chengfu Transcriptomic and genomic identification of spliceosomal genes from Euglena gracilis Acta Biochimica et Biophysica Sinica txcavata spliceosome intron transcriptome <italic>trans</italic>-splicing SF3B |
| title | Transcriptomic and genomic identification of spliceosomal genes from Euglena gracilis |
| title_full | Transcriptomic and genomic identification of spliceosomal genes from Euglena gracilis |
| title_fullStr | Transcriptomic and genomic identification of spliceosomal genes from Euglena gracilis |
| title_full_unstemmed | Transcriptomic and genomic identification of spliceosomal genes from Euglena gracilis |
| title_short | Transcriptomic and genomic identification of spliceosomal genes from Euglena gracilis |
| title_sort | transcriptomic and genomic identification of spliceosomal genes from euglena gracilis |
| topic | txcavata spliceosome intron transcriptome <italic>trans</italic>-splicing SF3B |
| url | https://www.sciengine.com/doi/10.3724/abbs.2023143 |
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