Architecture and Distribution of Introns in Core Genes of Four Fusarium Species
Removal of introns from transcribed RNA represents a crucial step during the production of mRNA in eukaryotes. Available whole-genome sequences and expressed sequence tags (ESTs) have increased our knowledge of this process and revealed various commonalities among eukaryotes. However, certain aspect...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Oxford University Press
2017-11-01
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| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.117.300344 |
| _version_ | 1829496314815053824 |
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| author | Mmatshepho M. Phasha Brenda D. Wingfield Martin P. A. Coetzee Quentin C. Santana Gerda Fourie Emma T. Steenkamp |
| author_facet | Mmatshepho M. Phasha Brenda D. Wingfield Martin P. A. Coetzee Quentin C. Santana Gerda Fourie Emma T. Steenkamp |
| author_sort | Mmatshepho M. Phasha |
| collection | DOAJ |
| description | Removal of introns from transcribed RNA represents a crucial step during the production of mRNA in eukaryotes. Available whole-genome sequences and expressed sequence tags (ESTs) have increased our knowledge of this process and revealed various commonalities among eukaryotes. However, certain aspects of intron structure and diversity are taxon-specific, which can complicate the accuracy of in silico gene prediction methods. Using core genes, we evaluated the distribution and architecture of Fusarium circinatum spliceosomal introns, and linked these characteristics to the accuracy of the predicted gene models of the genome of this fungus. We also evaluated intron distribution and architecture in F. verticillioides, F. oxysporum, and F. graminearum, and made comparisons with F. circinatum. Results indicated that F. circinatum and the three other Fusarium species have canonical 5′ and 3′ splice sites, but with subtle differences that are apparently not shared with those of other fungal genera. The polypyrimidine tract of Fusarium introns was also found to be highly divergent among species and genes. Furthermore, the conserved adenosine nucleoside required during the first step of splicing is contained within unique branch site motifs in certain Fusarium introns. Data generated here show that introns of F. circinatum, as well as F. verticillioides, F. oxysporum, and F. graminearum, are characterized by a number of unique features such as the CTHAH and ACCAT motifs of the branch site. Incorporation of such information into genome annotation software will undoubtedly improve the accuracy of gene prediction methods used for Fusarium species and related fungi. |
| first_indexed | 2024-12-16T07:28:37Z |
| format | Article |
| id | doaj.art-1e63bdc72e504897ac170e186cc0ad09 |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-16T07:28:37Z |
| publishDate | 2017-11-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-1e63bdc72e504897ac170e186cc0ad092022-12-21T22:39:25ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362017-11-017113809382010.1534/g3.117.30034422Architecture and Distribution of Introns in Core Genes of Four Fusarium SpeciesMmatshepho M. PhashaBrenda D. WingfieldMartin P. A. CoetzeeQuentin C. SantanaGerda FourieEmma T. SteenkampRemoval of introns from transcribed RNA represents a crucial step during the production of mRNA in eukaryotes. Available whole-genome sequences and expressed sequence tags (ESTs) have increased our knowledge of this process and revealed various commonalities among eukaryotes. However, certain aspects of intron structure and diversity are taxon-specific, which can complicate the accuracy of in silico gene prediction methods. Using core genes, we evaluated the distribution and architecture of Fusarium circinatum spliceosomal introns, and linked these characteristics to the accuracy of the predicted gene models of the genome of this fungus. We also evaluated intron distribution and architecture in F. verticillioides, F. oxysporum, and F. graminearum, and made comparisons with F. circinatum. Results indicated that F. circinatum and the three other Fusarium species have canonical 5′ and 3′ splice sites, but with subtle differences that are apparently not shared with those of other fungal genera. The polypyrimidine tract of Fusarium introns was also found to be highly divergent among species and genes. Furthermore, the conserved adenosine nucleoside required during the first step of splicing is contained within unique branch site motifs in certain Fusarium introns. Data generated here show that introns of F. circinatum, as well as F. verticillioides, F. oxysporum, and F. graminearum, are characterized by a number of unique features such as the CTHAH and ACCAT motifs of the branch site. Incorporation of such information into genome annotation software will undoubtedly improve the accuracy of gene prediction methods used for Fusarium species and related fungi.http://g3journal.org/lookup/doi/10.1534/g3.117.300344Fusariumintron splicingspliceosomal intronscis-elementsgene prediction |
| spellingShingle | Mmatshepho M. Phasha Brenda D. Wingfield Martin P. A. Coetzee Quentin C. Santana Gerda Fourie Emma T. Steenkamp Architecture and Distribution of Introns in Core Genes of Four Fusarium Species G3: Genes, Genomes, Genetics Fusarium intron splicing spliceosomal introns cis-elements gene prediction |
| title | Architecture and Distribution of Introns in Core Genes of Four Fusarium Species |
| title_full | Architecture and Distribution of Introns in Core Genes of Four Fusarium Species |
| title_fullStr | Architecture and Distribution of Introns in Core Genes of Four Fusarium Species |
| title_full_unstemmed | Architecture and Distribution of Introns in Core Genes of Four Fusarium Species |
| title_short | Architecture and Distribution of Introns in Core Genes of Four Fusarium Species |
| title_sort | architecture and distribution of introns in core genes of four fusarium species |
| topic | Fusarium intron splicing spliceosomal introns cis-elements gene prediction |
| url | http://g3journal.org/lookup/doi/10.1534/g3.117.300344 |
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