An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference.
The ITS2 gene class shows a high sequence divergence among its members that have complicated its annotation and its use for reconstructing phylogenies at a higher taxonomical level (beyond species and genus). Several alignment strategies have been implemented to improve the ITS2 annotation quality a...
Guardado en:
| Autores principales: | , , , , , , , |
|---|---|
| Formato: | article |
| Lenguaje: | EN |
| Publicado: |
Public Library of Science (PLoS)
2011
|
| Materias: | |
| Acceso en línea: | https://doaj.org/article/d21d467703db4c5886500106cf499991 |
| Etiquetas: |
Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
|
| id |
oai:doaj.org-article:d21d467703db4c5886500106cf499991 |
|---|---|
| record_format |
dspace |
| spelling |
oai:doaj.org-article:d21d467703db4c5886500106cf4999912021-11-18T07:35:43ZAn alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference.1932-620310.1371/journal.pone.0026638https://doaj.org/article/d21d467703db4c5886500106cf4999912011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22046320/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203The ITS2 gene class shows a high sequence divergence among its members that have complicated its annotation and its use for reconstructing phylogenies at a higher taxonomical level (beyond species and genus). Several alignment strategies have been implemented to improve the ITS2 annotation quality and its use for phylogenetic inferences. Although, alignment based methods have been exploited to the top of its complexity to tackle both issues, no alignment-free approaches have been able to successfully address both topics. By contrast, the use of simple alignment-free classifiers, like the topological indices (TIs) containing information about the sequence and structure of ITS2, may reveal to be a useful approach for the gene prediction and for assessing the phylogenetic relationships of the ITS2 class in eukaryotes. Thus, we used the TI2BioP (Topological Indices to BioPolymers) methodology [1], [2], freely available at http://ti2biop.sourceforge.net/ to calculate two different TIs. One class was derived from the ITS2 artificial 2D structures generated from DNA strings and the other from the secondary structure inferred from RNA folding algorithms. Two alignment-free models based on Artificial Neural Networks were developed for the ITS2 class prediction using the two classes of TIs referred above. Both models showed similar performances on the training and the test sets reaching values above 95% in the overall classification. Due to the importance of the ITS2 region for fungi identification, a novel ITS2 genomic sequence was isolated from Petrakia sp. This sequence and the test set were used to comparatively evaluate the conventional classification models based on multiple sequence alignments like Hidden Markov based approaches, revealing the success of our models to identify novel ITS2 members. The isolated sequence was assessed using traditional and alignment-free based techniques applied to phylogenetic inference to complement the taxonomy of the Petrakia sp. fungal isolate.Guillermin Agüero-ChapinAminael Sánchez-RodríguezPedro I Hidalgo-YanesYunierkis Pérez-CastilloReinaldo Molina-RuizKathleen MarchalVítor VasconcelosAgostinho AntunesPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 10, p e26638 (2011) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Medicine R Science Q |
| spellingShingle |
Medicine R Science Q Guillermin Agüero-Chapin Aminael Sánchez-Rodríguez Pedro I Hidalgo-Yanes Yunierkis Pérez-Castillo Reinaldo Molina-Ruiz Kathleen Marchal Vítor Vasconcelos Agostinho Antunes An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference. |
| description |
The ITS2 gene class shows a high sequence divergence among its members that have complicated its annotation and its use for reconstructing phylogenies at a higher taxonomical level (beyond species and genus). Several alignment strategies have been implemented to improve the ITS2 annotation quality and its use for phylogenetic inferences. Although, alignment based methods have been exploited to the top of its complexity to tackle both issues, no alignment-free approaches have been able to successfully address both topics. By contrast, the use of simple alignment-free classifiers, like the topological indices (TIs) containing information about the sequence and structure of ITS2, may reveal to be a useful approach for the gene prediction and for assessing the phylogenetic relationships of the ITS2 class in eukaryotes. Thus, we used the TI2BioP (Topological Indices to BioPolymers) methodology [1], [2], freely available at http://ti2biop.sourceforge.net/ to calculate two different TIs. One class was derived from the ITS2 artificial 2D structures generated from DNA strings and the other from the secondary structure inferred from RNA folding algorithms. Two alignment-free models based on Artificial Neural Networks were developed for the ITS2 class prediction using the two classes of TIs referred above. Both models showed similar performances on the training and the test sets reaching values above 95% in the overall classification. Due to the importance of the ITS2 region for fungi identification, a novel ITS2 genomic sequence was isolated from Petrakia sp. This sequence and the test set were used to comparatively evaluate the conventional classification models based on multiple sequence alignments like Hidden Markov based approaches, revealing the success of our models to identify novel ITS2 members. The isolated sequence was assessed using traditional and alignment-free based techniques applied to phylogenetic inference to complement the taxonomy of the Petrakia sp. fungal isolate. |
| format |
article |
| author |
Guillermin Agüero-Chapin Aminael Sánchez-Rodríguez Pedro I Hidalgo-Yanes Yunierkis Pérez-Castillo Reinaldo Molina-Ruiz Kathleen Marchal Vítor Vasconcelos Agostinho Antunes |
| author_facet |
Guillermin Agüero-Chapin Aminael Sánchez-Rodríguez Pedro I Hidalgo-Yanes Yunierkis Pérez-Castillo Reinaldo Molina-Ruiz Kathleen Marchal Vítor Vasconcelos Agostinho Antunes |
| author_sort |
Guillermin Agüero-Chapin |
| title |
An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference. |
| title_short |
An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference. |
| title_full |
An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference. |
| title_fullStr |
An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference. |
| title_full_unstemmed |
An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference. |
| title_sort |
alignment-free approach for eukaryotic its2 annotation and phylogenetic inference. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2011 |
| url |
https://doaj.org/article/d21d467703db4c5886500106cf499991 |
| work_keys_str_mv |
AT guillerminaguerochapin analignmentfreeapproachforeukaryoticits2annotationandphylogeneticinference AT aminaelsanchezrodriguez analignmentfreeapproachforeukaryoticits2annotationandphylogeneticinference AT pedroihidalgoyanes analignmentfreeapproachforeukaryoticits2annotationandphylogeneticinference AT yunierkisperezcastillo analignmentfreeapproachforeukaryoticits2annotationandphylogeneticinference AT reinaldomolinaruiz analignmentfreeapproachforeukaryoticits2annotationandphylogeneticinference AT kathleenmarchal analignmentfreeapproachforeukaryoticits2annotationandphylogeneticinference AT vitorvasconcelos analignmentfreeapproachforeukaryoticits2annotationandphylogeneticinference AT agostinhoantunes analignmentfreeapproachforeukaryoticits2annotationandphylogeneticinference AT guillerminaguerochapin alignmentfreeapproachforeukaryoticits2annotationandphylogeneticinference AT aminaelsanchezrodriguez alignmentfreeapproachforeukaryoticits2annotationandphylogeneticinference AT pedroihidalgoyanes alignmentfreeapproachforeukaryoticits2annotationandphylogeneticinference AT yunierkisperezcastillo alignmentfreeapproachforeukaryoticits2annotationandphylogeneticinference AT reinaldomolinaruiz alignmentfreeapproachforeukaryoticits2annotationandphylogeneticinference AT kathleenmarchal alignmentfreeapproachforeukaryoticits2annotationandphylogeneticinference AT vitorvasconcelos alignmentfreeapproachforeukaryoticits2annotationandphylogeneticinference AT agostinhoantunes alignmentfreeapproachforeukaryoticits2annotationandphylogeneticinference |
| _version_ |
1718423252461682688 |