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Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine

BACKGROUND: “Omics” approaches may provide useful information for a deeper understanding of speciation events, diversification and function innovation. This can be achieved by investigating the molecular similarities at sequence level between species, allowing the definition of ortholog and paralog...

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Autores principales: Ambrosino, Luca, Ruggieri, Valentino, Bostan, Hamed, Miralto, Marco, Vitulo, Nicola, Zouine, Mohamed, Barone, Amalia, Bouzayen, Mondher, Frusciante, Luigi, Pezzotti, Mario, Valle, Giorgio, Chiusano, Maria Luisa
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6266932/
https://www.ncbi.nlm.nih.gov/pubmed/30497367
http://dx.doi.org/10.1186/s12859-018-2420-y
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author Ambrosino, Luca
Ruggieri, Valentino
Bostan, Hamed
Miralto, Marco
Vitulo, Nicola
Zouine, Mohamed
Barone, Amalia
Bouzayen, Mondher
Frusciante, Luigi
Pezzotti, Mario
Valle, Giorgio
Chiusano, Maria Luisa
author_facet Ambrosino, Luca
Ruggieri, Valentino
Bostan, Hamed
Miralto, Marco
Vitulo, Nicola
Zouine, Mohamed
Barone, Amalia
Bouzayen, Mondher
Frusciante, Luigi
Pezzotti, Mario
Valle, Giorgio
Chiusano, Maria Luisa
author_sort Ambrosino, Luca
collection PubMed
description BACKGROUND: “Omics” approaches may provide useful information for a deeper understanding of speciation events, diversification and function innovation. This can be achieved by investigating the molecular similarities at sequence level between species, allowing the definition of ortholog and paralog genes. However, the spreading of sequenced genome, often endowed with still preliminary annotations, requires suitable bioinformatics to be appropriately exploited in this framework. RESULTS: We presented here a multilevel comparative approach to investigate on genome evolutionary relationships and peculiarities of two fleshy fruit species of relevant agronomic interest, Solanum lycopersicum (tomato) and Vitis vinifera (grapevine). We defined 17,823 orthology relationships between tomato and grapevine reference gene annotations. The resulting orthologs are associated with the detected paralogs in each species, permitting the definition of gene networks, useful to investigate the different relationships. The reconciliation of the compared collections in terms of an updating of the functional descriptions was also exploited. All the results were made accessible in ComParaLogs, a dedicated bioinformatics platform available at http://biosrv.cab.unina.it/comparalogs/gene/search. CONCLUSIONS: The aim of the work was to suggest a reliable approach to detect all similarities of gene loci between two species based on the integration of results from different levels of information, such as the gene, the transcript and the protein sequences, overcoming possible limits due to exclusive protein versus protein comparisons. This to define reliable ortholog and paralog genes, as well as species specific gene loci in the two species, overcoming limits due to the possible draft nature of preliminary gene annotations. Moreover, reconciled functional descriptions, as well as common or peculiar enzymatic classes and protein domains from tomato and grapevine, together with the definition of species-specific gene sets after the pairwise comparisons, contributed a comprehensive set of information useful to comparatively exploit the two species gene annotations and investigate on differences between species with climacteric and non-climacteric fruits. In addition, the definition of networks of ortholog genes and of associated paralogs, and the organization of web-based interfaces for the exploration of the results, defined a friendly computational bench-work in support of comparative analyses between two species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2420-y) contains supplementary material, which is available to authorized users.
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spelling pubmed-62669322018-12-05 Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine Ambrosino, Luca Ruggieri, Valentino Bostan, Hamed Miralto, Marco Vitulo, Nicola Zouine, Mohamed Barone, Amalia Bouzayen, Mondher Frusciante, Luigi Pezzotti, Mario Valle, Giorgio Chiusano, Maria Luisa BMC Bioinformatics Research BACKGROUND: “Omics” approaches may provide useful information for a deeper understanding of speciation events, diversification and function innovation. This can be achieved by investigating the molecular similarities at sequence level between species, allowing the definition of ortholog and paralog genes. However, the spreading of sequenced genome, often endowed with still preliminary annotations, requires suitable bioinformatics to be appropriately exploited in this framework. RESULTS: We presented here a multilevel comparative approach to investigate on genome evolutionary relationships and peculiarities of two fleshy fruit species of relevant agronomic interest, Solanum lycopersicum (tomato) and Vitis vinifera (grapevine). We defined 17,823 orthology relationships between tomato and grapevine reference gene annotations. The resulting orthologs are associated with the detected paralogs in each species, permitting the definition of gene networks, useful to investigate the different relationships. The reconciliation of the compared collections in terms of an updating of the functional descriptions was also exploited. All the results were made accessible in ComParaLogs, a dedicated bioinformatics platform available at http://biosrv.cab.unina.it/comparalogs/gene/search. CONCLUSIONS: The aim of the work was to suggest a reliable approach to detect all similarities of gene loci between two species based on the integration of results from different levels of information, such as the gene, the transcript and the protein sequences, overcoming possible limits due to exclusive protein versus protein comparisons. This to define reliable ortholog and paralog genes, as well as species specific gene loci in the two species, overcoming limits due to the possible draft nature of preliminary gene annotations. Moreover, reconciled functional descriptions, as well as common or peculiar enzymatic classes and protein domains from tomato and grapevine, together with the definition of species-specific gene sets after the pairwise comparisons, contributed a comprehensive set of information useful to comparatively exploit the two species gene annotations and investigate on differences between species with climacteric and non-climacteric fruits. In addition, the definition of networks of ortholog genes and of associated paralogs, and the organization of web-based interfaces for the exploration of the results, defined a friendly computational bench-work in support of comparative analyses between two species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2420-y) contains supplementary material, which is available to authorized users. BioMed Central 2018-11-30 /pmc/articles/PMC6266932/ /pubmed/30497367 http://dx.doi.org/10.1186/s12859-018-2420-y Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Ambrosino, Luca
Ruggieri, Valentino
Bostan, Hamed
Miralto, Marco
Vitulo, Nicola
Zouine, Mohamed
Barone, Amalia
Bouzayen, Mondher
Frusciante, Luigi
Pezzotti, Mario
Valle, Giorgio
Chiusano, Maria Luisa
Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine
title Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine
title_full Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine
title_fullStr Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine
title_full_unstemmed Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine
title_short Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine
title_sort multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6266932/
https://www.ncbi.nlm.nih.gov/pubmed/30497367
http://dx.doi.org/10.1186/s12859-018-2420-y
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