Ambrosino, Luca (2016) COMPARATIVE APPROACHES FOR PLANT GENOMES: UNRAVELING "INTRA" AND "INTER" SPECIES RELATIONSHIPS FROM PRELIMINARY GENE ANNOTATIONS. [Tesi di dottorato]

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Item Type: Tesi di dottorato
Lingua: English
Title: COMPARATIVE APPROACHES FOR PLANT GENOMES: UNRAVELING "INTRA" AND "INTER" SPECIES RELATIONSHIPS FROM PRELIMINARY GENE ANNOTATIONS
Creators:
CreatorsEmail
Ambrosino, Lucaluca.bioinfo@gmail.com
Date: 31 March 2016
Number of Pages: 133
Institution: Università degli Studi di Napoli Federico II
Department: Medicina Molecolare e Biotecnologie Mediche
Scuola di dottorato: Biotecnologie
Dottorato: Biologia computazionale e bioinformatica
Ciclo di dottorato: 28
Coordinatore del Corso di dottorato:
nomeemail
Cocozza, Sergiosergio.cocozza@gmail.com
Tutor:
nomeemail
Chiusano, Maria LuisaUNSPECIFIED
Date: 31 March 2016
Number of Pages: 133
Uncontrolled Keywords: Comparative genomics, orthologs, paralogs
Settori scientifico-disciplinari del MIUR: Area 05 - Scienze biologiche > BIO/11 - Biologia molecolare
Date Deposited: 13 Apr 2016 20:52
Last Modified: 17 May 2017 01:00
URI: http://www.fedoa.unina.it/id/eprint/11048

Abstract

Comparative genomics studies the differences and similarities between different species, to transfer biological information from model organisms to newly sequenced genomes, and to understand the evolutionary forces that drive changes in genomic features such as gene sequences, gene order or regulatory sequences. The detection of ortholog genes between different organisms is a key approach for comparative genomics. For example, gene function prediction is primarily based on the identification of orthologs. On the other hand, the detection of paralog genes is fundamental for gene functions innovation studies. The fast spreading of whole genome sequencing approaches strongly enhanced the need of reliable methods to detect orthologs and paralogs and to understand molecular evolution. In this thesis, methods for predicting orthology relationships and exploiting the biological knowledge included within sets of paralog genes are shown. Although the similarity search methods used to identify orthology or paralogy relationships are generally based on the comparison between protein sequences, this analysis can lead to errors due to the lack of a correct and exhaustive definition of such sequences in recently sequenced organisms with a still preliminary annotation. Here we present a methodology that predict orthologs between two species by sequence similarity searches based on mRNA sequences. Moreover, the features of a web-accessible database on paralog and singleton genes of the model plant Arabidopsis thaliana, developed in our lab, are described. Duplicated genes are organized into networks of paralogs, whose graphical display and analysis enable the investigation of gene families structural relationships and evolution. Consequently, we applied the developed methodologies to the cross comparison between some economically important plant species, such as tomato, potato and grapevine. The similarities between two distantly related species such as tomato and grapevine, belonging to two different clades, and the distinctive aspects between two closely related members of the family of Solanaceae, potato and tomato, are also highlighted. Understanding different and common mechanisms that underlie these crop species could provide valuable insights in plant physiology.

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