Tesi etd-03092020-101016
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Tipo di tesi
Dottorato
Autore
MARTURANO, GIOVANNI
URN
etd-03092020-101016
Titolo
Characterization of Long Terminal Repeat Retroelements and identification of exaptation events involving Transposable Elements in conifer genomes: a comparative approach
Settore scientifico disciplinare
Istituto di Scienze della Vita
Corso di studi
Istituto di Scienze della Vita - AGROBIOSCIENCES
Commissione
relatore ZUCCOLO, ANDREA
Membro Prof. CAVALLINI, ANDREA
Membro Prof. PE', MARIO ENRICO
Membro Dott. VENDRAMIN, GIOVANNI GIUSEPPE
Membro Prof. CAVALLINI, ANDREA
Membro Prof. PE', MARIO ENRICO
Membro Dott. VENDRAMIN, GIOVANNI GIUSEPPE
Parole chiave
- Conifers genome
- Exaptation
- Transposable elements
Data inizio appello
15/05/2020;
Disponibilità
completa
Riassunto analitico
Transposable elements (TEs) are sequences able to move in chromosomal sites different from the original one. They heavily contribute to the observed genome size variation across different species and constitute, through their spread within genomes, an endogenous source of variability contributing to the evolution of host genomes. When the activity of a TE confers a benefit to the host genome, that element may begin to evolve as a conventional sequence rather than through self-duplication. This process, called TE exaptation, leads to the creation of new genes defined as exapted transposable element genes (ETEs), that could play crucial roles in various biological systems.
We identified and characterized a total of 2400 complete and manually curated TEs belonging to 4 TE-groups (Ty1-copia,Ty3-gypsy, CACTA and LINE) within the genome of 6 gymnosperm species (Picea abies, Picea glauca, Pinus taeda, Pinus lambertiana and Pseudotsuga menziesii) and used in turn these information to investigate the exaptation events involving the TE component of genomes (especially LTR-retrotransposons) in species belonging to the Pinophyta division. Conifers have an ancient origin and large genomes, composed of a large fraction of old and highly diverged TEs. These features make them attractive subjects for studies aimed at identifying ETEs. Furthermore the paucity of genomic studies on conifers increases the interest of this research. In order to analyze these events, we adopted a comparative approach, by testing ETEs identified in conifers against a panel of species that covers about 400 million years of plant evolution and includes the bryophyite Physcomitrella patens, the ancient vascular plant Selaginella moellendorffii, the basal angiosperm Amborella trichopoda, the dicot angiosperm Vitis vinifera and the monocot angiosperm Oryza sativa. TE coding regions of elements belonging to a collection of P. abies complete and manually curated TEs were used to build Hidden Markov Models (HMMs) profiles, then used to search all the available aminoacidic sequences coded by annotated conifer genes. Genes coding for proteins showing similarity with TE-HMM profiles were further scrutinized for genetic attributes typical of genes (i.e. repetitiveness, expression, siRNA coverage and similarity with already known TEs) in order to identify putative ETE candidates.
In this research we identified 372 candidate ETEs in P. abies. In spite of their limited abundance in the host genome CACTA and LINE TEs were the source of a relatively high number of exaptation events (16% and 27% respectively). ETEs were subjected to purifying selection, suggesting that they are playing an important role for the evolution and functioning of host genomes. They mostly have catalytic and binding activities and are frequently involved in cellular and metabolic processes, 52% of them were conserved in all the species considered in this study and 31% of them were originated in gymnosperms
We identified and characterized a total of 2400 complete and manually curated TEs belonging to 4 TE-groups (Ty1-copia,Ty3-gypsy, CACTA and LINE) within the genome of 6 gymnosperm species (Picea abies, Picea glauca, Pinus taeda, Pinus lambertiana and Pseudotsuga menziesii) and used in turn these information to investigate the exaptation events involving the TE component of genomes (especially LTR-retrotransposons) in species belonging to the Pinophyta division. Conifers have an ancient origin and large genomes, composed of a large fraction of old and highly diverged TEs. These features make them attractive subjects for studies aimed at identifying ETEs. Furthermore the paucity of genomic studies on conifers increases the interest of this research. In order to analyze these events, we adopted a comparative approach, by testing ETEs identified in conifers against a panel of species that covers about 400 million years of plant evolution and includes the bryophyite Physcomitrella patens, the ancient vascular plant Selaginella moellendorffii, the basal angiosperm Amborella trichopoda, the dicot angiosperm Vitis vinifera and the monocot angiosperm Oryza sativa. TE coding regions of elements belonging to a collection of P. abies complete and manually curated TEs were used to build Hidden Markov Models (HMMs) profiles, then used to search all the available aminoacidic sequences coded by annotated conifer genes. Genes coding for proteins showing similarity with TE-HMM profiles were further scrutinized for genetic attributes typical of genes (i.e. repetitiveness, expression, siRNA coverage and similarity with already known TEs) in order to identify putative ETE candidates.
In this research we identified 372 candidate ETEs in P. abies. In spite of their limited abundance in the host genome CACTA and LINE TEs were the source of a relatively high number of exaptation events (16% and 27% respectively). ETEs were subjected to purifying selection, suggesting that they are playing an important role for the evolution and functioning of host genomes. They mostly have catalytic and binding activities and are frequently involved in cellular and metabolic processes, 52% of them were conserved in all the species considered in this study and 31% of them were originated in gymnosperms
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