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Imaging Intron Evolution

Intron evolution may be readily imaged through the combined use of the “dot plot” function of the NCBI BLAST, aligning two sequences at a time, and the Vertebrate “Multiz” alignment and conservation tool of the UCSC Genome Browser. With the NCBI BLAST, an ideal alignment of two highly conserved sequ...

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Autores principales: Panaro, Maria Antonietta, Calvello, Rosa, Miniero, Daniela Valeria, Mitolo, Vincenzo, Cianciulli, Antonia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9326662/
https://www.ncbi.nlm.nih.gov/pubmed/35893579
http://dx.doi.org/10.3390/mps5040053
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author Panaro, Maria Antonietta
Calvello, Rosa
Miniero, Daniela Valeria
Mitolo, Vincenzo
Cianciulli, Antonia
author_facet Panaro, Maria Antonietta
Calvello, Rosa
Miniero, Daniela Valeria
Mitolo, Vincenzo
Cianciulli, Antonia
author_sort Panaro, Maria Antonietta
collection PubMed
description Intron evolution may be readily imaged through the combined use of the “dot plot” function of the NCBI BLAST, aligning two sequences at a time, and the Vertebrate “Multiz” alignment and conservation tool of the UCSC Genome Browser. With the NCBI BLAST, an ideal alignment of two highly conserved sequences generates a diagonal straight line in the plot from the lower left corner to the upper right corner. Gaps in this line correspond to non-conserved sections. In addition, the dot plot of the alignment of a sequence with the same sequence after the removal of the Transposable Elements (TEs) can be observed along the diagonal gaps that correspond to the sites of TE insertion. The UCSC Genome Browser can graph, along the entire sequence of a single gene, the level of overall conservation in vertebrates. This level can be compared with the conservation level of the gene in one or more selected vertebrate species. As an example, we show the graphic analysis of the intron conservation in two genes: the mitochondrial solute carrier 21 (SLC25A21) and the growth hormone receptor (GHR), whose coding sequences are conserved through vertebrates, while their introns show dramatic changes in nucleotide composition and even length. In the SLC25A21, a few short but significant nucleotide sequences are conserved in zebrafish, Xenopus and humans, and the rate of conservation steadily increases from chicken/human to mouse/human alignments. In the GHR, a less conserved gene, the earlier indication of intron conservation is a small signal in chicken/human alignment. The UCSC tool may simultaneously display the conservation level of a gene in different vertebrates, with reference to the level of overall conservation in Vertebrates. It is shown that, at least in SLC25A21, the sites of higher conservation are not always coincident in chicken and zebrafish nor are the sites of higher vertebrate conservation.
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spelling pubmed-93266622022-07-28 Imaging Intron Evolution Panaro, Maria Antonietta Calvello, Rosa Miniero, Daniela Valeria Mitolo, Vincenzo Cianciulli, Antonia Methods Protoc Article Intron evolution may be readily imaged through the combined use of the “dot plot” function of the NCBI BLAST, aligning two sequences at a time, and the Vertebrate “Multiz” alignment and conservation tool of the UCSC Genome Browser. With the NCBI BLAST, an ideal alignment of two highly conserved sequences generates a diagonal straight line in the plot from the lower left corner to the upper right corner. Gaps in this line correspond to non-conserved sections. In addition, the dot plot of the alignment of a sequence with the same sequence after the removal of the Transposable Elements (TEs) can be observed along the diagonal gaps that correspond to the sites of TE insertion. The UCSC Genome Browser can graph, along the entire sequence of a single gene, the level of overall conservation in vertebrates. This level can be compared with the conservation level of the gene in one or more selected vertebrate species. As an example, we show the graphic analysis of the intron conservation in two genes: the mitochondrial solute carrier 21 (SLC25A21) and the growth hormone receptor (GHR), whose coding sequences are conserved through vertebrates, while their introns show dramatic changes in nucleotide composition and even length. In the SLC25A21, a few short but significant nucleotide sequences are conserved in zebrafish, Xenopus and humans, and the rate of conservation steadily increases from chicken/human to mouse/human alignments. In the GHR, a less conserved gene, the earlier indication of intron conservation is a small signal in chicken/human alignment. The UCSC tool may simultaneously display the conservation level of a gene in different vertebrates, with reference to the level of overall conservation in Vertebrates. It is shown that, at least in SLC25A21, the sites of higher conservation are not always coincident in chicken and zebrafish nor are the sites of higher vertebrate conservation. MDPI 2022-06-24 /pmc/articles/PMC9326662/ /pubmed/35893579 http://dx.doi.org/10.3390/mps5040053 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Panaro, Maria Antonietta
Calvello, Rosa
Miniero, Daniela Valeria
Mitolo, Vincenzo
Cianciulli, Antonia
Imaging Intron Evolution
title Imaging Intron Evolution
title_full Imaging Intron Evolution
title_fullStr Imaging Intron Evolution
title_full_unstemmed Imaging Intron Evolution
title_short Imaging Intron Evolution
title_sort imaging intron evolution
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9326662/
https://www.ncbi.nlm.nih.gov/pubmed/35893579
http://dx.doi.org/10.3390/mps5040053
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