Here we describe the mitochondrial genome of the golden mussel Limnoperna fortunei, an Asian biva... more Here we describe the mitochondrial genome of the golden mussel Limnoperna fortunei, an Asian bivalve which has become one of the most aggressive invasive species in Japan and South America. The mitochondrial genome of L. fortunei does not present conserved gene arrangement when compared to the other Mytilidae species suggesting a high degree of gene recombination in the mitochondria of this clade. In addition, the golden mussel mitogenome encodes two copies of tRNA(Lys) and presents a putative pseudogene for the atp8 gene sequence that encodes a 27 amino acid peptide containing an in-frame stop codon. The presence of this pseudogene raises the question as to whether atp8 is encoded in some bivalve mitochondrial genomes or not. The phylogenetic analysis of all complete mitochondrial genomes available from Mytilidae mussels confirmed the close evolutionary relationships among bivalves from the genus Mytilys and placed L. fortunei coming from a more ancestral branch on the family. The supermatrix phylogeny described used the concatenation of all 12 genes from the mitochondria and disputed the monophyly of the genus Perna, as Perna perna was shown to be more closely related to Brachidontes exustus than to Perna viridis. The comparative analysis of mitogenome synteny also confirmed the polyphyly of the genus Perna. The complete and annotated mitogenome has been published in GenBank under the accession number KP756905.
Among known bird species, oscines are one of the few groups that produce complex vocalizations du... more Among known bird species, oscines are one of the few groups that produce complex vocalizations due to vocal learning. One of the most conspicuous oscine passerines in southeastern South America is the Rufous-bellied Thrush, Turdus rufiventris. The complete mitochondrial genome of this species was sequenced with the Illumina HiSeq platform (Illumina Inc., San Diego, CA), assembled using MITObim software and annotated by MITOS web server and Artemis software. This mitogenome contained 16 669 bases, organized as 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a control region (d-loop). The sequencing of the Rufous-bellied Thrush mitochondrial genome is of particular interest for better understanding of population genetics and phylogeography of the Turdidae family.
Proceedings of the National Academy of Sciences, 2015
Rhodnius prolixus not only has served as a model organism for the study of insect physiology, but... more Rhodnius prolixus not only has served as a model organism for the study of insect physiology, but also is a major vector of Chagas disease, an illness that affects approximately seven million people worldwide. We sequenced the genome of R. prolixus, generated assembled sequences covering 95% of the genome (∼702 Mb), including 15,456 putative protein-coding genes, and completed comprehensive genomic analyses of this obligate blood-feeding insect. Although immune-deficiency (IMD)-mediated immune responses were observed, R. prolixus putatively lacks key components of the IMD pathway, suggesting a reorganization of the canonical immune signaling network. Although both Toll and IMD effectors controlled intestinal microbiota, neither affected Trypanosoma cruzi, the causal agent of Chagas disease, implying the existence of evasion or tolerance mechanisms. R. prolixus has experienced an extensive loss of selenoprotein genes, with its repertoire reduced to only two proteins, one of which is a selenocysteine-based glutathione peroxidase, the first found in insects. The genome contained actively transcribed, horizontally transferred genes from Wolbachia sp., which showed evidence of codon use evolution toward the insect use pattern. Comparative protein analyses revealed many lineage-specific expansions and putative gene absences in R. prolixus, including tandem expansions of genes related to chemoreception, feeding, and digestion that possibly contributed to the evolution of a blood-feeding lifestyle. The genome assembly and these associated analyses provide critical information on the physiology and evolution of this important vector species and should be instrumental for the development of innovative disease control methods.
Spiders possess distinctive evolutionary adaptations, such as venom and silk production, providin... more Spiders possess distinctive evolutionary adaptations, such as venom and silk production, providing an ample system for evolutionary and developmental studies of anatomical adaptation. Here we compare transcripts from 2 suborders of the Araneae order: ...
The complete sequence of the brown mussel Perna perna mitochondrial genome is described in this a... more The complete sequence of the brown mussel Perna perna mitochondrial genome is described in this article. It was sequenced in 1/11 of an Illumina HiSeq lane using Nextera multiplexing kit. The mitogenome was assembled using both (i) de novo assembly and (ii) referenced-based strategies with mitoMaker software. Perna perna mitogenome is a circular molecule of 18,415 bp in size, containing 12 protein-coding genes, 23 transfer RNAs, 2 ribossomal RNAs and several non-coding regions. As shown in the previous studies, Perna perna does not present the doubly uniparental inheritance system (DUI) of mitochondria and does not encode the ATPase8 gene, in accordance with other Mytilidae data.
The Alzheimer disease (AD) is a complex neurodegenerative disorder and it is the predominant caus... more The Alzheimer disease (AD) is a complex neurodegenerative disorder and it is the predominant cause of dementia in people over 65 years of age (1). Genetic risk factors for AD have been identified in the last years in search of major factors related to neurodegenerative process. Searching for a susceptibility loci, Myers et al. (2000) performed a genetic linkage study
The Alzheimer disease (AD) is a complex neurodegenerative disorder and it is the predominant caus... more The Alzheimer disease (AD) is a complex neurodegenerative disorder and it is the predominant cause of dementia in people over 65 years of age [1]. Genetic risk factors for AD have been identified in the last years in search of major factors related to ...
The methodology for evolutionary comparative analysis has developed over several decades. The met... more The methodology for evolutionary comparative analysis has developed over several decades. The methodology now includes familiar and powerful software tools for inferring phylogenetic trees, reconstructing ancestral states and comparing models of evolution. Lagging far behind however, are the informatics resources to facilitate integrative, large-scale, or automated analyses, especially for data other than molecular sequences. Because the informatics challenges of evolutionary analysis are similar to the challenges of ...
The Gene Ontology (GO) database annotates a large number of genes according to their functions (t... more The Gene Ontology (GO) database annotates a large number of genes according to their functions (the biological processes, molecular functions and cellular components in which they are involved). However, it is far from complete, and so there is a need for techniques that automatically assign GO functional categories to genes based on integration of available data. The present work describes one such technique, that uses a combination of sequence similarity and a similarity measure based on mutual information applied to cross ...
Here we describe the mitochondrial genome of the golden mussel Limnoperna fortunei, an Asian biva... more Here we describe the mitochondrial genome of the golden mussel Limnoperna fortunei, an Asian bivalve which has become one of the most aggressive invasive species in Japan and South America. The mitochondrial genome of L. fortunei does not present conserved gene arrangement when compared to the other Mytilidae species suggesting a high degree of gene recombination in the mitochondria of this clade. In addition, the golden mussel mitogenome encodes two copies of tRNA(Lys) and presents a putative pseudogene for the atp8 gene sequence that encodes a 27 amino acid peptide containing an in-frame stop codon. The presence of this pseudogene raises the question as to whether atp8 is encoded in some bivalve mitochondrial genomes or not. The phylogenetic analysis of all complete mitochondrial genomes available from Mytilidae mussels confirmed the close evolutionary relationships among bivalves from the genus Mytilys and placed L. fortunei coming from a more ancestral branch on the family. The supermatrix phylogeny described used the concatenation of all 12 genes from the mitochondria and disputed the monophyly of the genus Perna, as Perna perna was shown to be more closely related to Brachidontes exustus than to Perna viridis. The comparative analysis of mitogenome synteny also confirmed the polyphyly of the genus Perna. The complete and annotated mitogenome has been published in GenBank under the accession number KP756905.
Among known bird species, oscines are one of the few groups that produce complex vocalizations du... more Among known bird species, oscines are one of the few groups that produce complex vocalizations due to vocal learning. One of the most conspicuous oscine passerines in southeastern South America is the Rufous-bellied Thrush, Turdus rufiventris. The complete mitochondrial genome of this species was sequenced with the Illumina HiSeq platform (Illumina Inc., San Diego, CA), assembled using MITObim software and annotated by MITOS web server and Artemis software. This mitogenome contained 16 669 bases, organized as 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a control region (d-loop). The sequencing of the Rufous-bellied Thrush mitochondrial genome is of particular interest for better understanding of population genetics and phylogeography of the Turdidae family.
Proceedings of the National Academy of Sciences, 2015
Rhodnius prolixus not only has served as a model organism for the study of insect physiology, but... more Rhodnius prolixus not only has served as a model organism for the study of insect physiology, but also is a major vector of Chagas disease, an illness that affects approximately seven million people worldwide. We sequenced the genome of R. prolixus, generated assembled sequences covering 95% of the genome (∼702 Mb), including 15,456 putative protein-coding genes, and completed comprehensive genomic analyses of this obligate blood-feeding insect. Although immune-deficiency (IMD)-mediated immune responses were observed, R. prolixus putatively lacks key components of the IMD pathway, suggesting a reorganization of the canonical immune signaling network. Although both Toll and IMD effectors controlled intestinal microbiota, neither affected Trypanosoma cruzi, the causal agent of Chagas disease, implying the existence of evasion or tolerance mechanisms. R. prolixus has experienced an extensive loss of selenoprotein genes, with its repertoire reduced to only two proteins, one of which is a selenocysteine-based glutathione peroxidase, the first found in insects. The genome contained actively transcribed, horizontally transferred genes from Wolbachia sp., which showed evidence of codon use evolution toward the insect use pattern. Comparative protein analyses revealed many lineage-specific expansions and putative gene absences in R. prolixus, including tandem expansions of genes related to chemoreception, feeding, and digestion that possibly contributed to the evolution of a blood-feeding lifestyle. The genome assembly and these associated analyses provide critical information on the physiology and evolution of this important vector species and should be instrumental for the development of innovative disease control methods.
Spiders possess distinctive evolutionary adaptations, such as venom and silk production, providin... more Spiders possess distinctive evolutionary adaptations, such as venom and silk production, providing an ample system for evolutionary and developmental studies of anatomical adaptation. Here we compare transcripts from 2 suborders of the Araneae order: ...
The complete sequence of the brown mussel Perna perna mitochondrial genome is described in this a... more The complete sequence of the brown mussel Perna perna mitochondrial genome is described in this article. It was sequenced in 1/11 of an Illumina HiSeq lane using Nextera multiplexing kit. The mitogenome was assembled using both (i) de novo assembly and (ii) referenced-based strategies with mitoMaker software. Perna perna mitogenome is a circular molecule of 18,415 bp in size, containing 12 protein-coding genes, 23 transfer RNAs, 2 ribossomal RNAs and several non-coding regions. As shown in the previous studies, Perna perna does not present the doubly uniparental inheritance system (DUI) of mitochondria and does not encode the ATPase8 gene, in accordance with other Mytilidae data.
The Alzheimer disease (AD) is a complex neurodegenerative disorder and it is the predominant caus... more The Alzheimer disease (AD) is a complex neurodegenerative disorder and it is the predominant cause of dementia in people over 65 years of age (1). Genetic risk factors for AD have been identified in the last years in search of major factors related to neurodegenerative process. Searching for a susceptibility loci, Myers et al. (2000) performed a genetic linkage study
The Alzheimer disease (AD) is a complex neurodegenerative disorder and it is the predominant caus... more The Alzheimer disease (AD) is a complex neurodegenerative disorder and it is the predominant cause of dementia in people over 65 years of age [1]. Genetic risk factors for AD have been identified in the last years in search of major factors related to ...
The methodology for evolutionary comparative analysis has developed over several decades. The met... more The methodology for evolutionary comparative analysis has developed over several decades. The methodology now includes familiar and powerful software tools for inferring phylogenetic trees, reconstructing ancestral states and comparing models of evolution. Lagging far behind however, are the informatics resources to facilitate integrative, large-scale, or automated analyses, especially for data other than molecular sequences. Because the informatics challenges of evolutionary analysis are similar to the challenges of ...
The Gene Ontology (GO) database annotates a large number of genes according to their functions (t... more The Gene Ontology (GO) database annotates a large number of genes according to their functions (the biological processes, molecular functions and cellular components in which they are involved). However, it is far from complete, and so there is a need for techniques that automatically assign GO functional categories to genes based on integration of available data. The present work describes one such technique, that uses a combination of sequence similarity and a similarity measure based on mutual information applied to cross ...
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Papers by Francisco Prosdocimi