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Article
Open AccessDetection of ribonucleotides embedded in DNA by Nanopore sequencing
Ribonucleotides represent the most common non-canonical nucleotides found in eukaryotic genomes. The sources of chromosome-embedded ribonucleotides and the mechanisms by which unrepaired rNMPs trigger genome i...
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Article
Against the flow: Integrated taxonomy and environmental suitability of a cold-water species dispersing to warmer waters
The number of species dispersing to higher and/or lower latitudes, in association with temperature warming, is growing exponentially with only a few described opposite cases of dispersal to warmer regions. Her...
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Article
Open AccessHaploCoV: unsupervised classification and rapid detection of novel emerging variants of SARS-CoV-2
Accurate and timely monitoring of the evolution of SARS-CoV-2 is crucial for identifying and tracking potentially more transmissible/virulent viral variants, and implement mitigation strategies to limit their ...
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Article
Open AccessAn elongated COI fragment to discriminate botryllid species and as an improved ascidian DNA barcode
Botryllids are colonial ascidians widely studied for their potential invasiveness and as model organisms, however the morphological description and discrimination of these species is very problematic, leading ...
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Article
Open AccessExtensive mitochondrial gene rearrangements in Ctenophora: insights from benthic Platyctenida
Complete mitochondrial (mt) genomes have been sequenced for thousands of animals and represent a molecule of choice for many evolutionary studies. Nevertheless, some animal groups have remained under-sampled. ...
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Open AccessThe influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy
The rapid expansion of multicellular native and alien species outbreaks in aquatic and terrestrial ecosystems (bioinvasions) may produce significant impacts on bacterial community dynamics and nutrient pathways w...
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Open AccessBioinformatics in Italy: BITS2012, the ninth annual meeting of the Italian Society of Bioinformatics
The BITS2012 meeting, held in Catania on May 2-4, 2012, brought together almost 100 Italian researchers working in the field of Bioinformatics, as well as students in the same or related disciplines. About 90 ...
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Article
Open AccessAssessment of orthologous splicing isoforms in human and mouse orthologous genes
Recent discoveries have highlighted the fact that alternative splicing and alternative transcripts are the rule, rather than the exception, in metazoan genes. Since multiple transcript and protein variants exp...
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Article
Open AccessThe mitochondrial genome of Phallusia mammillata and Phallusia fumigata (Tunicata, Ascidiacea): high genome plasticity at intra-genus level
Within Chordata, the subphyla Vertebrata and Cephalochordata (lancelets) are characterized by a remarkable stability of the mitochondrial (mt) genome, with constancy of gene content and almost invariant gene o...
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Open AccessPhylogenetic analyses of complete mitochondrial genome sequences suggest a basal divergence of the enigmatic rodent Anomalurus
Phylogenetic relationships between Lagomorpha, Rodentia and Primates and their allies (Euarchontoglires) have long been debated. While it is now generally agreed that Rodentia constitutes a monophyletic sister...
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Article
Open AccessHuntingtin gene evolution in Chordata and its peculiar features in the ascidian Ciona genus
To gain insight into the evolutionary features of the huntingtin (htt) gene in Chordata, we have sequenced and characterized the full-length htt mRNA in the ascidian Ciona intestinalis, a basal chordate emerging ...
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Article
Complete mtDNA of Ciona intestinalis Reveals Extensive Gene Rearrangement and the Presence of an atp8 and an Extra trnM Gene in Ascidians
The complete mitochondrial genome (mtDNA) of the model organism Ciona intestinalis (Urochordata, Ascidiacea) has been amplified by long-PCR using specific primers designed on putative mitochondrial transcripts id...
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Article
Untranslated regions of mRNAs
Gene expression is finely regulated at the post-transcriptional level. Features of the untranslated regions of mRNAs that control their translation, degradation and localization include stem-loop structures, u...
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Article
Nucleotide Substitution Rate of Mammalian Mitochondrial Genomes
We present here for the first time a comprehensive study based on the analysis of closely related organisms to provide an accurate determination of the nucleotide substitution rate in mammalian mitochondrial ...
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Article
Evolution of thenad3-rps12 gene cluster in angiosperm mitochondria: Comparison of edited and unedited sequences
We have analyzed thenad3-rps12 locus for eight angiosperms in order to compare the utility of mitochondrial DNA and edited mRNA sequences in phylogenetic reconstruction. The two coding regions, containing from 25...
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Article
Evolution of the nad3-rps12 Gene Cluster in Angiosperm Mitochondria: Comparison of Edited and Unedited Sequences
We have analyzed the nad3-rps12 locus for eight angiosperms in order to compare the utility of mitochondrial DNA and edited mRNA sequences in phylogenetic reconstruction. The two coding regions, containing from ...
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Article
The guinea-pig is not a rodent
IN 1991 Graur et al. raised the question of whether the guinea-pig, Cavia porcellus, is a rodent1. They suggested that the guinea-pig and myomorph rodents diverged before the separation between myomorph rodents a...
