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Evolutionary features of the mitochondrial genome of Ascidiacea (Chordata, Tunicata) at short and long phylogenetic distances
No full textEvolutionary studies of the mitochondrial genome (mtDNA) have been widely used to
solve phylogenetic controversies and to analyse the mechanisms of whole genome evolution.
Indeed, the availability of several complete mtDNAs have provided, in addition to sequences
of single genes, several whole-genome characters useful to solve phylogenetic questions.
Moreover, the strong correlation between mitochondrial structural features and functional
processes like the replication and transcription of mtDNA increases the importance to deeply
investigate the mitochondrial genomic features. At present, the sequence sample of complete
mtDNAs is biased toward vertebrates, and the sampling within deuterostome groups, such as
hemichordates and tunicates is very poor. The mtDNA of tunicates, traditionally considered
the basal group of chordates, shows several differences from the mtDNAs of remaining
chordates and deuterostomes. Indeed, the tunicate mtDNA presents a different genetic code
compared to that of all other deuterostomes, and encodes for two additional tRNA genes,
trnG(AGR) and trnM(TAT). The trnG(AGR) gene is needed because of the different genetic
code and the second trnM gene is due to the usage of different tRNA-Met as initiator and
elongator. The most interesting feature of tunicate mtDNA is the high gene order variability
compared to remainimg deuterostomes. This extensive gene rearrangement has been found
even at intra genus level (Iannelli et al. 2007a; Iannelli et al. 2007b). However, the mtDNA
has been completely sequenced only in seven tunicate species: six ascidian species (two
Phallusia species and three Ciona species belonging to Phlebobranchiata order; and
Halocynthia roretzi belonging to Stolidobranchiata order) and the Thaliacea Doliolum
nationalis.
In order to deeper analyse the structural features and the evolution of tunicate mtDNA,
in this PhD project, we have sequenced the whole mtDNA of four ascidian species: the
Aplousobranchiata species Clavelina lepadiformis, Clavelina phlegraea (Polycitoridae
family), and Diplosoma listerianum (Didemnidae family); and the Phlebobranchiata species
Ascidiella aspersa (Ascidiidae family). The two Clavelina species and D. listerianum have
been selected in order to have the representatives of the unsampled Aplousobranchiata order
even at intra-genus level. The mtDNA of A. aspersa has been sequenced in order to verify if
the high number of gene rearrangements and the high GC content previously observed in
Phallusia species, belonging to the same family Ascidiidae, are typical features of all
Ascidiidae species. Thus, we have carried out comparative analyses of several mt features. also including the mtDNA of other ascidian species recently sequenced in our laboratory, and
the mtDNA of other deuterostome species available in the public databases.
All tunicate mtDNAs encode for the canonical mt genes but show a variable number
of tRNA genes. This is in accordance with the situation observed in remaining deuterostomes,
where only in few cases there is a variation of the protein gene number while changes of the
tRNA gene number is more frequent. Only the mtDNA of A. aspersa shows an additional
unassignable ORF of uncertain function.
Tunicate mtDNAs show a great variability of gene order, indeed no conserved gene
blocks are shared by all tunicates or by all ascidians. Gene rearrangements at intra-genus level
have been observed in all analyzed congeneric pairs but the extent of gene rearrangements
within the same genus seems to be less pronounced in the Aplousobranchiata order (the two
Clavelina species show the same gene order except for the position of one tRNA gene) than in
the other ascidian orders, although this observation could be the consequence of a still poor
taxon sampling.
The base composition is variable within tunicates and the GC content appears to
follow a taxon-specific trend: the GC content is low in Aplousobranchiata, variable in
Phlebobranchiata, and intermediate in Stolidobranchiata. As regard compositional asymmetry,
that is the distribution of complementary bases between the two strands, the different ascidian
mtDNAs show different behaviours: the AT- and GC-skews, parameters measuring the
compositional asymmetry, are close to zero in most species, thus indicating an almost
symmetric composition. However, in some ascidians the AT- and GC-skews show opposite
signs compared to vertebrates and several cephalochordates. In vertebrates, the compositional
asymmetry is related to the asymmetric mtDNA replication mechanism. Thus, the absence or
the opposite orientation of the compositional asymmetry in tunicates compared to vertebrates
can suggest a different replication mechanism that does not affect the base distribution
between the two strands. This hypothesis is also supported by the absence, in tunicates, of a
major non-coding region with size and features similar to the control region of vertebrates,
which is known to be involved in mtDNA replication and transcription.
All analysed mt features indicate strong differences between the mtDNA evolutionary
dynamics of tunicates and those of remaining deuterostomes but at present we can not
hypothesize which mechanisms are responsible of the fast mt evolutionary dynamics of
tunicates
Evolutionary mitogenomics of Chordata: the strange case of ascidians and vertebrates
No full textThe availability of almost one thousand complete mitochondrial genome (mtDNA) sequences of chordates provides an almost unique opportunity to analyse the evolution of this genome in the phylum Chordata, and to identify possible divergent evolutionary trends followed by the three chordate subphyla: Vertebrata, Cephalochordata and Tunicata.Here, we review some genome-level features of mtDNA, such as genetic code, gene content, genome architecture and gene strand asymmetry, mostly focusing on differences existing between tunicates and remaining chordates. Indeed, tunicate mtDNAs show a surprisingly high variability in several genome-level features, even though the current tunicate taxon sampling is absolutely insufficient and is focused mainly on the class Ascidiacea. On the contrary, a stabilization of the mtDNA structural and evolutionary features is observed in both cephalochordates and vertebrates, where genome-level features are almost invariant. Thus, different evolutionary dynamics, probably related to divergent functional constraints, have modelled the overall mtDNA structure and organization of the three chordate subphyla
Mitogenomics reveals a remarkably high intra-species substitution rate in the ascidian Botryllus schlosseri
No full textThe leitmotiv of mitochondrial genome (mtDNA) evolution in ascidians is the
hypervariability of many genomic features (such as gene order, nucleotide substitution
rate and tRNA gene content) even at short phylogenetic distances. As consequence, the
ascidian mtDNA has been proved to unambiguously discriminate between two cryptic
species of Ciona intestinalis. Here, we describe the mtDNA of a model species, the
colonial ascidian Botryllus schlosseri. Two specimens, one from California and one
from Italy, have been sequenced. We found that the mtDNA of B. schlosseri has a novel
gene order, completely different from other ascidians, and encodes for peculiar tRNAlike
structures. Surprisingly, the sequence divergence between the two specimens is up
to one order of magnitude higher (depending on the functional mt region) than the one
measured in other ascidian intra-species comparisons. However, this value is lower than
the one measured within genera, and between the two cryptic C. intestinalis species.
Thus, based on mtDNA, the Californian and Italian B. schlosseri specimens appear to
belong to a single species that is characterized by a remarkably high nucleotide
substitution rate
The fast evolutionary dynamics of ascidian mitochondrial genome: an exception to the general deuterostome evolutionary trend
No full text
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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