86,749 research outputs found
BONE STRENGTH OF DIFFERENT PIGS GENETIC TYPES
No full textThe aim of this study was to evaluate the bone strength in different genetic types of pigs.
Nowadays, in swine production it is rather common to obtain pigs with weak bones,
especially on the hind legs. This weakness causes fractures, which are correlated with
losses in carcass weight, hence economical aspects are involved as well, and regard to
significant animal welfare issues, too. Because of this, it was interesting to investigate what
are the causes of weakness in pig bones of the most important genetic types used in the
North European pig breeding, such as Duroc, Hampshire, Finnish Landrace and Norwegian Landrace. Bone and joint defects have been linked to high growth rate (different content in collagen), mainly of pigs. The responses of the mechanical properties
are also strongly related to feeding. Genetic factors are another probable cause of weakness and the fracture of bones, both linked to osteochondrosis, which is rather common in pigs.
In this study the bone strength and other geometrical and mechanical parameters, such as the bone mineral content (BMC), the bone mineral density (BMD), the thickness of the
ring bone, the cross sectional area and the compression force of the ring bone as well were evaluated. These mechanical parameters were evaluated in bone‟ rings, which were obtained from the middle shaft of each femur bone of pigs
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
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
The mitochondrial genome of <it>Phallusia mammillata </it>and <it>Phallusia fumigata </it>(Tunicata, Ascidiacea): high genome plasticity at intra-genus level
No full textAbstract Background 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 order, whereas the limited mitochondrial data on the subphylum Tunicata suggest frequent and extensive gene rearrangements, observed also within ascidians of the same genus. Results To confirm this evolutionary trend and to better understand the evolutionary dynamics of the mitochondrial genome in Tunicata Ascidiacea, we have sequenced and characterized the complete mt genome of two congeneric ascidian species, Phallusia mammillata and Phallusia fumigata (Phlebobranchiata, Ascidiidae). The two mtDNAs are surprisingly rearranged, both with respect to one another and relative to those of other tunicates and chordates, with gene rearrangements affecting both protein-coding and tRNA genes. The new data highlight the extraordinary variability of ascidian mt genome in base composition, tRNA secondary structure, tRNA gene content, and non-coding regions (number, size, sequence and location). Indeed, both Phallusia genomes lack the trnD gene, show loss/acquisition of DHU-arm in two tRNAs, and have a G+C content two-fold higher than other ascidians. Moreover, the mt genome of P. fumigata presents two identical copies of trnI, an extra tRNA gene with uncertain amino acid specificity, and four almost identical sequence regions. In addition, a truncated cytochrome b, lacking a C-terminal tail that commonly protrudes into the mt matrix, has been identified as a new mt feature probably shared by all tunicates. Conclusion The frequent occurrence of major gene order rearrangements in ascidians both at high taxonomic level and within the same genus makes this taxon an excellent model to study the mechanisms of gene rearrangement, and renders the mt genome an invaluable phylogenetic marker to investigate molecular biodiversity and speciation events in this largely unexplored group of basal chordates.</p
The mitochondrial genome of Phallusia mammillata and Phallusia fumigata (Tunicata, Ascidiacea): high genome plasticity at intra-genus level
No full textBackground: Within Chordata, the subphyla Vertebrata and Cephalochordata (Iancelets) are characterized by a remarkable stability of the mitochondrial (mt) genome, with constancy of gene content and almost invariant gene order, whereas the limited mitochondrial data on the subphylum Tunicata suggest frequent and extensive gene rearrangements, observed also within ascidians of the same genus. Results: To confirm this evolutionary trend and to better understand the evolutionary dynamics of the mitochondrial genome in Tunicata Ascidiacea, we have sequenced and characterized the complete mt genome of two congeneric ascidian species, Phallusia mammillata and Phallusia fumigata (Phlebobranchiata, Ascidiidae). The two mtDNAs are surprisingly rearranged, both with respect to one another and relative to those of other tunicates and chordates, with gene rearrangements affecting both protein-coding and tRNA genes. The new data highlight the extraordinary variability of ascidian mt genome in base composition, tRNA secondary structure, tRNA gene content, and non-coding regions (number, size, sequence and location). Indeed, both Phallusia genomes lack the trnD gene, show loss/acquisition of DHU-arm in two tRNAs, and have a G+C content two-fold higher than other ascidians. Moreover, the mt genome of P. fumigata presents two identical copies of trnI, an extra tRNA gene with uncertain amino acid specificity, and four almost identical sequence regions. In addition, a truncated cytochrome b, lacking a C-terminal tail that commonly protrudes into the mt matrix, has been identified as a new mt feature probably shared by all tunicates. Conclusion: The frequent occurrence of major gene order rearrangements in ascidians both at high taxonomic level and within the same genus makes this taxon an excellent model to study the mechanisms of gene rearrangement, and renders the mt genome an invaluable phylogenetic marker to investigate molecular biodiversity and speciation events in this largely unexplored group of basal chordates
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