Mitochondrial genomic landscape: A portrait of the mitochondrial genome 40 years after the first complete sequence

open3noNotwithstanding the initial claims of general conservation, mitochondrial genomes are a largely heterogeneous set of organellar chromosomes which displays a bewildering diversity in terms of structure, architecture, gene content, and functionality. The mitochondrial genome is typically described as a single chromosome, yet many examples of multipartite genomes have been found (for example, among sponges and diplonemeans); the mitochondrial genome is typically depicted as circular, yet many linear genomes are known (for example, among jellyfish, alveolates, and apicomplexans); the chromosome is normally said to be “small”, yet there is a huge variation between the smallest and the largest known genomes (found, for example, in ctenophores and vascular plants, respectively); even the gene content is highly unconserved, ranging from the 13 oxidative phosphorylation-related enzymatic subunits encoded by animal mitochondria to the wider set of mitochondrial genes found in jakobids. In the present paper, we compile and describe a large database of 27,873 mitochondrial genomes currently available in GenBank, encompassing the whole eukaryotic domain. We discuss the major features of mitochondrial molecular diversity, with special reference to nucleotide composition and compositional biases; moreover, the database is made publicly available for future analyses on the MoZoo Lab GitHub page.openFormaggioni A.; Luchetti A.; Plazzi F.Formaggioni A.; Luchetti A.; Plazzi F

Riding the wave: the SINE-specific V highly conserved domain spread into mammalian genomes exploiting the replication burst of MER6 DNA transposon.

Transposable elements are widely distributed within genomes where they may significantly impact their evolution and cell functions. Short interspersed elements (SINEs) are non-autonomous, fast-evolving elements, but some of them carry a highly conserved domain (HCD), whose sequence remained substantially unchanged throughout the metazoan evolution. SINEs carrying the HCD called V are absent in amniote genomes, but V-like sequences were found within the miniature inverted-repeat transposable element (MITE) MER6 in Homo sapiens. In the present work, the genomic distribution and evolution of MER6 are investigated, in order to reconstruct the origin of human V domain and to envisage its possible functional role. The analysis of 85 tetrapod genomes revealed that MER6 and its variant MER6A are found in primates, while only the MER6A variant was found in bats and eulipotyphlans. These MITEs appeared no longer active, in line with literature data on mammalian DNA transposons. Moreover, they appeared to have originated from a Mariner element found in turtles and from a V-SINE from bony fishes. MER6 insertions were found within genes and conserved in mRNAs: in line with previous hypothesis on functional role of HCDs, the MER6 V domain may be important for cell function also in mammals

The complete mitogenome of the European mantis, Mantis religiosa, from Italy: implications for the origin of North American mantis population

3openInternationalItalian coauthor/editorThe European mantis, Mantis religiosa L. (Mantodea Mantidae), is distributed all over Southern Europe, Africa and Asia, and has been reported as alien species in North America. Here we present the mitogenome sequence of an Italian individual and compare it with previously sequenced Chinese and Canadian samples. The assembled mitogenome has a length of 15,530 nucleotides and includes 13 protein coding genes, two ribosomal RNA genes, 23 tRNA genes (including the additional Arginine tRNA already observed in other M. religiosa mitogenomes), and the control region. Based on the inferred phylogenetic relationships, the Canadian sample is more closely related to the Italian than to the Chinese one, in line with the putative European origin of the North American invasive population. Time-calibrated phylogeny dated the divergence among extant European Mantis lineages at 2.33 million years ago, consistent with the first appearance of M. religiosa fossils. Our results support a European origin of the North American M. religiosa population and suggest that selective processes acting on mitogenome may have contributed to its adaptation in the new area.openLuchetti, A; Ometto, L; Rota Stabelli, O.Luchetti, A.; Ometto, L.; Rota Stabelli, O

Adjacent sequences disclose potential for intra-genomic dispersal of satellite DNA repeats and suggest a complex network with transposable elements

Satellite DNA (satDNA) sequences are typically arranged as arrays of tandemly repeated monomers. Due to the similarity among monomers, their organizational pattern and abundance, satDNAs are hardly accessible to structural and functional studies and still represent the most obscure genome component. Although many satDNA arrays of diverse length and even single monomers exist in the genome, surprisingly little is known about transition from satDNAs to other sequences. Studying satDNA monomers at junctions and identifying DNA sequences adjacent to them can help to understand the processes that (re)distribute satDNAs and significance that evolution of these sequence elements might have in creating the genomic landscape. We explored sets of randomly selected satDNA-harboring genomic fragments in four mollusc species to examine satDNA transition sites, and the nature of adjacent sequences. All examined junctions are characterized by abrupt transitions from satDNAs to other sequences. Among them, junctions of only one examined satDNA mapped non-randomly (within the palindrome), indicating that well-defined sequence feature is not a necessary prerequisite in the junction formation. In the studied sample, satDNA flanking sequences can be roughly classified into two groups. The first group is composed of anonymous DNA sequences which occasionally include short segments of transposable elements (TEs) as well as segments of other satDNA sequences. In the second group, satDNA repeats and the array flanking sequences are identified as parts of TEs of the Helitron superfamily. There, some array flanking regions hold fragmented satDNA monomers alternating with anonymous sequences of comparable length as missing monomer parts, suggesting a process of sequence reorganization by a mechanism able to excise short monomer parts and replace them with unrelated sequences. The observed architecture of satDNA transition sites can be explained as a result of insertion and/or recombination events involving short arrays of satDNA monomers and TEs, in combination with hypothetical transposition-related ability of satDNA monomers to be shuffled independently in the genome. We conclude that satDNAs and TEs can form a complex network of sequences which essentially share the propagation mechanisms and in synergy shape the genome

The Gene Targeting Approach of Small Fragment Homologous Replacement (SFHR) Alters the Expression Patterns of DNA Repair and Cell Cycle Control Genes

Cellular responses and molecular mechanisms activated by exogenous DNA that invades cells are only partially understood. This limits the practical use of gene targeting strategies. Small fragment homologous replacement (SFHR) uses a small exogenous wild-type DNA fragment to restore the endogenous wild-type sequence; unfortunately, this mechanism has a low frequency of correction. In this study, we used a mouse embryonic fibroblast cell line with a stably integrated mutated gene for enhanced green fluorescence protein. The restoration of a wild-type sequence can be detected by flow cytometry analysis. We quantitatively analyzed the expression of 84 DNA repair genes and 84 cell cycle control genes. Peculiar temporal gene expression patterns were observed for both pathways. Different DNA repair pathways, not only homologous recombination, as well as the three main cell cycle checkpoints appeared to mediate the cellular response. Eighteen genes were selected as highly significant target/effectors of SFHR. We identified a wide interconnection between SFHR, DNA repair, and cell cycle control. Our results increase the knowledge of the molecular mechanisms involved in cell invasion by exogenous DNA and SFHR. Specific molecular targets of both the cell cycle and DNA repair machineries were selected for manipulation to enhance the practical application of SFHR

Terminal-repeat retrotransposons in miniature (TRIMs) in bivalves

Terminal repeat retrotransposons in miniature (TRIMs) are small non-autonomous LTR retrotransposons consisting of two terminal direct repeats surrounding a short internal domain. The detection and characterization of these elements has been mainly limited to plants. Here we present the first finding of a TRIM element in bivalves, and among the first known in the kingdom Animalia. Class Bivalvia has high ecological and commercial importance in marine ecosystems and aquaculture, and, in recent years, an increasing number of genomic studies has addressed to these organisms. We have identified biv-TRIM in several bivalve species: Donax trunculus, Ruditapes decussatus, R. philippinarum, Venerupis corrugata, Polititapes rhomboides, Venus verrucosa, Dosinia exoleta, Glycymeris glycymeris, Cerastoderma edule, Magallana gigas, Mytilus galloprovincialis. biv-TRIM has several characteristics typical for this group of elements, exhibiting different variations. In addition to canonically structured elements, solo-TDRs and tandem repeats were detected. The presence of this element in the genome of each species is <1%. The phylogenetic analysis showed a complex clustering pattern of biv-TRIM elements, and indicates the involvement of horizontal transfer in the spreading of this elementXunta de Galicia | Ref. ED431C 2016-037Xunta de Galicia | Ref. ED481B/2018/091Ministarstvo Znanosti, Obrazovanja i Sporta | Ref. 098-0982913-275

A surge of late-occurring meiotic double-strand breaks rescues synapsis abnormalities in spermatocytes of mice with hypomorphic expression of SPO11

Meiosis is the biological process that, after a cycle of DNA replication, halves the cellular chromosome complement, leading to the formation of haploid gametes. Haploidization is achieved via two successive rounds of chromosome segregation, meiosis I and II. In mammals, during prophase of meiosis I, homologous chromosomes align and synapse through a recombination-mediated mechanism initiated by the introduction of DNA double-strand breaks (DSBs) by the SPO11 protein. In male mice, if SPO11 expression and DSB number are reduced below heterozygosity levels, chromosome synapsis is delayed, chromosome tangles form at pachynema, and defective cells are eliminated by apoptosis at epithelial stage IV at a spermatogenesis-specific endpoint. Whether DSB levels produced in Spo11 +/− spermatocytes represent, or approximate, the threshold level required to guarantee successful homologous chromosome pairing is unknown. Using a mouse model that expresses Spo11 from a bacterial artificial chromosome, within a Spo11 −/− background, we demonstrate that when SPO11 expression is reduced and DSBs at zygonema are decreased (approximately 40 % below wild-type level), meiotic chromosome pairing is normal. Conversely, DMC1 foci number is increased at pachynema, suggesting that under these experimental conditions, DSBs are likely made with delayed kinetics at zygonema. In addition, we provide evidences that when zygotene-like cells receive enough DSBs before chromosome tangles develop, chromosome synapsis can be completed in most cells, preventing their apoptotic elimination

Colony Breeding Structure of the Invasive Termite Reticulitermes urbis

Dissertação de Mestrado em Lazer, Património e Desenvolvimento apresentada ao Departamento de Geografia da Faculdade de Letras da Universidade de Coimbra.O turismo é uma atividade em expansão por todo o mundo, que representa 9% do PIB mundial e é considerada o quarto líder de exportações, de acordo com a OMT (2015). No entanto, assiste-se a uma alteração de consumos, devido à alteração de necessidades, motivada por uma elevação de rendimentos, cultura e escolaridade da população, mas também por alteração políticas e socioeconómicas. Assim, o turista atual procura novos destinos, que se diferenciem pela inovação, criatividade e autenticidade, alcançadas através dos seus recursos endógenos e singularidades. Desta forma, o desafio dos destinos turísticos situa-se na sua capacidade para competir no mercado global, através da diferenciação da oferta. O turismo cultural é o segmento turístico que mais se destaca e tem evoluído, em oposição ao turismo de massas, sobretudo em meio urbano. Contudo, importa encontrar novas estratégias que posicionem as cidades no mercado competitivo mundial, das quais se destacam os eventos. Nos últimos anos, os seus impactos ambientais e socioculturais têm ganho importância, justificando o seu papel enquanto produtos turísticos diferenciadores e autênticos, capazes de atrair novos nichos turísticos. Numa sociedade cada vez mais tecnológica, estes acontecimentos desempenham também um papel social relevante na promoção de interações e convívio humano. No entanto, a sua popularidade justifica-se devido aos seus impactos económicos e turísticos, que estimulam a competitividade entre destinos para a sua concretização, uma vez que os eventos são fenómenos centrais na sociedade atual, alvo de atenção constante dos meios de comunicação social e de partilha nas redes sociais pelos seus participantes, promovendo a divulgação e promoção do destino turístico. Ultimamente, a Figueira da Foz tem vindo a consolidar o seu calendário com eventos de projeção nacional e internacional, contribuindo também para a divulgação da sua imagem enquanto destino turístico. Nesse sentido, esta investigação incide na análise da sua oferta e seus impactos, bem como procura encontrar estratégias para que o município se assuma como um destino de eventos, tendo por base um enquadramento teórico que assenta na evolução do mercado turístico e na consolidação dos eventos enquanto produto competitivo.Tourism is a developing activity all over the world, which represents 9% of world GDP and is the fourth product most exported, in order with UNWTO (2015). However, patterns of consumption are changing because of changes in needs, motivated by higher incomes, culture and education of population, as well as by political and socioeconomic factors. This way, the actual tourist searches new destinies, which are able to distinguish themselves through innovation, creativity and authenticity, provided by endogenous resources and uniqueness of places. Nowadays, the challenge of the destinations is, therefore, the competitive capacity in world market, offering different products. Cultural tourism is the most important and increasing tourist segment in opposition of mass tourism, especially in urban environments. However, it is important for cities to find new strategies that could position them in the competitive world market, of which, events are the most appealing. Over the last years, their environmental and socioeconomic impacts are earning significance, justifying their role as authentic and different tourism products, capable of attracting new tourist niches. In a society increasingly technological, this happenings also have an important social role because they promote social interactions and sharing between people. However, their popularity is justified mainly because of their economic and tourism impacts, which increases the competitiveness of destinations for the organization of events, because they are central in the actual society, object of media attention and sharing in social networks, promoting and enhancing the tourism destination image. Lately, Figueira da Foz has had many demand for events with national and international projection, which also contributes for the promotion of its image as a tourism destination. This way, this investigation analyses its offer and impacts, as well as looks for new strategies capable of turning the municipality into a real event destination, while studies the evolution of tourism market and consolidation of events as a competitive tourism product

Terminal-Repeat Retrotransposons in Miniature (TRIMs) in bivalves

Terminal repeat retrotransposons in miniature (TRIMs) are small non-autonomous LTR retrotransposons consisting of two terminal direct repeats surrounding a short internal domain. The detection and characterization of these elements has been mainly limited to plants. Here we present the first finding of a TRIM element in bivalves, and among the first known in the kingdom Animalia. Class Bivalvia has high ecological and commercial importance in marine ecosystems and aquaculture, and, in recent years, an increasing number of genomic studies has addressed to these organisms. We have identified biv-TRIM in several bivalve species: Donax trunculus, Ruditapes decussatus, R. philippinarum, Venerupis corrugata, Polititapes rhomboides, Venus verrucosa, Dosinia exoleta, Glycymeris glycymeris, Cerastoderma edule, Magallana gigas, Mytilus galloprovincialis. biv-TRIM has several characteristics typical for this group of elements, exhibiting different variations. In addition to canonically structured elements, solo-TDRs and tandem repeats were detected. The presence of this element in the genome of each species is <1%. The phylogenetic analysis showed a complex clustering pattern of biv-TRIM elements, and indicates the involvement of horizontal transfer in the spreading of this element