Andrea Luchetti

University of Bologna | UNIBO · Department of Biological, Geological and Environmental Sciences BiGeA

Background Short interspersed nuclear elements (SINEs) are non-autonomous non-LTR retrotransposons widespread across eukaryotes. They exist both as lineage-specific, fast-evolving elements and as ubiquitous superfamilies characterized by highly conserved domains (HCD). Several of these superfamilies have been described in bivalves, however their ov...

The phylogeography and demographical history of Italian Formica pratensis populations were examined and compared with the Eurasian-wide dataset available for this species and the other red wood ant species Formica lugubris . Forty-eight workers belonging to eight populations from both Alps and Apennines were analysed sequencing a 1.5-kilobase mitoc...

The Canary Islands is a Macaronesian volcanic archipelago with a depauperate community of three species of Kalotermitidae, including Kalotermes dispar. A total of 54 Kalotermes colonies were collected from Gran Canaria, Tenerife, La Gomera, La Palma, and El Hierro islands. Soldiers and imagos were morphologically examined and sequenced for four mit...

After the loss of a trait, theory predicts that the molecular machinery underlying its phenotypic expression should decay. Yet, empirical evidence is contrasting. Here, we test the hypotheses that (1) the molecular ground plan of a lost trait could persist due to pleiotropic effects on other traits and (2) that gene co-expression network architectu...

Mastigusa is a genus of small palearctic spiders that has recently been moved to the family Cybaeidae after the first inclusion of the genus in a phylogenetic matrix. Three species are currently recognised: M. arietina, M. lucifuga and M. macrophthalma. The status and delimita-tion, though, has always been problematic due to inconsistency in the ch...

Reproduction is a key feature of all organisms, yet the way in which it is achieved varies greatly across the tree of life. One striking example of this variation is the stick insect genus Bacillus, in which five different reproductive modes have been described: sex, facultative and obligate parthenogenesis, and two highly unusual reproductive mode...

The subterranean termite Reticulitermes lucifugus (Rossi 1792) is distributed in Italy and southern France, both in natural and urban environments. It comprises three lineages: i) R. lucifugus lucifugus (Rossi 1792) in the mainland, ii) R. lucifugus corsicus Clement 1977 in Corsica, Provence, Sardinia and a portion of the Tyrrhenian coast of Italy,...

After the loss of a trait, theory predicts that the molecular machinery underlying its phenotypic expression should decay. Yet, empirical evidence is contrasting. Here, we test the hypotheses that (1) the molecular ground plan of a lost trait could persist due to pleiotropic effects on other traits and (2) that gene co-expression network architectu...

Bivalves are a diverse group of molluscs that have recently attained a central role in plenty of biological research fields, thanks to their peculiar life history traits. Here, we propose that bivalves should be considered as emerging model systems also in sex-determination (SD) studies, since they would allow to investigate: 1) the transition betw...

The presence of the spider genus Thyreosthenius Simon, 1884 (Linyphiidae) is for the first time confirmed in the Iberian Peninsula with an observation of the myrmecophile species T. biovatus (O. Pickard Cambridge, 1875). Four adult females and two sub-adult male specimens were collected inside mound nests belonging to the red wood ant species Formi...

Reproduction is a key feature of all organisms, yet the way in which it is achieved varies greatly across the tree of life. One striking example of this variation is the stick insect genus Bacillus, in which five different reproductive modes have been described: sex, facultative and obligate parthenogenesis, and two highly unusual reproductive mode...

Background Transposable elements (TEs) can represent one of the major sources of genomic variation across eukaryotes, providing novel raw materials for species diversification and innovation. While considerable effort has been made to study their evolutionary dynamics across multiple animal clades, molluscs represent a substantially understudied ph...

The palearctic spider genus Mastigusa Menge, 1854 is characterized by a remarkable morphology and wide ecological variability, with free-living, cave dwelling and myrmecophile populations known. This genus has a long and tangled taxonomic history and was placed in different families in the past, all belonging to the "marronoid clade" an informal gr...

The morphology of the Betancurian Dwarf Mantis Pseudoyersinia betancuriae Wiemers, 1993 is here presented with a redescription of both male and female, to better understand the taxonomy of this species within the tribe Amelini. The mating behaviour has been studied pairing different males and females in laboratory conditions, recording the occurren...

Hox and ParaHox genes (HPHGs) are key developmental genes that pattern regional identity along the anterior–posterior body axis of most animals. Here, we identified HPHGs in tadpole shrimps (Pancrustacea, Branchiopoda, Notostraca), an iconic example of the so-called “living fossils” and performed a comparative genomics analysis of HPHGs and the Hox...

The evolution of automixis - i.e., meiotic parthenogenesis - requires several features, including ploidy restoration after meiosis and maintenance of fertility. Characterizing the relative contribution of novel versus pre-existing genes and the similarities in their expression and sequence evolution is fundamental to understand the evolution of rep...

Termites (Insecta, Blattodea, Termitoidae) are a widespread and diverse group of eusocial insects known for their ability to digest wood matter. Herein, we report the draft genome of the subterranean termite Reticulitermes lucifugus, an economically important species and among the most studied taxa with respect to eusocial organisation and mating s...

The Phasmida genus Candovia comprises nine traditionally recognized species, all endemic to Australia. In this study, Candovia diversity is explored through molecular species-delimitation analyses using the COIFol gene fragment and phylogenetic inferences leveraging seven additional mitochondrial and nuclear loci. Molecular results were integrated...

Bivalve molluscs show a great variety of reproductive modes, ranging from strict gonochorism (i.e., species with separate male and female individuals) to simultaneous and sequential hermaphroditism. In addition, both genetic and environmental factors appear to determine sex in most bivalve species studied to date, albeit heteromorphic sex chromosom...

Ants belonging to the Formica rufa species group, counting 10 representatives in Europe, are often referred to as red wood ants (RWAs). These dominant, mound building species are known to host in their nests an extremely diverse fauna of associated myr- mecophilic arthropods, among which are the two W-Palaearctic spider species Mastigusa arietina (...

The salticid spider Habrocestum graecum Dalmas, 1920, until now only known from Greece, is for the first time recorded in Italy. Observations on ecology and behavior are also reported and pictures of its habitus and genitalia are provided. Furthermore, the first DNA barcode sequence for H. graecumis produced and made publicly available. The species...

The concept that complex ancestral traits can never be recovered after their loss is still widely accepted, despite phylogenetic and molecular approaches suggest instances where phenotypes may have been lost throughout the evolutionary history of a clade and subsequently reverted back in derived lineages. One of the first and most notable examples...

Here we provide the very first genomic characterization of HPHGs in the two tadpole shrimp (Branchiopoda, Notostraca) living genera, Triops and Lepidurus. Tadpole shrimps are pretty charismatic crustaceans for they show an outstanding morphological and ecological stasis and an ancient origin dating back to the Permian. Recent comparative genomics a...

The West-Palaearctic Colobopsis ant populations have long been considered a single species (Colobopsis truncata). We studied the diversity of this species by employing a multidisciplinary approach and combining data from our surveys, museum and private collections, and citizen science platforms. As a result, we have revealed the existence of a seco...

The class Branchiopoda, whose origin dates back to Cambrian, includes ~ 1200 species which mainly occupy freshwater habitats. The phylogeny and systematics of the class have been debated for long time, until recent phylogenomic analyses allowed to better clarify the relationships among major clades. Based on these data, the clade Anostraca (fairy a...

The myth of a “typical” mitochondrial genome (mtDNA) is a rock-hard belief in the field of genetics, at least for the animal kingdom [...]

This analysis presents five genome assemblies of four Notostraca taxa. Notostraca origin dates to the Permian/Upper Devonian and the extant forms show a striking morphological similarity to fossil taxa. The comparison of sequenced genomes with other Branchiopoda genomes shows that, despite the morphological stasis, Notostraca share a dynamic genome...

Inferring the selective forces that orthologous genes underwent across different lineages can help us understand the evolutionary processes that have shaped their extant diversity and the phenotypes they underlie. The most widespread metric to estimate the selection regimes of coding genes—across sites and phylogenies—is the ratio of nonsynonymous...

Notwithstanding 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 multipar...

Inferring the selective forces that different ortholog genes underwent across different lineages can make us understand the evolutionary processes which shaped their extant diversity. The more widespread metric to estimate coding sequences selection regimes across across their sites and species phylogeny is the ratio of nonsynonymous to synonymous...

A bstract The concept that complex ancestral traits can never be re-acquired after their loss has grown popular since its initial formulation and it’s often referred to as Dollo’s law. Nonetheless, several macroevolutionary evidences - along with molecular ones - suggest instances where complex phenotypes could have been lost throughout a clade evo...

Phasmatodea species diversity lies almost entirely within its suborder Euphasmatodea, which exhibits a pantropical distribution and is considered to derive from a recent and rapid evolutionary radiation. To shed light on Euphasmatodea origins and diversification, we assembled the mitogenomes of 17 species from transcriptomic sequencing data and ana...

The stick-insect genus Pijnackeria includes four diploid bisexual and two polyploid (3n, 4n) parthenogenetic species. Earlier analyses of the tetraploid parthenogen P. hispanica using mitochondrial markers allowed tracing its maternal ancestry to Pijnackeria originis, while no maternal nuclear contribution was found, thus suggesting an androgenetic...

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 firs...

Background The crustacean class Branchiopoda includes fairy shrimps, clam shrimps, tadpole shrimps, and water fleas. Branchiopods, which are well known for their great variety of reproductive strategies, date back to the Cambrian and extant taxa can be mainly found in freshwater habitats, also including ephemeral ponds. Mitochondrial genomes of the...

Stingless bees often associate with termites, while association with ants is uncommon due to the high costs related to the aggressiveness of ants. Few combative genera of stingless bees can associate with a larger number of hosts, including ants. Here, we describe for the first time the association between a stingless bee (Partamona testacea) and t...

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....

Thousands of eukaryotes transcriptomes have been generated, mainly to investigate nuclear genes expression, and the amount of available data is constantly increasing. A neglected but promising use of this large amount of data is to assemble organelle genomes. To assess the reliability of this approach, we attempted to reconstruct complete mitochond...

Although DNA transposons often generated internal deleted derivatives such as miniature inverted-repeat transposable elements (MITEs), short internally deleted elements (SIDEs) derived from non-long terminal repeat retrotransposons are rare. Here, we found a novel SIDE, named Persaeus, that originated from the chicken repeat 1 (CR1) retrotransposon...

Crustaceans of the order Notostraca (Branchiopoda) are distributed worldwide and are known for the remarkable morphological stasis between their extant and Permian fossil species. Moreover, these crustaceans show relevant ecological traits and a wide range of reproductive strategies. However, genomic studies on notostracans are fairly limited. Here...

Background: Transposable elements (TEs) are common and often present with high copy numbers in cellular genomes. Unlike in cellular organisms, TEs were previously thought to be either rare or absent in viruses. Almost all reported TEs display only one or two copies per viral genome. In addition, the discovery of pandoraviruses with genomes up to 2...

Biological invasions are among key factors of ecological changes, and social insects appear as highly successful invasive animals. Subterranean termites of the holarctic genus Reticulitermes are present in Europe with six native and one invasive (the nearctic R. flavipes) species. The species R. urbis shows a disjunct distribution in the Western Ba...

European dry-wood termites belong to the genus Kalotermes (Kalotermitidae), one of the two termite genera in Europe. Until the recent description of two new species, Kalotermes italicus in Italy and Kalotermes phoenicae in the eastern Mediterranean area, Kalotermes flavicollis was the only taxon known in this region. The presence of additional enti...

Short interspersed elements (SINEs) are non-autonomous retrotransposons. Although they usually show fast evolutionary rates, in some instances highly conserved domains (HCDs) have been observed in elements with otherwise divergent sequences and from distantly related species. Here we document the life history of two HCD-SINE families in the elephan...

Horizontal transfer (HT) is an event in which the genetic material is transferred from one species to another, even if distantly related, and it has been demonstrated as a possible essential part of the lifecycle of transposable elements (TEs). However, previous studies on the non-LTR R2 retrotransposon, a metazoan-wide distributed element, indicat...

Background 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...

Transposable elements (TEs) are self-replicating, mobile DNA sequences which constitute a significant fraction of eukaryotic genomes. They are generally considered selfish DNA, as their replication and random insertion may have deleterious effects on genome functionalities, although some beneficial effects and evolutionary potential have been recog...