Daniel García Souto

University of Vigo | UVIGO · Department of Biochemistry, Genetics and Immunology

L1 retrotransposition is a significant source of genomic variation in human epithelial tumours, which can contribute to tumorigenesis. However, fundamental questions about the causes and consequences of L1 activity in cancer genomes remain unresolved, primarily due to the limitations of short-read sequencing technologies. Here, we employ multiplatf...

The dynamics of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) transmission are influenced by a variety of factors, including social restrictions and the emergence of distinct variants. In this study, we delve into the origins and dissemination of the Alpha, Delta, and Omicron‐BA.1 variants of concern in Galicia, northwest Spain. For...

Poster presented at the 48th FEBS congress (Federation of European Biochemical Societies) in Milan (Italy) and at the 23th Young Scientist Forum in Pavia (Italy) in 2024 thanks to a FEBS travel grant awarded to Alicia L Bruzos.

Cancer is a multifaceted genetic disease characterized by the acquisition of several essential hallmarks. Notably, certain cancers exhibit horizontal transmissibility, observed across mammalian species and diverse bivalves, the latter referred to as hemic neoplasia. Within this complex landscape, epigenetic mechanisms such as histone modifications...

Research on bivalves is fast-growing, including genome-wide analyses and genome sequencing. Several characteristics qualify oysters as a valuable model to explore repetitive DNA sequences and their genome organization. Here we characterize the satellitomes of five species in the family Ostreidae (Crassostrea angulata, C. virginica, C. hongkongensis...

The Atlantic dog whelk, Nucella lapillus, is a marine snail that exhibits divergent evolution in response to habitat adaptation, resulting in distinct populations at the phenotypic, genotypic, and karyotypic levels. In this study, we utilized short- and long-read NGS data to perform a de novo assembly of the entire mitochondrial genome of N. lapill...

The Atlantic Whelk, Nucella lapillus, is a marine snail that exhibits divergent evolution in response to habitat adaptation, resulting in distinct populations at the phenotypic, genotypic, and karyotypic levels. In this study, we utilized short-and long-read NGS data to perform a de novo assembly of the entire mitochondrial genome of N. lapillus an...

The dynamics of SARS-CoV-2 transmission are influenced by a variety of factors, including social restrictions and the emergence of distinct variants. In this study, we delve into the origins and dissemination of the Alpha, Delta, and Omicron variants of concern in Galicia, northwest Spain. For this, we leveraged genomic data collected by the EPICOV...

Rising occurrence of extreme warming events are profoundly impacting ecosystems, altering their functioning and services with significant socio-economic consequences. Particularly susceptible to heatwaves are intertidal shellfish beds, located in estuarine areas already stressed by factors such as rainfall events, red tides, eutrophication, and pol...

In this study, we investigated the integration of Human Herpesvirus 8 (HHV-8) into the human genome using the primary effusion lymphoma (PEL) cell line BC-3. Through next-generation sequencing (NGS) data from multiple independent sequencing runs, we identified two highly supported HHV-8 integrants. These integrants encompassed a region of human chr...

Transmissible cancers are malignant cell lineages that spread clonally between individuals. Several such cancers, termed bivalve transmissible neoplasia (BTN), induce leukemia-like disease in marine bivalves. This is the case of BTN lineages affecting the common cockle, Cerastoderma edule, which inhabits the Atlantic coasts of Europe and northwest...

Cover featuring transmissible leukemia-like cancer in the marine species Cerastoderma edule and Mya arenaria is characterized by long-term tolerance as well as genomic instability. See Bruzos et al. and Hart et al. and the accompanying News & Views article by Schönbichler & Bergthaler. Link: https://www.nature.com/natcancer/volumes/4/issues/11

The plastic ability for a range of phenotypes to be exhibited by the same genotype allows organisms to respond to environmental variation and may modulate fitness in novel environments. Differing capacities for phenotypic plasticity within a population, apparent as genotype by environment interactions (GxE), can therefore have both ecological and e...

There are sex differences in microglia, which can maintain sex‐related gene expression and functional differences in the absence of circulating sex steroids. The angiotensin type 2 (AT2) receptors mediate anti‐inflammatory actions in different tissues, including brain. In mice, we performed RT‐PCR analysis of microglia isolated from adult brains an...

Transmissible cancers are malignant cell clones that spread among individuals through transfer of living cancer cells. Several such cancers, collectively known as bivalve transmissible neoplasia (BTN), are known to infect and cause leukaemia in marine bivalve molluscs. This is the case of BTN clones affecting the common cockle, Cerastoderma edule ,...

In a recent contribution in this journal [1], the subspecies Lumbricus rubellus friendoides Bouché, 1972 [2], was raised to species rank, and a new name was proposed for this species, Lumbricus heracleus Briones et al., 2022. The authors want to clarify here that the valid name of this species, following the rules of Zoological Nomenclature (Articl...

Clonally transmissible cancers are tumour lineages that are transmitted between individuals via the transfer of living cancer cells. In marine bivalves, leukaemia-like transmissible cancers, called hemic neoplasia (HN), have demonstrated the ability to infect individuals from different species. We performed whole-genome sequencing in eight warty ve...

Lumbricus friendi is a lumbricid earthworm mainly found in western Europe, considerably less well studied than its close relative L. terrestris and until now, has not been a subject of taxonomical debate. However, its disjointed geographical distribution suggesting striking similarities to the Celtic fringes and of the so-called "Lusitanian" specie...

Most cancers are characterized by the somatic acquisition of genomic rearrangements during tumour evolution that eventually drive the oncogenesis. Here, using multiplatform sequencing technologies, we identify and characterize a remarkable mutational mechanism in human hepatocellular carcinoma caused by Hepatitis B virus, by which DNA molecules fro...

The coronavirus disease 2019 (COVID-19) pandemic has affected the world radically since 2020. Spain was one of the European countries with the highest incidence during the first wave. As a part of a consortium to monitor and study the evolution of the epidemic, we sequenced 2,170 samples, diagnosed mostly before lockdown measures. Here, we identifi...

Following its emergence in late 2019, the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)1,2 has been tracked via phylogenetic analysis of viral genome sequences in unprecedented detail3–5. While the virus spread globally in early 2020 before borders closed, intercontinental travel has since been greatly reduced. However, wit...

Several features already qualified the invasive bivalve species Crassostrea gigas as a valuable non-standard model organism in genome research. C. gigas is characterized by the low contribution of satellite DNAs (satDNAs) vs. mobile elements and has an extremely low amount of heterochromatin, predominantly built of DNA transposons. In this work, we...

Most cancers are characterized by the somatic acquisition 52 of genomic rearrangements during tumour evolution that eventually drive the oncogenesis. There are different mutational mechanisms causing structural variation, some of which are specific to particular cancer types. Here, using multiplatform sequencing technologies, we identify and charac...

Clonally transmissible cancers are tumour lineages that are transmitted between individuals via the transfer of living cancer cells. In marine bivalves, leukemia-like transmissible cancers, called hemic neoplasia, have demonstrated the ability to infect individuals from different species. We performed whole-genome sequencing in eight warty venus cl...

Epigenetic modifications such as DNA methylation have been shown to participate in plastic responses to environmental change in a wide range of organisms, including scleractinian corals. Unfortunately, the current understanding of the links between environmental signals, epigenetic modifications, and the subsequent consequences for acclimatory phen...

Segments of the genome enriched in repetitive sequences still present a challenge and are omitted in genome assemblies. For that reason, the exact composition of DNA sequences underlying the heterochromatic regions and the active centromeres are still unexplored for many organisms. The centromere is a crucial region of eukaryotic chromosomes respon...

About half of all cancers have somatic integrations of retrotransposons. Here, to characterize their role in oncogenesis, we analyzed the patterns and mechanisms of somatic retrotransposition in 2,954 cancer genomes from 38 histological cancer subtypes within the framework of the Pan-Cancer Analysis of Whole Genomes (PCAWG) project. We identified 1...

About half of all cancers have somatic integrations of retrotransposons. Here, to characterize their role in oncogenesis, we analyzed the patterns and mechanisms of somatic retrotransposition in 2,954 cancer genomes from 38 histological cancer subtypes within the framework of the Pan-Cancer Analysis of Whole Genomes (PCAWG) project. We identified 1...

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...

Cockles, Cerastoderma edule frequently suffer high prevalence of disseminated neoplasia throughout its geographical distribution. However, a natural population with gonadal neoplasia has never been detected before. Germinoma prevalences of 15.4% were found in Denmark populations using histopathological techniques. This germinoma affects only male c...

The recent discovery of clonally transmissible cancers, somatic cell lineages capable of infecting other individuals through the physical transfer of living cells, means having a great model to study cancer metastasis. Disseminated neoplasia, a leukaemia-like cancer is found in multiple bivalve species around the world, including cockles and by ana...

Periwinkles of the family Littorinidae (Children, 1834) are common members of seashore littoral communities worldwide. Although the family is composed of more than 200 species belonging to 18 genera, chromosome numbers have been described in only eleven of them. A molecular cytogenetic analysis of nine periwinkle species, the rough periwinkles Litt...

DNA methylation is the best studied epigenetic marker, being essential in regulating gene expression and gene silencing in the eukaryotic genome. Different cell types have specific and pre-established DNA methylation profiles according to their organic function. Alterations in this profile may lead to cell malfunction, illness and, ultimately, tumo...

Clonally transmissible cancers are somatic cell lineages transmitted between individuals via the transfer of living cancer cells. There are only three known types of naturally occurring clonally transmissible cancers, one of which is a leukaemia-like cancer found in cockles, called disseminated neoplasia (DN). Using DN as a model to identify the ge...

Cockle Cerastoderma edule is a species of great commercial interest in Galicia, lt is one of the bivalve species with more annual catches and, therefore, has a high economic and ecological importance in this region. Pathological studies associated with cockle mortality events in Galicia detected high prevalence of a pathological condition known as...

Due to its extraordinary longevity and wide distribution, the ocean quahog Arctica islandica has become an important species model in both aging and environmental change research. Notwithstanding that, most genetic studies on ocean quahogs have been focused on fishery related, phylogeographic and phylogenetic aspects but nothing is known about thei...

Wedge shells belonging to the Donacidae family are the dominant bivalves in exposed beaches in almost all areas of the world. Typically, two or more sympatric species of wedge shells differentially occupy intertidal, sublittoral, and offshore coastal waters in any given locality. A molecular cytogenetic analysis of two sympatric and closely related...

Background Although Tellinidae is one of the largest and most diverse families of bivalves, its taxonomy is utterly chaotic. This is mainly due to the morphological diversity and homoplasy displayed by their shells and to the scarcity of the molecular phylogenetic studies performed on them. A molecular cytogenetic analysis of four tellin shell spec...

Tandemly repeated DNAs usually constitute significant portions of eukaryotic genomes. In bivalves, however, repetitive DNAs are habitually not widespread. In our search for abundant repetitive DNAs in trough shells, we discovered a novel satellite DNA, SSUsat, which constitutes at least 1.3% of the genome of Spisula subtruncata. As foreseen by the...

Transmissible cancers are somatic cell lineages that spread between individuals via the physical transfer of living cancer cells, becoming able to survive in time through multiple generations due to an unlimited proliferation among host population. To our knowledge, only eight transmissible cancers have been reported in nature. The oldest one of...

La accesibilidad a las técnicas de secuenciación masiva (NGS), hasta hace poco restringidas a estudios de biomedicina, están revolucionando los estudios genéticos. En este estudio se presentan datos preliminares del tamaño del genoma del berberecho Cerastoderma edule, punto de partida para la obtención del genoma de referencia de esta especie. La s...

La accesibilidad a las técnicas de secuenciación masiva (NGS), hasta hace poco restringidas a estudios de biomedicina, están revolucionando los estudios genéticos. En este estudio se presentan datos preliminares del tamaño del genoma del berberecho Cerastoderma edule, punto de partida para la obtención del genoma de referencia de esta especie. La s...

The common octopus, Octopus vulgaris, is a good candidate for aquaculture but a sustainable production is still unviable due to an almost total mortality during the paralarvae stage. DNA methylation regulates gene expression in the eukaryotic genome, and has been shown to exhibit plasticity throughout O. vulgaris life cycle, changing profiles from...

The striped venus clams Chamelea gallina and C. striatula are commercially important bivalves inhabiting European and North African coastal waters. The taxonomic status of these taxa has been the subject of debate for decades. In order to elucidate this issue, we generated 5S and 28S ribosomal RNA and H3 histone gene probes and mapped them by fluor...

Massive algal proliferations known as Harmful Algal Blooms (HABs) represent one of the most important threats to coastal areas. Among them, the so-called Florida Red Tides (FRTs, caused by blooms of the dinoflagellate Karenia brevis and associated brevetoxins) are particularly detrimental in the southeastern U.S., causing high mortality rates and a...

PCR conditions used in the amplification of COI, 16S rRNA gene, ITS2, histone H3 and 5S and 28S rRNA genes.

The family Mactridae is composed of a diverse group of marine organisms, commonly known as trough shells or surf clams, which illustrate a global distribution. Although this family includes some of the most fished and cultured bivalve species, their chromosomes are poorly studied. In this work, we analyzed the chromosomes of Spisula solida, Spisula...

The European hake (Merluccius merluccius) is a highly valuable and intensely fished species in which a long-term alive stock has been established in captivity for aquaculture purposes. Due to their huge economic importance, genetic studies on hakes were mostly focused on phylogenetic and phylogeographic aspects; however chromosome numbers are still...

Digenetic trematodes are the largest group of internal metazoan parasites, but their chromosomes are poorly studied. Although chromosome numbers and/or karyotypes are known for about 300 of the 18,000 described species, molecular cytogenetic knowledge is mostly limited to the mapping of telomeric sequences and/or of major rDNA clusters in 9 species...

Histone H3 gene clusters have been described as highly conserved chromosomal markers in invertebrates. Surprisingly, in bivalves remarkable interspecific differences were found among the eight mussels and between the two clams in which histone H3 gene clusters have already been located. Although the family Veneridae comprises 10 % of the species of...

Zoledronic acid effectively reduces skeletal events in patients with metastatic disease. The results of pre-clinical and emerging clinical data suggest an additional activity of zoledronic acid as an antitumor agent, interfering with the growth and dissemination of malignant cells. However, the mechanisms by which zoledronic acid impairs tumor prog...