Biology subjects

Manousaki, T.

Publications and source records attributed to Manousaki, T..

9 recordsLinked to original sources

bioRxiv2026

The epigenomic landscape of deep lineage divergence: The case of the European sea bass

BackgroundUnderstanding the role of non-coding genomic variation in speciation remains a major challenge in evolutionary biology. Here, we investigated whether regulatory elements contribute to this process between Atlantic and Mediterranean lineages of European sea bass (Dicentrarchus labrax), a well-characterized case-study near speciation where barriers to introgression exist in the presence of connectivity between diverging populations. ResultsWe generated a novel, highly contiguous genome assembly, which was annotated at the epigenomic level using ATAC-seq and ChIP-seq with six embryonic developmental stages and five tissue types in adult fish, identifying thousands of promoters, enhancers, and open chromatin regions. Integrating this annotation with whole-genome sequence data from 65 individuals across three geographically distinct populations, we identified 57,505 outlier SNPs and 332 structural variants (SVs) showing elevated differentiation between Atlantic and East Mediterranean lineages. Outlier SVs affected key regulatory elements and coding genes, while outlier SNPs were enriched in regulatory elements, particularly enhancers active in adult tissues. Local genomic divergence correlated positively with regulatory element density, especially on chromosomes 1, 9, and 18, which are enriched in genes related to osmoregulation, immune response, and oxidative stress -- processes relevant to adaptation across contrasting marine environments. ConclusionsThese findings support a major role for regulatory variation in driving deep lineage divergence through local adaptation.

evolutionary biology↗

bioRxiv2025

ERGA-BGE genome of Noah's Ark shell (Arca noae Linnaeus, 1758), a Mediterranean bivalve species

Arca noae, also known as the Noahs Ark clam, is a bivalve mollusk found in the shallow coastal waters of the Mediterranean Sea and the eastern Atlantic Ocean. This species plays a crucial ecological role by filtering plankton and organic particles from the water, helping maintain water quality and supporting nutrient cycling in marine ecosystems. It is also an important food source for various marine predators, including fish and crustaceans, thereby contributing to the coastal food web. Arca noae is notably resilient to environmental stressors, such as temperature fluctuations, changes in salinity, and pollution, making it a valuable model species for studying how bivalves adapt and respond to stress. While it is not commonly harvested commercially, Arca noae is of great interest to marine researchers due to its ability to thrive in diverse coastal habitats. The reference genome of Arca noae will thus provide important evolutionary insights. The entirety of the genome sequence was assembled into 19 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 1.5 Gb, composed of 257 contigs and 119 scaffolds, with contig and scaffold N50 values of 20.5 Mb and 84.7 Mb, respectively.

genomics↗

bioRxiv2025

ERGA-BGE genome of Pinctada radiata (Leach, 1814): one of the first Lessepsian migrants

Pinctada radiata, commonly known as the Gulf pearl oyster, is a species of pearl oyster found primarily in the warm waters of the Red Sea, the Persian Gulf, and parts of the Indian Ocean. Pinctada radiata contributes to marine ecosystems by filtering water, which helps maintain water quality and supports other marine life. This species is the first bivalve Lessepsian migrant, having migrated from the Red Sea to the Mediterranean Sea via the Suez Canal. The reference genome of Pinctada radiata could help identify genes enabling adaptation to varying temperatures and salinities, facilitating survival in diverse and newly colonized habitats allowing comparisons with other bivalves to uncover shared and unique genetic adaptations. Additionally, the genome could support targeted management practices and conservation initiatives, such as habitat restoration and selective breeding, ensuring the long-term sustainability of P. radiata. The entirety of the genome sequence was assembled into 14 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 0.93 Gb, composed of 220 contigs and 44 scaffolds, with contig and scaffold N50 values of 8.1 Mb and 63.8 Mb, respectively.

genomics↗

bioRxiv2023

Extensive Loss and Gain of Conserved Non-Coding Elements during Early Teleost Evolution

Conserved Non-coding Elements (CNE) in vertebrates are enriched around transcription factor loci associated with development. However, loss and rapid divergence of CNEs has been reported in teleost fish, albeit taking only few genomes into consideration. Taking advantage of the recent increase in high-quality teleost genomes, we focus on studying the evolution of teleost CNEs, carrying out targeted genomic alignments and comparisons within the teleost phylogeny to detect CNEs and reconstruct the ancestral teleost CNE repertoire. This teleost-centric approach confirms previous observations of extensive vertebrate CNE loss early in teleost evolution, but also reveals massive CNE gain in the teleost stem-group over 300 million years ago. Using synteny-based association to link CNEs to their putatively regulated target genes, we show the most teleost gained CNEs are found in the vicinity of orthologous loci involved in transcriptional regulation and embryonic development that are also associated with CNEs in other vertebrates. Moreover, teleost and vertebrate CNEs share a highly similar motif and transcription factor binding site vocabulary. We suggest that early teleost CNE gains reflect a restructuring of the ancestral CNE repertoire through both extreme divergence and de novo emergence. Finally, we support newly identified pan-teleost CNEs have potential for accurate resolution of teleost phylogenetic placements in par with coding sequences, unlike ancestral only elements shared with spotted gar. This work provides new insight into CNE evolution with great value for follow-up work on phylogenomics, comparative genomics and the study of gene regulation evolution in teleosts.

genomics↗

bioRxiv2023

Near-chromosome level genome assembly of devil firefish, Pterois miles

Devil firefish (Pterois miles), a member of Scorpaenidae family, is one of the most successful marine non-native species, dominating around the world, that was rapidly spread into the Mediterranean Sea, through the Suez Canal, originating from the Indian Ocean. Even though lionfishes (Scorpaenidae) are identified among the most prosperous marine invaders, within this taxonomic group, the genomic resources are scant, while reference genome assemblies are totally absent. Here, we built and analyzed the first reference genome assembly of P. miles and explored its evolutionary background. The resulting genome assembly consisted of 660 contigs and scaffolds (N50 = 14,5 Mb) with a total size of about 902 Mb, while delivering 98% BUSCO completeness. We identified and described the large amount of transposable elements present in the genome and based on genomic data we constructed the first teleost phylogeny which includes a member of genus Pterois. The high-quality and contiguity de novo genome assembly built herein provides a valuable resource for future studies in species biology and ecology, lionfish phylogeny, the influence of transposable elements on the evolution of vertebrate genomes and fish toxins evolution.

genomics↗

bioRxiv2022

Chromosome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution

The meagre, Argyrosomus regius, has recently become a species of increasing economic interest for the Mediterranean aquaculture and there is ongoing work to boost production efficiency through selective breeding. Access to the complete genomic sequence will provide an essential resource for studying quantitative trait-associated loci and exploring the genetic diversity of different wild populations and aquaculture stocks in more detail. Here, we present the first complete genome for A. regius, produced through a combination of long and short read technologies and an efficient in-house developed pipeline for assembly and polishing. Scaffolding using previous linkage map data allowed us to reconstruct a chromosome level assembly with high completeness, complemented with gene annotation and repeat masking. We use this new resource to study the evolution of the meagre genome and other Sciaenids, via a comparative analysis of 25 high-quality teleost genomes. Combining a rigorous investigation of gene duplications with base-wise conservation analysis, we identify candidate loci related to immune, fat metabolism and growth adaptations in the meagre. Following phylogenomic reconstruction, we show highly conserved synteny within Sciaenidae. In contrast, we report rapidly evolving syntenic rearrangements and gene copy changes in the sex-related dmrt1 neighbourhood in meagre and other members of the family. These novel genomic datasets and findings will add important new tools for aquaculture studies and greatly facilitate husbandry and breeding work in the species.

genomics↗

bioRxiv2020

Development and validation of a combined species SNP array for the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata)

SNP arrays are powerful tools for high-resolution studies of the genetic basis of complex traits, facilitating both population genomic and selective breeding research. The European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata) are the two most important fish species for Mediterranean aquaculture. While selective breeding programmes increasingly underpin stocky supply for this industry, genomic selection is not yet widespread. Genomic selection has major potential to expedite genetic gain, in particular for traits practically impossible to measure on selection candidates, such as disease resistance and fillet yield. The aim of our study was to design a combined-species 60K SNP array for both European seabass and gilthead seabream, and to validate its performance on farmed and wild populations from numerous locations throughout the species range. To achieve this, high coverage Illumina whole genome sequencing of pooled samples was performed for 24 populations of European seabass and 27 populations of gilthead seabream. This resulted in a database of ~20 million SNPs per species, which were then filtered to identify high-quality variants and create the final set for the development of the MedFish SNP array. The array was then tested by genotyping a subset of the discovery populations and demonstrated a high conversion rate to functioning polymorphic assays on the array (92% in seabass: 89% in seabream) and repeatability (99.4 - 99.7%). The platform interrogates ~30K markers in each fish species, includes features such as SNPs previously shown to be associated with performance traits, and is enriched for SNPs predicted to alter protein function. The array was demonstrated to be effective at detecting population structure across a wide range of fish populations from diverse geographical origins, and to examine the extent of haplotype sharing among Mediterranean fish farms. Therefore, the MedFish array enables efficient and accurate high-throughput genotyping for genome-wide distributed SNPs on each fish species, and will facilitate stock management, population genomics approaches, and acceleration of selective breeding through genomic selection.

genomics↗

bioRxiv2020

Building a high-quality reference genome assembly for the the eastern Mediterranean Sea invasive sprinter Lagocephalus sceleratus (Tetraodontiformes, Tetraodontidae)

The Tetraodontidae family encompasses several species which attract scientific interest in terms of their ecology and evolution. However, the genomic resources and especially reference assemblies are sparse for the members of the family. In this study, we focus on the silver-cheeked toadfish (Lagocephalus sceleratus) a well-known invasive sprinter that has invaded and spread throughout the Eastern and part of the Western Mediterranean Sea from the Red Sea through the Suez Canal within a decade. We sequenced the genome of L. sceleratus using a single MinION flow cell for the main assembly, and Illumina reads for polishing the assembly. The resulted assembly consisted of 241 contigs (N50 = 11,3 Mb) with a total size of 360 Mb and yielded 98% BUSCO completeness. The high-quality genome assembly built here is expected to set the ground for future studies on this focal species invasive biology.

genomics↗

bioRxiv2019

Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling

Sparidae (Teleostei: Spariformes) are a family of fish constituted by approximately 150 species with high popularity and commercial value, such as porgies and seabreams. Although the phylogeny of this family has been investigated multiple times, its position among other teleost groups remains ambiguous. Most studies have used a single or few genes to decipher the phylogenetic relationships of sparids. Here, we conducted a phylogenomic attempt to resolve the position of the family using five recently available Sparidae gene-sets and 26 available fish proteomes from species with a sequenced genome, to ensure higher quality of the predicted genes. A thorough phylogenomic analysis suggested that Tetraodontiformes (puffer fish, sunfish) are the closest relatives to sparids than all other groups used, a finding that contradicts our previous phylogenomic analysis that proposed the yellow croaker and the european seabass as closest taxa of sparids. By analytically comparing the methodologies applied in both cases, we show that this discordance is not due to different orthology assignment algorithms; on the contrary, we prove that it is caused by the increased taxon sampling of the present study, outlining the great importance of this aspect in phylogenomic analyses in general.

evolutionary biology↗