Vasilis Papadogiannis

@article{iliopoulou_extensive_2024,
title = {Extensive Loss and Gain of Conserved Noncoding Elements During Early Teleost Evolution},
author = {Elisavet Iliopoulou and Vasileios Papadogiannis and Costas S Tsigenopoulos and Tereza Manousaki},
editor = {Bonnie Fraser},
url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/04/2024-Iliopoulou-GBE-23.pdf
https://academic.oup.com/gbe/article/doi/10.1093/gbe/evae061/7655401},
doi = {10.1093/gbe/evae061},
issn = {1759-6653},
year = {2024},
date = {2024-04-24},
urldate = {2024-04-24},
journal = {Genome Biology and Evolution},
volume = {16},
number = {4},
pages = {evae061},
abstract = {Abstract
Conserved noncoding elements in vertebrates are enriched around transcription factor loci associated with development. However, loss and rapid divergence of conserved noncoding elements 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 conserved noncoding elements, carrying out targeted genomic alignments and comparisons within the teleost phylogeny to detect conserved noncoding elements and reconstruct the ancestral teleost conserved noncoding elements repertoire. This teleost-centric approach confirms previous observations of extensive vertebrate conserved noncoding elements loss early in teleost evolution, but also reveals massive conserved noncoding elements gain in the teleost stem-group over 300 million years ago. Using synteny-based association to link conserved noncoding elements to their putatively regulated target genes, we show the most teleost gained conserved noncoding elements are found in the vicinity of orthologous loci involved in transcriptional regulation and embryonic development that are also associated with conserved noncoding elements in other vertebrates. Moreover, teleost and vertebrate conserved noncoding elements share a highly similar motif and transcription factor binding site vocabulary. We suggest that early teleost conserved noncoding element gains reflect a restructuring of the ancestral conserved noncoding element repertoire through both extreme divergence and de novo emergence. Finally, we support newly identified pan-teleost conserved noncoding elements 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 conserved noncoding element evolution with great value for follow-up work on phylogenomics, comparative genomics, and the study of gene regulation evolution in teleosts.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{kitsoulis_near-chromosome_2023,
title = {Near-chromosome level genome assembly of devil firefish, Pterois miles},
author = {Christos V Kitsoulis and Vasileios Papadogiannis and Jon B Kristoffersen and Elisavet Kaitetzidou and Aspasia Sterioti and Costas S Tsigenopoulos and Tereza Manousaki},
url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/08/2023-Kitsoulis-PeerCJ-43.pdf
https://peercommunityjournal.org/articles/10.24072/pcjournal.295/},
doi = {10.24072/pcjournal.295},
issn = {2804-3871},
year = {2023},
date = {2023-08-29},
urldate = {2023-08-31},
journal = {Peer Community Journal},
volume = {3},
pages = {e64},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{papadogiannis_chromosome_2023b,
title = {Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution},
author = {Vasileios Papadogiannis and Tereza Manousaki and Orestis Nousias and Alexandros Tsakogiannis and Jon B Kristoffersen and Constantinos C Mylonas and Costas Batargias and Dimitrios Chatziplis and Costas S Tsigenopoulos},
url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/07/2023-Papadogiannis-FrontGen-34.pdf
https://www.frontiersin.org/articles/10.3389/fgene.2022.1081760/full},
doi = {10.3389/fgene.2022.1081760},
issn = {1664-8021},
year = {2023},
date = {2023-07-03},
urldate = {2023-07-03},
journal = {Frontiers in Genetics},
volume = {13},
pages = {1081760},
abstract = {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. The 696 Mb long assembly has an N50 = 27.87 Mb and an L50 = 12, with 92.85% of its length placed in 24 chromosomes. 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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{papadogiannis_chromosome_2023,
title = {Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution},
author = {Vasileios Papadogiannis and Tereza Manousaki and Orestis Nousias and Alexandros Tsakogiannis and Jon B Kristoffersen and Constantinos C Mylonas and Costas Batargias and Dimitrios Chatziplis and Costas S Tsigenopoulos},
url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/01/2023-Papadogiannis-FinGenetics-4.pdf
https://www.frontiersin.org/articles/10.3389/fgene.2022.1081760/full},
doi = {10.3389/fgene.2022.1081760},
issn = {1664-8021},
year = {2023},
date = {2023-01-10},
urldate = {2023-01-11},
journal = {Frontiers in Genetics},
volume = {13},
pages = {1081760},
abstract = {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. The 696 Mb long assembly has an N50 = 27.87 Mb and an L50 = 12, with 92.85% of its length placed in 24 chromosomes. 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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{papadogiannis_hmx_2022,
title = {Hmx gene conservation identifies the origin of vertebrate cranial ganglia},
author = {Vasileios Papadogiannis and Alessandro Pennati and Hugo J Parker and Ute Rothbächer and Cedric Patthey and Marianne E Bronner and Sebastian M Shimeld},
url = {https://www.nature.com/articles/s41586-022-04742-w.epdf?sharing_token=0xZJF5h0PJfpVUdefAf4R9RgN0jAjWel9jnR3ZoTv0PSCAbGc3qtbGpsTuLrcmb7ttAtuhgvjAvX1_k8Ag7g7vn007aa4q9FN_-aaVkwteXRU-W2Z6yGfxXTk4K9POn9sdB02QtTVBOCYrkTIU4SKKE5Vu5NqJLHbbWXMbZGPEI%3D
https://www.nature.com/articles/s41586-022-04742-w},
doi = {10.1038/s41586-022-04742-w},
issn = {0028-0836, 1476-4687},
year = {2022},
date = {2022-05-01},
urldate = {2022-07-29},
journal = {Nature},
volume = {605},
number = {7911},
pages = {701--705},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{zafeiropoulos_0s_2021,
title = {0s and 1s in marine molecular research: a regional HPC perspective},
author = {Haris Zafeiropoulos and Anastasia Gioti and Stelios Ninidakis and Antonis Potirakis and Savvas Paragkamian and Nelina Angelova and Aglaia Antoniou and Theodoros Danis and Eliza Kaitetzidou and Panagiotis Kasapidis and Jon Bent Kristoffersen and Vasileios Papadogiannis and Christina Pavloudi and Quoc Viet Ha and Jacques Lagnel and Nikos Pattakos and Giorgos Perantinos and Dimitris Sidirokastritis and Panagiotis Vavilis and Georgios Kotoulas and Tereza Manousaki and Elena Sarropoulou and Costas S Tsigenopoulos and Christos Arvanitidis and Antonios Magoulas and Evangelos Pafilis},
url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/08/2021-Zafeiropoulos-GiGa-63.pdf
https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giab053/6353916},
doi = {10.1093/gigascience/giab053},
issn = {2047-217X},
year = {2021},
date = {2021-01-01},
urldate = {2021-08-23},
journal = {GigaScience},
volume = {10},
number = {8},
pages = {giab053},
abstract = {Abstract
High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade’s experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility’s future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{danis_genome_2021,
title = {Genome Analysis of Lagocephalus sceleratus: Unraveling the Genomic Landscape of a Successful Invader},
author = {Theodoros Danis and Vasileios Papadogiannis and Alexandros Tsakogiannis and Jon B Kristoffersen and Daniel Golani and Dimitris Tsaparis and Aspasia Sterioti and Panagiotis Kasapidis and Georgios Kotoulas and Antonios Magoulas and Costas S Tsigenopoulos and Tereza Manousaki},
url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/01/2021-Danis-FrontGen-84.pdf
https://www.frontiersin.org/article/10.3389/fgene.2021.790850},
doi = {10.3389/fgene.2021.790850},
issn = {1664-8021},
year = {2021},
date = {2021-01-01},
urldate = {2022-01-12},
journal = {Frontiers in Genetics},
volume = {12},
pages = {2481},
abstract = {The Tetraodontidae family encompasses several species which attract scientific interest in terms of their ecology and evolution. The silver-cheeked toadfish (Lagocephalus sceleratus) is a well-known “invasive sprinter” that has invaded and spread, in less than a decade, throughout the Eastern and part of the Western Mediterranean Sea from the Red Sea through the Suez Canal. In this study, we built and analysed the first near-chromosome level genome assembly of L. sceleratus and explored its evolutionary landscape. Through a phylogenomic analysis, we positioned L. sceleratus closer to T. nigroviridis, compared to other members of the family, while gene family evolution analysis revealed that genes associated with the immune response have experienced rapid expansion, providing a genetic basis for studying how L. sceleratus is able to achieve highly successful colonisation. Moreover, we found that voltage-gated sodium channel (NaV 1.4) mutations previously connected to tetrodotoxin resistance in other pufferfishes are not found in L. sceleratus, highlighting the complex evolution of this trait. The high-quality genome assembly built here is expected to set the ground for future studies on the species biology.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}