{"entity": "researcher", "timestamp": "2026-08-14T12:42:17.157Z", "family": "Palaiokostas", "given": "Christos", "initials": "C", "orcid": "0000-0002-4480-4612", "affiliations": ["Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/a1d6c65f53a8434cb1d5dd4c7bf5d444.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/a1d6c65f53a8434cb1d5dd4c7bf5d444"}}, "publications": [{"entity": "publication", "iuid": "c0b630a30a1a46ce900790a05a054996", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0b630a30a1a46ce900790a05a054996.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0b630a30a1a46ce900790a05a054996"}}, "title": "Assessing Sperm Quality Parameters in Mass\u2010Spawning Norwegian Arctic Charr", "authors": [{"family": "Kurta", "given": "Khrystyna", "initials": "K", "orcid": "0000-0002-9852-1896", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ba96d1e78654b6992ef1c25035e93da.json"}}, {"family": "Beir\u00e3o", "given": "Jos\u00e9", "initials": "J"}, {"family": "Thomason", "given": "Benjamin", "initials": "B"}, {"family": "Palaiokostas", "given": "Christos", "initials": "C", "orcid": "0000-0002-4480-4612", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1d6c65f53a8434cb1d5dd4c7bf5d444.json"}}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Aquaculture Fish &amp; Fisheries", "issn": "2693-8847", "volume": "5", "issue": "4", "issn-l": null}, "abstract": null, "doi": "10.1002/aff2.70111", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T07:02:14.701Z", "modified": "2025-09-09T13:12:28.648Z"}, {"entity": "publication", "iuid": "54e65a8ce2c94cf5ac271086444360f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/54e65a8ce2c94cf5ac271086444360f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/54e65a8ce2c94cf5ac271086444360f9"}}, "title": "Sperm DNA methylation landscape and its links to male fertility in a non-model teleost using EM-seq.", "authors": [{"family": "Pappas", "given": "Fotis", "initials": "F", "orcid": "0000-0003-3696-5069", "researcher": {"href": "https://publications.scilifelab.se/researcher/238d355f0f5f4dd798fdc7f58d4c5a41.json"}}, {"family": "Johnsson", "given": "Martin", "initials": "M", "orcid": "0000-0003-1262-4585", "researcher": {"href": "https://publications.scilifelab.se/researcher/02b768197c08422aaad526f35c526eaf.json"}}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-5131-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ce81c314db47c8ad63c3ed38dffcb3.json"}}, {"family": "Debes", "given": "Paul V", "initials": "PV", "orcid": "0000-0003-4491-9564", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1887c01f5b343e19e398b3fcd96ba14.json"}}, {"family": "Palaiokostas", "given": "Christos", "initials": "C", "orcid": "0000-0002-4480-4612", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1d6c65f53a8434cb1d5dd4c7bf5d444.json"}}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "volume": "134", "issue": "5", "pages": "293-305", "issn-l": "0018-067X"}, "abstract": "Differential DNA methylation due to epigenetic phenomena is crucial in regulating gene expression. Understanding the consequences of such differential expression on sperm quality parameters may provide insights into the underlying mechanisms of male reproductive success. Nonetheless, male fertility in fish remains understudied despite its critical importance to overall reproductive success in nature and captivity. This study investigated the DNA methylation landscape in spermatozoa of domesticated Arctic charr (Salvelinus alpinus) and its associations with sperm quality parameters. Computer assisted-semen analysis (CASA) was performed in 47 sperm samples of farmed Arctic charr, followed by enzymatic methylation sequencing (EM-seq). Our results showed that the DNA of Arctic charr sperm is highly methylated (mean value of ~86%), though variations were observed in genomic features involved in gene regulation. Methylation at variable CpG sites exhibited regional correlation decaying by physical distance, while methylation similarities among individuals were strongly coupled with genetic variation and mirrored pedigree structure. Comethylation network analyses for promoters, CpG islands and first introns revealed genomic modules significantly correlated with sperm quality traits (p < 0.05; Bonferroni adjusted), with distinct patterns suggesting a resource trade-off between sperm concentration and kinematics. Furthermore, annotation and gene-set enrichment analysis highlighted biological mechanisms related to spermatogenesis, cytoskeletal regulation, and mitochondrial function, all vital to sperm physiology. These findings suggest that DNA methylation is a critical and fundamental factor influencing male fertility in Arctic charr, providing insights into the underlying mechanisms of male reproductive success.", "doi": "10.1038/s41437-025-00756-y", "pmid": "40097595", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12056074"}, {"db": "pii", "key": "10.1038/s41437-025-00756-y"}], "notes": [], "created": "2025-09-08T06:59:19.759Z", "modified": "2025-11-14T11:06:34.293Z"}, {"entity": "publication", "iuid": "b63ebec5607f49219d63cb4bcce20f95", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b63ebec5607f49219d63cb4bcce20f95.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b63ebec5607f49219d63cb4bcce20f95"}}, "title": "Genetic diversity insights from population genomics and machine learning tools for Nordic Arctic charr (Salvelinus alpinus) populations", "authors": [{"family": "Palaiokostas", "given": "Christos", "initials": "C", "orcid": "0000-0002-4480-4612", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1d6c65f53a8434cb1d5dd4c7bf5d444.json"}}, {"family": "Kurta", "given": "Khrystyna", "initials": "K"}, {"family": "Pappas", "given": "Fotis", "initials": "F"}, {"family": "Jeuthe", "given": "Henrik", "initials": "H"}, {"family": "Hagen", "given": "\u00d8rjan", "initials": "\u00d8"}, {"family": "Beir\u00e3o", "given": "Jos\u00e9", "initials": "J"}, {"family": "Janhunen", "given": "Matti", "initials": "M"}, {"family": "Kause", "given": "Antti", "initials": "A"}], "type": "journal-article", "published": "2024-12-00", "journal": {"title": "Aquaculture Reports", "issn": "2352-5134", "volume": "39", "pages": "102495", "issn-l": "2352-5134"}, "abstract": null, "doi": "10.1016/j.aqrep.2024.102495", "pmid": null, "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-12T10:39:01.587Z", "modified": "2025-12-04T19:36:52.855Z"}, {"entity": "publication", "iuid": "b6c8b4628a8b4d1e9ad4c1345f3d8d26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b6c8b4628a8b4d1e9ad4c1345f3d8d26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b6c8b4628a8b4d1e9ad4c1345f3d8d26"}}, "title": "Genetic diversity patterns in farmed rainbow trout (Oncorhynchus mykiss) populations using genome-wide SNP and haplotype data.", "authors": [{"family": "Longo", "given": "Alessio", "initials": "A"}, {"family": "Kurta", "given": "Khrystyna", "initials": "K"}, {"family": "Vanhala", "given": "Tytti", "initials": "T"}, {"family": "Jeuthe", "given": "Henrik", "initials": "H"}, {"family": "de Koning", "given": "Dirk-Jan", "initials": "DJ"}, {"family": "Palaiokostas", "given": "Christos", "initials": "C", "orcid": "0000-0002-4480-4612", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1d6c65f53a8434cb1d5dd4c7bf5d444.json"}}], "type": "journal article", "published": "2024-02-00", "journal": {"title": "Anim Genet", "issn": "1365-2052", "volume": "55", "issue": "1", "pages": "87-98", "issn-l": "0268-9146"}, "abstract": "Rainbow trout is one of the most popular aquaculture species worldwide, with a long history of domestication. However, limited information exists about the genetic diversity of farmed rainbow trout populations globally, with most available reports relying on low-throughput genotyping technologies. Notably, no information exists about the genetic diversity status of farmed rainbow trout in Sweden. Double-digest restriction-site-associated DNA sequencing was performed on more than 500 broodfish from two leading producers in Sweden and from the country's national breeding program. Following the detection of single nucleotide polymorphisms (SNPs), genetic diversity was studied by using either individual SNPs (n = 8680; one SNP retained per 300 bp sequence reads) or through SNP haplotypes (n = 20 558; all SNPs retained in 300 bp sequence reads). Similar amounts of genetic diversity were found amongst the three populations when individual SNPs were used. Furthermore, principal component analysis and discriminant analysis of principal components suggested two genetic clusters with the two industry populations grouped together. Genetic differentiation based on the FST fixation index was ~0.01 between the industry populations and ~0.05 when those were compared with the breeding program. Preliminary estimates of effective population size (Ne ) and inbreeding (based on runs of homozygosity; FROH ) were similar amongst the three populations (Ne \u2248 50-80; median FROH \u2248 0.11). Finally, the haplotype-based analysis suggested that animals from the breeding program had higher shared coancestry levels than those from the other two populations. Overall, our study provides novel insights into the genetic diversity and structure of Sweden's three main farmed rainbow trout populations, which could guide their future management.", "doi": "10.1111/age.13378", "pmid": "37994156", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "RefSeq", "key": "GCA_013265735.3"}], "notes": [], "created": "2024-03-21T08:48:47.551Z", "modified": "2024-03-21T08:48:47.647Z"}, {"entity": "publication", "iuid": "091bc2001e6e49a1a25c43f310e57220", "links": {"self": {"href": "https://publications.scilifelab.se/publication/091bc2001e6e49a1a25c43f310e57220.json"}, "display": {"href": "https://publications.scilifelab.se/publication/091bc2001e6e49a1a25c43f310e57220"}}, "title": "Whole-genome re-sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia.", "authors": [{"family": "Pappas", "given": "Fotis", "initials": "F"}, {"family": "Kurta", "given": "Khrystyna", "initials": "K"}, {"family": "Vanhala", "given": "Tytti", "initials": "T"}, {"family": "Jeuthe", "given": "Henrik", "initials": "H"}, {"family": "Hagen", "given": "\u00d8rjan", "initials": "\u00d8"}, {"family": "Beir\u00e3o", "given": "Jos\u00e9", "initials": "J"}, {"family": "Palaiokostas", "given": "Christos", "initials": "C", "orcid": "0000-0002-4480-4612", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1d6c65f53a8434cb1d5dd4c7bf5d444.json"}}], "type": "journal article", "published": "2023-04-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "16", "issue": "4", "pages": "797-813", "issn-l": "1752-4571"}, "abstract": "Arctic charr (Salvelinus alpinus) is a niche-market high-value species for Nordic aquaculture. Similar to other salmonids, both anadromous and landlocked populations are encountered. Whole-genome re-sequencing (22X coverage) was performed on two farmed populations of anadromous (Sigerfjord; n = 24) and landlocked (Arctic Superior; n = 24) origin from Norway and Sweden respectively. More than 5 million SNPs were used to study their genetic diversity and to scan for selection signatures. The two populations were clearly distinguished through principal component analysis, with the mean fixation index being ~0.12. Furthermore, the levels of genomic inbreeding estimated from runs of homozygosity were 6.23% and 8.66% for the Norwegian and the Swedish population respectively. Biological processes that could be linked to selection pressure associated primarily with the anadromous background and/or secondarily with domestication were suggested. Overall, our study provided insights regarding the genetic composition of two main strains of farmed Arctic charr from Scandinavia. At the same time, ample genomic resources were produced in the magnitude of millions of SNPs that could assist the transition of Nordic Arctic charr farming in the genomics era.", "doi": "10.1111/eva.13537", "pmid": "37124091", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10130564"}, {"db": "pii", "key": "EVA13537"}], "notes": [], "created": "2023-11-29T11:32:33.735Z", "modified": "2023-11-29T11:32:33.768Z"}]}