Chromosome genome 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...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-01-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.1081760/full |
| _version_ | 1797956500786774016 |
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| author | Vasileios Papadogiannis Tereza Manousaki Orestis Nousias Orestis Nousias Alexandros Tsakogiannis Jon B. Kristoffersen Constantinos C. Mylonas Costas Batargias Dimitrios Chatziplis Costas S. Tsigenopoulos |
| author_facet | Vasileios Papadogiannis Tereza Manousaki Orestis Nousias Orestis Nousias Alexandros Tsakogiannis Jon B. Kristoffersen Constantinos C. Mylonas Costas Batargias Dimitrios Chatziplis Costas S. Tsigenopoulos |
| author_sort | Vasileios Papadogiannis |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-10T23:51:00Z |
| format | Article |
| id | doaj.art-1b28a256407a481989679c789dacdacc |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-10T23:51:00Z |
| publishDate | 2023-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-1b28a256407a481989679c789dacdacc2023-01-10T18:36:12ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-01-011310.3389/fgene.2022.10817601081760Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolutionVasileios Papadogiannis0Tereza Manousaki1Orestis Nousias2Orestis Nousias3Alexandros Tsakogiannis4Jon B. Kristoffersen5Constantinos C. Mylonas6Costas Batargias7Dimitrios Chatziplis8Costas S. Tsigenopoulos9Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology Biotechnology and Aquaculture (IMBBC), Heraklion, Crete, GreeceHellenic Centre for Marine Research (HCMR), Institute of Marine Biology Biotechnology and Aquaculture (IMBBC), Heraklion, Crete, GreeceHellenic Centre for Marine Research (HCMR), Institute of Marine Biology Biotechnology and Aquaculture (IMBBC), Heraklion, Crete, GreeceDepartment of Biology, University of Crete, Heraklion, Crete, GreeceHellenic Centre for Marine Research (HCMR), Institute of Marine Biology Biotechnology and Aquaculture (IMBBC), Heraklion, Crete, GreeceHellenic Centre for Marine Research (HCMR), Institute of Marine Biology Biotechnology and Aquaculture (IMBBC), Heraklion, Crete, GreeceHellenic Centre for Marine Research (HCMR), Institute of Marine Biology Biotechnology and Aquaculture (IMBBC), Heraklion, Crete, GreeceDepartment of Biology, University of Patras, Patras, GreeceDepartment of Agriculture, International Hellenic University (IHU), Thessaloniki, GreeceHellenic Centre for Marine Research (HCMR), Institute of Marine Biology Biotechnology and Aquaculture (IMBBC), Heraklion, Crete, GreeceThe 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.https://www.frontiersin.org/articles/10.3389/fgene.2022.1081760/fullgenomemeagreArgyrosomus regiussciaenidaeadaptationevolution |
| spellingShingle | Vasileios Papadogiannis Tereza Manousaki Orestis Nousias Orestis Nousias Alexandros Tsakogiannis Jon B. Kristoffersen Constantinos C. Mylonas Costas Batargias Dimitrios Chatziplis Costas S. Tsigenopoulos Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution Frontiers in Genetics genome meagre Argyrosomus regius sciaenidae adaptation evolution |
| title | Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution |
| title_full | Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution |
| title_fullStr | Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution |
| title_full_unstemmed | Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution |
| title_short | Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution |
| title_sort | chromosome genome assembly for the meagre argyrosomus regius reveals species adaptations and sciaenid sex related locus evolution |
| topic | genome meagre Argyrosomus regius sciaenidae adaptation evolution |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.1081760/full |
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