A new Merluccius polli reference genome to investigate the effects of global change in West African waters
Genome resources have become crucial to assess genome-wide level of variation as well as to detect adaptive variation. This is particularly important for studying diversity in marine species inhabiting regions highly affected by accelerated climate warming and pollution, also known as global change....
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-04-01
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| Series: | Frontiers in Marine Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmars.2023.1111107/full |
| _version_ | 1797840595517964288 |
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| author | Juan L. Mateo Carmen Blanco-Fernandez Eva Garcia-Vazquez Gonzalo Machado-Schiaffino |
| author_facet | Juan L. Mateo Carmen Blanco-Fernandez Eva Garcia-Vazquez Gonzalo Machado-Schiaffino |
| author_sort | Juan L. Mateo |
| collection | DOAJ |
| description | Genome resources have become crucial to assess genome-wide level of variation as well as to detect adaptive variation. This is particularly important for studying diversity in marine species inhabiting regions highly affected by accelerated climate warming and pollution, also known as global change. A greater awareness of the impacts of global change is urgently needed to ensure sustainable marine fisheries. Despite recent efforts, there are still many gaps in fish reference genomes, both geographical and taxonomic. Here, we sequence, assemble and annotate the genome of Merluccius polli. The total length of this new assembly (~582 Kb, N50 = 168Kb) is approximately 40% longer and much less fragmented than a previous version. Even though it might not be intrinsic of this species, low level of heterozygosity (1.16 SNPs/Kb) and low proportion of repeat content (9.21%) was found in this genome. This hake species has a wide latitudinal distribution; therefore, it is exposed to a changing temperature gradient and to a variety of contaminants in part of its distribution along West African coast. Special emphasis was laid on the identification and characterization of candidate genes known to respond to different stressors (depth, temperature, hypoxia, and heavy metals) happening along its geographical distribution. A total of 68 of the selected candidate genes known to be associated with responses to these stressors were found in the current assembly of the genome, and their predicted sequence can be considered as full-length. Therefore, it is expected that this genome would serve as a tool to further investigations of global change in one of the most stressed marine regions in the planet. |
| first_indexed | 2024-04-09T16:17:25Z |
| format | Article |
| id | doaj.art-c7ff46df6c1f40c18397ca8c392397df |
| institution | Directory Open Access Journal |
| issn | 2296-7745 |
| language | English |
| last_indexed | 2024-04-09T16:17:25Z |
| publishDate | 2023-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Marine Science |
| spelling | doaj.art-c7ff46df6c1f40c18397ca8c392397df2023-04-24T04:23:25ZengFrontiers Media S.A.Frontiers in Marine Science2296-77452023-04-011010.3389/fmars.2023.11111071111107A new Merluccius polli reference genome to investigate the effects of global change in West African watersJuan L. Mateo0Carmen Blanco-Fernandez1Eva Garcia-Vazquez2Gonzalo Machado-Schiaffino3Department of Informatics, University of Oviedo, Oviedo, SpainDepartment of Functional Biology, University of Oviedo, Oviedo, SpainDepartment of Functional Biology, University of Oviedo, Oviedo, SpainDepartment of Functional Biology, University of Oviedo, Oviedo, SpainGenome resources have become crucial to assess genome-wide level of variation as well as to detect adaptive variation. This is particularly important for studying diversity in marine species inhabiting regions highly affected by accelerated climate warming and pollution, also known as global change. A greater awareness of the impacts of global change is urgently needed to ensure sustainable marine fisheries. Despite recent efforts, there are still many gaps in fish reference genomes, both geographical and taxonomic. Here, we sequence, assemble and annotate the genome of Merluccius polli. The total length of this new assembly (~582 Kb, N50 = 168Kb) is approximately 40% longer and much less fragmented than a previous version. Even though it might not be intrinsic of this species, low level of heterozygosity (1.16 SNPs/Kb) and low proportion of repeat content (9.21%) was found in this genome. This hake species has a wide latitudinal distribution; therefore, it is exposed to a changing temperature gradient and to a variety of contaminants in part of its distribution along West African coast. Special emphasis was laid on the identification and characterization of candidate genes known to respond to different stressors (depth, temperature, hypoxia, and heavy metals) happening along its geographical distribution. A total of 68 of the selected candidate genes known to be associated with responses to these stressors were found in the current assembly of the genome, and their predicted sequence can be considered as full-length. Therefore, it is expected that this genome would serve as a tool to further investigations of global change in one of the most stressed marine regions in the planet.https://www.frontiersin.org/articles/10.3389/fmars.2023.1111107/fullgenomeglobal changecandidate genesenvironmental challengesBenguela hake |
| spellingShingle | Juan L. Mateo Carmen Blanco-Fernandez Eva Garcia-Vazquez Gonzalo Machado-Schiaffino A new Merluccius polli reference genome to investigate the effects of global change in West African waters Frontiers in Marine Science genome global change candidate genes environmental challenges Benguela hake |
| title | A new Merluccius polli reference genome to investigate the effects of global change in West African waters |
| title_full | A new Merluccius polli reference genome to investigate the effects of global change in West African waters |
| title_fullStr | A new Merluccius polli reference genome to investigate the effects of global change in West African waters |
| title_full_unstemmed | A new Merluccius polli reference genome to investigate the effects of global change in West African waters |
| title_short | A new Merluccius polli reference genome to investigate the effects of global change in West African waters |
| title_sort | new merluccius polli reference genome to investigate the effects of global change in west african waters |
| topic | genome global change candidate genes environmental challenges Benguela hake |
| url | https://www.frontiersin.org/articles/10.3389/fmars.2023.1111107/full |
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