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The project Squalomix aims at unveiling the unique evolutionary trajectory of chondrichthyans (sharks, rays, and chimaeras) and is sustained by tight collaborations involving academic sequencing core facilities, marine stations, and public aquariums. By means of multimodal omics and molecular evolutionary approaches, it tackles biological questions in various fields including developmental biology and comparative physiology.
| Accession | PRJNA707598 |
| Type | Umbrella project |
| Publications (total 8) Less... | - Yamaguchi K et al., "Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization.", Genome Res, 2023 Sep;33(9):1527-1540
More...- Yamaguchi K et al., "Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization.", Genome Res, 2023 Sep;33(9):1527-1540
- Ohishi Y et al., "Egg Yolk Protein Homologs Identified in Live-Bearing Sharks: Co-Opted in the Lecithotrophy-to-Matrotrophy Shift?", Genome Biol Evol, 2023 Mar 3;15(3)
- Yamaguchi K et al., "Whale shark rhodopsin adapted to deep-sea lifestyle by a substitution associated with human disease.", Proc Natl Acad Sci U S A, 2023 Mar 28;120(13):e2220728120
- Kuraku S "Shark and ray genomics for disentangling their morphological diversity and vertebrate evolution.", Dev Biol, 2021 Sep;477:262-272
- Yamaguchi K et al., "Visual and nonvisual opsin genes of sharks and other nonosteichthyan vertebrates: Genomic exploration of underwater photoreception.", J Evol Biol, 2021 Jun;34(6):968-976
- Uno Y et al., "Cell culture-based karyotyping of orectolobiform sharks for chromosome-scale genome analysis.", Commun Biol, 2020 Nov 6;3(1):652
- Hara Y et al., "Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates.", Nat Ecol Evol, 2018 Nov;2(11):1761-1771
- Published online: Nishimura O et al., "Squalomix: shark and ray genome analysis consortium and its data sharing platform", F1000Research, 2022;11
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| Submission | Registration date: 8-Mar-2021
Squalomix |
| Related Resources | |
| Relevance | Evolution |
Project Data:
| Resource Name | Number
of Links |
|---|
| Sequence data |
| Nucleotide (total) | 55309 |
| WGS master | 7 |
| TSA master | 1 |
| Genomic DNA | 2 |
| Transcript | 54344 |
| SRA Experiments | 240 |
| Protein Sequences | 40304 |
| Publications |
| PubMed | 9 |
| PMC | 5 |
| Other datasets |
| BioSample | 204 |
| Assembly | 7 |
Squalomix Project encompasses the following 10 sub-projects:
| Project Type | Number of Projects |
| Genome sequencing |
3
3
6
|
BioProject
accession | Assembly
level | Name | Title |
|---|
| PRJNA1075468 | SRA or Trace | Chimaera phantasma genome sequencing and analysis | Chimaera phantasma genome sequencing and analysis (National Insitute of Genetics) | | PRJDB16029 | SRA or Trace | Cololabis saira | Molecular-level investigation of the Pacific saury (Molecular Life History Laboratory,...) | | PRJNA1027303 | Chromosomes | Cololabis saira | Cololabis saira Genome sequencing and assembly (National Insitute of Genetics) | | PRJNA1054198 | Chromosomes | Cololabis saira | Cololabis saira RefSeq Genome sequencing and assembly (NCBI) | | PRJDB6260 | SRA or Trace | Elasmobranchii | Elasmobranch shark genome evolution (Phyloinformatics Unit, Division...) | | PRJNA703743 | Chromosomes | Squalomix Project: Stegostoma fasciatum & Rhincodon typus | Squalomix Project: Stegostoma fasciatum & Rhincodon typus (Squalomix) |
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| Umbrella project | 1 |
|
| transcriptome | 3 |
|