Pipelines, code and ressources for creating a fully haplotype-resolved T2T assembly of the African catfish (Clarias gariepinus) combining PacBio HiFi, ONT long reads and Hi-C data.
-
Big guy regarding Salmon genome - Craig Primmer
-
Sex-specific lipid profiles in the muscle of Atlantic salmon juveniles
-
2016 The Atlantic salmon genome provides insights into rediploidization
-
2022 | A haplotype-resolved draft genome of the European sardine (Sardina pilchardus) | 10x Genomics | paper
-
2021 | Asian Red-Tail Catfish | Hemibagrus wyckioides | Illumina + Nanopore + PacBio HiFi + Hi-C | paper
-
2021 | striped catfish | Pangasianodon hypophthalmus | Illumina + Nanopore + Hi-C | striped catfish updated genome paper
-
2020 | African Arowana Genome Provides Insights on Ancient Teleost Evolution | stLFR + ONT + Hi-C| paper
-
2020 | Freshwater Apex Predator Wels Catfish | Silurus glanis | 10x Genomics | freshwater apex genome paper
-
2019 | giant devil catfish | Bagarius yarrelli | Illumina + PacBio | giant devil genome paper
-
2018 | Chinese Yellow Catfish | Pelteobagrus fulvidraco | Illumina + PacBio | paper
-
2018 | walking catfish | Clarias batrachus | Illumina | ALLPATHS-LG | paper
-
2018 | yellow catfish | Pelteobagrus fulvidraco | Illumina + PacBio + Hi-C | Yellow catfish genome paper
-
2018 | striped catfish| Pangasianodon hypophthalmus | Platanus | Illumina | Genes level comparison | stripped catfish paper
-
2016 | Channel catfish | Ictalurus punctatus | MASURCA | Illumina + PacBio CLR | Summary stats | Catfish paper
-
unknown |A Review | Whole-Genome Duplication in Teleost Fishes and Its Evolutionary Consequences
-
2006 Fish Genomes, Comparative Genomics and Vertebrate Evolution
Hence, teleost fishes display a high level of genomic plasticity
- 2001 Comparative genomics provides evidence for an ancient genome duplication event in fish
- 2006 Fish Genomes, Comparative Genomics and Vertebrate Evolution
.....convincing evidence that all teleosts are derived from a common tetraploid fish ancestor
The evolutionary rate of duplicate fish genes appears to be determined by 3 forces: 1) fish proteins evolve faster than mammalian orthologs; 2) the genes kept in double after genome duplication represent the subset under strongest purifying selection; and 3) following duplication, there is an asymmetric acceleration of evolutionary rate in one of the paralogs.
Idea: We might trace the evolutionary history of stearoyl-CoA desaturase since they are involved in food dieatary supplement
- 2012 Polyploidy in Fish and the Teleost Genome Duplication
- 2020 The lasting after-effects of an ancient polyploidy on the genomes of teleosts
The ancestor of most teleost fishes underwent a whole-genome duplication event three hundred million years ago. Despite its antiquity, the effects of this event are evident both in the structure of teleost genomes and in how the surviving duplicated genes still operate to drive form and function
... after the teleost-specific third round WGD (3R WGD)........
The teleost 3R WGD, which occurred about 320 mya, played an important role in the diversification of ancient teleosts (Yang et al., 2016). Therefore, polyploid fish species can be used to study post-WGD genome evolution and to determine the contribution of WGD to speciation and environmental adaptation (Chen et al., 2019). Re-diploidization is an essential post-WGD evolutionary process, which differentiates and stabilizes duplicated genomes (Lien et al., 2016).
The channel catfish haploid genome contains 29 chromosomes with an estimated 1.0 Gb of DNA 13,14 (Supplementary Fig. 1), and this diploid species is assumed to have undergone the teleost-specific genome duplication (TSGD) 15,16
Tetraploydization/Rediploidization | Sex Determination | TE evolution
All teleost fish species descend from an ancient round of whole genome duplication (WGD), dated 320 Mya (Jaillon et al. 2004). This dramatic evolutionary event, referred to as the teleost specific genome duplication (TGD), doubled all chromosomes and genes present in the teleost ancestor. The TGD has left a significant imprint on extant teleost genomes: while most duplicated genes have returned to a single-copy state, an important fraction of teleost genes remain in two copies, called ohnologs.
Importantly, the redundancy in fish genomes can be appreciated at the macrosyntenic level, where remnants of ancestrally duplicated chromosomes form runs of large duplicated regions (Postlethwait et al. 2000; Taylor et al. 2003; Jaillon et al. 2004)
In particular, autopolyploidization and allopolyploidization differentially shape the rediploidization process, i.e. how the polyploid genome returns to a largely diploid state over time.
The retention of redundant gene copies is also affected by the nature of the polyploidization event
we might have also rentention of duplicated genes in the african catfish that is why the busco duplicated orthologs rate is still high
For the comparative phylogenomics we might need to use SCORPIOs pipeline due to the duplication of gene in teleost that can biased the tree inference.
Yes...The functional attributes of the retained genes and also african catfish specific genes. What make the African catfish particular?
Ok I think this is easy. 1) Identify paralogs in all catfish and classify them. ====> Check if some families of important genes are contained in this list. ====> Analyze their comparative evolution. 2) Analyse positive selection/evolution of paralogs in catfish. 3) Which genes are retained? What are their function? loss of function? Neofunctionalization?
- Evolution of some key genes among catfishes (which genes might be of general interest, hence considered as key genes for catfishes??)