Initial data release and announcement of the 10,000 Fish Genomes Project (Fish10K)

Abstract

Background: With more than 30,000 species, fish-including bony, jawless, and cartilaginous fish-are the largest vertebrate group, and include some of the earliest vertebrates. Despite their critical roles in many ecosystems and human society, fish genomics lags behind work on birds and mammals. This severely limits our understanding of evolution and hinders progress on the conservation and sustainable utilization of fish.

Results: Here, we announce the Fish10K project, a portion of the Earth BioGenome Project aiming to sequence 10,000 representative fish genomes in a systematic fashion within 10 years, and we officially welcome collaborators to join this effort. As a step towards this goal, we herein describe a feasible workflow for the procurement and storage of biospecimens, as well as sequencing and assembly strategies.

Conclusions: To illustrate, we present the genomes of 10 fish species from a cohort of 93 species chosen for technology development.

Keywords: Fish10K; evolution; fish; genome sequencing; phylogenetics; stLFR.

Figure 1:

Assembly statistics of fish genomes in public databases. (a) Summary of genome size. (b, c) N50 statistics. A scaffold is a set of contigs linked together with gaps introduced in between. N50 is the median contig size of the genomic assembly. It's a metric that could be used to evaluate the quality of genome assembly.

Figure 2:

The sequencing and assembly strategies. In the preferred strategy (Strategy II), high-quality DNA fragments (≥40Kb) are used to construct a stLFR library, which is sequenced using the DNBSEQ platform. Low–sequencing depth long reads are only used to improve the continuity of highly complex regions (increase the contig N50). In the alternative Strategy I, high-depth long reads are used to construct contigs, while low-depth stLFR reads are used to polish the contig and link the scaffolds. Hi-C data are used to generate a chromosome-level assembly.

Figure 3:

The roadmap and organization of Fish10K. Fish10K is divided into 3 phases, based on the evolutionary relationship of fish, and 3 working groups (steering committee, scientific groups, and species groups).

Figure 4:

Phylogenetics tree of fish. Jawed vertebrates (gnathostomes) are divided into 2 major groups: cartilaginous fish (Chondrichthyes; in orange) and bony vertebrates (Osteichthyes; in blue and green). Bony fish are grouped into 2 subgroups (Sarcopterygii; green) and (Actinopterygii; blue). The number of families and species in the 5 largest orders are labeled. The remaining 10 orders of bony fish (Caproiformes, Callionymiformes, Gobiesociformes, Icosteiformes, Lepisosteiformes, Moroniformes, Scombrolabraciformes, Scorpaeniformes, Trachichthyiformes, and Trachiniformes) and 2 orders of cartilaginous fish (Rhinopristiformes and Squatiniformes) are not included in the phylogenetic tree, due to their uncertain positions.