1,000 Fish Transcriptome (Fish-T1K) Project -- Progress and Challenges

Fishes represent over 50% of the global vertebrate biodiversity but are relatively underrepresented in genome studies, with only about 23 genomes and 185 transcriptomes published so far. We have, therefore, initiated a “Transcriptomes of 1,000 Fishes” (Fish-T1K) project, an international effort devoted to collecting tissue samples and sequencing transcriptomes of 1000 ray-finned fish species. This project was officially launched by China National Genebank (CNBG, www.cngb.org) and BGI-Shenzhen (www.genomics.cn) in November 2013 and has now attracted more than 30 scientists from 20 institutions and 5 countries worldwide to get involved in the project.

A major challenge for Fish-T1K is the availability of fresh tissues for representative species covering major taxa of ray-finned fishes. We have been making efforts in establishing a collaborative global network for fish collection, storage, transportation and RNA extraction.As on November 2014, 7,000 genome-quality fish tissue samples have been collected, representing 62% (44/71) orders and 28% (112/398) families of ray-finned fishes, as per Betancur, et al. 2013. In order to facilitate quality-sample collection from North America, we are establishing a ‘hub’ at the National Museum of Natural History (NMNH, www.mnh.si.edu), Washington DC, with a streamlined protocol for reception of tissue samples, cryopreservation, RNA extraction, and shipping RNA samples to BGI-Shenzhen for sequencing.

The main research project of Fish-T1K is to “reconstruct fish tree of life”. At least two representative species from each of the 71 orders (or at least one from each of the 398 families) will be sequenced. This new comprehensive molecular phylogeny of all fish species will verify existing phylogenetic hypotheses and resolve relationships of hitherto difficult-to-resolve fish lineages thereby providing a phylogenetic framework for better understanding the evolution of fishes. In addition to the main project, several sub-projects such as venom gene evolution, vision gene evolution, etc. will be undertaken by using appropriate tissues from selected species of ray-finned fishes. We are looking for collaborators who can propose subprojects, arrange for tissue samples and take the lead in analyzing and publishing the data.

Currently, FishT1K is establishing standards for tissue collection, storage, transportation, RNA extraction, sequence assembly, ortholog prediction, and over all data management. The guidelines developed will be published on our website (www.fisht1k.org) so that all the collaborators can adopt the same standard practices. So far, we have sequenced 40 species covering 19 orders of ray-finned fishes, and RNA from an additional 68 species have been extracted.