COMMENTARY Open Access
Fish-T1K (Transcriptomes of 1,000 Fishes)
Project: large-scale transcriptome data for
fish evolution studies
Ying Sun1,2*†, Yu Huang2†, Xiaofeng Li2†, Carole C. Baldwin3, Zhuocheng Zhou4, Zhixiang Yan5, Keith A. Crandall6,
Yong Zhang2, Xiaomeng Zhao2, Min Wang2,7, Alex Wong8, Chao Fang2, Xinhui Zhang2, Hai Huang9,
Jose V. Lopez10, Kirk Kilfoyle10, Yong Zhang1, Guillermo Ortí6*, Byrappa Venkatesh11* and Qiong Shi2,7,12*
Abstract
Ray-finned fishes (Actinopterygii) represent more than 50 % of extant vertebrates and are of great evolutionary,
ecologic and economic significance, but they are relatively underrepresented in ‘omics studies. Increased availability
of transcriptome data for these species will allow researchers to better understand changes in gene expression, and
to carry out functional analyses. An international project known as the “Transcriptomes of 1,000 Fishes” (Fish-T1K)
project has been established to generate RNA-seq transcriptome sequences for 1,000 diverse species of ray-finned
fishes. The first phase of this project has produced transcriptomes from more than 180 ray-finned fishes, representing
142 species and covering 51 orders and 109 families. Here we provide an overview of the goals of this project and the
work done so far.
Keywords: Fish-T1K, Fish, Transcriptome, RNA, Database, Biodiversity
Background
Ray-finned fishes (Actinopterygii) are the most diverse
and abundant group of extant vertebrates. Thus far, ap-
proximately 32,900 fish species are recorded in FishBase
[1]. Fishes encompass enormous variation in morph-
ology, physiology and ecology. They are of great eco-
nomic and medical significance as a primary source of
protein for people worldwide, as a novel source of active
ingredients in pharmaceuticals [2], and as evolutionary
models for specific human diseases and conditions [3].
However, genomic resources for fishes are relatively
underrepresented and published genetic data represent
only a small fraction of extant fish species. So far, the
whole genomes of only 38 fish species have been pub-
lished (Additional file 1) and, although the number is
growing (Additional file 2), searching the National Cen-
ter for Biotechnology Information (NCBI)’s Sequence
Read Archive (SRA) database for “fish AND transcrip-
tome” yields 16,975 transcriptomes of only 242 fish spe-
cies (Table 1). A lack of genomic resources for most fish
species motivated us to generate large-scale fish tran-
scriptome data and establish a database that may be
used by scientists around the world. To this end, we ini-
tiated the “Transcriptomes of 1,000 Fishes” (Fish-T1K)
project, an effort devoted to sequencing the transcrip-
tomes of 1,000 different species of ray-finned fishes.
Fish-T1K
Fish-T1K is an international, collaborative and non-
profit initiative officially launched by BGI and the China
National Genebank (CNGB) in November 2013. The ob-
jective is to generate RNA-seq transcriptome sequences
for 1,000 diverse fish species to help scientists unravel
the mysteries of fish evolution, and pursue innovative
approaches and strategies for addressing challenges in
* Correspondence: ying_sun09@icloud.com; gorti@email.gwu.edu; mcbbv@
imcb.a-star.edu.sg; shiqiong@genomics.cn
†Equal contributors
1State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals
and Guangdong Provincial Key Laboratory for Aquatic Economic Animals,
School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
6Department of Biological Sciences, The George Washington University,
Washington, DC 20052, USA
11Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
2Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of
Molecular Breeding in Marine Economic Animals, BGI, Shenzhen 518083, China
Full list of author information is available at the end of the article
© 2016 Sun et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and
reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to
the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver
(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Sun et al. GigaScience  (2016) 5:18 
DOI 10.1186/s13742-016-0124-7
fish breeding, disease control and prevention, seafood
safety, and biodiversity conservation.
Through this project, an integrated biobank will be
established, incorporating a high-level bio-repository and
a large-scale transcriptome database. The biobank will col-
lect and store fish genetic resources including vouchers
and frozen tissues, DNA and RNA nucleotides, together
with related sample information documented according to
standard operating procedures (SOPs). A companion data-
base, committed to being the world’s largest database of
fish transcriptomes, has already been established and pro-
vides access to the sequences via BLAST search.
The Fish-T1K consortium
More than 40 scientists from 25 institutions across seven
countries are active members of the Fish-T1K project
(Fig. 1; Additional file 3). The Steering Committee con-
sists of six core consortium members who are recog-
nized experts in ichthyology, taxonomy, bioinformatics,
phylogenetics, and evolution. In addition to the head of-
fice at BGI in Shenzhen, China, we have also established
a hub at the Smithsonian National Museum of Natural
History (NMNH) in Washington DC, USA, to facilitate
quality sample collection from North America.
Species selection
Fish-T1K proposes to sequence 1,000 different ray-finned
fish species representing all the orders and major families
[4], and filling important gaps in the phylogenetic tree.
Table 1 List of fish species with published transcriptome data
in NCBI’s SRA, and those generated by Fish-T1K
Order No. of species
in SRA
No. of species
in Fish-T1K
No. of new species
generated by
Fish-T1K
Cypriniformes 42 5 3
Cyprinodontiformes 33 2 0
Perciformes 21 9 9
Cichliformes 15 2 2
Salmoniformes 14 0 0
Order-level incertae
sedis in Eupercaria
9 2 2
Pleuronectiformes 9 2 1
Osteoglossiformes 8 4 2
Siluriformes 8 9 8
Clupeiformes 6 1 1
Syngnathiformes 6 5 5
Gymnotiformes 5 2 1
Acipenseriformes 4 1 1
Anabantiformes 4 4 4
Anguilliformes 4 4 3
Centrarchiformes 4 4 3
Scombriformes 4 2 2
Beloniformes 3 2 2
Characiformes 3 6 6
Gadiformes 3 1 1
Order-level incertae
sedis in Ovalentaria
3 5 5
Tetraodontiformes 3 4 4
Carangiformes 2 2 1
Amiiformes 1 1 0
Batrachoidiformes 1 1 1
Blenniiformes 1 4 4
Esociformes 1 0 0
Labriformes 1 3 2
Lepisosteiformes 1 2 2
Ophidiiformes 1 2 2
Osmeriformes 1 0 0
Pempheriformes 1 2 2
Polypteriformes 1 3 3
Spariformes 1 2 2
Synbranchiformes 1 2 2
Argentiniformes 0 1 1
Atheriniformes 0 2 2
Aulopiformes 0 2 2
Chaetodontiformes 0 1 1
Elopiformes 0 1 1
Ephippiformes 0 2 2
Table 1 List of fish species with published transcriptome data
in NCBI’s SRA, and those generated by Fish-T1K (Continued)
Galaxiiformes 0 1 1
Gobiiformes 0 3 3
Holocentriformes 0 3 3
Kurtiformes 0 2 2
Lepidogalaxiiformes 0 1 1
Lobotiformes 0 1 1
Lophiiformes 0 2 2
Mugiliformes 0 2 2
Order-level incertae
sedis in
Carangimorphariae
0 3 3
Order-level incertae
sedis in
Percomorpharia
0 12 12
Percopsiformes 0 1 1
Uranoscopiformes 0 1 1
Zeiformes 0 1 1
others (Chondrichthyes
and Sarcopterygii)
17 / /
All 242 142 128
Sun et al. GigaScience  (2016) 5:18 
2
Species that are endangered, of great economic and med-
ical significance, or exhibit extreme phenotypes will also
be targeted. Candidate species will be decided based on
their importance and availability, while the target number
will be a compromise between scientific needs and prac-
tical limitations such as financial constraints and availabil-
ity of specimens.
Subprojects
To maximize usage of these transcripts, Fish-T1K has
launched several subprojects to address specific ques-
tions in fish evolution. The major research goal of Fish-
T1K is to reconstruct a comprehensive molecular
phylogeny of ray-finned fishes to further resolve and test
existing phylogenetic hypotheses. Additional subprojects
include analysis of the evolutionary genomics of fish
venoms, evolution of the annual life cycle in killifishes,
and adaptations related to marine-to-freshwater transi-
tions/migration.
SOPs and best practices
In the past two years, the Fish-T1K Team has estab-
lished a series of SOPs, approved by BGI’s Institutional
Review Board on Bioethics and Biosafety (No. BGI-IRB
15139), to ensure high quality sampling is achieved. Ad-
hering to these SOPs means that all of our genetic re-
sources, data and associated metadata are appropriately
obtained, documented, and stored, which is helpful in
establishing and optimizing standards common to large-
scale transcriptome and genome sequencing projects.
Transcriptome data from multiple tissues of five fishes
were generated as a pilot quality control test (Additional
file 4). Accordingly, total RNA is now routinely extracted
from gills and other tissues of interest, and approxi-
mately 3.5 Gb of raw data are generated for each sample.
Clean reads are assembled de novo into contigs with
SOAPdenovo-Trans (v1.3) [5], and the final assembled
transcripts are used for annotation, ortholog prediction
and other analyses.
Current RNA sequencing progress
The Fish-T1K team has established a collaborative global
network for collecting specimens. As of January 2016,
7,000 high quality fish samples were collected from
Australia, the Caribbean, Denmark, Singapore, the UK,
USA, and many places in China such as the Tibetan
Plateau, Sanya, and the Yellow Sea. From these 7,000
samples, RNA samples were extracted from 142 ray-
finned species covering 51 orders and 109 families, and
around 180 transcriptomes have been produced (Table 1;
Additional file 5). Meanwhile, more RNA samples from
other species are being isolated and sequenced.
Website and database
The official Fish-T1k website [6] is equipped with a data-
base for BLAST search. The website provides detailed
information about the Fish-T1K project, and particular
sample information (RNA quality, sample provider, etc.)
and data quality (raw data size, scaffold size and number,
etc.) are presented in the database. Users can access the
BLAST tool and download sequences of interest. Data
Fig. 1 Distribution of Fish-T1K Consortium members. See detailed information of these numbered institutions in Additional file 3
Sun et al. GigaScience  (2016) 5:18 
3
will be uploaded periodically as sample collection and
transcriptome sequencing progresses.
Data sharing policy and data availability
All sequences generated from Fish-T1K will be deposited
in NCBI and GigaDB in addition to the Fish-T1K data-
base, following the Fort Lauderdale rules [7] and To-
ronto International Data Release Workshop guidelines
[8], and will be released at least in the time of publica-
tion of any resulting papers. We plan to peer review and
publish the SOP and method papers, will be published
and we’re expecting publications for some of the on-
going subprojects are also expected in one the coming
year or sooner.
Fish-T1K membership
All are welcome to participate in Fish-T1K and to propose
new subprojects; these should address a major question in
fish evolution and lead to (a) significant publication(s). In-
terested researchers can email fisht1k@genomics.cn with
a brief proposal. The significance, question(s) to be ad-
dressed and fishes/tissues to be sequenced and analyzed
should be included. On acceptance of a proposal, the lead
scientist(s) will be asked to collect any fish tissues that are
not already in our list, and to be in charge of analyzing
and publishing the generated data.
Conclusions
Similar initiatives already exist to sequence the tran-
scriptomes of large numbers of plants (1KP [9]) and in-
sects (1KITE [10]). They have been well received and
have been useful in establishing Fish-T1K. Although
some progress has already been made, the Fish-T1K is at
an early stage. We will continue to expand the scope of
the project: in the first phase we aim to cover all orders,
and all families in the second phase. More species will
be added as required by subprojects. As the world’s first
large-scale transcriptome database exclusively for fish,
Fish-T1K will greatly enhance the study of fish biology,
and eventually contribute efforts towards global fish bio-
diversity conservation and the sustainable utilization of
natural fish resources.
Additional files
Additional file 1: List of fishes with published genome data. (DOCX 30 kb)
Additional file 2: Number of fish species with newly published
transcriptomes in SRA of the NCBI from 2009 to 2015. (TIF 4045 kb)
Additional file 3: List of the current Fish-T1K Consortium members.
(DOCX 19 kb)
Additional file 4: Transcriptome data of five species for quality control.
(DOCX 20 kb)
Additional file 5: List of fishes with transcriptome data generated by
Fish-T1K. (XLSX 87 kb)
Abbreviations
1KITE: 1 K Insect Transcriptome Evolution; 1KP: 1000 Plants;
Fish-T1K: transcriptomes of 1,000 Fishes; NGS: next-generation sequencing;
RNA-seq: RNA sequencing; SOPs: standard operating procedures.
SRA: Sequence Read Archive.; SRA: Sequence Read Archive.
Competing interests
The authors declare that they have no competing interests.
Authors’ contributions
YS drafted the original text with detailed input from YH, XL, GO, BV and QS.
All authors have read and approved the final manuscript and participated in
Fish-T1K.
Acknowledgements
We wish to acknowledge the Fish-T1K Consortium members, partners,
advisors and supporters who have made Fish-T1K possible. We would also
like to thank Junxing Yang from the Kunming Institute of Zoology of the
Chinese Academy of Sciences, Qiang Lin from South China Sea Institute of
Oceanology of the Chinese Academy of Sciences, Carol Stepien from the
University of Toledo, Luiz Rocha from the California Academy of Sciences,
Donald Stewart from the State University of New York College of
Environmental Science and Forestry, and Andrew Thompson from The
George Washington University for their tremendous support with sample
collection.
Funding
This work was supported by China 863 Projects (No. 2012AA10A407 &
2014AA093501), Shenzhen and Hong Kong Innovation Circle Project (No.
SGLH20131010105856414), Shenzhen Special Program for Future Industrial
Development (No. JSGG20141020113728803), Shenzhen Special Program for
Bio-industry Development (Nos. HY20130205008 and NYSW20130326010014)
and Special Project on the Integration of Industry, Education and Research of
Guangdong Province (No. 2013B090800017). A grant from the Smithsonian In-
stitution (Biogenomics/GGI) to C. Baldwin, G. Orti, and R. Betancur provides par-
tial funding for RNA extractions at the NMNH (Washington, DC, USA).
Author details
1State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals
and Guangdong Provincial Key Laboratory for Aquatic Economic Animals,
School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
2Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of
Molecular Breeding in Marine Economic Animals, BGI, Shenzhen 518083, China.
3National Museum of Natural History, Smithsonian Institution, Washington, DC
20560, USA. 4China Fisheries Association, Beijing 100000, China. 5China National
Genebank, Shenzhen, 518083, China. 6Department of Biological Sciences, The
George Washington University, Washington, DC 20052, USA. 7BGI-Zhenjiang
Institute of Hydrobiology, Zhenjiang 212000, China. 8BGI-Hong Kong, Hong
Kong 999077, China. 9Sanya Science and Technology Academy for Crop Winter
Multiplication, Hainan 572000, China. 10Oceanographic Center, Nova
Southeastern University, Fort Lauderdale 33004, USA. 11Institute of Molecular
and Cell Biology, A*STAR, Singapore 138673, Singapore. 12College of Life
Sciences, Shenzhen University, Shenzhen 518060, China.
Received: 10 December 2015 Accepted: 14 April 2016
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