Fish-T1K (Transcriptomes of 1,000 Fishes) Project: Large-Scale Transcriptome Data for Fish Evolution Studies

Ying Sun; Yu Huang; Xiaofeng Li; Carole C. Baldwin; Zhuocheng Zhou; Zhixiang Yan; Keith A. Crandall; Yong Zhang; Xiaomeng Zhao; Min Wang; Alex Wong; Chao Fang; Xinhui Zhang; Hai Huang; Jose V Lopez; Kirk Kilfoyle; Yong Zhang; Guillermo Orti; Byrappa Venkatesh; Qiong Shi

doi:10.1186/s13742-016-0124-7

Fish-T1K (Transcriptomes of 1,000 Fishes) Project: Large-Scale Transcriptome Data for Fish Evolution Studies

Ying Sun
, Yu Huang
, Xiaofeng Li
, Carole C. Baldwin
, Zhuocheng Zhou
, Zhixiang Yan
, Keith A. Crandall
, Yong Zhang
, Xiaomeng Zhao
, Min Wang
, Alex Wong
, Chao Fang
, Xinhui Zhang
, Hai Huang
, Jose V Lopez
, Kirk Kilfoyle
, Yong Zhang
, Guillermo Orti
, Byrappa Venkatesh
, Qiong Shi

Department of Biological Sciences

Research output: Contribution to journal › Article › peer-review

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.

Original language	American English
Article number	18
Journal	GigaScience
Volume	5
Issue number	1
DOIs	https://doi.org/10.1186/s13742-016-0124-7
State	Published - May 3 2016

Bibliographical note

Publisher Copyright:
© 2016 Sun et al.

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 Institution (Biogenomics/GGI) to C. Baldwin, G. Orti, and R. Betancur provides partial funding for RNA extractions at the NMNH (Washington, DC, USA).

Funders	Funder number
China 863 Projects	2014AA093501, 2012AA10A407
Integration of Industry, Education and Research of Guangdong Province	2013B090800017
Shenzhen Special Program for Bio-industry Development	HY20130205008, NYSW20130326010014
Shenzhen Special Program for Future Industrial Development	JSGG20141020113728803
Shenzhen and Hong Kong Innovation Circle Project	SGLH20131010105856414
National Science Foundation	1541554
Smithsonian Institution
National Museum of Natural History

ASJC Scopus Subject Areas

General Medicine

Keywords

Biodiversity
Database
Fish
Fish-T1K
RNA
Transcriptome
Gene Expression Profiling/methods
Geography
Species Specificity
Databases, Genetic
International Cooperation
Fishes/classification
Animals
Research/organization & administration
Evolution, Molecular
Sequence Analysis, RNA/methods

Disciplines

Genetics and Genomics

Access to Document

10.1186/s13742-016-0124-7

http://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0124-7

Cite this

Sun, Y., Huang, Y., Li, X., Baldwin, C. C., Zhou, Z., Yan, Z., Crandall, K. A., Zhang, Y., Zhao, X., Wang, M., Wong, A., Fang, C., Zhang, X., Huang, H., Lopez, J. V., Kilfoyle, K., Zhang, Y., Orti, G., Venkatesh, B., & Shi, Q. (2016). Fish-T1K (Transcriptomes of 1,000 Fishes) Project: Large-Scale Transcriptome Data for Fish Evolution Studies. GigaScience, 5(1), Article 18. https://doi.org/10.1186/s13742-016-0124-7

Sun, Y, Huang, Y, Li, X, Baldwin, CC, Zhou, Z, Yan, Z, Crandall, KA, Zhang, Y, Zhao, X, Wang, M, Wong, A, Fang, C, Zhang, X, Huang, H, Lopez, JV, Kilfoyle, K, Zhang, Y, Orti, G, Venkatesh, B & Shi, Q 2016, 'Fish-T1K (Transcriptomes of 1,000 Fishes) Project: Large-Scale Transcriptome Data for Fish Evolution Studies', GigaScience, vol. 5, no. 1, 18. https://doi.org/10.1186/s13742-016-0124-7

@article{f191128924544b028a02e1698c2b62fd,

title = "Fish-T1K (Transcriptomes of 1,000 Fishes) Project: Large-Scale Transcriptome Data for Fish Evolution Studies",

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 {\textquoteleft}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 = "Biodiversity, Database, Fish, Fish-T1K, RNA, Transcriptome, Gene Expression Profiling/methods, Geography, Species Specificity, Databases, Genetic, International Cooperation, Fishes/classification, Animals, Research/organization \& administration, Evolution, Molecular, Sequence Analysis, RNA/methods",

author = "Ying Sun and Yu Huang and Xiaofeng Li and Baldwin, \{Carole C.\} and Zhuocheng Zhou and Zhixiang Yan and Crandall, \{Keith A.\} and Yong Zhang and Xiaomeng Zhao and Min Wang and Alex Wong and Chao Fang and Xinhui Zhang and Hai Huang and Lopez, \{Jose V\} and Kirk Kilfoyle and Yong Zhang and Guillermo Orti and Byrappa Venkatesh and Qiong Shi",

note = "Publisher Copyright: {\textcopyright} 2016 Sun et al.",

year = "2016",

month = may,

day = "3",

doi = "10.1186/s13742-016-0124-7",

language = "American English",

volume = "5",

journal = "GigaScience",

issn = "2047-217X",

number = "1",

}

TY - JOUR

T1 - Fish-T1K (Transcriptomes of 1,000 Fishes) Project: Large-Scale Transcriptome Data for Fish Evolution Studies

AU - Sun, Ying

AU - Huang, Yu

AU - Li, Xiaofeng

AU - Baldwin, Carole C.

AU - Zhou, Zhuocheng

AU - Yan, Zhixiang

AU - Crandall, Keith A.

AU - Zhang, Yong

AU - Zhao, Xiaomeng

AU - Wang, Min

AU - Wong, Alex

AU - Fang, Chao

AU - Zhang, Xinhui

AU - Huang, Hai

AU - Lopez, Jose V

AU - Kilfoyle, Kirk

AU - Zhang, Yong

AU - Orti, Guillermo

AU - Venkatesh, Byrappa

AU - Shi, Qiong

PY - 2016/5/3

Y1 - 2016/5/3

N2 - 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.

AB - 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.

KW - Biodiversity

KW - Database

KW - Fish

KW - Fish-T1K

KW - RNA

KW - Transcriptome

KW - Gene Expression Profiling/methods

KW - Geography

KW - Species Specificity

KW - Databases, Genetic

KW - International Cooperation

KW - Fishes/classification

KW - Animals

KW - Research/organization & administration

KW - Evolution, Molecular

KW - Sequence Analysis, RNA/methods

UR - https://nsuworks.nova.edu/cnso_bio_facarticles/389

UR - http://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0124-7

UR - https://www.scopus.com/pages/publications/84992416483

UR - https://www.scopus.com/pages/publications/84992416483#tab=citedBy

U2 - 10.1186/s13742-016-0124-7

DO - 10.1186/s13742-016-0124-7

M3 - Article

C2 - 27144000

SN - 2047-217X

VL - 5

JO - GigaScience

JF - GigaScience

IS - 1

M1 - 18

ER -

Fish-T1K (Transcriptomes of 1,000 Fishes) Project: Large-Scale Transcriptome Data for Fish Evolution Studies

Abstract

Bibliographical note

Funding

ASJC Scopus Subject Areas

Keywords

Disciplines

Access to Document

Other files and links

Fingerprint

Cite this