Fish-T1K (Transcriptomes of 1,000 Fishes) Project: large-scale transcriptome data for fish evolution studies

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

doi:10.1186/s13742-016-0124-7

Cited by 49 publications

(40 citation statements)

References 6 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Taxonomic Sampling and RNA Sequencing. A total of 131 transcriptomes included in this study were newly sequenced as a part of the Transcriptomes of 1,000 Fishes Project (Fish-T1K) (20). Specimens representing all major lineages of fishes were collected in the field by numerous colleagues around the world (SI Appendix, Table S1).…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

Hughes

Ortı́

Huang

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

496

607

View full text Add to dashboard Cite

Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genome-scale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We apply phylogenetic tests designed to trace the effect of whole-genome duplication events on gene trees and find paralogy-free loci using a bioinformatics approach. Genome-wide data support the structure of the fish phylogeny, and hypothesis-testing procedures appropriate for phylogenomic datasets using explicit gene genealogy interrogation settle some long-standing uncertainties, such as the branching order at the base of the teleosts and among early euteleosts, and the sister lineage to the acanthomorph and percomorph radiations. Comprehensive fossil calibrations date the origin of all major fish lineages before the end of the Cretaceous.

show abstract

Section: Methodsmentioning

confidence: 99%

“…To expand currently available genomic resources for fishes, we established an international consortium (20) to sequence transcriptomes sampled from a wide taxonomic diversity (https://db. cngb.org/fisht1k/).…”

Section: This Article Is a Pnas Direct Submissionmentioning

confidence: 99%

Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

Hughes

Ortı́

Huang

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

496

607

View full text Add to dashboard Cite

show abstract

“…For example, a supermatrix of 1,110 genes from 22 actinopterygians was assembled to resolve controversies regarding the evolution of the Otocephalan group (Dai et al, 2018). Recently, the international project “Transcriptomes of 1,000 Fishes” (Fish-T1K) (Sun et al, 2016) published a massive phylogenomic analysis including more than 300 fish species (Hughes et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling

Natsidis

Tsakogiannis

Pavlidis

et al. 2019

Preprint

View full text Add to dashboard Cite

19Sparidae (Teleostei: Spariformes) are a family of fish constituted by approximately 150 20 species with high popularity and commercial value, such as porgies and seabreams. Although 21 the phylogeny of this family has been investigated multiple times, its position among other 22 teleost groups remains ambiguous. Most studies have used a single or few genes to decipher 23 the phylogenetic relationships of sparids. Here, we conducted a phylogenomic attempt to 24 resolve the position of the family using five recently available Sparidae gene-sets and 26 25 available fish proteomes from species with a sequenced genome, to ensure higher quality of 26 the predicted genes. A thorough phylogenomic analysis suggested that Tetraodontiformes 27 (puffer fish, sunfish) are the closest relatives to sparids than all other groups used, a finding 28 that contradicts our previous phylogenomic analysis that proposed the yellow croaker and the 29 european seabass as closest taxa of sparids. By analytically comparing the methodologies 30 applied in both cases, we show that this discordance is not due to different orthology 31 assignment algorithms; on the contrary, we prove that it is caused by the increased taxon 32 sampling of the present study, outlining the great importance of this aspect in phylogenomic 33 analyses in general. 34 35 Keywords: Sparidae; fish phylogenomics; orthology assignment; jackknife phylogeny test; 36 taxon sampling; 37Teleostei represent the dominant group within ray-finned fish (Actinopterygii), with 39 more than 26,000 extant species. Their evolution has been extensively studied through past 40 decades, using a variety of data including fossil records, morphological characters and 41 molecular data, leading to a gradual resolution of teleost phylogeny (Betancur-R. et al., 2013(Betancur-R. et al., 42 & 2017. 43 With the continuous emergence of new whole-genome sequences, phylogenomic 44 techniques are applied to characterise the evolutionary relationships among species. Whole-45 genome information can help in resolving uncertain nodes, as well as provide stronger evidence 46 on already established relationships. Regarding fish phylogeny, several genome-wide 47 approaches have been implemented so far. One of the first efforts to study ray-finned fish 48 phylogenomics was conducted by (Li et al., 2007). Since then, several studies have been 49 published using not only gene markers, but also noncoding elements such as the work of 50 (Faircloth et al., 2013) who used UCE (ultra-conserved elements) to investigate the 51 diversification of basal clades in ray-finned fish. Most genome papers include a phylogenomic 52 analysis albeit with limited taxon sampling (e.g. Vij et al., 2016 and Xu et al., 2017), while the 53 use of whole-transcriptome data is being employed to uncover phylogenetic relationships of 54 specific taxonomic groups as well (Dai et al., 2018; Rodgers et al., 2018). With the emergence 55 of new genomes and the possibilities of modern sequencing technologies, bigger datasets are ...

show abstract

“…With few exceptions, all fish have genes for IgM, IgD, and most for IgT. Representative sequences for the IgT were used to search the Fish-T1K (Sun et al, 2016) repository that contains transcriptome sequences for 124 fish species, shown in Table S3. Additionally, a bibliographic search was carried out since 2005 to identify the different IgT that have been published in teleosts (see Table S2).…”

Section: Resultsmentioning

confidence: 99%

Immunoglobulin T genes in Neopterygii

Mirete-Bachiller

Olivieri

Gambón-Deza

2020

Preprint

View full text Add to dashboard Cite

In teleost fishes there are three immunoglobulin isotypes named immunoglobulin M (IgM), D (IgD) and T (IgT). IgT has been the last to be described and is considered a teleosts-fish specific isotype. From the recent availability of genome sequences of fishes, an in-depth analysis of Actinopterygii immunoglobulin heavy chain genes was undertaken. With the aid of a bioinformatics pipeline, a machine learning software, CHfinder, was developed that identifies the coding exons of the CH domains of fish immunoglobulins. Using this pipeline, a high number of such sequences were obtained from teleosts and holostean fishes. IgT was found in teleost and holostean fishes that had not been previously described. A phylogenetic analysis reveals that IgT CH1 exons are similar to the IgM CH1. This analysis also demonstrates that the other three domains (CH2, CH3 and CH4) were not generated by recent duplication processes of IgM in Actinopterygii, indicating it is an immunoglobulin with an earlier origin.

show abstract

Fish-T1K (Transcriptomes of 1,000 Fishes) Project: large-scale transcriptome data for fish evolution studies

Cited by 49 publications

References 6 publications

Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling

Immunoglobulin T genes in Neopterygii

Contact Info

Product

Resources

About