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Goldfish, one of the first animals domesticated for ornamental purposes, experience huge morphological variation, of which the number changes in tailfins and the loss of dorsal fins is the most impressive due to their important functions in fish. In the present study, a transcriptome analysis of the tailfins of Grass- (with complete dorsal fin and a single tailfin), and Egg-goldfish (loss of dorsal fin and double tail fins) was carried out to determine the sequence variants, to detect differential gene expression patterns in transcriptomes, and to characterize the effects of selection and identify target genes under selection. In total, 124,808,475 and 101,965,939 high quality reads were obtained from the tailfins of Grass- and Egg-goldfish, respectively, and 114,796 unigenes were further assembled from over 33.48 Gb nucleotides. A large portion of unigenes related to various primary and secondary metabolite pathways were identified, and the differentially expressed genes (DEGs) between the tailfins from Grass- and Egg-goldfish were also generally enriched in the metabolite pathways, for instant, the PI3K−Akt signalling pathway, the MAPK signalling pathway, osteoclast differentiation, and the dorso-ventral axis formation, all relating to cell proliferation, growth, and differentiation. These identified DEGs (HOXA2b, HOXB13a, paired mesoderm homeobox protein 1-like isoform X2 (PRRX2), zinc finger E-box-binding homeobox 1-like isoform X3 (ZEB1), and homeobox protein (Meis1), presumably played an important role in the development of the double tail fins during the artificial selection for ornamental purposes.
Keywords
goldfish, high-throughput sequencing, morphological variation, gene expression difference
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Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
- tableS1.xlsx
Table S1 unigenes were significantly down-regulated (log2-FC ≤ -1, q-value < 0.05, TMM-normalized FPKM > 0.3) in tailfin of Grass-goldfish vs. Egg-goldfish
- tableS2.xlsx
Table S2 unigenes were significantly up-regulated (log2-FC ≤ -1, q-value < 0.05, TMM-normalized FPKM > 0.3) in tailfin of Grass-goldfish vs. Egg-goldfish
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This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Research Article
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 22 Apr, 2021
No community comments so far
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Marine and Freshwater Biology
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Goldfish, one of the first animals domesticated for ornamental purposes, experience huge morphological variation, of which the number changes in tailfins and the loss of dorsal fins is the most impressive due to their important functions in fish. In the present study, a transcriptome analysis of the tailfins of Grass- (with complete dorsal fin and a single tailfin), and Egg-goldfish (loss of dorsal fin and double tail fins) was carried out to determine the sequence variants, to detect differential gene expression patterns in transcriptomes, and to characterize the effects of selection and identify target genes under selection. In total, 124,808,475 and 101,965,939 high quality reads were obtained from the tailfins of Grass- and Egg-goldfish, respectively, and 114,796 unigenes were further assembled from over 33.48 Gb nucleotides. A large portion of unigenes related to various primary and secondary metabolite pathways were identified, and the differentially expressed genes (DEGs) between the tailfins from Grass- and Egg-goldfish were also generally enriched in the metabolite pathways, for instant, the PI3K−Akt signalling pathway, the MAPK signalling pathway, osteoclast differentiation, and the dorso-ventral axis formation, all relating to cell proliferation, growth, and differentiation. These identified DEGs (HOXA2b, HOXB13a, paired mesoderm homeobox protein 1-like isoform X2 (PRRX2), zinc finger E-box-binding homeobox 1-like isoform X3 (ZEB1), and homeobox protein (Meis1), presumably played an important role in the development of the double tail fins during the artificial selection for ornamental purposes.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
- tableS1.xlsx
Table S1 unigenes were significantly down-regulated (log2-FC ≤ -1, q-value < 0.05, TMM-normalized FPKM > 0.3) in tailfin of Grass-goldfish vs. Egg-goldfish
- tableS2.xlsx
Table S2 unigenes were significantly up-regulated (log2-FC ≤ -1, q-value < 0.05, TMM-normalized FPKM > 0.3) in tailfin of Grass-goldfish vs. Egg-goldfish
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