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| Status |
Public on Apr 01, 2024 |
| Title |
Dynamic co-evolution of transposable elements and the piRNA pathway in East African cichlid fishes |
| Organisms |
Oreochromis niloticus; Haplochromis burtoni; Astatotilapia calliptera; Maylandia zebra; Tropheops sp. 'mauve'; Pundamilia nyererei |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. Orthology inference revealed an expansion of piwil1 genes in Lake Malawi cichlids, likely driven by PiggyBac TEs. The expanded piwil1 copies have signatures of positive selection and retain amino acid residues essential for catalytic activity. Furthermore, the gonads of African cichlids express a Piwi-interacting RNA (piRNA) pathway that target TEs. We define the genomic sites of piRNA production in African cichlids and find divergence in closely related species, in line with fast evolution of piRNA-producing loci. Our findings suggest dynamic co-evolution of TEs and host silencing pathways in the African cichlid radiations. We propose that this co-evolution has contributed to cichlid genomic diversity.
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| Overall design |
To profile transposable element expression in the East African cichlid radiation, we have sequenced mRNA from ovaries, testes, and brains of cichlid species representative of the three East African Great Lakes, as well as of Nile Tilapia (Orechromis niloticus) an outgroup to radiating cichlids.
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| Contributor(s) |
Almeida MV, Price JL, Miska EA |
| Citation(s) |
38617250 |
| Submission date |
Jan 09, 2024 |
| Last update date |
May 02, 2024 |
| Contact name |
Miguel Vasconcelos Almeida |
| E-mail(s) |
miguelddv.almeida@gmail.com, mdd34@cam.ac.uk
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| Organization name |
University of Cambridge
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| Department |
Department of Biochemistry
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| Street address |
Tennis Court Road
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| City |
Cambridge |
| ZIP/Postal code |
CB2 1GA |
| Country |
United Kingdom |
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| Platforms (6)
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| GPL29385 |
Illumina NovaSeq 6000 (Oreochromis niloticus) |
| GPL30104 |
Illumina NovaSeq 6000 (Astatotilapia calliptera) |
| GPL34066 |
Illumina NovaSeq 6000 (Maylandia zebra) |
| GPL34067 |
Illumina NovaSeq 6000 (Tropheops sp. 'mauve') |
| GPL34068 |
Illumina NovaSeq 6000 (Haplochromis burtoni) |
| GPL34069 |
Illumina NovaSeq 6000 (Pundamilia nyererei) |
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| Samples (40)
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| GSM8008055 |
A. calliptera, ovary, rep4 |
| GSM8008056 |
A. calliptera, testes, rep1 |
| GSM8008057 |
A. calliptera, testes, rep2 |
| GSM8008058 |
A. calliptera, testes, rep3 |
| GSM8008059 |
A. calliptera, testes, rep4 |
| GSM8008060 |
M. zebra, testes, rep1 |
| GSM8008061 |
M. zebra, testes, rep2 |
| GSM8008062 |
T. mauve, testes, rep1 |
| GSM8008063 |
T. mauve, testes, rep2 |
| GSM8008064 |
T. mauve, testes, rep3 |
| GSM8008065 |
T. mauve, testes, rep4 |
| GSM8008066 |
A. calliptera, female brain, rep1 |
| GSM8008067 |
A. calliptera, female brain, rep2 |
| GSM8008068 |
A. calliptera, female brain, rep3 |
| GSM8008069 |
A. calliptera, male brain, rep1 |
| GSM8008070 |
A. calliptera, male brain, rep2 |
| GSM8008071 |
A. calliptera, male brain, rep3 |
| GSM8008072 |
A. burtoni, ovary, rep1 |
| GSM8008073 |
A. burtoni, ovary, rep2 |
| GSM8008074 |
A. burtoni, ovary, rep4 |
| GSM8008075 |
A. burtoni, testes, rep1 |
| GSM8008076 |
A. burtoni, testes, rep2 |
| GSM8008077 |
A. burtoni, testes, rep3 |
| GSM8008078 |
A. burtoni, testes, rep4 |
| GSM8008079 |
P. nyererei, ovary, rep1 |
| GSM8008080 |
P. nyererei, ovary, rep2 |
| GSM8008081 |
P. nyererei, ovary, rep3 |
| GSM8008082 |
P. nyererei, testes, rep1 |
| GSM8008083 |
P. nyererei, testes, rep2 |
| GSM8008084 |
P. nyererei, testes, rep3 |
| GSM8008085 |
P. nyererei, testes, rep4 |
| GSM8008086 |
O. niloticus, ovary, rep1 |
| GSM8008087 |
O. niloticus, ovary, rep2 |
| GSM8008088 |
O. niloticus, ovary, rep3 |
| GSM8008089 |
O. niloticus, testes, rep1 |
| GSM8008090 |
O. niloticus, testes, rep2 |
| GSM8008091 |
O. niloticus, testes, rep3 |
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| Relations |
| BioProject |
PRJNA1062739 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE252805_NormCounts_mRNA_TEs_Abur.txt.gz |
47.3 Kb |
(ftp)(http) |
TXT |
| GSE252805_NormCounts_mRNA_TEs_Acal.txt.gz |
54.5 Kb |
(ftp)(http) |
TXT |
| GSE252805_NormCounts_mRNA_TEs_Malawi_curatedTEAnnotation.txt.gz |
66.0 Kb |
(ftp)(http) |
TXT |
| GSE252805_NormCounts_mRNA_TEs_Onil.txt.gz |
45.8 Kb |
(ftp)(http) |
TXT |
| GSE252805_NormCounts_mRNA_TEs_Pnye.txt.gz |
45.8 Kb |
(ftp)(http) |
TXT |
| GSE252805_lengthScaledTPM_mRNA_Acal_brain_gonads.txt.gz |
2.0 Mb |
(ftp)(http) |
TXT |
| GSE252805_rawCounts_mRNA_Acal_brain_gonads.txt.gz |
732.2 Kb |
(ftp)(http) |
TXT |
| GSE252805_rawCounts_mRNA_GenesAndTEs_Abur.txt.gz |
341.0 Kb |
(ftp)(http) |
TXT |
| GSE252805_rawCounts_mRNA_GenesAndTEs_Acal.txt.gz |
411.9 Kb |
(ftp)(http) |
TXT |
| GSE252805_rawCounts_mRNA_GenesAndTEs_Malawi_curatedTEAnnotation.txt.gz |
638.6 Kb |
(ftp)(http) |
TXT |
| GSE252805_rawCounts_mRNA_GenesAndTEs_Onil.txt.gz |
365.9 Kb |
(ftp)(http) |
TXT |
| GSE252805_rawCounts_mRNA_GenesAndTEs_Pnye.txt.gz |
328.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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