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| Status |
Public on Aug 24, 2020 |
| Title |
Identification and characterization of microRNAs (miRNAs) and their transposable element origins in the saltwater crocodile, Crocodylus porosus |
| Organism |
Crocodylus porosus |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
MicroRNAs (miRNAs) are 18-24 nucleotide autonomous regulatory RNA molecules found in all eukaryotes. They are involved in the regulation of a multitude of genetic and biological pathways through post transcriptional gene silencing and/or translational repression. Previous data has suggested a slow evolutionary rate for the saltwater crocodile (Crocodylus porosus) over the past several million years when compared to its closest extant relatives, the birds. Understanding genome regulation, adaptive capabilities and physiological features in the saltwater crocodile in the context of relatively slow genomic change thus holds significant potential for the investigation of genomics, evolution and adaptive studies. Utilizing eleven different tissue types and sixteen small RNA libraries, we report a catalog of 644 miRNAs in the saltwater crocodile with > 78% of miRNAs being potentially novel to crocodilians. We also predicted and identified targets for the miRNAs as well as analyzed the relationship of the miRNA repertoire to transposable elements (TEs) in the saltwater crocodile that showed an increased association of DNA transposons with miRNA biogenesis when compared to retrotransposons. Phylogenetic analysis of C. porosus miRNA expectedly revealed highest number of miRNAs in sister crocodilian clades of the American Alligator and the Indian Gharial. This work reports the first comprehensive analysis of miRNAs in Crocodylus porosus for and addresses the potential impacts of miRNAs in regulating the genome in the saltwater crocodile as well as supporting the role of TEs as a source for miRNAs, adding to the increasing evidence that TEs play a significant role in the evolution of gene regulation.
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| Overall design |
Construction of Illumina Deep sequening small RNA libraries in 11 different tissue typoes in the C porosus and bioinformatic analysis to predict C porosus known and novel miRNAs, their targets, expression profiles and other genomic features of the miRNAs in the C porosus
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| Contributor(s) |
Ghosh A, Platt RN, Vandewege MW, Isberg SR, Glenn TC, Peterson DG, Hsu C, Finger JW, Kieran T, Gongora J, Tabassum R, Ray DA |
| Citation(s) |
32485163 |
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| Submission date |
May 13, 2020 |
| Last update date |
Aug 24, 2020 |
| Contact name |
ARNAB GHOSH |
| Organization name |
Texas Tech University
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| Department |
Biology
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| Street address |
2500 Broadway
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| City |
Lubbock |
| State/province |
Texas |
| ZIP/Postal code |
79409 |
| Country |
USA |
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| Platforms (1) |
| GPL28534 |
Illumina HiSeq 2500 (Crocodylus porosus) |
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| Samples (60)
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| Relations |
| BioProject |
PRJNA632490 |
| SRA |
SRP261402 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE150461_Data_process_GEO_May2020_Ghosh_Ray.xlsx |
75.6 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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