| Accession |
PRJCA003510 |
| Title |
A high-quality draft genome of white-blotched river stingray (Potamotrygon leopoldi) |
| Relevance |
Evolution |
| Data types |
Whole genome sequencing
Genome sequencing and assembly
Raw sequence reads
Genome sequencing
|
| Organisms |
Potamotrygon leopoldi
|
| Description |
White-blotched river stingray (Potamotrygon leopoldi) is a rare freshwater cartilaginous fish with unique biological features. For its disc-like body shape and bizarre color pattern, P. leopoldi is sometimes kept as an aquarium pet. In this study, we present its high-quality draft genome of 4.39 Gb, which has contig N50 of 4.33 Gbp and scaffold N50 of 4.35 Gbp in size. Our analysis shows that P. leopoldi is slow- evolving, diverged from elephant shark about 96 million years ago. Compared genomic data to five other fish species, two gene families related to immune system, immunoglobulin heavy constant delta genes, and T-cell receptor alpha/delta variable genes, stand out expanded in P. leopoldi, suggesting robustness in response to freshwater pathogens in adapting novel environments, whereas seven Hox genes shared by the others are found missing in P. leopoldi. Our RNA-seq data from six P. leopoldi tissues exhibit more diversified expression as compared with the same tissues of mammals. Moreover, we find that both P. leopoldi and elephant shark appear lost a unique vitamin D-binding protein gene. A knockdown zebrafish model of this gene validates involvement of hard skeleton formation. The P. leopoldi genome data, joining to more than 30 fish genomes, serve as an information bonanza for fish and evolution biologists. |
| Sample scope |
Monoisolate |
| Release date |
2020-09-22 |
| Publication |
| PubMed ID |
Article title |
Journal name |
DOI |
Year |
| 36470576
|
Draft Genome of White-blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation
|
Genomics, Proteomics & Bioinformatics
|
10.1016/j.gpb.2022.11.005
|
2022
|
|
|
| Grants |
| Agency |
program |
Grant ID |
Grant title |
| 上海南睦林生物科技有限公司
|
|
N/A
|
|
|
|
| Submitter |
Libing
Shen (libingshen12@fudan.edu.cn)
|
| Organization |
Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences |
| Submission date |
2020-09-22 |
