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| Status |
Public on Jun 01, 2017 |
| Title |
Sequencing of the stomach-less ballan wrasse (Labrus berggylta) genome and transcriptomic characterization of the intestine |
| Organism |
Labrus bergylta |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Stomach-less fishes comprise a diverse phylogenetic group within the teleosts indicating that the organ has been lost several times during evolution. In the present project we have combined Illumina short read platform with the PacBio long read platform to sequence the ballan wrasse (Labrus bergylta) genome and its intestinal transcriptome. The genome was applied to investigate the elimination and conservation of genes related to stomach function and appetite regulation in wrasse in relation to the loss of stomach in this species. We have sequenced the transcriptome of four intestinal segments from six ballan wrasse (Labrus bergylta) for the purpose of identifying possible functional organization along the wrasse intestine. The transcriptomic reads were mapped against the newly assembled genome. The analysis revealed a transcriptional gradient showing genes involved in nutrient digestion and uptake being highly expressed in the anterior intestine and declining towards the end of the intestine. The last segment, hind-gut, had the most distinct expression between the four segments with increased expression of genes coding for proteins involved in lysosomal activity, antigen presenting and vitamin b12 uptake. Overall, our results suggests that the wrasse entire digestive system is comparable to the small intestine of mammals with regards to gene expression missing both a stomach and colon. Gene expression related to colon in humans such as MS4A12 were found in the last segment. The genome analysis also confirmed the lack of genes coding for gastric proteins such as gastric lipase, pepsin, gastrin and ghrelin. Although ghrelin is not only related to stomach, ghrelin was missing in all stomach-less fish species with the exception of cyprinid. Ghrelin is currently the only known orexigenic hormone.
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| Overall design |
Six ballan wrasse (Labrus bergylta) were collected from a commercial fish farm. Four segments of the intestine from the anterior to the posterior part was sampled from each fish. RNA from each segment were sequenced seperatly and analyzed.
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| Contributor(s) |
Lie KK, Tørresen OK, Solbakken MH, Tooming-Klunderud A, Nederbragt L, Sæle Ø |
| Citation(s) |
29510660 |
| |
| Submission date |
Jan 05, 2017 |
| Last update date |
Feb 19, 2020 |
| Contact name |
Kai Kristoffer Lie |
| E-mail(s) |
kli@hi.no
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| Organization name |
Institute of Marine research
|
| Department |
Feed Safety
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| Street address |
Pobox 2029 Nordnes
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| City |
Bergen |
| State/province |
Hordaland |
| ZIP/Postal code |
5817 |
| Country |
Norway |
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| Platforms (1) |
| GPL22892 |
Illumina HiSeq 2000 (Labrus bergylta) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA360275 |
| SRA |
SRP096123 |
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