Journal Article
Discovery of putative long non‑coding RNAs expressed in the eyes of Astyanax mexicanus (Actinopterygii: Characidae)
Batista da Silva, I., Barbosa, D.A., Kavalco, K.F., Nunes, L.R., Pasa, R. and Menegidio, F.B.
Record Number:
6246
Year:
2023
Journal:
Scientific Reports
Pages:
1-16
Volume:
13:12051
Abstract:
Astyanax mexicanus is a well-known model species, that has two morphotypes, cavefish, from
subterranean rivers and surface fish, from surface rivers. They are morphologically distinct due to
many troglomorphic traits in the cavefish, such as the absence of eyes. Most studies on A. mexicanus
are focused on eye development and protein-coding genes involved in the process. However,
lncRNAs did not get the same attention and very little is known about them. This study aimed to
fill this knowledge gap, identifying, describing, classifying, and annotating lncRNAs expressed in
the embryo’s eye tissue of cavefish and surface fish. To do so, we constructed a concise workflow to
assemble and evaluate transcriptomes, annotate protein-coding genes, ncRNAs families, predict
the coding potential, identify putative lncRNAs, map them and predict interactions. This approach
resulted in the identification of 33,069 and 19,493 putative lncRNAs respectively mapped in cavefish
and surface fish. Thousands of these lncRNAs were annotated and identified as conserved in human
and several species of fish. Hundreds of them were validated in silico, through ESTs. We identified
lncRNAs associated with genes related to eye development. This is the case of a few lncRNAs
associated with sox2, which we suggest being isomorphs of the SOX2-OT, a lncRNA that can regulate
the expression of sox2. This work is one of the first studies to focus on the description of lncRNAs in A.
mexicanus, highlighting several lncRNA targets and opening an important precedent for future studies
focusing on lncRNAs expressed in A. mexicanus.
Times Cited:
1
Relevent Species: