Development of SNVs and indels markers mined out of the first multi-organ transcriptomes from Hypancistrus zebra (Loricariidae), an endangered Amazonian catfish

Abstract

Hypancistrus zebra is a catfish, endemic from the Xingu River, threatened with extinction due to the impacts of Belo Monte dam, of its illegal capture, of gold mining activities and of climate change. Currently, there are three nucleotide sequences from this species in GenBank, what impedes the development of genetic markers to assist on its conservation. A total of 217 million RNA-Seq reads from seven organs were sequenced and used to assemble 566,607 transcripts, including 98% of BUSCO vertebrates orthologs, 11,321 transcripts with SNVs and 1,724 transcripts with indels. Three transcripts with SNVs and five transcripts with indels were validated as the best candidate markers to conservation practices. This work illustrates the use of transcriptomics in conservation, by the development of a bigger toolbox for an endangered fish, and shall further contribute to studies on this and others related species reproduction, physiology, and adaptability to environmental changes.