A broad genomic panel of microsatellite loci from Brycon orbignyanus (Characiformes: Bryconidae) an endangered migratory Neotropical fish

Abstract

A broad panel of tens of thousands of microsatellite loci is unveiled for an endangered piracema (i.e. migratory) South American fish, Brycon orbignyanus. Once one of the main fisheries resources in the Platine Basin, it is now almost extinct in nature and focus of intense aquaculture activity. A total of 178.2 million paired-end reads (90 bases long) were obtained through the use of sequencing-by-synthesis (from a primary genomic library of 500 bp DNA fragments) and is made available through NCBI’s Sequence Read Archive, SRA accession SRX3350440. Short reads were assembled de novo and screening for perfect microsatellite motifs revealed more than 81 thousands unique microsatellite loci, for which primer pairs were proposed. A total of 29 polymorphic microsatellite markers were already previously validated for this panel. A partial genomic assembly is hereby presented and these genomic resources are publicly made available. These data will foster the rapid development of hundreds of new DNA markers for genetic diversity studies, conservation initiatives and management practices for this important and depleted species. The availability of such preliminary genomic data will also be of use in the areas of bioinformatics, ecology, genetics and evolution.

Genomic approach for conservation and the sustainable management of endangered species of the Amazon

“…In this study, we identified a total of 95,098 microsatellites based on sequences of the complete genome of A. gigas, a value close to that found for Monopterus albus (99,293) [32] and much larger than what was found for Brycon orbignyanus (81,241) [31]. These differences probably are due to the size of the databases, search criteria and bioinformatics tools used to identify the microsatellites [35].…”

“…The rapid development of sequencing technologies allowed the obtention of complete genome sequences from an increasing number of species [30], which is an excellent source for identification of microsatellite markers already used in several species [30,31,32,33,34].…”

“…Population genetics data are undoubtedly the most important component of the baseline of any conservation and management plan [53]. The broad microsatellite panel developed for A. gigas opens perspectives for studies in as many fields as bioinformatics, ecology, genetics, evolution, and comparative studies among species [31]. And the multiplex system designed for A. gigas allows an accurate, faster, cost-effective, and affordable genotyping for low-income laboratories and conservation studies focusing on this species.…”

Genomic approach for conservation and the sustainable management of endangered species of the Amazon

“…The rapid development of sequencing technologies allowed the obtention of complete genome sequences from an increasing number of species [ 33 ], which is an excellent source for identification of microsatellite markers already used in several species [ 34 – 38 ]. However, the use of sequencing Technologies demands laboratories equipped with high infrastructure and skilled personal resources, which in many cases does not match the reality of several laboratories in the Amazon region.…”

Microsatellite multiplex systems for Brycon orbignyanus (Characiformes: Bryconidae)

“…Rodriguez-Rodriguez et al, 2010;Lopera-Barrero et al, 2010, 2014Ashikaga et al, 2015;Carmo et al, 2015;Castro et al, 2017). This yields a restricted number of usable loci and can lead to increasing artefactual noise in the analyses (Carmo et al, 2015).With the unveiling of the first 29 microsatellite loci from B. orbignyanus (Arias et al, 2016), by the application of next-generation sequencing (NGS) pipelines (Yazbeck et al, 2018), more reliable genetic analysis systems for this species can now be developed, in order to accelerate the profiling of extant and cultivated stocks in this threatened species. Recently, seven polymorphic microsatellite loci were also developed by means of traditional cloning methods, involving a microsatellite-enriched library prepared with hybridization capture process, and their transferability assayed, along five other new markers, in Brycon gouldingi and B. falcatus (Souza et al, 2018).…”