Variação genômica em Paracheirodon axelrodi (Schultz, 1956) (Characiformes: Characidae)

Abstract

Within the order Characiformes, Characidae is the largest and most diverse family of fish in the Neotropical region and represents more than 50% of the total taxonomic diversity described for the order. It is in the streams, seasonally flooded forests and interfluvial fields along the basins of the Negro and Orinoco rivers that one of the most emblematic species in freshwater fishkeeping is found: the cardinal tetra Paracheirodon axelrodi. Millions of individuals are exported every year from their countries of origin. However, the consequences of this extraction are still unclear from a population and genetic point of view. Furthermore, regional and global climate disturbances make the future of the species uncertain. Thus, the objective of this work was to generate a reference genome for the species and provide preliminary data that can guide assessment and management strategies for natural populations and also serve as a timestamp of the current situation in which the species finds itself for future comparisons in the coming decades. Five samples collected in natural environments, georeferenced and deposited in biological collections in Brazil were sequenced using the PCR Free Whole Genome Sequencing method. From the raw sequencing data, we used bioinformatics pipelines to (1) De Novo assembly and annotate mitogenomes and (2) map reads to the reference genome of the Mexican tetra Astyanax mexicanus. Through De Novo assembly methodology we obtained five circular mitogenomes with an average size of 16,891 ± 92 bp, with characteristics and organization typical of other teleost fish mitogenomes. The annotation of the mitogenomes revealed differences in relation to the mitogenomes of P. axelrodi already available in GenBank, such as the lengths of the COX2 and CYTB genes and the presence of 3 to 11 repetitive elements at the 5' end of the mitochondrial DNA control region, which may be due either to population variation or the difficulty of bioinformatics algorithms to deal with repetitive sequences. Through the reference-guided methodology, about 75% of the five sample’s reads (~17.3 Gigabases) were mapped to the Mexican tetra genome, covering about 35% of its total length (1.4 Gigabases). Population structure analyses based on SNPs indicate that there is structure between the sampled locations – Santa Isabel do Rio Negro and Barcelos – where FST values are in the order of 10% and K values were between 4 and 5. The historical demography of the species was also estimated, indicating a sharp decline in effective population size after the Last Interglacial followed by a constant decline throughout the Last Glacial period, without an evident recovery during the Holocene.