Whole Genome Sequencing of the Pirarucu (Arapaima gigas) Supports Independent Emergence of Major Teleost Clades

Abstract

The Pirarucu (Arapaima gigas) is one of the world’s largest freshwater fishes and member of the superorder Osteoglossomorpha (bonytongues), one of the oldest lineages of ray-finned fishes. This species is an obligate air-breather found in the basin of the Amazon River with an attractive potential for aquaculture. Its phylogenetic position among bony fishes makes the Pirarucu a relevant subject for evolutionary studies of early teleost diversification. Here, we present, for the first time, a draft genome version of the A. gigas genome, providing useful information for further functional and evolutionary studies. The A. gigas genome was assembled with 103-Gb raw reads sequenced in an Illumina platform. The final draft genome assembly was ∼661 Mb, with a contig N50 equal to 51.23 kb and scaffold N50 of 668 kb. Repeat sequences accounted for 21.69% of the whole genome, and a total of 24,655 protein-coding genes were predicted from the genome assembly, with an average of nine exons per gene. Phylogenomic analysis based on 24 fish species supported the postulation that Osteoglossomorpha and Elopomorpha (eels, tarpons, and bonefishes) are sister groups, both forming a sister lineage with respect to Clupeocephala (remaining teleosts). Divergence time estimations suggested that Osteoglossomorpha and Elopomorpha lineages emerged independently in a period of ∼30 Myr in the Jurassic. The draft genome of A. gigas provides a valuable genetic resource for further investigations of evolutionary studies and may also offer a valuable data for economic applications.

Assessing the sex-related genomic composition difference using a K-mer-based approach: a case of study in Arapaima gigas (Pirarucu)

“…In this study, we have noticed the existence of k-mers over or underrepresented in one of the sexes, indicating potential differences in the genetic composition between males and females of A. gigas . The difference is not so expressive, which corroborates with the reports that estimate 0.01% [14] to 0.1% [15] of the genome of this species as linked to the sexual determination. The four sequences reported in this work (Figure 3) are all part of repetitive sequences.…”

“…But elucidating these mechanisms in fish is challenging, since most of them, including A. gigas , do not bear a typical sex chromosome in their genome [16, 17] and the difference of the genome sequences between samples of opposite sex seems to be minimal. The first genome sequencing of A. gigas [14] did not find significant differences between the genomic content of male and female samples. The second one [15] suggested the XY system for A. gigas , but their results conflict with the genome data of the first one.…”

“…For the following analyses, genomic data were used from four adult Arapaima gigas representatives, two males (M1 and M2) and two females (F1 and F2). All samples were collected from Bioproject PRJEB22808 available in National Center for Biotechnology Information (NCBI) database [14]. The quality of the reads was verified with the help of FastQC (v. 0.11.4) [18], and low-quality reads were trimmed with the help of the Sickle paired-end (v. 1.33) [19].…”

“…For this, the establishment of a molecular genetic marker related to sexual differentiation would be an advantageous tool. Previous analysis of the Arapaima gigas genome found no genes associated with the identification of the sex determination system of these individuals [14, 15]. And chromosomal characterization studies could not distinguishable cytologically a sex chromosome in Arapaima gigas [16, 17].…”

Three genomes of Osteoglossidae shed light on ancient teleost evolution

“…1b ). Firstly, we calculated the divergence time of S. formosus and the common ancestor of H. niloticus and A. gigas at ∼106.1 Mya (± 20 Mya) [3, 8, 23], which is coincided with the separated time of South America and Africa continents by Afro-South American drift at ∼110 Mya[5]. At the original of separated time, the ancestor of S. formosus might live in South America.…”