Cytogenetics, genomics and biodiversity of the South American and African Arapaimidae fish family (Teleostei, Osteoglossiformes)

Abstract

Osteoglossiformes represents one of the most ancestral teleost lineages, currently widespread over almost all continents, except for Antarctica. However, data involving advanced molecular cytogenetics or comparative genomics are yet largely limited for this fish group. Therefore, the present investigations focus on the osteoglossiform family Arapaimidae, studying a unique fish model group with advanced molecular cytogenetic genomic tools. The aim is to better explore and clarify certain events and factors that had impact on evolutionary history of this fish group. For that, both South American and African representatives of Arapaimidae, namely Arapaima gigas and Heterotis niloticus, were examined. Both species differed markedly by diploid chromosome numbers, with 2n = 56 found in A. gigas and 2n = 40 exhibited by H. niloticus. Conventional cytogenetics along with fluorescence in situ hybridization revealed some general trends shared by most osteoglossiform species analyzed thus far, such as the presence of only one chromosome pair bearing 18S and 5S rDNA sites and karyotypes dominated by acrocentric chromosomes, resembling thus the patterns of hypothetical ancestral teleost karyotype. Furthermore, the genomes of A. gigas and H. niloticus display remarkable divergence in terms of repetitive DNA content and distribution, as revealed by comparative genomic hybridization (CGH). On the other hand, genomic diversity of single copy sequences studied through principal component analyses (PCA) based on SNP alleles genotyped by the DArT seq procedure demonstrated a very low genetic distance between the South American and African Arapaimidae species; this pattern contrasts sharply with the scenario found in other osteoglossiform species. Underlying evolutionary mechanisms potentially explaining the obtained data have been suggested and discussed.

Three genomes of Osteoglossidae shed light on ancient teleost evolution

“…Based on the high quality draft genome assembly, we also sequenced 21.23 Gb data of a Hi-C library and anchored 647.59 Mb (∼96.80% of the whole assembly) scaffold sequences onto 20 chromosomes ( Fig. 1a, Supplemental table 3 ), consistent with the reported H. niloticus ’s karyotype[11]. To double check the taxonomy information of this sequencing sample, we assembled a complete H. niloticus mitochondria genome of 16.55 Kb using MitoZ[21], which was phylogenetically closest to published H. niloticus mitochondria genome.…”

“…Osteoglossidae contains four genera Arapaima, Heterotis, Osteoglossum and Scleropages. The Heterotis niloticus , the only omnivore in Osteoglossiformes[10, 11], together with its sister species Arapaima gigas and Scleropages formosus form a good example to investigate the genetic basis of this ancient teleost clade[12]. H. niloticus lives in Africa while A. gigas mainly distributes in South America and S. formosus distributes in Southeast Asia, characterized by several morphological differences.…”

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

“…Introspection of these mechanisms in A. gigas has an appeal because this species plays an important role in the economy of the north region of Brazil [12, 13]. 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.…”

“…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]. In this study, we proposed to asses the genomic composition of A. gigas using a k-mer-based approach to identify regions in excess or missing in one of the sexes.…”

African Arowana Genome Provides Insights on Ancient Teleost Evolution

“…African arowana (or African bonytongue, Heterotis niloticus ), pirarucu ( Arapaima gigas ), and Asian arowana ( Scleropages formosus ) are three representative species of Osteoglossidae in Osteoglossiformes with some morphological differences ( Adite et al., 2017 ; Axelrod et al., 1986 ; saint-Paul, 1986 ). African arowana is the only omnivore in Osteoglossiformes ( Adite et al., 2013 ; Oliveira et al., 2019 ), distributing majorly in Africa, compared to pirarucu mainly in South America and Asian arowana in Southeast Asia. Despite their differences in habitats and morphology, these three species are relatively closely related with similar behaviors and physiological characters ( Monentcham et al., 2009 ; Núñez et al., 2011 ; Scott and Fuller, 1976 ), making them good representative species for investigating the genetic basis of the ancient teleost clade ( Betancur et al., 2017 ).…”