De novo transcriptome based on next-generation sequencing reveals candidate genes with sex-specific expression in Arapaima gigas (Schinz, 1822), an ancient Amazonian freshwater fish

Abstract

BackgroundThe Arapaima (Arapaima gigas) is one of the world's largest freshwater bony fish, and is found in the rivers of the Amazon basin. This species is a potential aquaculture resource, although reproductive management in captivity is limited in particular due to the lack of external sexual dimorphism. In this study, using the 454 Roche platform (pyrosequencing) techniques, we evaluated a major portion of the transcriptome of this important Amazonian species.ResultsFour libraries obtained from the liver and skin tissue of juvenile specimens (representing males and females separately) were sequenced, yielding 5,453,919 high-quality reads. The de novo transcriptome assembly resulted in 175,792 contigs, with 51,057 significant blast hits. A total of 38,586 transcripts were mapped by Gene Ontology using Blast2GO. We identified 20,219 genes in the total transcriptome (9,551 in the liver and 16,818 in the skin). The gene expression analyses indicated 105 genes in the liver and 204 in the skin with differentiated expression profiles, with 95 being over-expressed in the females and 214 in the males. The log2 Fold Change and heatmap based on Reads Per Kilobase per Million mapped reads (RPKM) revealed that the gene expression in the skin is highly differentiated between male and female arapaima, while the levels of expression in the liver are similar between the sexes.ConclusionTranscriptome analysis based on pyrosequencing proved to be a reliable tool for the identification of genes with differentiated expression profiles between male and female arapaima. These results provide useful insights into the molecular pathways of sexual dimorphism in this important Amazonian species, and for comparative analyses with other teleosts.

Morphological characterization of pirarucu Arapaima gigas (Schinz, 1822) gonadal differentiation

“…However, no technology exists today to manipulate the reproduction of pirarucu, and this situation means a huge hindrance and delay for the commercial production of the species. Because the main bottleneck is the reproduction in captivity, most of these studies on the species aimed at understanding patterns and mechanisms of sex determination, molecular differentiation, and gonadal activity of A. gigas (Almeida, Ianella, Faria, Paiva, & Caetano, ; Du et al, ; Prado‐Lima & Val, ; Torati et al, ; Torati, Lima, Kirschnik, & Migaud, ; Watanabe et al, ). However, sex determination and regulation of the sexual maturation remain largely unknown in the species (Almeida et al, ).…”

Characterization and analysis of the transcriptome inArapaima gigasusing multi-tissue RNA-sequencing

“…Arapaima gigas , also known as Pirarucu or Paiche, is one of the largest freshwater fishes in South America, whose adults body weight can reach up to 250 kg [1] and a length of up to three meters [2] [3]. It belongs to the bonytongues (order Osteoglossiformes) [2] [4] and it is naturally distributed in Amazonas and Tocantins-Araguaia basins [1] [3] [4], and it has also been introduced into the Bolivian Amazon [3] [5]. This emblematic fish has been an extensive economic resource for communities and is an attractive candidate for aquaculture development [1] [2].…”

“…In the wild, this air-breather fish lives preferentially in lentic environments [7], tolerates low oxygen levels dissolved in the water and is less susceptible to ammonia or nitrite intoxication [2]. The reproduction behavior is complex, which includes breeding pairs, nest building and parental care, and significant external sexual dimorphism is not displayed [1] [3]. Methods usually used for sexual identification include biopsy, ultrasonography and endoscopy [8].…”

“…Recently, due to the rapid development of next-generation sequencing technologies, genome and transcriptome analysis become powerful tools for identifying candidate genes [9] related to these important traits, and it has provided an advancement in availability of arapaima genomics and transcriptomics resources [3]. The ability to elucidate the basis of complex traits has been dramatically improved by the availability of reference genomes for A. gigas [2] [4].…”

“…To date, their major impact has been through enabling evolutionary analysis and application of analysis of gene family dynamics. The availability of the de novo transcriptome [3] has also enabled performing differential gene expression analysis. Unfortunately, there is still a lack of knowledge about molecular and biochemical mechanisms involved in its fast growth, metabolism and sexual development, which interfered in the widespread establishment of A. gigas in aquaculture [2].…”