Menu
How can the answer be improved?
We have sequenced the genome of the largest freshwater fish species of the world, the arapaima. Analysis of gene family dynamics and signatures of positive selection identified genes involved in the specific adaptations and unique features of this iconic species, in particular it’s large size and fast growth. Genome sequences from both sexes combined with RAD-tag analyses from other males and females led to the isolation of male-specific scaffolds and supports an XY sex determination system in arapaima. Whole transcriptome sequencing showed that the product of the gland-like secretory organ on the head surface of males and females may not only provide nutritional fluid for sex-unbiased parental care, but that the organ itself has a more specific function in males, which engage more in parental care.
The Amazonian freshwater fish arapaima ( Arapaima gigas) has a most remarkable biology. This legendary fish can reach a body length of almost 3 meters placing it the largest freshwater fish, exhibits the fastest known growth rates, and – supporting its importance for aquaculture – has the best food conversion so far recorded in fish. Known as pirarucu in Brazil and paiche in Peru, it belongs to the bonytongues (Order Osteoglossiformes), one of the most basally diverging lineages of the teleost fish. Its natural distribution covers most of the Amazon River basin in Peru and Brazil, and it has been introduced as an aquaculture species to other rivers in tropical South America.
As an obligate air-breathing fish obtaining up to 95% of its oxygen uptake by breathing, it is able to tolerate extremely low oxygen levels in the water, and is less susceptible to ammonia or nitrite intoxication due to its degenerated gills.The combination of unusual adaptations make arapaima a promising candidate for aquaculture. But so far, it has not been established widely in aquaculture, partially due to deficits in knowledge about its sexual development, allowing controlled reproduction in captivity, and lack of information about the molecular and biochemical mechanisms involved in its fast and gigantic growth. So far, genomic resources are sparse and far below what is available for other important aquaculture fish. In South America arapaima is a high-priced fish for commercial fisheries. Sadly, the drastic decline in natural stocks and genetic bottlenecks brought arapaima towards the brink of extinction and illicit poaching - despite its status of protection - continues to threaten remaining populations. Destruction of its natural habitats through various causes is also contributing to the immanent threat of extinction of this iconic species.Gigantism and muscle growth separate arapaima (2.5 m, 100 kg) from its relative, the much smaller Asian arowana Scleropages formosus. During the first year, juvenile arapaima exhibits the fastest growth rates recorded in fish, reaching weights between 10 to 15 kg at an extraordinary efficient food conversion rate (FCR.
Genome assembly and annotationWe used a whole genome shotgun approach with Illumina technology (Hiseq2500) to sequence the genome of one male and one female at 58.6 and 59.8x coverage, respectively (Fig. ). The DNA was extracted from fin tissues, and the libraries were produced using the Truseq DNA Nano sample preparation kit.
The DISCOVAR (version 52488) assembly resulted in 52,688 scaffolds with size ranging from 138 bp to 2,146 kb for the female (average size 13 kb, N50 315 kb); for male, 60,055 scaffolds with size ranging from 192 bp to 3,323 kb (average size 12 kb, N50 285 kb). The total size of the male assembly is 666 Mb and of the female 664 Mb compared to the estimated 790 Mb from cytometric C-value measurements.Based on the Benchmarking Universal Single-Copy Orthologs (BUSCO) method from the vertebrate database, the completeness of the male assembly is estimated to being 96.1% and in that of the female 95.7% (Table ). Because of its higher contiguity, we chose the male assembly for annotation. With our own in-house assembly pipeline (Fig. ), we predicted 26,755 genes, out of which 21,701 (81.1%) were identified with known Pfam protein domains. BUSCO analysis revealed 2,471 (95.5%) out of 2,586 conserved vertebrate genes to be annotated and complete (Table ).Analysis of repeats in the male genome assembly revealed that repetitive elements constitute 16.46% of the genome, which is in the range of other teleost genomes of similar size.
One category of repetitive elements, the transposable elements (TEs), are always of interest with regards to their important role in the evolution of genes, gene networks, and genomes. In male arapaima, TEs account for 16.21% of the male and 16.77% of the female genome (Table ).
![Arapaima habitat Arapaima habitat](http://www.scielo.br/img/revistas/ni/v11n2//1679-6225-ni-11-02-0341-gf06.jpg)
To investigate TE dynamics, we calculated the distribution of TEs based on Kimura Distance for European eel (Fig. ), arapaima (Fig. ) and Asian arowana, the only other sequenced osteoglossomorph genome (Fig. ), as an approximation of relative ages of TEs. Two major transposition bursts are apparent. The older one comprises all major classes, while the more recent burst mainly affected DNA elements (Fig. ). After the first burst, all other families obviously contracted to the lower levels observed today. Compared to other teleosts, the Kimura profile of arapaima also follows the pattern of “generally one or two main bursts” with some significant interspecific differences. Usually, if there are two bursts, they are similar with either one major class or all classes contributing in a similar way to the expansion.
However, arapaima is so far unique amongst the analyzed vertebrate genomes with one burst of mainly DNA transposons and another one to which all classes of TEs contributed. Interspersed repeat landscape for arapaima, Asian arowana and European eel and phylogenetic tree. ( A– C) The interspersed repeat landscape, revealing the copy-divergence analysis of TE classes, based on Kimura distances. Percentages of TEs in genomes (Y-axis) are clustered based on their Kimura values (X-axis; K-values from 0 to 50; arbitrary values). Older copies are located on the right side of the graphs while rather recent copies are located on the left side. ( A) is for European eel, ( B) arapaima, ( C) Asian arowana. ( D) The phylogenetic tree, generated using 234 one-to-one ortholog protein sequences.
Values at the nodes are Maximum Likelihood bootstrap p.
Arapaima Fish Facts and Information Arapaima gigas Introduction to Arapaima FishThe Arapaima Fish is one that has many legends surrounding it. One of them is that it is a man eater. However, no such credibility has been given to those stories. It is one of the largest freshwater fish found in the world.
![Largest Largest](/uploads/1/2/5/3/125362014/520341092.png)
They can be up to 6 ½ feet long and they can weigh around 220 pounds. There have been reports of larger ones but they can’t be confirmed. This is a common type of fish that people eat in South America. Arapaima Fish DescriptionThe Arapaima Fish is shaped like a torpedo.
Their bodies are black and they have reddish markings on them. They also feature large scales. The mouth is turned upwards which helps with feeding as they consume food from the surface. ClassActinopterygiiOrderOsteoglossiformesFamilyOsteoglossidaeSubfamilyHeterotidinaeGenusArapaimaConservation statusData DeficientArapaima Fish DistributionSouth America is the location of the Arapaima Fish.
They live in locations around the Amazon River basin. They are also found in tributaries all around this area. They are very common in the flood plains after the rainy season. They have a limited distribution though due to the rapid flow of water and even waterfalls.
They aren’t able to navigate in such territories. Arapaima Fish BehaviorThey have to come to the surface for air. They enjoy water temperatures of 75 degrees or higher. When the water is cooler they may not eat and they may not be able to survive.
The Arapaima Fish is very aggressive and they are continually on the move. They don’t seem to really have a home range – they simply live where they are able to survive. Arapaima Fish – Arapaima gigas / Photo taken by George Chernilevsky Arapaima Fish FeedingThey are. The majority of their diet consists of other fish. They will consume anything that they can get though. This includes small mammals and various species of birds. The mouth is turned upwards and they will feed close to the surface of the water.
When birds or mammals are found there looking for their own prey they can very quickly become a meal for the Arapaima Fish.They have a very bony tongue that allows them to get food. They also have tiny teeth that are very sharp. Most of their food is consumed whole though. They don’t use those teeth to be able to tear off pieces so what they prey on has to be small enough to swallow. Arapaima Fish ReproductionIt is very hard to get information about what draws males and females to each other during mating due to where they live. It is known that the water cycle has a great deal to do with when they will lay eggs and if those eggs will survive.
The lay their eggs when the water levels are low in the water.They build a small nest in the muddy bottom area of the river. The eggs will hatch as the waters increase and flooding occurs. When there is no such flooding though the eggs won’t be able to survive. The female will circle around the area of her eggs often to help protect them from various predators.
Spawning occurs in shallow lakes, chiefly during the months of October and November. Approximately 2/3 of them will be consumed though by various predators early on. They can live in captivity for a period of time from 15 to 20 years. Arapaima Fish ConservationDue to commercial fishing, the number of them in Brazil have been significantly reduced. The law now says that only the native people of Brazil can hunt them and use them for food. All other people have to catch and release them or they can be in trouble with the law. Even with such conservation efforts though it is going to take time for the number of them to increase.
To help with the demand for this type of fish as food, there are now farms where the Arapaima Fish are raised in captivity for that purpose.