9 best Arapaima gigas images on Pinterest Freshwater fish, Fishing and Nature
Typically the Pirarucu (Arapaima gigas) is among the world’s greatest freshwater fish and member of typically the superorder Osteoglossomorpha (bonytongues), a single of the oldest lineages of ray-finned fishes. This species is an obligate air-breather found in typically the basin of the Amazon . com River by having an attractive prospective for aquaculture. Its phylogenetic position among bony these people own in makes the Pirarucu another subject for evolutionary scientific studies of early teleost diversity. Here, we present, for the first time, a draft genome variation of the A. gigas genome, providing useful details for more functional and evolutionary studies. The A. gigas genome was assembled with 103-Gb raw reads sequenced in an Illumina platform. The final draft genome assemblage was ∼661 Mb, with the contig N50 equal to 51. 23 kb and scaffold N50 of 668 kb. Repeat sequences accounted for 21. 69% of the whole genome, and also a total of twenty four, 655 protein-coding genes had been predicted from the genome assembly, with an average regarding nine exons per gene. Phylogenomic analysis based upon 24 fish species supported the postulation that Osteoglossomorpha and Elopomorpha (eels, tarpons, and bonefishes) are sibling groups, both forming the sister lineage with respect to Clupeocephala (remaining teleosts). Divergence period estimations suggested that Osteoglossomorpha and Elopomorpha lineages appeared independently in a period of ∼30 Myr in the particular Jurassic. The draft genome of A. gigas provides a valuable genetic resource with regard to further investigations of major studies and may likewise give you a valuable data for financial applications.
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Arapaima gigas, also known as Pirarucu or Paiche, is one of the world’s biggest freshwater fishes (Wijnstekers 2011) whose body length plus weight may attain some. 5 m (15 ft) and two hundred Kg (440 lb), respectively (Nelson 1994; Froese and Pauly 2018). The genus Arapaima emerged in the Amazon online floodplain basin and is usually presently distributed in Brazil, Colombia, Ecuador, and Peru (Hrbek et al. june 2006, 2007; Froese and Pauly 2018), and also inside Thailand and Malaysia wherever it has been released for commercial fishing (Froese and Pauly 2018). Arapaima gigas local name (Pirarucu) derives from your indigenous Tupi words “pira” and “urucum” for “fish” and “red, ” respectively, presumably referring to its red butt scales flecks or its reddish flesh (Marsden 1994; Godinho et al. 2005). The peculiarity of its breathing apparatus is characteristic regarding this Amazonian fish, comprising gills and a lung-like tissue devised for air-breathing based on a modified in addition to enlarged swim bladder (Burnie and Wilson 2001; Brauner et al. 2004). Typically the Pirarucu has an interesting market value because of less fat and low bone content. Overfishing practices inside the Amazonian region led to the banning of Pirarucu commercialization by the Brazilian federal government in 2001, although intake with the native population is usually currently permitted under stringent size and seasoning regulations (Bayley and Petrere 1989). Its main supply is usually provided by wild-caught fish and fish farming conducted by riverbank population associated with the Amazonas (Froese in addition to Pauly 2018). Aquaculture creation is attractive due in order to high carcass yields and rapid juvenile growth, along with yearlings reaching up to be able to 10 kg (22 lb) (Almeida et al. 2013).
Arapaima, Arapaima gigas, Pirarucu, Paiche Fish Guide
Arapaima gigas belongs to the superorder Osteoglossomorpha of bony-tongued fishes whose tongue consists of sharp bony teeth regarding disabling and shredding preys (Sanford and Lauder 1990; Burnie and Wilson 2001). Along with Elopomorpha (eels in addition to tarpons) and Clupeocephala (most of extant fish species), the Osteoglossomorpha comprises a single of the three major teleosts groups whose phylogenetic position has been debatable (Le et al. 93; Inoue et al. 2003; Near et al. 2012; Betancur-R 2013; Faircloth ou al. 2013; Chen ou al. 2015; Hughes ainsi que al. 2018). Fossil data and some early molecular studies, including a current comprehensive analysis of > 300 Actinopterygii species (Hughes et al. 2018), positioned Osteoglossomorpha because the oldest teleost group (Greenwood 1970; Inoue et al. 2003), whilst other studies put Elopomorpha as the most ancestral one (Near et 's. 2012; Betancur-R 2013; Faircloth et al. 2013). Recently, a phylogenetic study based on whole genome sequencing in the bony-tongued Asian arowana (Scleropages formosus) suggested that the particular branching of Elopomorpha in addition to Osteoglossomorpha occurred almost at the same time, positioning them as sister lineages of Clupeocephala (Bian 2016). Within this framework, the genome of typically the Pirarucu provides new insights to study the historical past of teleosts as properly as providing useful information for sustainable exploration associated with this giant Amazon fish. Here, we present typically the first whole genome assembly, gene annotation, and phylogenomic inference of the Pirarucu which should facilitate the molecular characterization and conservation of this economically important seafood species.
Arapaima Gigas
Test Collection and SequencingGenomic DNA was extracted from peripheral blood samples regarding four adult individuals (two males and two females) of Arapaima gigas: NCBI taxonomy ID 113544, FishBase ID: 2076. All selections were collected in compliance with the standards of the Federal University associated with Pará animal protocol. All of us applied a whole-genome shotgun sequencing strategy using 2 short-insert libraries (400 and 500 bp) in an Illumina HiSeq 2500 platform according to the manufacturer’s instructions (Illumina, San Diego, CA). HiSeq Rapid SBS Kits (FC-402-4021) and HiSeq Rapid Bunch Kits (PE-402-4002) were utilized to sequence paired-end read of 2 × 250 base pairs. Read quality was checked out using FastQC, version zero. 11. 4 (Andrews 2010), and low-quality reads have been trimmed with Sickle paired-end (pe), version 1. 33 (Joshi and Fass 2011), under default parameters.Genome Size Estimation and Sobre Novo AssemblageGenome dimension was estimated based on the k-mer spectrum with all the following formula: G= (N×(L−K + 1)−B)/D. Where N is typically the total read count, L may be the read length, Nited kingdom is k-mer length (K = 31), B is the total low-frequency (frequency ≤1) k-mer count, D is the k-mer depth, and Gary the gadget guy is the genome dimension. Jellyfish 2. 2. 6 (Marçais and Kingsford 2011) was used to count number k-mer frequencies of top quality sequencing reads.Genome assembly was performed using SOAPdenovo2 (version 2. 04) (Luo et al. 2012) beneath default parameters (127mer version). Three assemblies were carried out: 1) using all reads; 2) with reads coming from male samples; and 3) with reads from female samples. Subsequently, gaps have been filled using Redundants (Pryszcz and Gabaldón 2016) making use of three-run scaffolding steps: first of all with all the default value of minimum read pairs to be able to joining contigs (5 pairs), subsequently rerunning with previous data having a minimum value of four read sets and, finally, utilizing a minimum of three read pairs. Assembly quality and data were assessed with QUAST (version 4. 4) (Gurevich et al. 2013).
Big Fishes of the World: ARAPAIMA PIRARUCU Arapaima gigas
Evaluation of Genome CompletenessAssembly quality was measured by assessing gene completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO) (Simão et 's. 2015) based on some, 584 BUSCO groups produced from Actinopterygii orthologs.Do it again AnalysisTransposable elements (TEs) and other repetitive factors of the Pirarucu genome were identified by the combined, homology-based method and a de novo réflexion approach. Initially, tandem repeats were identified with Tandem Repeats Finder 4. 09 (Benson 1999) with the following parameters: “Match=2, Mismatch=7, Delta=7, PM=80, PI=10, Minscore=50, and MaxPerid=2, 000. ” Additionally, a de novo repeat library was built with RepeatModeler 1. zero. 9 and LTR_FINDER (Xu and Wang 2007), plus filtered with LTR_retriever (Ou and Jiang 2017) under default parameters. Subsequently, identified and novel transposable components were identified by umschlüsselung the assembled sequences for the Repbase TE 22. 05 (Bao et al. 2015) and de novo replicate libraries using RepeatMasker four. 0 (Tarailo-Graovac and Chen 2009). In addition, we annotated TE-related proteins making use of RepeatProteinMask 4. 0 (Tarailo-Graovac and Chen 2009).Gene Structure and Function AnnotationGenome annotation was carried out with the MAKER2 pipeline (Holt and Yandell 2011) in a two-pass iteration. First, homology annotation was carried out with protein data through Homo sapiens (human), Danio rerio (zebrafish), Takifugu rubripes (Japanese fugu), Tetraodon nigroviridis (spotted green pufferfish), Gasterosteus aculeatus (three-spined stickleback), Oryzias latipes (Japanese medaka), Latimeria chalumnae (coelacanth) (Ensembl launch 88), together with Scleropages formosus (Asian arowana) protein sequences from NCBI RefSeq annotation data. Subsequently, sobre novo annotations were carried out using the homology-based outcomes achieved in the first step. We also used the RepeatModeller 1. 0. nine (Smit and Hubley 2008) to build a de novo repeat library with default parameters. The GFF output from the first step was used in order to train the SNAP 20131129 (Korf 2004) and AUGUSTUS 3. 2. 3 (Stanke et al. 2008) predictors. GeneMark-ES 4. 32 (Lomsadze et al. 2005) had been trained using the genome assembly itself. InterProScan five. 24-63. 0 (Jones et al. 2014) was operate on the protein output associated with MAKER, providing gene ontologies and classifying protein domain names and families. Protein result was compared using BOOST against the NCBI NR database (available on May 29, 2017) for determining putative gene names. Blast2GO v5 (Conesa et ing. 2005) was subsequently used to obtain Gene Ontology mapping and annotation (supplementary file S2, Supplementary Material online).