Arapaima Gigas
The particular Pirarucu (Arapaima gigas) is among the world’s most significant freshwater fish and member of the superorder Osteoglossomorpha (bonytongues), one of the oldest lineages of ray-finned fishes. This specific species is an obligate air-breather found in the basin of the Amazon . com River having an attractive prospective for aquaculture. Its phylogenetic position among bony these people own in makes the Pirarucu another subject for evolutionary research of early teleost diversification. Here, we present, initially, a draft genome version of the A. gigas genome, providing useful info for further functional and major studies. The A. gigas genome was assembled along with 103-Gb raw reads sequenced within an Illumina platform. The particular final draft genome assemblage was ∼661 Mb, with a contig N50 equal to fifty-one. 23 kb and scaffold N50 of 668 kb. Repeat sequences accounted for 21. 69% of the whole genome, along with a total of twenty four, 655 protein-coding genes were predicted from the genome assembly, by having 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 sibling groups, both forming the sister lineage with respect to Clupeocephala (remaining teleosts). Divergence moment estimations suggested that Osteoglossomorpha and Elopomorpha lineages surfaced independently in a amount of ∼30 Myr in the particular Jurassic. The draft genome of any. gigas provides a valuable genetic resource regarding further investigations of evolutionary studies and may likewise provide a valuable data for financial applications.
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Arapaima gigas — Wikipédia
Arapaima gigas, also known as Pirarucu or Paiche, is a single of the world’s most significant freshwater fishes (Wijnstekers 2011) whose body length in addition to weight may attain four. 5 m (15 ft) and 2 hundred Kg (440 lb), respectively (Nelson 1994; Froese and Pauly 2018). The genus Arapaima emerged in the Amazon floodplain basin and will be presently distributed in Brazil, Colombia, Ecuador, and Peru (Hrbek et al. 2005, 2007; Froese and Pauly 2018), and also in Thailand and Malaysia exactly where it has been introduced for commercial fishing (Froese and Pauly 2018). Arapaima gigas local name (Pirarucu) derives through the indigenous Tupi words “pira” and “urucum” for “fish” and “red, ” respectively, presumably referring to its red end scales flecks or to their reddish flesh (Marsden 1994; Godinho et al. 2005). The peculiarity of its inhaling and exhaling apparatus is characteristic associated with this Amazonian fish, including gills and a lung-like tissue devised for air-breathing derived from a modified in addition to enlarged swim bladder (Burnie and Wilson 2001; Brauner et al. 2004). The Pirarucu has an appealing market value because of low-fat and low bone articles. Overfishing practices inside the Amazonian region led to the banning of Pirarucu commercialization by the Brazilian authorities in 2001, although intake from the native population is usually currently permitted under stringent size and seasoning regulations (Bayley and Petrere 1989). Its main supply is provided by wild-caught species of fish and fish farming performed by riverbank population associated with the Amazonas (Froese and Pauly 2018). Aquaculture manufacturing is attractive due in order to high carcass yields and rapid juvenile growth, along with yearlings reaching up in order to 10 kg (22 lb) (Almeida et al. 2013).
Big Fishes of the World: ARAPAIMA PIRARUCU Arapaima gigas
Arapaima gigas belongs to the superorder Osteoglossomorpha of bony-tongued fishes whose tongue includes sharp bony teeth for disabling and shredding preys (Sanford and Lauder 1990; Burnie and Wilson 2001). Along with Elopomorpha (eels and tarpons) and Clupeocephala (most of extant fish species), the Osteoglossomorpha comprises a single of the three main teleosts groups whose phylogenetic position has been questionable (Le et al. 93; Inoue et al. 2003; Near et al. 2012; Betancur-R 2013; Faircloth et al. 2013; Chen et al. 2015; Hughes ainsi que al. 2018). Fossil information and some early molecular studies, including a latest comprehensive analysis of > 300 Actinopterygii species (Hughes et al. 2018), put Osteoglossomorpha because the oldest teleost group (Greenwood 1970; Inoue et al. 2003), although other studies positioned Elopomorpha as the most ancestral one (Near et ing. 2012; Betancur-R 2013; Faircloth et al. 2013). Lately, a phylogenetic study based on whole genome sequencing in the bony-tongued Asian arowana (Scleropages formosus) suggested that typically the branching of Elopomorpha plus Osteoglossomorpha occurred almost simultaneously, inserting them as sibling lineages of Clupeocephala (Bian 2016). Within this framework, the genome of typically the Pirarucu provides new information to study the evolutionary history of teleosts as nicely as providing useful information for sustainable exploration associated with this giant Amazon fish. Here, we present typically the first whole genome assemblage, gene annotation, and phylogenomic inference of the Pirarucu which should facilitate the molecular characterization and conservation regarding this economically important species of fish species.
Arapaima Gigas
Test Collection and SequencingGenomic DNA was extracted coming from peripheral blood samples associated with four adult individuals (two males and two females) of Arapaima gigas: NCBI taxonomy ID 113544, FishBase ID: 2076. All samples were collected in compliance with the standards of the Federal University associated with Pará animal protocol. We all applied a whole-genome shotgun sequencing strategy using two short-insert libraries (400 plus 500 bp) in an Illumina HiSeq 2500 platform according to be able to the manufacturer’s instructions (Illumina, San Diego, CA). HiSeq Rapid SBS Kits (FC-402-4021) and HiSeq Rapid Group Kits (PE-402-4002) were applied to sequence paired-end read of 2 × 250 base pairs. Read quality was checked 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 Para Novo AssemblyGenome sizing was estimated based about the k-mer spectrum using the following formula: G= (N×(L−K + 1)−B)/D. Where N is the particular total read count, L may be the read length, K is k-mer length (K = 31), B is the overall low-frequency (frequency ≤1) k-mer count, D is the k-mer depth, and Gary the gadget guy is the genome size. Jellyfish 2. 2. six (Marçais and Kingsford 2011) was used to depend k-mer frequencies of superior quality sequencing reads.Genome assemblage was performed using SOAPdenovo2 (version 2. 04) (Luo et al. 2012) below default parameters (127mer version). Three assemblies were conducted: 1) using all reads; 2) with reads from male samples; and 3) with reads from woman samples. Subsequently, gaps had been filled using Redundants (Pryszcz and Gabaldón 2016) making use of three-run scaffolding steps: first of all using the default value associated with minimum read pairs to joining contigs (5 pairs), subsequently rerunning with prior data having a minimum value of four read pairs and, finally, utilizing a minimal of three read pairs. Assembly quality and statistics were assessed with QUAST (version 4. 4) (Gurevich et al. 2013).
Pirarucu, Arapaima Arapaima gigas Aquarismo Paulista
Assessment of Genome CompletenessSet up quality was measured by simply assessing gene completeness along with Benchmarking Universal Single-Copy Orthologs (BUSCO) (Simão et 's. 2015) based on four, 584 BUSCO groups derived 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 annotation approach. Initially, tandem repeats were identified with Conjunction Repeats Finder 4. 2009 (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 developed with RepeatModeler 1. zero. 9 and LTR_FINDER (Xu and Wang 2007), and filtered with LTR_retriever (Ou and Jiang 2017) below default parameters. Subsequently, known and novel transposable elements were identified by umschlüsselung the assembled sequences to 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, all of us annotated TE-related proteins using 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 performed with protein data from 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 discharge 88), together with Scleropages formosus (Asian arowana) proteins sequences from NCBI RefSeq annotation data. Subsequently, de novo annotations were performed using the homology-based results achieved in the very first step. We also used the RepeatModeller 1. 0. nine (Smit and Hubley 2008) to build a sobre novo repeat library along with default parameters. The GFF output from the 1st step was used 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 5. 24-63. 0 (Jones ou al. 2014) was operate on the protein output of MAKER, providing gene ontologies and classifying protein domains and families. Protein result was compared using BLAST against the NCBI NR database (available on Might 29, 2017) for identifying putative gene names. Blast2GO v5 (Conesa et ing. 2005) was subsequently used to obtain Gene Ontology mapping and annotation (supplementary file S2, Supplementary Materials online).
