Pirarucu, Arapaima Arapaima gigas Aquarismo Paulista
The particular Pirarucu (Arapaima gigas) is probably the world’s biggest freshwater these people own in and member of the superorder Osteoglossomorpha (bonytongues), a single of the oldest lineages of ray-finned fishes. This species is an obligate air-breather found in the basin of the Amazon online River with an attractive potential for aquaculture. Its phylogenetic position among bony fish makes the Pirarucu another subject for evolutionary research of early teleost diversification. Here, we present, for the first time, a draft genome edition of the A. gigas genome, providing useful info for even more functional and major studies. The A. gigas genome was assembled along with 103-Gb raw reads sequenced in a Illumina platform. The final draft genome set up was ∼661 Mb, with a contig N50 corresponding 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 24, 655 protein-coding genes had been predicted from the genome assembly, with an average of nine exons per gene. Phylogenomic analysis based on 24 fish species backed the postulation that Osteoglossomorpha and Elopomorpha (eels, tarpons, and bonefishes) are sister groups, both forming a new sister lineage regarding Clupeocephala (remaining teleosts). Divergence time estimations suggested that Osteoglossomorpha and Elopomorpha lineages emerged independently in a amount of ∼30 Myr in the particular Jurassic. The draft genome of the. gigas provides a valuable genetic resource for further investigations of evolutionary studies and may also give a valuable data with regard to monetary applications.
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Arapaima gigas Merifish Aquariums.
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 2 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 Brazilian, Colombia, Ecuador, and Peru (Hrbek et al. june 2006, 2007; Froese and Pauly 2018), and also inside Thailand and Malaysia 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 mentioning to its red end scales flecks or to their reddish flesh (Marsden year 1994; Godinho et al. 2005). The peculiarity of its breathing apparatus is characteristic regarding this Amazonian fish, including gills and a lung-like tissue devised for air-breathing derived from a modified plus enlarged swim bladder (Burnie and Wilson 2001; Brauner et al. 2004). The Pirarucu has an interesting market value because of its low-fat and low bone content. 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 currently permitted under stringent size and seasoning regulations (Bayley and Petrere 1989). Its main supply will be provided by wild-caught seafood and fish farming carried out by riverbank population regarding the Amazonas (Froese in addition to Pauly 2018). Aquaculture production is attractive due to be able to high carcass yields and rapid juvenile growth, with yearlings reaching up to be able to 10 kg (22 lb) (Almeida et al. 2013).
Arapaima gigas — Wikipédia
Arapaima gigas belongs to typically 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). Together with Elopomorpha (eels in addition to tarpons) and Clupeocephala (most of extant fish species), the Osteoglossomorpha comprises one of the three main teleosts groups whose phylogenetic position has been questionable (Le et al. 93; Inoue et al. 2003; Near et al. spring 2012; Betancur-R 2013; Faircloth ou al. 2013; Chen et al. 2015; Hughes et al. 2018). Fossil records and some early molecular studies, including a latest comprehensive analysis of > 300 Actinopterygii species (Hughes et al. 2018), put Osteoglossomorpha since the oldest teleost group (Greenwood 1970; Inoue et al. 2003), although other studies put Elopomorpha as the most ancestral one (Near et al. 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 typically the branching of Elopomorpha plus Osteoglossomorpha occurred almost at the same time, putting them as sibling lineages of Clupeocephala (Bian 2016). Within this framework, the genome of the particular Pirarucu provides new ideas to study the historical past of teleosts as nicely as providing useful information for sustainable exploration regarding this giant Amazon seafood. Here, we present the first whole genome set up, gene annotation, and phylogenomic inference of the Pirarucu that ought to facilitate the molecular characterization and conservation associated with this economically important seafood species.
File:Arapaima gigas 01.JPG Wikimedia Commons
Test Collection and SequencingGenomic DNA was extracted coming from peripheral blood samples of four adult individuals (two males and two females) of Arapaima gigas: NCBI taxonomy ID 113544, FishBase ID: 2076. All selections were collected in agreement with the standards associated with the Federal University regarding Pará animal protocol. We 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 using FastQC, version 0. 11. 4 (Andrews 2010), and low-quality reads have been trimmed with Sickle paired-end (pe), version 1. thirty-three (Joshi and Fass 2011), under default parameters.Genome Size Estimation and Para Novo AssemblageGenome sizing was estimated based about the k-mer spectrum with all the following formula: G= (N×(L−K + 1)−B)/D. Where N is the particular total read count, D will be the read length, Nited kingdom is k-mer length (K = 31), B is the complete low-frequency (frequency ≤1) k-mer count, D is the particular k-mer depth, and H is the genome dimension. Jellyfish 2. 2. 6 (Marçais and Kingsford 2011) was used to count number k-mer frequencies of high-quality sequencing reads.Genome assemblage was performed using SOAPdenovo2 (version 2. 04) (Luo et al. 2012) beneath default parameters (127mer version). Three assemblies were conducted: 1) using all says; 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: to begin with with all the default value of minimum read pairs to be able to joining contigs (5 pairs), subsequently rerunning with earlier data having a minimum worth of four read pairs and, finally, using a minimum of three read pairs. Assembly quality and statistics were assessed with QUAST (version 4. 4) (Gurevich et al. 2013).
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Evaluation of Genome CompletenessSet up quality was measured by simply assessing gene completeness along with Benchmarking Universal Single-Copy Orthologs (BUSCO) (Simão et al. 2015) based on four, 584 BUSCO groups produced from Actinopterygii orthologs.Repeat AnalysisTransposable elements (TEs) and other repetitive elements of the Pirarucu genome were identified by the combined, homology-based method in addition to a de novo observation approach. Initially, tandem repeats were identified with Conjunction Repeats Finder 4. 2009 (Benson 1999) with the particular 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 constructed 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, known and novel transposable factors 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, we annotated TE-related proteins using RepeatProteinMask 4. 0 (Tarailo-Graovac and Chen 2009).Gene Structure and Function ObservationGenome annotation was performed 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, sobre novo annotations were performed using the homology-based outcomes achieved in the very 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 1st 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) has been trained using the genome assembly itself. InterProScan five. 24-63. 0 (Jones ainsi que al. 2014) was run on the protein output associated with MAKER, providing gene ontologies and classifying protein domains and families. Protein result was compared using BOOST against the NCBI NR database (available on May 29, 2017) for identifying putative gene names. Blast2GO v5 (Conesa et ing. 2005) was subsequently utilized to obtain Gene Ontology mapping and annotation (supplementary file S2, Supplementary Materials online).