Arapaima gigas 120 kg ,Amazonie YouTube
Typically the Pirarucu (Arapaima gigas) is probably the world’s greatest freshwater fish and member of typically the superorder Osteoglossomorpha (bonytongues), one of the oldest lineages of ray-finned fishes. This specific species is an obligate air-breather found in typically the basin of the Amazon . com River with an attractive potential for aquaculture. Its phylogenetic position among bony fishes makes the Pirarucu a relevant subject for evolutionary studies of early teleost diversification. Here, we present, for the first time, a draft genome version of the A. gigas genome, providing useful details for even more functional and major studies. The A. gigas genome was assembled with 103-Gb raw reads sequenced in a Illumina platform. The particular final draft genome set up was ∼661 Mb, with the contig N50 comparable 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 about 24 fish species supported the postulation that Osteoglossomorpha and Elopomorpha (eels, tarpons, and bonefishes) are sibling groups, both forming the sister lineage regarding Clupeocephala (remaining teleosts). Divergence moment estimations suggested that Osteoglossomorpha and Elopomorpha lineages appeared independently in a length of ∼30 Myr in the particular Jurassic. The draft genome of the. gigas provides a new valuable genetic resource with regard to further investigations of evolutionary studies and may furthermore give you a valuable data regarding economical applications.
Rangking: 29
Size: 557.5KB
Width: 2333
Height: 1556
Arapaima gigas — Wikipédia
Arapaima gigas, also known as Pirarucu or Paiche, is 1 of the world’s most significant freshwater fishes (Wijnstekers 2011) whose body length and 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 . com floodplain basin and is usually presently distributed in Brazil, Colombia, Ecuador, and Peru (Hrbek et al. 2005, 2007; Froese and Pauly 2018), and also within Thailand and Malaysia exactly where it has been launched for commercial fishing (Froese and Pauly 2018). Arapaima gigas local name (Pirarucu) derives from the indigenous Tupi words “pira” and “urucum” for “fish” and “red, ” respectively, presumably referring to its red tail scales flecks or to the reddish flesh (Marsden year 1994; Godinho et al. 2005). The peculiarity of its inhaling and exhaling apparatus is characteristic associated with this Amazonian fish, comprising 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 due to its less fat and low bone content. Overfishing practices in the Amazonian region led to the banning of Pirarucu commercialization by the Brazilian federal government in 2001, although consumption by the native population is currently permitted under strict size and seasoning rules (Bayley and Petrere 1989). Its main supply is usually provided by wild-caught seafood and fish farming conducted by riverbank population regarding the Amazonas (Froese plus Pauly 2018). Aquaculture creation is attractive due in order to high carcass yields plus rapid juvenile growth, along with yearlings reaching up to be able to 10 kg (22 lb) (Almeida et al. 2013).
Arapaima gigas — Wikipédia
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). Combined with Elopomorpha (eels and tarpons) and Clupeocephala (most of extant fish species), the Osteoglossomorpha comprises one of the three primary 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 ou al. 2015; Hughes et al. 2018). Fossil data 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), whilst other studies put Elopomorpha as the most primitive one (Near et 's. 2012; Betancur-R 2013; Faircloth et al. 2013). Recently, a phylogenetic study depending on whole genome sequencing from the bony-tongued Asian arowana (Scleropages formosus) suggested that the branching of Elopomorpha in addition to Osteoglossomorpha occurred almost simultaneously, positioning them as sibling lineages of Clupeocephala (Bian 2016). Within this circumstance, the genome of the Pirarucu provides new information to study the historical past of teleosts as nicely as providing useful info for sustainable exploration associated with this giant Amazon seafood. Here, we present typically 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.Arapaima gigas — Wikipédia
Test Collection and SequencingGenomic DNA was extracted through peripheral blood samples associated with 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 associated with the Federal University of Pará animal protocol. All of us applied a whole-genome shotgun sequencing strategy using 2 short-insert libraries (400 plus 500 bp) in a Illumina HiSeq 2500 platform according in order 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 used to sequence paired-end study of 2 × 250 base sets. Read quality was checked using FastQC, version zero. 11. 4 (Andrews 2010), and low-quality reads were trimmed with Sickle paired-end (pe), version 1. thirty-three (Joshi and Fass 2011), under default parameters.Genome Size Estimation and Para Novo AssemblageGenome dimension was estimated based upon the k-mer spectrum using the following formula: G= (N×(L−K + 1)−B)/D. Where N is typically the total read count, L will be the read length, E is k-mer length (K = 31), B is the total low-frequency (frequency ≤1) k-mer count, D is the k-mer depth, and H is the genome size. Jellyfish 2. 2. 6th (Marçais and Kingsford 2011) was used to depend k-mer frequencies of top quality sequencing reads.Genome assemblage 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 through male samples; and 3) with reads from female samples. Subsequently, gaps had been filled using Redundants (Pryszcz and Gabaldón 2016) making use of three-run scaffolding steps: first of all with the default value regarding minimum read pairs in order to joining contigs (5 pairs), subsequently rerunning with prior data with a minimum benefit of four read sets and, finally, by using a minimal of three read sets. Assembly quality and stats were assessed with QUAST (version 4. 4) (Gurevich et al. 2013).Arapaima Gigas
Examination of Genome CompletenessSet up quality was measured by assessing gene completeness along with Benchmarking Universal Single-Copy Orthologs (BUSCO) (Simão et ing. 2015) based on four, 584 BUSCO groups produced from Actinopterygii orthologs.Replicate AnalysisTransposable elements (TEs) and other repetitive factors of the Pirarucu genome were identified by a combined, homology-based method in addition to a de novo observation approach. Initially, tandem repeats were identified with Conjunction 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 constructed with RepeatModeler 1. zero. 9 and LTR_FINDER (Xu and Wang 2007), and filtered with LTR_retriever (Ou and Jiang 2017) beneath default parameters. Subsequently, identified and novel transposable elements were identified by mapping the assembled sequences towards the Repbase TE 22. 05 (Bao et al. 2015) and de novo repeat libraries using RepeatMasker 4. 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. 1st, 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 release 88), together with Scleropages formosus (Asian arowana) proteins sequences from NCBI RefSeq annotation data. Subsequently, sobre novo annotations were carried out using the homology-based results achieved in the 1st 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 very 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 5. 24-63. 0 (Jones ou al. 2014) was operate on the protein output associated with MAKER, providing gene ontologies and classifying protein domain names and families. Protein output 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 utilized to obtain Gene Ontology mapping and annotation (supplementary file S2, Supplementary Materials online).