Arapaima gigas : Pirarucu
The Pirarucu (Arapaima gigas) is one of the world’s greatest freshwater fish and member of typically the superorder Osteoglossomorpha (bonytongues), 1 of the oldest lineages of ray-finned fishes. This species is an obligate air-breather found in the particular basin of the Amazon River having an attractive possible for aquaculture. Its phylogenetic position among bony fish makes the Pirarucu another subject for evolutionary scientific studies of early teleost variation. 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 together with 103-Gb raw reads sequenced within an Illumina platform. Typically the final draft genome assembly was ∼661 Mb, with a contig N50 equal to 51. 23 kb and scaffold N50 of 668 kb. Repeat sequences accounted for 21. 69% of the whole genome, and a total of twenty four, 655 protein-coding genes have been predicted from the genome assembly, with an average regarding nine exons per gene. Phylogenomic analysis based on 24 fish species reinforced the postulation that Osteoglossomorpha and Elopomorpha (eels, tarpons, and bonefishes) are cousin groups, both forming a new sister lineage with respect to Clupeocephala (remaining teleosts). Divergence time estimations suggested that Osteoglossomorpha and Elopomorpha lineages emerged independently in a length of ∼30 Myr in the Jurassic. The draft genome of any. gigas provides a valuable genetic resource with regard to further investigations of evolutionary studies and may likewise provide a valuable data regarding monetary applications.
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Fish That Can Survive Piranha Bites Inspire New Types Of Body Armour
Arapaima gigas, also known as Pirarucu or Paiche, is 1 of the world’s most significant freshwater fishes (Wijnstekers 2011) whose body length in addition to weight may attain 4. 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. 2005, 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 from your indigenous Tupi words “pira” and “urucum” for “fish” and “red, ” respectively, presumably referring to its red end scales flecks in order to their reddish flesh (Marsden year 1994; Godinho et al. 2005). The peculiarity from the breathing apparatus is characteristic regarding this Amazonian fish, comprising gills and a lung-like tissue devised for air-breathing based on a modified and enlarged swim bladder (Burnie and Wilson 2001; Brauner et al. 2004). Typically the Pirarucu has an attractive market value because of less fat and low bone content. Overfishing practices inside the Amazonian region led to the particular banning of Pirarucu commercialization by the Brazilian authorities in 2001, although intake with the native population is 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 carried out by riverbank population of the Amazonas (Froese in addition to Pauly 2018). Aquaculture manufacturing is attractive due in order to high carcass yields in addition to rapid juvenile growth, together with yearlings reaching up to 10 kg (22 lb) (Almeida et al. 2013).
Arapaima Gigas
Arapaima gigas belongs to the superorder Osteoglossomorpha of bony-tongued fishes whose tongue contains sharp bony teeth regarding 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 primary teleosts groups whose phylogenetic position has been debatable (Le et al. 93; Inoue et al. the year 2003; Near et al. 2012; Betancur-R 2013; Faircloth et al. 2013; Chen ou al. 2015; Hughes ou al. 2018). Fossil records and some early molecular studies, including a recent 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 primitive one (Near et ing. 2012; Betancur-R 2013; Faircloth et al. 2013). Recently, a phylogenetic study depending on whole genome sequencing of the bony-tongued Asian arowana (Scleropages formosus) suggested that typically the branching of Elopomorpha and Osteoglossomorpha occurred almost simultaneously, inserting them as sibling lineages of Clupeocephala (Bian 2016). Within this context, the genome of typically the Pirarucu provides new insights to study the historical past of teleosts as nicely as providing useful info for sustainable exploration of this giant Amazon species of fish. Here, we present the particular first whole genome assembly, gene annotation, and phylogenomic inference of the Pirarucu which should facilitate the molecular characterization and conservation associated with this economically important species of fish species.
Big Fishes of the World: ARAPAIMA PIRARUCU Arapaima gigas
Trial 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 regarding the Federal University associated with Pará animal protocol. We all applied a whole-genome shotgun sequencing strategy using two short-insert libraries (400 in addition to 500 bp) in an 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 Cluster Kits (PE-402-4002) were applied to sequence paired-end go through of 2 × 250 base pairs. Read quality was checked using FastQC, version 0. 11. 4 (Andrews 2010), and low-quality reads had been trimmed with Sickle paired-end (pe), version 1. thirty-three (Joshi and Fass 2011), under default parameters.Genome Size Estimation and Para Novo AssemblyGenome sizing was estimated based on the k-mer spectrum with the following formula: G= (N×(L−K + 1)−B)/D. Where N is the total read count, T may be the read length, E is k-mer length (K = 31), B is the total low-frequency (frequency ≤1) k-mer count, D is typically the k-mer depth, and Gary the gadget guy is the genome sizing. Jellyfish 2. 2. 6th (Marçais and Kingsford 2011) was used to count k-mer frequencies of top quality sequencing reads.Genome assembly 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 women samples. Subsequently, gaps have been filled using Redundants (Pryszcz and Gabaldón 2016) using three-run scaffolding steps: to begin with with all the default value of minimum read pairs to joining contigs (5 pairs), subsequently rerunning with previous data with a minimum worth of four read sets 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 with Benchmarking Universal Single-Copy Orthologs (BUSCO) (Simão et al. 2015) based on some, 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 plus a de novo annotation approach. Initially, tandem repeats were identified with Conjunction Repeats Finder 4. 09 (Benson 1999) with typically 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) 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 some. 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) inside a two-pass iteration. 1st, homology annotation was carried out 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) protein sequences from NCBI RefSeq annotation data. Subsequently, de novo annotations were performed using the homology-based results achieved in the first step. We also used 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) was trained using the genome assembly itself. InterProScan five. 24-63. 0 (Jones ou al. 2014) was run 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 al. 2005) was subsequently utilized to obtain Gene Ontology mapping and annotation (supplementary file S2, Supplementary Materials online).
