Arapaima Gigas
Typically the Pirarucu (Arapaima gigas) is one of the world’s most significant freshwater fish and member of the particular superorder Osteoglossomorpha (bonytongues), 1 of the oldest lineages of ray-finned fishes. This species is an obligate air-breather found in typically the basin of the Amazon River having an attractive prospective for aquaculture. Its phylogenetic position among bony fish makes the Pirarucu another subject for evolutionary scientific studies of early teleost variation. Here, we present, for the first time, a draft genome version of the A. gigas genome, providing useful details for further functional and evolutionary studies. The A. gigas genome was assembled with 103-Gb raw reads sequenced in an Illumina platform. The final draft genome set up was ∼661 Mb, with a new contig N50 corresponding to 51. 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 had been predicted from the genome assembly, by having an average regarding nine exons per gene. Phylogenomic analysis based on 24 fish species backed the postulation that Osteoglossomorpha and Elopomorpha (eels, tarpons, and bonefishes) are cousin groups, both forming a sister lineage regarding Clupeocephala (remaining teleosts). Divergence moment estimations suggested that Osteoglossomorpha and Elopomorpha lineages emerged independently in a amount of ∼30 Myr in typically the Jurassic. The draft genome of A. gigas provides a new valuable genetic resource with regard to further investigations of major studies and may furthermore provide a valuable data regarding financial applications.
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Arapaima gigas — Wikipédia
Arapaima gigas, also known as Pirarucu or Paiche, is 1 of the world’s greatest freshwater fishes (Wijnstekers 2011) whose body length in addition to weight may attain some. 5 m (15 ft) and 200 Kg (440 lb), respectively (Nelson 1994; Froese and Pauly 2018). The genus Arapaima emerged in the Amazon floodplain basin and is usually presently distributed in Brazilian, Colombia, Ecuador, and Peru (Hrbek et al. 2006, 2007; Froese and Pauly 2018), and also within Thailand and Malaysia where it has been launched 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 tail scales flecks in order to their reddish flesh (Marsden year 1994; Godinho et al. 2005). The peculiarity of its inhaling and exhaling apparatus is characteristic of 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 appealing market value because of low-fat and low bone content material. Overfishing practices in the Amazonian region led to the particular banning of Pirarucu commercialization by the Brazilian government in 2001, although intake with the native population is usually currently permitted under strict size and seasoning restrictions (Bayley and Petrere 1989). Its main supply will be provided by wild-caught species of fish and fish farming carried out by riverbank population associated with the Amazonas (Froese plus Pauly 2018). Aquaculture manufacturing is attractive due to be able to high carcass yields plus rapid juvenile growth, along with yearlings reaching up to 10 kg (22 lb) (Almeida et al. 2013).
17 Best images about Arapaima on Pinterest Fish swimming, Search and Peru
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). Combined 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. the year 2003; Near et al. 2012; Betancur-R 2013; Faircloth ainsi que al. 2013; Chen ou al. 2015; Hughes ainsi que al. 2018). Fossil records and some early molecular studies, including a latest comprehensive analysis of > 300 Actinopterygii species (Hughes et al. 2018), located Osteoglossomorpha because the oldest teleost group (Greenwood 1970; Inoue et al. 2003), while other studies positioned Elopomorpha as the most ancestral one (Near et ing. 2012; Betancur-R 2013; Faircloth et al. 2013). Just lately, a phylogenetic study depending on whole genome sequencing in the bony-tongued Asian arowana (Scleropages formosus) suggested that the branching of Elopomorpha plus Osteoglossomorpha occurred almost concurrently, positioning them as sister lineages of Clupeocephala (Bian 2016). Within this circumstance, the genome of typically the Pirarucu provides new insights to study the historical past of teleosts as nicely as providing useful details for sustainable exploration associated with this giant Amazon species of fish. Here, we present the particular first whole genome set up, 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.
Giant Arapaima Arapaima gigas ZooChat
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 examples were collected in accordance with the standards regarding the Federal University regarding Pará animal protocol. We applied a whole-genome shotgun sequencing strategy using a couple of short-insert libraries (400 in addition to 500 bp) in a Illumina HiSeq 2500 platform according 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 utilized to sequence paired-end go through of 2 × 250 base sets. Read quality was checked out 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 Sobre Novo AssemblageGenome dimension 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, T is the read length, K is k-mer length (K = 31), B is the complete 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. 6 (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) beneath default parameters (127mer version). Three assemblies were performed: 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) applying three-run scaffolding steps: to begin with with the default value of minimum read pairs in order to joining contigs (5 pairs), subsequently rerunning with earlier data having a minimum benefit of four read pairs and, finally, utilizing a minimum of three read pairs. Assembly quality and data were assessed with QUAST (version 4. 4) (Gurevich et al. 2013).
File:Arapaima gigas 01.JPG Wikimedia Commons
Assessment of Genome CompletenessAssemblage quality was measured simply by assessing gene completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO) (Simão et 's. 2015) based on four, 584 BUSCO groups derived from Actinopterygii orthologs.Replicate AnalysisTransposable elements (TEs) and other repetitive elements of the Pirarucu genome were identified by the combined, homology-based method and a de novo observation approach. Initially, tandem repeats were identified with Conjunction Repeats Finder 4. 09 (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 developed with RepeatModeler 1. zero. 9 and LTR_FINDER (Xu and Wang 2007), plus filtered with LTR_retriever (Ou and Jiang 2017) beneath default parameters. Subsequently, recognized and novel transposable factors were identified by umschlüsselung the assembled sequences for the Repbase TE 22. 05 (Bao et al. 2015) and de novo replicate libraries using RepeatMasker 4. 0 (Tarailo-Graovac and Chen 2009). In addition, we all annotated TE-related proteins making use of RepeatProteinMask 4. 0 (Tarailo-Graovac and Chen 2009).Gene Structure and Function ObservationGenome 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, sobre 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 first 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 operate on the protein output of MAKER, providing gene ontologies and classifying protein domain names and families. Protein output was compared using BLAST against the NCBI NR database (available on May 29, 2017) for determining putative gene names. Blast2GO v5 (Conesa et 's. 2005) was subsequently utilized to obtain Gene Ontology mapping and annotation (supplementary file S2, Supplementary Materials online).