Osteoglossomorpha Wikipedia
The Pirarucu (Arapaima gigas) is one of the world’s biggest freshwater fishes and member of the particular superorder Osteoglossomorpha (bonytongues), 1 of the oldest lineages of ray-finned fishes. This particular species is an obligate air-breather found in the basin of the Amazon online River having 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, initially, a draft genome variation of the A. gigas genome, providing useful info for even more functional and major studies. The A. gigas genome was assembled together with 103-Gb raw reads sequenced in a Illumina platform. The final draft genome set up was ∼661 Mb, with the contig N50 corresponding to fifty-one. 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 of nine exons per gene. Phylogenomic analysis based upon 24 fish species supported the postulation that Osteoglossomorpha and Elopomorpha (eels, tarpons, and bonefishes) are cousin groups, both forming the sister lineage regarding Clupeocephala (remaining teleosts). Divergence time estimations suggested that Osteoglossomorpha and Elopomorpha lineages emerged independently in a length of ∼30 Myr in typically the Jurassic. The draft genome of A. gigas provides a new valuable genetic resource regarding further investigations of major studies and may likewise give a valuable data for economical applications.
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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 will be presently distributed in Brazil, 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 through the indigenous Tupi words “pira” and “urucum” for “fish” and “red, ” respectively, presumably referring to its red tail scales flecks or their reddish flesh (Marsden 1994; Godinho et al. 2005). The peculiarity of its breathing apparatus is characteristic regarding 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). Typically the Pirarucu has an appealing market value because of its less fat and low bone content. Overfishing practices in the Amazonian region led to typically the banning of Pirarucu commercialization by the Brazilian authorities in 2001, although consumption with the native population is currently permitted under rigid size and seasoning rules (Bayley and Petrere 1989). Its main supply is usually provided by wild-caught seafood and fish farming performed by riverbank population regarding the Amazonas (Froese in addition to Pauly 2018). Aquaculture manufacturing is attractive due to high carcass yields plus rapid juvenile growth, along with yearlings reaching up to 10 kg (22 lb) (Almeida et al. 2013).
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Arapaima gigas belongs to typically 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 plus tarpons) and Clupeocephala (most of extant fish species), the Osteoglossomorpha comprises a single of the three main teleosts groups whose phylogenetic position has been controversial (Le et al. 93; Inoue et al. 2003; Near et al. this year; Betancur-R 2013; Faircloth et al. 2013; Chen ainsi que al. 2015; Hughes ou al. 2018). Fossil data and some early molecular studies, including a current comprehensive analysis of > 300 Actinopterygii species (Hughes et al. 2018), positioned Osteoglossomorpha since 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). Lately, a phylogenetic study based on whole genome sequencing in the bony-tongued Asian arowana (Scleropages formosus) suggested that the branching of Elopomorpha and Osteoglossomorpha occurred almost at the same time, positioning them as sibling lineages of Clupeocephala (Bian 2016). Within this circumstance, the genome of typically the Pirarucu provides new information to study the evolutionary history of teleosts as well as providing useful info for sustainable exploration associated with this giant Amazon species of fish. Here, we present the 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.
Pirarucu, Arapaima Arapaima gigas Aquarismo Paulista
Trial 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 samples were collected in compliance with the standards associated with the Federal University associated with Pará animal protocol. We applied a whole-genome shotgun sequencing strategy using two short-insert libraries (400 and 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 Group Kits (PE-402-4002) were applied to sequence paired-end go through of 2 × 250 base sets. Read quality was checked out using FastQC, version zero. 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 Set upGenome dimension was estimated based about the k-mer spectrum using the following formula: G= (N×(L−K + 1)−B)/D. Where N is the total read count, L may be the read length, E is k-mer length (K = 31), B is the overall low-frequency (frequency ≤1) k-mer count, D is the particular k-mer depth, and G is the genome sizing. Jellyfish 2. 2. 6th (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 conducted: 1) using all says; 2) with reads through male samples; and 3) with reads from women samples. Subsequently, gaps had been filled using Redundants (Pryszcz and Gabaldón 2016) using three-run scaffolding steps: to begin with with all the default value regarding minimum read pairs to joining contigs (5 pairs), subsequently rerunning with earlier data using a minimum benefit of four read sets and, finally, by using a minimum of three read pairs. Assembly quality and statistics were assessed with QUAST (version 4. 4) (Gurevich et al. 2013).
Arapaima Gigas
Evaluation 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 4, 584 BUSCO groups extracted 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 réflexion approach. Initially, tandem repeats were identified with Tandem 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), in addition to filtered with LTR_retriever (Ou and Jiang 2017) below default parameters. Subsequently, recognized and novel transposable elements were identified by mapping 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 annotated TE-related proteins applying 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) inside 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 outcomes achieved in the 1st step. We also used the RepeatModeller 1. 0. nine (Smit and Hubley 2008) to build a sobre novo repeat library 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) had been trained using the genome assembly itself. InterProScan five. 24-63. 0 (Jones et 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 GREAT TIME against the NCBI NR database (available on May 29, 2017) for identifying putative gene names. Blast2GO v5 (Conesa et al. 2005) was subsequently used to obtain Gene Ontology mapping and annotation (supplementary file S2, Supplementary Materials online).