Арапайма гигантская или пираруку лат. Arapaima gigas
The particular Pirarucu (Arapaima gigas) is one of the world’s most significant freshwater fishes and member of the superorder Osteoglossomorpha (bonytongues), one of the oldest lineages of ray-finned fishes. This particular species is an obligate air-breather found in the basin of the Amazon River with an attractive possible for aquaculture. Its phylogenetic position among bony fish makes the Pirarucu another subject for evolutionary scientific studies of early teleost diversification. Here, we present, the first time, a draft genome edition of the A. gigas genome, providing useful information for further functional and major studies. The A. gigas genome was assembled along with 103-Gb raw reads sequenced in a Illumina platform. Typically the final draft genome assembly was ∼661 Mb, with a 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, 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 sibling groups, both forming a sister lineage regarding Clupeocephala (remaining teleosts). Divergence period estimations suggested that Osteoglossomorpha and Elopomorpha lineages surfaced independently in a length of ∼30 Myr in the particular Jurassic. The draft genome of A. gigas provides the valuable genetic resource for further investigations of major studies and may also provide a valuable data for monetary applications.
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Arapaima gigas, also known as Pirarucu or Paiche, is one of the world’s most significant freshwater fishes (Wijnstekers 2011) whose body length plus 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 floodplain basin and will be presently distributed in Brazil, Colombia, Ecuador, and Peru (Hrbek et al. june 2006, 2007; Froese and Pauly 2018), and also in Thailand and Malaysia where it has been released 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 mentioning to its red tail scales flecks in order to their reddish flesh (Marsden 1994; Godinho et al. 2005). The peculiarity of its inhaling and exhaling apparatus is characteristic regarding this Amazonian fish, including gills and a lung-like tissue devised for air-breathing derived from a modified and enlarged swim bladder (Burnie and Wilson 2001; Brauner et al. 2004). The particular Pirarucu has an interesting market value due to its less fat and low bone articles. Overfishing practices in the Amazonian region led to the particular banning of Pirarucu commercialization by the Brazilian government in 2001, although intake by the native population is currently permitted under stringent size and seasoning rules (Bayley and Petrere 1989). Its main supply will be provided by wild-caught seafood and fish farming conducted by riverbank population of the Amazonas (Froese and Pauly 2018). Aquaculture creation is attractive due in order to high carcass yields in addition to rapid juvenile growth, with yearlings reaching up in order to 10 kg (22 lb) (Almeida et al. 2013).
Pirarucu, Arapaima Arapaima gigas Aquarismo Paulista
Arapaima gigas belongs to the particular superorder Osteoglossomorpha of bony-tongued fishes whose tongue includes sharp bony teeth for disabling and shredding preys (Sanford and Lauder 1990; Burnie and Wilson 2001). Together 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 controversial (Le et al. 1993; Inoue et al. the year 2003; Near et al. spring 2012; Betancur-R 2013; Faircloth ainsi que al. 2013; Chen et al. 2015; Hughes et 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), whilst other studies put Elopomorpha as the most primitive one (Near et al. 2012; Betancur-R 2013; Faircloth et al. 2013). Recently, a phylogenetic study according to whole genome sequencing of the bony-tongued Asian arowana (Scleropages formosus) suggested that the branching of Elopomorpha in addition to Osteoglossomorpha occurred almost concurrently, positioning them as cousin lineages of Clupeocephala (Bian 2016). Within this circumstance, the genome of the particular Pirarucu provides new insights to study the historical past of teleosts as nicely as providing useful info for sustainable exploration regarding this giant Amazon species of fish. Here, we present the first whole genome assembly, gene annotation, and phylogenomic inference of the Pirarucu that ought to facilitate the molecular characterization and conservation regarding this economically important species of fish species.
Arapaima gigas Merifish Aquariums.
Test Collection and SequencingGenomic DNA was extracted coming from peripheral blood samples associated with four adult individuals (two males and two females) of Arapaima gigas: NCBI taxonomy ID 113544, FishBase ID: 2076. All examples were collected in compliance with the standards of the Federal University regarding Pará animal protocol. All of us applied a whole-genome shotgun sequencing strategy using 2 short-insert libraries (400 plus 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 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 had been trimmed with Sickle paired-end (pe), version 1. thirty-three (Joshi and Fass 2011), under default parameters.Genome Size Estimation and Sobre Novo AssemblyGenome sizing was estimated based on the k-mer spectrum with all the following formula: G= (N×(L−K + 1)−B)/D. Where N is the particular total read count, L will be the read length, K is k-mer length (K = 31), B is the overall low-frequency (frequency ≤1) k-mer count, D is the k-mer depth, and G is the genome dimension. Jellyfish 2. 2. 6 (Marçais and Kingsford 2011) was used to count number k-mer frequencies of top quality sequencing reads.Genome assembly was performed using SOAPdenovo2 (version 2. 04) (Luo et al. 2012) under default parameters (127mer version). Three assemblies were conducted: 1) using all reads; 2) with reads coming from male samples; and 3) with reads from female samples. Subsequently, gaps were filled using Redundants (Pryszcz and Gabaldón 2016) making use of three-run scaffolding steps: to begin with with the default value associated with minimum read pairs to be able to joining contigs (5 pairs), subsequently rerunning with earlier data with a minimum value of four read pairs and, finally, utilizing a minimal of three read sets. Assembly quality and data were assessed with QUAST (version 4. 4) (Gurevich et al. 2013).
Pirarucu, Arapaima Arapaima gigas Aquarismo Paulista
Evaluation of Genome CompletenessAssembly quality was measured by simply assessing gene completeness together with Benchmarking Universal Single-Copy Orthologs (BUSCO) (Simão et al. 2015) based on four, 584 BUSCO groups produced from Actinopterygii orthologs.Replicate AnalysisTransposable elements (TEs) and other repetitive components 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 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 built 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 do it again libraries using RepeatMasker 4. 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) within 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 release 88), together with Scleropages formosus (Asian arowana) proteins sequences from NCBI RefSeq annotation data. Subsequently, de novo annotations were carried out 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 along with default parameters. The GFF output from the very 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 5. 24-63. 0 (Jones et al. 2014) was run on the protein output of MAKER, providing gene ontologies and classifying protein domains and families. Protein result was compared using BLAST against the NCBI NR database (available on Might 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 Material online).