ALIEN FISH SPECIES 22 APR 2014 FISHYOLOGY

ALIEN FISH SPECIES 22 APR 2014 FISHYOLOGY

The Pirarucu (Arapaima gigas) is one of the world’s biggest freshwater fish and member of the superorder Osteoglossomorpha (bonytongues), a single of the oldest lineages of ray-finned fishes. This particular species is an obligate air-breather found in the particular basin of the Amazon River with an attractive potential for aquaculture. Its phylogenetic position among bony fish makes the Pirarucu a relevant subject for evolutionary research of early teleost diversification. Here, we present, the first time, a draft genome version of the A. gigas genome, providing useful information for further functional and major studies. The A. gigas genome was assembled together with 103-Gb raw reads sequenced in an Illumina platform. Typically the final draft genome assembly was ∼661 Mb, with a 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 also a total of twenty four, 655 protein-coding genes had been predicted from the genome assembly, with an average regarding nine exons per gene. Phylogenomic analysis based upon 24 fish species supported the postulation that Osteoglossomorpha and Elopomorpha (eels, tarpons, and bonefishes) are sibling groups, both forming a sister lineage with respect to Clupeocephala (remaining teleosts). Divergence time estimations suggested that Osteoglossomorpha and Elopomorpha lineages surfaced independently in a period of ∼30 Myr in the particular Jurassic. The draft genome of the. gigas provides a valuable genetic resource with regard to further investigations of evolutionary studies and may furthermore give you a valuable data regarding monetary applications.

Rangking: 30

Size: 179.2KB

Width: 800

Height: 536

17 Best images about Arapaima on Pinterest Fish swimming, Search and Peru

Arapaima gigas, also known as Pirarucu or Paiche, is a single of the world’s most significant freshwater fishes (Wijnstekers 2011) whose body length and weight may attain four. 5 m (15 ft) and 200 Kg (440 lb), respectively (Nelson 1994; Froese and Pauly 2018). The genus Arapaima emerged in the Amazon . com floodplain basin and is presently distributed in Brazilian, Colombia, Ecuador, and Peru (Hrbek et al. 2005, 2007; Froese and Pauly 2018), and also inside Thailand and Malaysia wherever 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 end scales flecks in order to its reddish flesh (Marsden 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 produced from a modified plus enlarged swim bladder (Burnie and Wilson 2001; Brauner et al. 2004). The Pirarucu has an attractive market value because of its low-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 intake by the native population is usually currently permitted under strict size and seasoning rules (Bayley and Petrere 1989). Its main supply will be provided by wild-caught species of fish and fish farming performed by riverbank population associated with the Amazonas (Froese plus Pauly 2018). Aquaculture creation is attractive due in order to high carcass yields plus rapid juvenile growth, together with yearlings reaching up in order to 10 kg (22 lb) (Almeida et al. 2013).

Arapaima Wikipedia

Arapaima gigas belongs to the particular 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 plus tarpons) and Clupeocephala (most of extant fish species), the Osteoglossomorpha comprises one of the three primary teleosts groups whose phylogenetic position has been controversial (Le et al. 93; Inoue et al. 2003; Near et al. 2012; Betancur-R 2013; Faircloth et al. 2013; Chen ainsi que 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), 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). Lately, a phylogenetic study based on whole genome sequencing of the bony-tongued Asian arowana (Scleropages formosus) suggested that the particular branching of Elopomorpha and Osteoglossomorpha occurred almost concurrently, positioning them as cousin lineages of Clupeocephala (Bian 2016). Within this circumstance, the genome of the particular Pirarucu provides new ideas to study the historical past of teleosts as well as providing useful info for sustainable exploration associated with this giant Amazon fish. 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 of this economically important seafood species.

File:Arapaima Arapaima gigas 3.jpg Wikimedia Commons

Sample 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 associated with Pará animal protocol. All of us applied a whole-genome shotgun sequencing strategy using 2 short-insert libraries (400 and 500 bp) in a Illumina HiSeq 2500 platform according to be able 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 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. 33 (Joshi and Fass 2011), under default parameters.Genome Size Estimation and Sobre Novo AssemblyGenome dimension was estimated based upon the k-mer spectrum with all the following formula: G= (N×(L−K + 1)−B)/D. Where N is typically the total read count, T will be the read length, K is k-mer length (K = 31), B is the total low-frequency (frequency ≤1) k-mer count, D is the particular k-mer depth, and Gary the gadget guy is the genome dimension. Jellyfish 2. 2. six (Marçais and Kingsford 2011) was used to depend k-mer frequencies of top quality sequencing reads.Genome assembly 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 coming from male samples; and 3) with reads from women samples. Subsequently, gaps have been filled using Redundants (Pryszcz and Gabaldón 2016) making use of three-run scaffolding steps: first of all with all the default value associated with minimum read pairs in order to joining contigs (5 pairs), subsequently rerunning with prior data with a minimum worth of four read sets and, finally, by using a minimal of three read pairs. Assembly quality and stats were assessed with QUAST (version 4. 4) (Gurevich et al. 2013).

Arapaima Arapaima gigas MegaFishingThailand

Assessment of Genome CompletenessSet up quality was measured by simply assessing gene completeness together with Benchmarking Universal Single-Copy Orthologs (BUSCO) (Simão et ing. 2015) based on 4, 584 BUSCO groups extracted from Actinopterygii orthologs.Do it again AnalysisTransposable elements (TEs) and other repetitive components 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 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 built with RepeatModeler 1. 0. 9 and LTR_FINDER (Xu and Wang 2007), and filtered with LTR_retriever (Ou and Jiang 2017) beneath default parameters. Subsequently, recognized and novel transposable factors were identified by umschlüsselung the assembled sequences towards the Repbase TE 22. 05 (Bao et al. 2015) and de novo repeat libraries using RepeatMasker some. 0 (Tarailo-Graovac and Chen 2009). In addition, we annotated TE-related proteins using RepeatProteinMask 4. 0 (Tarailo-Graovac and Chen 2009).Gene Structure and Function AnnotationGenome annotation was performed with the MAKER2 pipeline (Holt and Yandell 2011) in a two-pass iteration. Very 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 RepeatModeller 1. 0. 9 (Smit and Hubley 2008) to build a de novo repeat library 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 five. 24-63. 0 (Jones et al. 2014) was run on the protein output associated with MAKER, providing gene ontologies and classifying protein domains and families. Protein result was compared using BOOST against the NCBI NR database (available on Might 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 Material online).