Of Fish Scales and Adaptable Armor – The Things That XRays Can Tell You Berkeley Lab
The Pirarucu (Arapaima gigas) is among the world’s biggest freshwater fish and member of the 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 . com River by having an attractive potential for aquaculture. Its phylogenetic position among bony fish makes the Pirarucu another subject for evolutionary studies of early teleost variation. Here, we present, for the first time, a draft genome edition of the A. gigas genome, providing useful info for more functional and evolutionary studies. The A. gigas genome was assembled along with 103-Gb raw reads sequenced in an Illumina platform. Typically the final draft genome assemblage was ∼661 Mb, with a new 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 were predicted from the genome assembly, with an average of nine exons per gene. Phylogenomic analysis based upon 24 fish species backed the postulation that Osteoglossomorpha and Elopomorpha (eels, tarpons, and bonefishes) are sister groups, both forming a new sister lineage regarding Clupeocephala (remaining teleosts). Divergence time estimations suggested that Osteoglossomorpha and Elopomorpha lineages appeared independently in a period of ∼30 Myr in typically the Jurassic. The draft genome of any. gigas provides a valuable genetic resource regarding further investigations of evolutionary studies and may also provide a valuable data with regard to financial applications.
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Pirarucu, Arapaima Arapaima gigas Aquarismo Paulista
Arapaima gigas, also known as Pirarucu or Paiche, is 1 of the world’s biggest freshwater fishes (Wijnstekers 2011) whose body length plus 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 online floodplain basin and is presently distributed in Brazil, Colombia, Ecuador, and Peru (Hrbek et al. 2005, 2007; Froese and Pauly 2018), and also inside Thailand and Malaysia wherever 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 butt scales flecks or its reddish flesh (Marsden 1994; Godinho et al. 2005). The peculiarity of its inhaling apparatus is characteristic of this Amazonian fish, composed of 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 interesting market value due to its low-fat and low bone content. Overfishing practices in the Amazonian region led to typically the banning of Pirarucu commercialization by the Brazilian federal government in 2001, although consumption by the native population will be currently permitted under strict size and seasoning restrictions (Bayley and Petrere 1989). Its main supply will be provided by wild-caught fish and fish farming performed by riverbank population regarding the Amazonas (Froese plus Pauly 2018). Aquaculture production is attractive due in order to high carcass yields in addition to rapid juvenile growth, along with yearlings reaching up to be able to 10 kg (22 lb) (Almeida et al. 2013).
File:Arapaima gigas 01.JPG Wikimedia Commons
Arapaima gigas belongs to typically the superorder Osteoglossomorpha of bony-tongued fishes whose tongue contains sharp bony teeth with regard to disabling and shredding preys (Sanford and Lauder 1990; Burnie and Wilson 2001). Together with Elopomorpha (eels in addition to tarpons) and Clupeocephala (most of extant fish species), the Osteoglossomorpha comprises one of the three main teleosts groups whose phylogenetic position has been questionable (Le et al. 1993; Inoue et al. the year 2003; Near et al. 2012; Betancur-R 2013; Faircloth ainsi que al. 2013; Chen ainsi que al. 2015; Hughes et al. 2018). Fossil records and some early molecular studies, including a current comprehensive analysis of > 300 Actinopterygii species (Hughes et al. 2018), located Osteoglossomorpha since the oldest teleost group (Greenwood 1970; Inoue et al. 2003), while other studies located Elopomorpha as the most our ancestors one (Near et ing. 2012; Betancur-R 2013; Faircloth et al. 2013). Lately, a phylogenetic study according to whole genome sequencing from the bony-tongued Asian arowana (Scleropages formosus) suggested that the branching of Elopomorpha in addition to Osteoglossomorpha occurred almost concurrently, positioning them as sibling lineages of Clupeocephala (Bian 2016). Within this circumstance, the genome of typically the Pirarucu provides new ideas to study the historical past of teleosts as nicely as providing useful details for sustainable exploration regarding this giant Amazon species of fish. Here, we present typically the first whole genome assemblage, gene annotation, and phylogenomic inference of the Pirarucu which should facilitate the molecular characterization and conservation associated with this economically important seafood species.
17 Best images about Arapaima on Pinterest Fish swimming, Search and Peru
Test Collection and SequencingGenomic DNA was extracted 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 samples were collected in agreement with the standards associated with the Federal University regarding 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 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 using FastQC, version 0. 11. 4 (Andrews 2010), and low-quality reads had been trimmed with Sickle paired-end (pe), version 1. 33 (Joshi and Fass 2011), under default parameters.Genome Size Estimation and De Novo AssemblageGenome 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, D is 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 size. Jellyfish 2. 2. six (Marçais and Kingsford 2011) was used to count number k-mer frequencies of top quality sequencing reads.Genome set up 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) making use of three-run scaffolding steps: to begin with using the default value of minimum read pairs to joining contigs (5 pairs), subsequently rerunning with previous data using a minimum worth of four read pairs and, finally, utilizing a minimum of three read sets. Assembly quality and stats were assessed with QUAST (version 4. 4) (Gurevich et al. 2013).
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Examination of Genome CompletenessSet up quality was measured by assessing gene completeness together with Benchmarking Universal Single-Copy Orthologs (BUSCO) (Simão et ing. 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 a combined, homology-based method plus a de novo annotation approach. Initially, tandem repeats were identified with Tandem 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 constructed 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, identified 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 four. 0 (Tarailo-Graovac and Chen 2009). In addition, all of us annotated TE-related proteins applying 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. First, 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) protein 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 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) has been trained using the genome assembly itself. InterProScan five. 24-63. 0 (Jones ou al. 2014) was operate on the protein output associated with MAKER, providing gene ontologies and classifying protein domains 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 ing. 2005) was subsequently used to obtain Gene Ontology mapping and annotation (supplementary file S2, Supplementary Materials online).
