Salmo trutta

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M. Fibla - One of the best experts on this subject based on the ideXlab platform.

  • De novo assembly of the Brown trout (Salmo trutta m. fario) brain and muscle transcriptome: transcript annotation, tissue differential expression profile and SNP discovery.
    BMC research notes, 2020
    Co-Authors: Joan Fibla, Neus Oromi, Mariona Pascual-pons, Jose Luis Royo, Antoni Palau, M. Fibla
    Abstract:

    OBJECTIVES The Brown trout is a Salmonid species with a high commercial value in Europe. Life history and spawning behaviour include resident (Salmo trutta m. fario) and migratory (Salmo trutta m. trutta) ecotypes. The main objective is to apply RNA-seq technology in order to obtain a reference transcriptome of two key tissues, brain and muscle, of the riverine trout Salmo trutta m. fario. Having a reference transcriptome of the resident form will complement genomic resources of Salmonid species. DATA DESCRIPTION We generate two cDNA libraries from pooled RNA samples, isolated from muscle and brain tissues of adult individuals of Salmo trutta m. fario, which were sequenced by Illumina technology. Raw reads were subjected to de-novo transcriptome assembly using Trinity, and coding regions were predicted by TransDecoder. A final set of 35,049 non-redundant ORF unigenes were annotated. Tissue differential expression analysis was evaluated by Cuffdiff. A False Discovery Rate (FDR) ≤ 0.01 was considered for significant differential expression, allowing to identify key differentially expressed unigenes. Finally, we have identified SNP variants that will be useful tools for population genomic studies.

Abolhasan Rezaei - One of the best experts on this subject based on the ideXlab platform.

  • Studies of mitochondrial genomics in Salmo trutta fario
    Mitochondrial DNA. Part B Resources, 2017
    Co-Authors: Abolhasan Rezaei, Sheyda Akhshabi
    Abstract:

    Salmo trutta fario population is an important species for aquaculture and livestock industry. Moreover, these species were used for studies on the molecular markers. Mitochondrial genomic is also beneficial for phylogenetic studies in Salmonid species. They applied maternal traits for mitogenome, whereas paternal traits related to nuclear genomics. It will be genetically highly divergent indicating that they may represent distinct and potentially locally adapted gene pools (Apostolidis et al., 2011). Evolutionary history has been studied on the Salmo taxa such as brown trout, Salmo salar, Salmo trutta populations (Kottelat & Freyhof, 2007; Simonovic et al., 2007).

  • Studies on the Mitochondrial Genomics in Salmo trutta caspius Population in Three Rivers of Caspian Sea
    Journal of Fisheries & Livestock Production, 2017
    Co-Authors: Abolhasan Rezaei, Sheyda Akhshabi
    Abstract:

    Mitochondrial DNA is suitable for phylogenetic studies. Hence in this study mitochondrial DNA genes in Salmo trutta caspius were sequenced and deposited in Genbank. Six sequences of S.t. caspius mitochondrial ATPase 6 gene with accession nos. LC011387.1, LC154842- LC154847 and the full length of the mitochondrial genome in S.t. caspius (accession no. LC011387.1) were deposited in Genbank. Sequences were aligned between S.t. caspius and Salmo trutta by BLAST program. Although results showed a high homology between both sequences, but single nucleotide variations between ND genes in S.t. caspius and Salmo trutta were observed. S.t. caspius, S. trutta, and Salmo salar sequences were converted into a circular map in an online system named Organellar Genome DRAW (http://ogdraw. mpimp-golm.mpg.de). Maps created by OGDRAW were different for S.t. caspius, S. trutta and S. salar. Moreover, Maximum Parsimony method was conducted for evolutionary analysis using MEGA 6.0 program tree between S.t. caspius and other Salmonids. The results showed that S.t. caspius, Salmo trutta, Salmo trutta fario and S. trutta are covered in a group. On the other hand, results of evolutionary analysis using Tajima's test were conducted in MEGA 6.0 program for three sequencing including, S.t. caspius, S.t. trutta specimen voucher Nor 00, and S.t. fario used as an outgroup for equality of evolutionary rate. Comparison of partial mitochondrial sequence in Iranian S.t. caspius population was performed between three regions [Tonekabon (Cheshmekileh Roud), Ramsar (Safa Roud) and Talesh (Nav roud)]. The results showed that except for one single nucleotide mutation in the partial sequence of mitochondria of S.t. caspius [Ramsar (Safa Roud)], there has been 100% homology between them. In conclusion, the mitochondrial genome homology of S.t. caspius and other Salmonids were high, though some SNPs were observed between S.t. caspius and other Salmonid species.

  • Phylogenetic analysis of NADH dehydrogenase subunit 1(NADH 1) gene in Salmo trutta caspius
    Journal of entomology and zoology studies, 2015
    Co-Authors: Abolhasan Rezaei
    Abstract:

    The NADH 1 gene in the Salmo trutta caspius has been sequenced, characterized and deposited in Genbank, Accession Number LC011387. In this study we compared NADH 1 gene between Salmo trutta caspius, Salmo trutta trutta, accession number (AM910409.1), Salmo salar (KF792729.1) and Oncorhynchus mykiss (DQ288268.1) by DNAMAN program and NCBI Network system separately. According to DNAMAN program analysis, we found 23 SNPs and 98% similarity between Salmo trutta caspius and Salmo trutta trutta, 67 SNPs and 92% similarity between Salmo trutta caspius and Salmo salar, 126 SNPs and 86% similarity between Salmo trutta caspius and Oncorhynchus mykiss. Amino acid sequences also were determined by DNAMAN program. Between Salmo trutta caspius and Salmo trutta trutta, 3 SNPs, between Salmo trutta caspius and Salmo salar 14 SNPs, and between Salmo trutta caspius and Oncorhynchus mykiss, 17 SNPs were observed. In this study we concluded that the rate of homology between Salmo trutta trutta and Salmo trutta caspius is more than its homology with Salmo salar and Oncorhynchus mykiss, so these results show that Salmo trutta caspius had originated from Salmo trutta.

  • Investigation and characterization of the 16S rRNA gene in the Salmo trutta fario and Salmo trutta caspius
    Egyptian Academic Journal of Biological Sciences B. Zoology, 2013
    Co-Authors: Abolhasan Rezaei
    Abstract:

    S rRNA gene in the Salmo trutta fario and Salmo trutta caspius has been polymerized, characterized and compared with within and between of Salmonids species. The full lengths of 16S rRNA gene in species of Salmons were sequenced approximately 1.7 kb and deposited in GenBank. We designed one pair of primer for amplification of 16S rRNA gene in species of s.t.caspius and s. t. fario. In present study, DNA extracted from muscles of s. t. fario and s.t.caspius for amplification of the 16S rRNA gene. After running PCR on the gel, against the PCR product had taken photo by Gel DOC. The results are shown there was high homology between solmonids, because we got PCR product around 1700bp equal of full length of 16S rRNA gene that reported in GenBank. However, the homology of PCR products were very high, but the shape of s. t. fario with s.t.caspius is different, s.t.fario has red to purple color dots on the skin but regards Salmo salar and s.t. caspius have grey to black dots colors on the skin.

  • Studies of Cytochrome b nucleotide sequence variation in the Salmo trutta fario
    Egyptian Academic Journal of Biological Sciences. C Physiology and Molecular Biology, 2012
    Co-Authors: Abolhasan Rezaei
    Abstract:

    The cytochrome b gene in the Salmo trutta fario has been sequenced and characterized and deposited in GeneBank, Accession Number (JN995186), the gene of cytochrome b approximately 1.2 kb. and consists of one exon from first to end of the gene, as found for all of Salmonids including, Salmo salar, Salmo trutta caspius, Salmo trutta fario that reported in GeneBank. There were the first to end of gene repetitive regions C-G that was unique for cytochrome b gene. At this study DNA extracted from muscles of Salmo trutta fario, after running PCR on the gel, the PCR products purify and sequenced. The fragments aligned with BLAST Network system, the results are shown there were high homology between solmonids, the rate of homology between Salmo salar 93%, Salmo trutta caspius almost 95% and Salmo fario (was reported in GeneBank) 93%. However, the homology of sequences were very high, but the shape of Salmo trutta fario and other Salmonids different, Salmo trutta fario has red to purple color dots on the skin but regards Salmo salar and Salmo trutta caspius have grey to black dots colors on the skin.

Ulo Faremo - One of the best experts on this subject based on the ideXlab platform.

Joan Fibla - One of the best experts on this subject based on the ideXlab platform.

  • De novo assembly of the Brown trout (Salmo trutta m. fario) brain and muscle transcriptome: transcript annotation, tissue differential expression profile and SNP discovery.
    BMC research notes, 2020
    Co-Authors: Joan Fibla, Neus Oromi, Mariona Pascual-pons, Jose Luis Royo, Antoni Palau, M. Fibla
    Abstract:

    OBJECTIVES The Brown trout is a Salmonid species with a high commercial value in Europe. Life history and spawning behaviour include resident (Salmo trutta m. fario) and migratory (Salmo trutta m. trutta) ecotypes. The main objective is to apply RNA-seq technology in order to obtain a reference transcriptome of two key tissues, brain and muscle, of the riverine trout Salmo trutta m. fario. Having a reference transcriptome of the resident form will complement genomic resources of Salmonid species. DATA DESCRIPTION We generate two cDNA libraries from pooled RNA samples, isolated from muscle and brain tissues of adult individuals of Salmo trutta m. fario, which were sequenced by Illumina technology. Raw reads were subjected to de-novo transcriptome assembly using Trinity, and coding regions were predicted by TransDecoder. A final set of 35,049 non-redundant ORF unigenes were annotated. Tissue differential expression analysis was evaluated by Cuffdiff. A False Discovery Rate (FDR) ≤ 0.01 was considered for significant differential expression, allowing to identify key differentially expressed unigenes. Finally, we have identified SNP variants that will be useful tools for population genomic studies.

J.l. Baglinière - One of the best experts on this subject based on the ideXlab platform.

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