The complete mitochondrial genome of perch
            <i>Perca fluviatilis</i>
            (Perciformes: Percidae)

Yang, Ruibin; Ma, Zhihong; Beliczky, Gábor; Havasi, Máté; Bercsényi, Miklós

doi:10.3109/19401736.2014.971303

Cited by 4 publications

(5 citation statements)

References 6 publications

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Section: Types Of Genetic Variationmentioning

confidence: 99%

“…The same approach was also applied to discover new microsatellite loci in perch (Pukk et al, 2014). However, the recent breakthrough in high throughput sequencing technologies along with the decrease in sequencing costs has considerably increased the number of mitochondrial (Yang et al, 2016), nuclear (Table 1) and transcriptome data sets of perch (Table 2). In turn, access to the reference genome assembly has helped to discover hundreds of thousands of SNPs in perch (Ozerov et al, 2022) and fuelled the development of the Axiom SNP array platform (MultiFishSNPChip_1.0) which consists of nearly 4000 SNPs (Figure 3).…”

Section: Available Genomic Resourcesmentioning

confidence: 99%

“…The first available whole-mitochondrial genome assembly of perch was deposited to the NCBI GenBank in 2015 by Yang et al (2016). At the time of writing this review, there were six whole-mitochondrial genome assemblies available at the NCBI GenBank.…”

Section: Whole-mitochondrial Genomesmentioning

confidence: 99%

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Unlocking the genome of perch – From genes to ecology and back again

Vasemägi

Ozerov

Noreikienė

et al. 2023

Ecology of Freshwater Fish

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Eurasian perch Perca fluviatilis has been a popular model species for decades in the fields of aquatic ecology, community dynamics, behaviour, physiology and ecotoxicology. Yet, despite extensive research, the progress of integrating genomic perspective into existing ecological knowledge in perch has been relatively modest. Meanwhile, the emergence of high‐throughput sequencing technologies has completely changed the methods for genetic variation assessment and conducting biodiversity and evolutionary research. During the last 5 years, three genome assemblies of P. fluviatilis have been generated, allowing substantial advancement of our understanding of the interactions between ecological and evolutionary processes at the whole‐genome level. We review the past progress, current status and potential future impact of the genomic resources and tools for ecological research in Eurasian perch focusing on the utility of recent whole‐genome assemblies. Furthermore, we demonstrate the power of genome‐wide approaches and newly developed tools and outline recent cases where genomics have contributed to new ecological and evolutionary knowledge. We explore how the availability of reference assembly enables the efficient application of various statistical tools, and how genomic approaches can provide novel insights into resource polymorphism, host–parasite interactions and to genetic and phenotypic changes associated with climate change and harvesting‐induced evolution. In summary, we call for increased integration of genomic tools into ecological research for perch, as well as for other fish species, which is likely to yield novel insights into processes linking the adaptation and plasticity to ecosystem functioning and environmental change.

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Section: Types Of Genetic Variationmentioning

confidence: 99%

Section: Available Genomic Resourcesmentioning

confidence: 99%

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Unlocking the genome of perch – From genes to ecology and back again

Vasemägi

Ozerov

Noreikienė

et al. 2023

Ecology of Freshwater Fish

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“…The analysed 627 bp ATP6 region consisted of one nucleotide before the first codon, 195 codons of the ATP6 fragment, and two nucleotides (TA) that acted as a stop codon before the 13 codons that represented part of the cox3 gene (Supplementary Document S2). The first nucleotide A after the mentioned TA sequence was used by both genes as a stop and start codon, respectively [69]. Of the 20 amino acids, only C was not coded by the studied fragment.…”

Section: Protein Sequence Variability Of the Mtdna Atp6 Regionmentioning

confidence: 99%

“…Moreover, the number of whole mtDNA genomes that have been sequenced is increasing [46]. The maternally transmitted mtDNA genome [68] of perch is 16,537 bp in length and consists of 37 genes and two non-coding regions [69], like the mtDNA genomes of most other known fish species [70]. In addition, species-specific DNA microsatellites have been created to examine various European and Asian perch populations [71][72][73][74].…”

Section: Introductionmentioning

confidence: 99%

Trends of Eurasian Perch (Perca fluviatilis) mtDNA ATP6 Region Genetic Diversity within the Hydro-Systems of the Eastern Part of the Baltic Sea in the Anthropocene

Ragauskas,

Ignatavičienė,

Rakauskas

et al. 2023

Animals

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The intraspecific genetic diversity of freshwater fish inhabiting hydro-systems of the macrogeographic area spreading from the Black to Baltic Seas requires comprehensive investigation from fundamental and practical perspectives. The current study focused on the involvement of the mtDNA ATP6 region in the adaptability and microevolution of Perca fluviatilis within phylogeographic and anthropogenic contexts. We sequenced a 627 bp fragment encompassing the ATP6 region and used it for genetic analysis of 193 perch caught in Latvia, Lithuania, Belarus, and Ukraine, representing natural and anthropogenically impacted populations. We evaluated patterns of intraspecific genetic diversity in the ATP6 region and phylogeographic trends within the studied area compared with previously established D-loop trends. Evaluation of ATP6 coding sequence variability revealed that among 13 newly detected haplotypes, only two were caused by non-synonymous substitutions of amino acids of the protein. PCoA revealed three genetic groups (I–III) based on the ATP6 region that encompassed four previously described genetic groups established based on the mtDNA D-loop. The two mtDNA regions (D-loop and ATP6) have microevolved at least partially independently. Prolonged anthropogenic impacts may generate new point mutations at the ATP6 locus, but this phenomenon could be mainly concealed by natural selection and reparation processes.

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The complete mitochondrial genome of Sillago sihama (Perciformes: Sillaginidae)

Siyal

Xiao

Song

et al. 2015

Mitochondrial DNA Part A

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In this study, the complete mitochondrial genome (mitogenome) sequence of Sillago sihama has been determined by long polymerase chain reaction and primer walking methods. The complete mitochondrial genome is a circular molecule of 17 003 bp in length and contains 37 mitochondrial genes and a control region. Within the control region, we identified the variable number tandem repeats, as well as the termination-associated sequence domain (TAS), the central conserved sequence block domains (CSB-F∼CSB-A) and the conserved sequence block domains (CSB-1, CSB-2, and CSB-3).

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The complete mitochondrial genome of perch Perca fluviatilis (Perciformes: Percidae)

Cited by 4 publications

References 6 publications

Unlocking the genome of perch – From genes to ecology and back again

Unlocking the genome of perch – From genes to ecology and back again

Trends of Eurasian Perch (Perca fluviatilis) mtDNA ATP6 Region Genetic Diversity within the Hydro-Systems of the Eastern Part of the Baltic Sea in the Anthropocene

The complete mitochondrial genome of Sillago sihama (Perciformes: Sillaginidae)

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