Mitogenomics of the suborder Cottoidei (Teleostei: Perciformes): Improved assemblies, mitogenome features, phylogeny, and ecological implications

Maduna, Simo N.; Vivian‐Smith, Adam; Jónsdóttir, Ólöf Dóra Bartels; Imsland, Albert K.; Klütsch, Cornelya F. C.; Nyman, Tommi; Eiken, Hans Geir; Hagen, Snorre B.

doi:10.1016/j.ygeno.2022.110297

Cited by 5 publications

(7 citation statements)

References 104 publications

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“…2013 ; Betancur-R et al . 2017 ; Maduna et al . 2022 ) and was expected to be approximately equally dissimilar to threespine stickleback and lumpfish.…”

Section: Resultsmentioning

confidence: 99%

“…2022 ) and was expected to be approximately equally dissimilar to threespine stickleback and lumpfish. Maduna et al . (2022) added a phylogenetic analysis to their study that incorporated fossil data, in particular, a 13 million-year-old stickleback.…”

Section: Resultsmentioning

confidence: 99%

“…While often called Alaskan black cod, they are more closely related to stickleback, sculpins, and lumpfish (suborder Cottioidei) than to cod (order Gadiformes) ( Betancur-R et al . 2017 ; Maduna et al . 2022 ).…”

Section: Introductionmentioning

confidence: 99%

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Sablefish (Anoplopoma fimbria) chromosome-level genome assembly

Flores

Christensen

Campbell³

et al. 2023

G3: Genes, Genomes, Genetics

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Sablefish (Anoplopoma fimbria) are in the suborder Cottioidei, which also includes stickleback and lumpfish. This species inhabits coastal regions of the northeastern and northwestern Pacific Ocean from California to Japan. A commercial fishery for sablefish began to flourish in the 1960s, though a downward trend in stock biomass and landings has been observed since 2010. Aquaculture protocols have been developed for sablefish; eggs and sperm from wild-caught and hatchery-reared captive broodstock are used to generate offspring that reach market size in about two years. Parentage analyses show that survival in aquaculture varies among families. Growth rate and disease resistance also vary among individuals and cohorts, but the extent to which genetics and the environment contribute to this variation is unclear. The sablefish genome assembly reported here will form the foundation for SNP-based surveys designed to detect genetic markers associated with survival, growth rate, and pathogen resistance. Beyond its contribution to sablefish domestication, the sablefish genome can be a resource for the management of the wild sablefish fishery. The assembly generated in this study had a length of 653 Mbp, a scaffold N50 of 26.74 Mbp, a contig N50 of 2.57 Mbp, and contained more than 98% of the 3640 Actinopterygii core genes. We placed 620.9 Mbp (95% of the total) onto 24 chromosomes using a genetic map derived from six full-sib families and Hi-C contact data.

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“…2013 ; Betancur-R et al . 2017 ; Maduna et al . 2022 ) and was expected to be approximately equally dissimilar to threespine stickleback and lumpfish.…”

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Sablefish (Anoplopoma fimbria) chromosome-level genome assembly

Flores

Christensen

Campbell³

et al. 2023

G3: Genes, Genomes, Genetics

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“…These PCGs play important roles in the electron transport chain, which produces nearly 95% of adenosine triphosphate (ATP) for essential energy production [3]. Two ribosomal RNAs (rRNAs), L and S (rrnL and rrnS), 22 tRNAs, and one putative main noncoding region (mNCR) are also present [4,5]. Compared with signal-based molecular markers, complete mitogenomes contain more biological information and can allow the interference…”

Section: Introductionmentioning

confidence: 99%

Analysis of the Overlength Main Noncoding Region in Metacarcinus magister (Decapoda: Brachyura) and a Phylogenetic Study of the Cancroidea Species

Wang,

Xu,

Zheng

et al. 2024

Genes

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Complete mitochondrial genomes (mitogenomes) can provide important information regarding the molecular evolution and phylogenetic relationships of marine invertebrates, especially in Brachyura. Only one Cancroidea species of mitogenomes has been sequenced before; in this research, the mitogenomic characteristics of Metacarcinus magister (Cancridae: Cancroidea) are newly studied. The length of the M. magister mitogenome was 48,820 bp, and it contained the typical 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. We performed a series of analyses on the characteristics of the mNCR of M. magister. The phylogenetics, life circumstances, and selective pressures were all analyzed to explain the formation of this length, which revealed the length of the M. magister mitogenome to be approximately three times greater than the normal length of Brachyuran mitogenomes. Phylogenetic analyses based on a dataset of 215 Decapodan mitogenomes indicated that all Eriphioidea crabs were clustered together as a group. Moreover, the rearrangement mechanism of the Cancroidea species was predicted to provide stronger evidence for the phylogenetic analysis. In general, the results obtained in this study will contribute to a better understanding of the cause of the unusual length of the M. magister mitogenome and provide new insights into the phylogeny of Brachyura.

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“…This distribution allows for the identification of SNPs without UMIs, even at medium-sequence coverage [30]. Only a few reports have used ONT Amplicon-Seq to elucidate the genetic variation in eukaryotic genes [34][35][36]. For example, Nanopore Amplicon-Seq has been used to validate IGVH mutations in clinical studies of FFPE (Nz66) gliomas.…”

Section: Introductionmentioning

confidence: 99%

Nanopore Amplicon Sequencing Allows Rapid Identification of Glutenin Allelic Variants in a Wheat Collection

Polkhovskaya,

Gruzdev,

Moskalev

et al. 2023

Agronomy

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Genetic variation in high molecular weight glutenin (HMW-GS) genes is tightly linked with the breadmaking quality of wheat. Hundreds of different alleles have been identified in HMW-GS genes worldwide. Such huge variability makes it difficult to distinguish them using conventional genotyping methods (for example, SDS-PAGE, SNP detection, etc.). Here, we exploited the nanopore amplicon sequencing technique (Amplicon-Seq) to uncover genetic variants distributed along the full-length sequence of six HMW-GSs, including the promoter and protein-coding regions. We analyzed 23 wheat accessions for allelic variants of HMW-GSs using the Amplicon-Seq and SDS-PAGE methods. We obtained sufficient (>50×) target gene coverage by ONT reads in just one hour. Using the obtained data, we identified numerous single nucleotide polymorphisms and InDels in the protein coding and promoter regions. Moreover, Amplicon-Seq allowed for the identification of new alleles (Glu-A1x1-T) of the Glu-1Ax gene that could not be recognized by SDS-PAGE. Collectively, our results showed that Amplicon-Seq is a rapid, multiplexed, and efficient method for high-throughput genotyping of full-length genes in large and complex genomes. This opens new avenues for the assessment of target gene variation to select novel alleles and create unique combinations of desirable traits in plant breeding programs.

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Mitogenomics of the suborder Cottoidei (Teleostei: Perciformes): Improved assemblies, mitogenome features, phylogeny, and ecological implications

Cited by 5 publications

References 104 publications

Sablefish (Anoplopoma fimbria) chromosome-level genome assembly

Sablefish (Anoplopoma fimbria) chromosome-level genome assembly

Analysis of the Overlength Main Noncoding Region in Metacarcinus magister (Decapoda: Brachyura) and a Phylogenetic Study of the Cancroidea Species

Nanopore Amplicon Sequencing Allows Rapid Identification of Glutenin Allelic Variants in a Wheat Collection

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