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Tianxiang Gao - One of the best experts on this subject based on the ideXlab platform.
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chromosome level genome assembly of burbot lota lota provides insights into the evolutionary adaptations in freshwater
Molecular Ecology Resources, 2021Co-Authors: Zhiqiang Han, Manhong Liu, Qi Liu, Hao Zhai, Shijun Xiao, Tianxiang GaoAbstract:The burbot (Lota lota) is the only member of the order Gadiformes adapted solely to freshwater. This species has the widest longitudinal range among freshwater fish worldwide. Burbot serves as a good model for studies on adaptive genome evolution from marine to freshwater environments. However, a high-quality reference genome of burbot has not yet been released. Here, the first chromosome-level genome of burbot was constructed using PacBio long sequencing and Hi-C technology. A total of 95.24 Gb polished PacBio sequences were generated, and the preliminary genome assembly was 575.83 Mb in size with a contig N50 size of 2.15 Mb. The assembled sequences were anchored to 22 pseudochromosomes by using Hi-C data. The final assembled genome after Hi-C correction was 575.92 Mb, with a contig N50 of 2.01 Mb and a scaffold N50 of 22.10 Mb. A total of 22,067 protein-coding genes were predicted, 94.82% of which were functionally annotated. Phylogenetic analyses indicated that burbot diverged with the Atlantic cod approximately 43.8 million years ago. In addition, 377 putative genes that appear to be under positive selection in burbot were identified. These positively selected genes might be involved in the adaptation to the freshwater environment. These genome data provide an invaluable resource for the ecological and evolutionary study of the order Gadiformes.
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The complete mitochondrial genome of Lota lota (Gadiformes: Gadidae).
Mitochondrial DNA, 2014Co-Authors: Nan Zhang, Na Song, Tianxiang GaoAbstract:In this study, the complete mitochondrial genome (mitogenome) sequence of Lota lota has been determined by long polymerase chain reaction and primer walking methods. The mitogenome is a circular molecule of 16,547 bp in length and contains 37 mitochondrial genes including 13 protein-coding genes, 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA) and a control region as other bony fishes. Within the control region, we identified the termination-associated sequence domain (TAS), the central conserved sequence block domains (CSB-F and CSB-D), and the conserved sequence block domains (CSB-1, CSB-2 and CSB-3).
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the complete mitochondrial genome of lota lota Gadiformes gadidae from the burqin river in china
Mitochondrial DNA, 2014Co-Authors: Nan Zhang, Na Song, Tianxiang GaoAbstract:In this study, the complete mitochondrial genome (mitogenome) sequence of Lota lota has been determined by long polymerase chain reaction and primer walking methods. The mitogenome is a circular molecule of 16,519 bp in length and contains 37 mitochondrial genes including 13 protein-coding genes, 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA) and a control region as other bony fishes. Within the control region, we identified the termination-associated sequence domain (TAS), the central conserved sequence block domains (CSB-F and CSB-D), and the conserved sequence block domains (CSB-1, CSB-2 and CSB-3).
Adela Roavaron - One of the best experts on this subject based on the ideXlab platform.
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confronting sources of systematic error to resolve historically contentious relationships a case study using gadiform fishes teleostei paracanthopterygii Gadiformes
Systematic Biology, 2020Co-Authors: Adela Roavaron, Rebecca B Dikow, Giorgio Carnevale, Luke Tornabene, Carole C Baldwin, Eric J HiltonAbstract:Reliable estimation of phylogeny is central to avoid inaccuracy in downstream macroevolutionary inferences. However, limitations exist in the implementation of concatenated and summary coalescent approaches, and Bayesian and full coalescent inference methods may not yet be feasible for computation of phylogeny using complicated models and large datasets. Here, we explored methodological (e.g., optimality criteria, character sampling, model selection) and biological (e.g., heterotachy, branch length heterogeneity) sources of systematic error that can result in biased or incorrect parameter estimates when reconstructing phylogeny by using the gadiform fishes as a model clade. Gadiformes include some of the most economically important fishes in the world (e.g., Cods, Hakes, and Rattails). Despite many attempts, a robust higher-level phylogenetic framework was lacking due to limited character and taxonomic sampling, particularly from several species-poor families that have been recalcitrant to phylogenetic placement. We compiled the first phylogenomic dataset, including 14,208 loci (>2.8 M bp) from 58 species representing all recognized gadiform families, to infer a time-calibrated phylogeny for the group. Data were generated with a gene-capture approach targeting coding DNA sequences from single-copy protein-coding genes. Species-tree and concatenated maximum-likelihood analyses resolved all family-level relationships within Gadiformes. While there were a few differences between topologies produced by the DNA and the amino acid datasets, most of the historically unresolved relationships among gadiform lineages were consistently well resolved with high support in our analyses regardless of the methodological and biological approaches used. However, at deeper levels, we observed inconsistency in branch support estimates between bootstrap and gene and site coefficient factors (gCF, sCF). Despite numerous short internodes, all relationships received unequivocal bootstrap support while gCF and sCF had very little support, reflecting hidden conflict across loci. Most of the gene-tree and species-tree discordance in our study is a result of short divergence times, and consequent lack of informative characters at deep levels, rather than incomplete lineage sorting (ILS). We use this phylogeny to establish a new higher-level classification of Gadiformes as a way of clarifying the evolutionary diversification of the order. We recognize 17 families in five suborders: Bregmacerotoidei, Gadoidei, Ranicipitoidei, Merluccioidei, and Macrouroidei (including two subclades). A time-calibrated analysis using 15 fossil taxa suggests that Gadiformes evolved ∼79.5 million years ago (Ma) in the late Cretaceous, but that most extant lineages diverged after the Cretaceous-Paleogene (K-Pg) mass extinction (66 Ma). Our results reiterate the importance of examining phylogenomic analyses for evidence of systematic error that can emerge as a result of unsuitable modeling of biological factors and/or methodological issues, even when datasets are large and yield high support for phylogenetic relationships.
Vaz-dos-santos, André Martins - One of the best experts on this subject based on the ideXlab platform.
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Atlas of marine bony fish otoliths (Sagittae) of Southeastern - Southern Brazil Part I: Gadiformes (Macrouridae, Moridae, Bregmacerotidae, Phycidae and Merlucciidae); Part II: Perciformes (Carangidae, Sciaenidae, Scombridae and Serranidae)
Universidade de São Paulo. Instituto Oceanográfico, 2014Co-Authors: Rossi-wongtschowski, Carmen Lucia Del Bianco, Santificetur César, Siliprandi, Carolina Correia, Brenha, Marina Rito, Gonsales, Silvia De Almeida, Vaz-dos-santos, André MartinsAbstract:The drawings, detailed pictures, precise descriptions and measurements that characterize otoliths must be made available for studies in various areas, including taxonomy, phylogeny, ecology, fisheries, paleontology, diversity, predator-prey relationships and modeling. The Collection of Teleostei Fish Otoliths of Southeastern-Southern Brazil (COSS-Brasil) of IOUSP contains 45,000 pairs of otoliths from 210 species. This publication is the first in a series that will constitute an atlas of Teleostei otoliths for southeastern-southern Brazil and presents the results of the morphologic and morphometric analyses of 11 Gadiformes and 36 Perciformes species by means of the most commonly used features, measurements and indices. Three otoliths of each species were illustrated and photographed whenever possible. The frequency of occurrence was calculated for each characteristic by total length classes (TL), and the ontogenetic differences were analyzed (multiple χ2 test; significance 0.05). Morphometric analyses were conducted for each characteristic per total length (TL) class and for the whole sample, and the ontogenetic differences were analyzed.A disponibilidade de desenhos, fotos detalhadas, descrições precisas e medidas que caracterizem os otólitos são ferramentas imprescindíveis para diversas áreas: taxonomia, filogenia, ecologia, pesca, paleontologia, diversidade, relações presa/predador e modelagem. Da Coleção de Otólitos de Peixes Teleósteos da Região Sudeste-Sul do Brasil (COSS-Brasil), IOUSP, constam quarenta e cinco mil pares relativos a 210 espécies. Esta publicação é a primeira de uma série que constituirá um atlas de otólitos para Teleostei da região sudeste-sul brasileira e apresenta os resultados de análises morfológicas e morfométricas de 11 espécies de Gadiformes e 36 de Perciformes das medidas e índices usualmente realizados. Foram desenhados e fotografados três otólitos de cada espécie sempre que possível. A frequência de ocorrência foi calculada por classes de comprimento total (TL) e para toda a amostra, e diferenças ontogenéticas foram analisadas
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Atlas of marine bony fish otoliths (Sagittae) of Southeastern - Southern Brazil Part I: Gadiformes (Macrouridae, Moridae, Bregmacerotidae, Phycidae and Merlucciidae); Part II: Perciformes (Carangidae, Sciaenidae, Scombridae and Serranidae)
'FapUNIFESP (SciELO)', 2014Co-Authors: Rossi-wongtschowski, Carmen Lucia Del Bianco, Siliprandi, Carolina Correia, Brenha, Marina Rito, Gonsales, Silvia De Almeida, Vaz-dos-santos, André MartinsAbstract:The drawings, detailed pictures, precise descriptions and measurements that characterize otoliths must be made available for studies in various areas, including taxonomy, phylogeny, ecology, fisheries, paleontology, diversity, predator-prey relationships and modeling. The Collection of Teleostei Fish Otoliths of Southeastern-Southern Brazil (COSS-Brasil) of IOUSP contains 45,000 pairs of otoliths from 210 species. This publication is the first in a series that will constitute an atlas of Teleostei otoliths for southeastern-southern Brazil and presents the results of the morphologic and morphometric analyses of 11 Gadiformes and 36 Perciformes species by means of the most commonly used features, measurements and indices. Three otoliths of each species were illustrated and photographed whenever possible. The frequency of occurrence was calculated for each characteristic by total length classes (TL), and the ontogenetic differences were analyzed (multiple χ2 test; significance 0.05). Morphometric analyses were conducted for each characteristic per total length (TL) class and for the whole sample, and the ontogenetic differences were analyzed
Ole K Torresen - One of the best experts on this subject based on the ideXlab platform.
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genomic architecture of haddock melanogrammus aeglefinus shows expansions of innate immune genes and short tandem repeats
BMC Genomics, 2018Co-Authors: Ole K Torresen, Marine S O Brieuc, Monica Hongro Solbakken, Elin Sorhus, Alexander J Nederbragt, Kjetill S Jakobsen, Sonnich Meier, Rolf B Edvardsen, Sissel JentoftAbstract:Increased availability of genome assemblies for non-model organisms has resulted in invaluable biological and genomic insight into numerous vertebrates, including teleosts. Sequencing of the Atlantic cod (Gadus morhua) genome and the genomes of many of its relatives (Gadiformes) demonstrated a shared loss of the major histocompatibility complex (MHC) II genes 100 million years ago. An improved version of the Atlantic cod genome assembly shows an extreme density of tandem repeats compared to other vertebrate genome assemblies. Highly contiguous assemblies are therefore needed to further investigate the unusual immune system of the Gadiformes, and whether the high density of tandem repeats found in Atlantic cod is a shared trait in this group. Here, we have sequenced and assembled the genome of haddock (Melanogrammus aeglefinus) – a relative of Atlantic cod – using a combination of PacBio and Illumina reads. Comparative analyses reveal that the haddock genome contains an even higher density of tandem repeats outside and within protein coding sequences than Atlantic cod. Further, both species show an elevated number of tandem repeats in genes mainly involved in signal transduction compared to other teleosts. A characterization of the immune gene repertoire demonstrates a substantial expansion of MCHI in Atlantic cod compared to haddock. In contrast, the Toll-like receptors show a similar pattern of gene losses and expansions. For the NOD-like receptors (NLRs), another gene family associated with the innate immune system, we find a large expansion common to all teleosts, with possible lineage-specific expansions in zebrafish, stickleback and the codfishes. The generation of a highly contiguous genome assembly of haddock revealed that the high density of short tandem repeats as well as expanded immune gene families is not unique to Atlantic cod – but possibly a feature common to all, or most, codfishes. A shared expansion of NLR genes in teleosts suggests that the NLRs have a more substantial role in the innate immunity of teleosts than other vertebrates. Moreover, we find that high copy number genes combined with variable genome assembly qualities may impede complete characterization of these genes, i.e. the number of NLRs in different teleost species might be underestimates.
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Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats
BMC Genomics, 2018Co-Authors: Ole K Torresen, Marine S O Brieuc, Monica Hongro Solbakken, Elin Sorhus, Alexander J Nederbragt, Kjetill S Jakobsen, Sonnich Meier, Rolf B Edvardsen, Sissel JentoftAbstract:Background Increased availability of genome assemblies for non-model organisms has resulted in invaluable biological and genomic insight into numerous vertebrates, including teleosts. Sequencing of the Atlantic cod ( Gadus morhua ) genome and the genomes of many of its relatives (Gadiformes) demonstrated a shared loss of the major histocompatibility complex ( MHC ) II genes 100 million years ago. An improved version of the Atlantic cod genome assembly shows an extreme density of tandem repeats compared to other vertebrate genome assemblies. Highly contiguous assemblies are therefore needed to further investigate the unusual immune system of the Gadiformes, and whether the high density of tandem repeats found in Atlantic cod is a shared trait in this group. Results Here, we have sequenced and assembled the genome of haddock ( Melanogrammus aeglefinus) – a relative of Atlantic cod – using a combination of PacBio and Illumina reads. Comparative analyses reveal that the haddock genome contains an even higher density of tandem repeats outside and within protein coding sequences than Atlantic cod. Further, both species show an elevated number of tandem repeats in genes mainly involved in signal transduction compared to other teleosts. A characterization of the immune gene repertoire demonstrates a substantial expansion of MCHI in Atlantic cod compared to haddock. In contrast, the Toll-like receptors show a similar pattern of gene losses and expansions. For the NOD-like receptors ( NLRs ), another gene family associated with the innate immune system, we find a large expansion common to all teleosts, with possible lineage-specific expansions in zebrafish, stickleback and the codfishes. Conclusions The generation of a highly contiguous genome assembly of haddock revealed that the high density of short tandem repeats as well as expanded immune gene families is not unique to Atlantic cod – but possibly a feature common to all, or most, codfishes. A shared expansion of NLR genes in teleosts suggests that the NLRs have a more substantial role in the innate immunity of teleosts than other vertebrates. Moreover, we find that high copy number genes combined with variable genome assembly qualities may impede complete characterization of these genes, i.e. the number of NLRs in different teleost species might be underestimates.
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evolution of the immune system influences speciation rates in teleost fishes
Nature Genetics, 2016Co-Authors: Martin Malmstrom, Ole K Torresen, Alexander J Nederbragt, Michael Matschiner, Bastiaan Star, Larsgustav Snipen, Thomas F Hansen, Helle Tessand Baalsrud, Reinhold Hanel, Walter SalzburgerAbstract:Teleost fishes constitute the most species-rich vertebrate clade and exhibit extensive genetic and phenotypic variation, including diverse immune defense strategies. The genomic basis of a particularly aberrant strategy is exemplified by Atlantic cod, in which a loss of major histocompatibility complex (MHC) II functionality coincides with a marked expansion of MHC I genes. Through low-coverage genome sequencing (9-39×), assembly and comparative analyses for 66 teleost species, we show here that MHC II is missing in the entire Gadiformes lineage and thus was lost once in their common ancestor. In contrast, we find that MHC I gene expansions have occurred multiple times, both inside and outside this clade. Moreover, we identify an association between high MHC I copy number and elevated speciation rates using trait-dependent diversification models. Our results extend current understanding of the plasticity of the adaptive immune system and suggest an important role for immune-related genes in animal diversification.
Sissel Jentoft - One of the best experts on this subject based on the ideXlab platform.
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genomic architecture of haddock melanogrammus aeglefinus shows expansions of innate immune genes and short tandem repeats
BMC Genomics, 2018Co-Authors: Ole K Torresen, Marine S O Brieuc, Monica Hongro Solbakken, Elin Sorhus, Alexander J Nederbragt, Kjetill S Jakobsen, Sonnich Meier, Rolf B Edvardsen, Sissel JentoftAbstract:Increased availability of genome assemblies for non-model organisms has resulted in invaluable biological and genomic insight into numerous vertebrates, including teleosts. Sequencing of the Atlantic cod (Gadus morhua) genome and the genomes of many of its relatives (Gadiformes) demonstrated a shared loss of the major histocompatibility complex (MHC) II genes 100 million years ago. An improved version of the Atlantic cod genome assembly shows an extreme density of tandem repeats compared to other vertebrate genome assemblies. Highly contiguous assemblies are therefore needed to further investigate the unusual immune system of the Gadiformes, and whether the high density of tandem repeats found in Atlantic cod is a shared trait in this group. Here, we have sequenced and assembled the genome of haddock (Melanogrammus aeglefinus) – a relative of Atlantic cod – using a combination of PacBio and Illumina reads. Comparative analyses reveal that the haddock genome contains an even higher density of tandem repeats outside and within protein coding sequences than Atlantic cod. Further, both species show an elevated number of tandem repeats in genes mainly involved in signal transduction compared to other teleosts. A characterization of the immune gene repertoire demonstrates a substantial expansion of MCHI in Atlantic cod compared to haddock. In contrast, the Toll-like receptors show a similar pattern of gene losses and expansions. For the NOD-like receptors (NLRs), another gene family associated with the innate immune system, we find a large expansion common to all teleosts, with possible lineage-specific expansions in zebrafish, stickleback and the codfishes. The generation of a highly contiguous genome assembly of haddock revealed that the high density of short tandem repeats as well as expanded immune gene families is not unique to Atlantic cod – but possibly a feature common to all, or most, codfishes. A shared expansion of NLR genes in teleosts suggests that the NLRs have a more substantial role in the innate immunity of teleosts than other vertebrates. Moreover, we find that high copy number genes combined with variable genome assembly qualities may impede complete characterization of these genes, i.e. the number of NLRs in different teleost species might be underestimates.
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Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats
BMC Genomics, 2018Co-Authors: Ole K Torresen, Marine S O Brieuc, Monica Hongro Solbakken, Elin Sorhus, Alexander J Nederbragt, Kjetill S Jakobsen, Sonnich Meier, Rolf B Edvardsen, Sissel JentoftAbstract:Background Increased availability of genome assemblies for non-model organisms has resulted in invaluable biological and genomic insight into numerous vertebrates, including teleosts. Sequencing of the Atlantic cod ( Gadus morhua ) genome and the genomes of many of its relatives (Gadiformes) demonstrated a shared loss of the major histocompatibility complex ( MHC ) II genes 100 million years ago. An improved version of the Atlantic cod genome assembly shows an extreme density of tandem repeats compared to other vertebrate genome assemblies. Highly contiguous assemblies are therefore needed to further investigate the unusual immune system of the Gadiformes, and whether the high density of tandem repeats found in Atlantic cod is a shared trait in this group. Results Here, we have sequenced and assembled the genome of haddock ( Melanogrammus aeglefinus) – a relative of Atlantic cod – using a combination of PacBio and Illumina reads. Comparative analyses reveal that the haddock genome contains an even higher density of tandem repeats outside and within protein coding sequences than Atlantic cod. Further, both species show an elevated number of tandem repeats in genes mainly involved in signal transduction compared to other teleosts. A characterization of the immune gene repertoire demonstrates a substantial expansion of MCHI in Atlantic cod compared to haddock. In contrast, the Toll-like receptors show a similar pattern of gene losses and expansions. For the NOD-like receptors ( NLRs ), another gene family associated with the innate immune system, we find a large expansion common to all teleosts, with possible lineage-specific expansions in zebrafish, stickleback and the codfishes. Conclusions The generation of a highly contiguous genome assembly of haddock revealed that the high density of short tandem repeats as well as expanded immune gene families is not unique to Atlantic cod – but possibly a feature common to all, or most, codfishes. A shared expansion of NLR genes in teleosts suggests that the NLRs have a more substantial role in the innate immunity of teleosts than other vertebrates. Moreover, we find that high copy number genes combined with variable genome assembly qualities may impede complete characterization of these genes, i.e. the number of NLRs in different teleost species might be underestimates.
