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Masaki Miya - One of the best experts on this subject based on the ideXlab platform.
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Mitochondrial Gene Orders of “saccopharyngiform” fishes.
2018Co-Authors: Jan Y. Poulsen, Michael J. Miller, Tetsuya Sado, Reinhold Hanel, Katsumi Tsukamoto, Masaki MiyaAbstract:Highly similar Gene Orders are present in Neocyema, Saccopharynx and Eurypharynx compared to Cyema and the highly rearranged Monognathus, and these Orders all differ from the more typical Gene Orders of the Serrivomeridae, Nemichthyidae, and Anguillidae and other vertebrates.
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Resolving deep-sea pelagic saccopharyngiform eel mysteries: Identification of Neocyema and Monognathidae leptocephali and establishment of a new fish family "Neocyematidae" based on larvae, adults and mitogenomic Gene Orders - Fig 3
2018Co-Authors: Jan Y. Poulsen, Michael J. Miller, Tetsuya Sado, Reinhold Hanel, Katsumi Tsukamoto, Masaki MiyaAbstract:Leptocephalus larvae of saccopharyngiform fishes known until the present study (A–F). A, Eurypharynx (WH404_906) 25.3 mm. B, Saccopharynx (WH342_1580) 40.0 mm. C, Cyema (WH404_82) 26.2 mm. D, “Leptocephalus holti” Type I (KH-11-6_184) 15.4 mm. E, “Leptocephalus holti” Type II (WH342_418) 38.0 mm. F, “Leptocephalus holti” Type III (MSM41_1404) 27.1 mm. Scale bars 5 mm.
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Resolving deep-sea pelagic saccopharyngiform eel mysteries: Identification of Neocyema and Monognathidae leptocephali and establishment of a new fish family "Neocyematidae" based on larvae, adults and mitogenomic Gene Orders - Fig 2
2018Co-Authors: Jan Y. Poulsen, Michael J. Miller, Tetsuya Sado, Reinhold Hanel, Katsumi Tsukamoto, Masaki MiyaAbstract:Line-illustrations of leptocephalus larvae of meso- and bathypelagic anguilliform families (A–K). A, Cyema (Cyematidae). B, “Leptocephalus holti”. C, Monognathidae (metamorphic stage). D, Unidentified saccopharyngiform. E, Saccopharynx (Saccopharyngidae). F, Eurypharynx (Eurypharyngidae). G, Serrivomer beani (Serrivomeridae). H, Nemichthys curvirostris (Nemichthyidae). I, Avocettina infans (Nemichthyidae). J, Derichthys serpentinus (Derichthyidae). K, Nessorhamphus ingolfianus (Derichthyidae). The dotted line separates the saccopharyngiform larvae from the larvae of other meso- and bathy-pelagic eel families. Illustrations A, C, D, F–K are reproduced or modified from Böhlke [1], B is modified from Smith and Miller [24], and E is modified from Castle [84] with permission under a CC BY license, from the Sears Foundation for Marine Research original copyright 1989, illustrator Mary H. Fuges, Yale University, and the American Society of Ichthyologists and Herpetologists, Lawrence, Kansas, respectively.
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Resolving deep-sea pelagic saccopharyngiform eel mysteries: Identification of Neocyema and Monognathidae leptocephali and establishment of a new fish family "Neocyematidae" based on larvae, adults and mitogenomic Gene Orders - Fig 4
2018Co-Authors: Jan Y. Poulsen, Michael J. Miller, Tetsuya Sado, Reinhold Hanel, Katsumi Tsukamoto, Masaki MiyaAbstract:A Leptocephalus larva (WH342_1248, 22.5 mm) of Neocyema erythrosoma from the Sargasso Sea that has unique orange pigment spots (A–D). A, Whole specimen, 22.5 mm TL. B, Head region. C, Esophagus, liver, stomach region. D, End of the gut region. Scale bar 5 mm.
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Resolving deep-sea pelagic saccopharyngiform eel mysteries: Identification of Neocyema and Monognathidae leptocephali and establishment of a new fish family "Neocyematidae" based on larvae, adults and mitogenomic Gene Orders
2018Co-Authors: Jan Y. Poulsen, Michael J. Miller, Tetsuya Sado, Reinhold Hanel, Katsumi Tsukamoto, Masaki MiyaAbstract:Deep-sea midwater “saccopharyngiform” eels of the families Cyematidae, Monognathidae, Eurypharyngidae and Saccopharyngidae (order Anguilliformes) are extraordinary fishes having major skeletal reductions and modifications compared to the General anguilliform body structure. Little is known about most aspects of the systematics, phylogeny, and ecology of these families, and few of the approximately 30 species described from adult specimens have been matched with their leptotocephalus larvae. Based on mitogenomic sequence data from rare new specimens, we show that the long-speculated-about larval form referred to as “Leptocephalus holti”, which was thought to possibly be the larva of the rare orange-colored eels of Neocyema (5 known specimens; speculated to belong to the Cyematidae) are actually the larvae of the one-jaw eels of the family Monognathidae. One of the 5 types of L. holti larvae that were collected in the Pacific is Genetically matched with Monognathus jesperseni, but multiple species exist based on larval sequence data and the morphology of adult specimens. A rare leptocephalus from the Sargasso Sea, with unique morphological characteristics including many small orange spots on the gut, was found to be the larva of Neocyema, which is presently only known from the Atlantic Ocean. We demonstrate that Neocyema constitutes a separate family being most closely related to Eurypharyngidae and Saccopharyngidae based on mitogenomic DNA sequences and unique mitochondrial Gene Orders.
Jijun Tang - One of the best experts on this subject based on the ideXlab platform.
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reconstruction of ancestral Gene Orders using probabilistic and Gene encoding approaches
PLOS ONE, 2014Co-Authors: Ning Yang, Lingxi Zhou, Jijun TangAbstract:Current tools used in the reconstruction of ancestral Gene Orders often fall into event-based and adjacency-based methods according to the principles they follow. Event-based methods such as GRAPPA are very accurate but with extremely high complexity, while more recent methods based on Gene adjacencies such as InferCARsPro is relatively faster, but often produces an excessive number of chromosomes. This issue is mitigated by newer methods such as GapAdj, however it sacrifices a considerable portion of accuracy. We recently developed an adjacency-based method in the probabilistic framework called PMAG to infer ancestral Gene Orders. PMAG relies on calculating the conditional probabilities of Gene adjacencies that are found in the leaf genomes using the Bayes' theorem. It uses a novel transition model which accounts for adjacency changes along the tree branches as well as a re-rooting procedure to prevent any information loss. In this paper, we improved PMAG with a new method to assemble Gene adjacencies into valid Gene Orders, using an exact solver for traveling salesman problem (TSP) to maximize the overall conditional probabilities. We conducted a series of simulation experiments using a wide range of configurations. The first set of experiments was to verify the effectiveness of our strategy of using the better transition model and re-rooting the tree under the targeted ancestral genome. PMAG was then thoroughly compared in terms of three measurements with its four major competitors including InferCARsPro, GapAdj, GASTS and SCJ in order to assess their performances. According to the results, PMAG demonstrates superior performance in terms of adjacency, distance and assembly accuracies, and yet achieves comparable running time, even all TSP instances were solved exactly. PMAG is available for free at http://phylo.cse.sc.edu.
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Probabilistic Reconstruction of Ancestral Gene Orders with Insertions and Deletions
IEEE ACM Transactions on Computational Biology and Bioinformatics, 2014Co-Authors: Fei Hu, Lingxi Zhou, Jun Zhou, Jijun TangAbstract:Changes of Gene orderings have been extensively used as a signal to reconstruct phylogenies and ancestral genomes. Inferring the Gene order of an extinct species has a wide range of applications, including the potential to reveal more detailed evolutionary histories, to determine Gene content and ordering, and to understand the consequences of structural changes for organismal function and species divergence. In this study, we propose a new adjacency-based method, PMAG + , to infer ancestral genomes under a more General model of Gene evolution involving Gene insertions and deletions (indels), in addition to Gene rearrangements. PMAG + improves on our previous method PMAG by developing a new approach to infer ancestral Gene contents and reducing the adjacency assembly problem to an instance of TSP. We designed a series of experiments to extensively validate PMAG + and compared the results with the most recent and comparable method GapAdj. According to the results, ancestral Gene contents predicted by PMAG + coincides highly with the actual contents with error rates less than 1 percent. Under various degrees of indels, PMAG + consistently achieves more accurate prediction of ancestral Gene Orders and at the same time, produces contigs very close to the actual chromosomes.
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reconstructing ancestral genomic Orders using binary encoding and probabilistic models
International Symposium on Bioinformatics Research and Applications, 2013Co-Authors: Lingxi Zhou, Fei Hu, Jijun TangAbstract:Changes of Gene ordering under rearrangements have been extensively used as a signal to reconstruct phylogenies and ancestral genomes. Inferring the Gene order of an extinct species has the potential in revealing a more detailed evolutionary history of species descended from it. Current tools used in ancestral reconstruction may fall into parsimonious and probabilistic methods according to the criteria they follow. In this study, we propose a new probabilistic method called PMAG to infer the ancestral genomic Orders by calculating the conditional probabilities of Gene adjacencies using Bayes’ theorem. The method incorporates a transition model designed particularly for genomic rearrangement scenarios, a reroot procedure to relocate the root to the target ancestor that is inferred as well as a greedy algorithm to connect adjacencies with high conditional probabilities into valid Gene Orders.
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a mixture framework for inferring ancestral Gene Orders
BMC Genomics, 2012Co-Authors: Yiwei Zhang, Jijun TangAbstract:Background Inferring Gene Orders of ancestral genomes has the potential to provide detailed information about the recent evolution of species descended from them. Current popular tools to infer ancestral genome data (such as GRAPPA and MGR) are all parsimony-based direct optimization methods with the aim to minimize the number of evolutionary events. Recently a new method based on the approach of maximum likelihood is proposed. The current implementation of these direct optimization methods are all based on solving the median problems and achieve more accurate results than the maximum likelihood method. However, both GRAPPA and MGR are extremely time consuming under high rearrangement rates. The maximum likelihood method, on the contrary, runs much faster with less accurate results.
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phyloGenetic reconstruction from complete Gene Orders of whole genomes
Asia-Pacific Bioinformatics Conference, 2007Co-Authors: Krister M Swenson, Jijun Tang, William Arndt, Bernard M E MoretAbstract:Reference LCBB-CONF-2007-003 URL: http://sunflower.kuicr.kyoto-u.ac.jp/apbc2008/ Record created on 2007-10-13, modified on 2017-05-12
Katsumi Tsukamoto - One of the best experts on this subject based on the ideXlab platform.
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Mitochondrial Gene Orders of “saccopharyngiform” fishes.
2018Co-Authors: Jan Y. Poulsen, Michael J. Miller, Tetsuya Sado, Reinhold Hanel, Katsumi Tsukamoto, Masaki MiyaAbstract:Highly similar Gene Orders are present in Neocyema, Saccopharynx and Eurypharynx compared to Cyema and the highly rearranged Monognathus, and these Orders all differ from the more typical Gene Orders of the Serrivomeridae, Nemichthyidae, and Anguillidae and other vertebrates.
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Resolving deep-sea pelagic saccopharyngiform eel mysteries: Identification of Neocyema and Monognathidae leptocephali and establishment of a new fish family "Neocyematidae" based on larvae, adults and mitogenomic Gene Orders - Fig 3
2018Co-Authors: Jan Y. Poulsen, Michael J. Miller, Tetsuya Sado, Reinhold Hanel, Katsumi Tsukamoto, Masaki MiyaAbstract:Leptocephalus larvae of saccopharyngiform fishes known until the present study (A–F). A, Eurypharynx (WH404_906) 25.3 mm. B, Saccopharynx (WH342_1580) 40.0 mm. C, Cyema (WH404_82) 26.2 mm. D, “Leptocephalus holti” Type I (KH-11-6_184) 15.4 mm. E, “Leptocephalus holti” Type II (WH342_418) 38.0 mm. F, “Leptocephalus holti” Type III (MSM41_1404) 27.1 mm. Scale bars 5 mm.
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Resolving deep-sea pelagic saccopharyngiform eel mysteries: Identification of Neocyema and Monognathidae leptocephali and establishment of a new fish family "Neocyematidae" based on larvae, adults and mitogenomic Gene Orders - Fig 2
2018Co-Authors: Jan Y. Poulsen, Michael J. Miller, Tetsuya Sado, Reinhold Hanel, Katsumi Tsukamoto, Masaki MiyaAbstract:Line-illustrations of leptocephalus larvae of meso- and bathypelagic anguilliform families (A–K). A, Cyema (Cyematidae). B, “Leptocephalus holti”. C, Monognathidae (metamorphic stage). D, Unidentified saccopharyngiform. E, Saccopharynx (Saccopharyngidae). F, Eurypharynx (Eurypharyngidae). G, Serrivomer beani (Serrivomeridae). H, Nemichthys curvirostris (Nemichthyidae). I, Avocettina infans (Nemichthyidae). J, Derichthys serpentinus (Derichthyidae). K, Nessorhamphus ingolfianus (Derichthyidae). The dotted line separates the saccopharyngiform larvae from the larvae of other meso- and bathy-pelagic eel families. Illustrations A, C, D, F–K are reproduced or modified from Böhlke [1], B is modified from Smith and Miller [24], and E is modified from Castle [84] with permission under a CC BY license, from the Sears Foundation for Marine Research original copyright 1989, illustrator Mary H. Fuges, Yale University, and the American Society of Ichthyologists and Herpetologists, Lawrence, Kansas, respectively.
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Resolving deep-sea pelagic saccopharyngiform eel mysteries: Identification of Neocyema and Monognathidae leptocephali and establishment of a new fish family "Neocyematidae" based on larvae, adults and mitogenomic Gene Orders - Fig 4
2018Co-Authors: Jan Y. Poulsen, Michael J. Miller, Tetsuya Sado, Reinhold Hanel, Katsumi Tsukamoto, Masaki MiyaAbstract:A Leptocephalus larva (WH342_1248, 22.5 mm) of Neocyema erythrosoma from the Sargasso Sea that has unique orange pigment spots (A–D). A, Whole specimen, 22.5 mm TL. B, Head region. C, Esophagus, liver, stomach region. D, End of the gut region. Scale bar 5 mm.
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Resolving deep-sea pelagic saccopharyngiform eel mysteries: Identification of Neocyema and Monognathidae leptocephali and establishment of a new fish family "Neocyematidae" based on larvae, adults and mitogenomic Gene Orders
2018Co-Authors: Jan Y. Poulsen, Michael J. Miller, Tetsuya Sado, Reinhold Hanel, Katsumi Tsukamoto, Masaki MiyaAbstract:Deep-sea midwater “saccopharyngiform” eels of the families Cyematidae, Monognathidae, Eurypharyngidae and Saccopharyngidae (order Anguilliformes) are extraordinary fishes having major skeletal reductions and modifications compared to the General anguilliform body structure. Little is known about most aspects of the systematics, phylogeny, and ecology of these families, and few of the approximately 30 species described from adult specimens have been matched with their leptotocephalus larvae. Based on mitogenomic sequence data from rare new specimens, we show that the long-speculated-about larval form referred to as “Leptocephalus holti”, which was thought to possibly be the larva of the rare orange-colored eels of Neocyema (5 known specimens; speculated to belong to the Cyematidae) are actually the larvae of the one-jaw eels of the family Monognathidae. One of the 5 types of L. holti larvae that were collected in the Pacific is Genetically matched with Monognathus jesperseni, but multiple species exist based on larval sequence data and the morphology of adult specimens. A rare leptocephalus from the Sargasso Sea, with unique morphological characteristics including many small orange spots on the gut, was found to be the larva of Neocyema, which is presently only known from the Atlantic Ocean. We demonstrate that Neocyema constitutes a separate family being most closely related to Eurypharyngidae and Saccopharyngidae based on mitogenomic DNA sequences and unique mitochondrial Gene Orders.
Aïda Ouangraoua - One of the best experts on this subject based on the ideXlab platform.
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procars progressive reconstruction of ancestral Gene Orders
BMC Genomics, 2015Co-Authors: Amandine Perrin, Jean-stéphane Varré, Samuel Blanquart, Aïda OuangraouaAbstract:In the context of ancestral Gene order reconstruction from extant genomes, there exist two main computational approaches: rearrangement-based, and homology-based methods. The rearrangement-based methods consist in minimizing a total rearrangement distance on the branches of a species tree. The homology-based methods consist in the detection of a set of potential ancestral contiguity features, followed by the assembling of these features into Contiguous Ancestral Regions (CARs). In this paper, we present a new homology-based method that uses a progressive approach for both the detection and the assembling of ancestral contiguity features into CARs. The method is based on detecting a set of potential ancestral adjacencies iteratively using the current set of CARs at each step, and constructing CARs progressively using a 2-phase assembling method. We show the usefulness of the method through a reconstruction of the boreoeutherian ancestral Gene order, and a comparison with three other homology-based methods: AnGeS, InferCARs and GapAdj. The program, written in Python, and the dataset used in this paper are available at http://bioinfo.lifl.fr/procars/ .
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ProCARs: Progressive Reconstruction of Ancestral Gene Orders
2014Co-Authors: Amandine Perrin, Jean-stéphane Varré, Samuel Blanquart, Aïda OuangraouaAbstract:Background: In the context of ancestral Gene order reconstruction from extant genomes, there exist two main computational approaches: rearrangement-based, and homology-based methods. The rearrangement-based methods consist in minimizing a total rearrangement distance on the branches of a species tree. The homology-based methods consist in the detection of a set of potential ancestral contiguity features, followed by the assembling of these features into Contiguous Ancestral Regions (CARs). Results: In this paper, we present a new homology-based method that uses a progressive approach for both the detection and the assembling of ancestral contiguity features into CARs. The method is based on detecting a set of potential ancestral adjacencies iteratively using the current set of CARs at each step, and constructing CARs progressively using a 2-phase assembling method. We show the usefulness of the method through a reconstruction of the boreoeutherian ancestral Gene order, and a comparison with three other homology-based methods: AnGeS, InferCARs and GapAdj. The program is written in Python, and the dataset used in this paper are available at http://bioinfo.lifl.fr/procars/.
Peter F. Stadler - One of the best experts on this subject based on the ideXlab platform.
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Genetic aspects of mitochondrial genome evolution
Molecular Phylogenetics and Evolution, 2013Co-Authors: Matthias Bernt, Anke Braband, Bernd Schierwater, Peter F. StadlerAbstract:Many years of extensive studies of metazoan mitochondrial genomes have established differences in Gene arrangements and Genetic codes as valuable phyloGenetic markers. Understanding the underlying mechanisms of replication, transcription and the role of the control regions which cause e.g. different Gene Orders is important to assess the phyloGenetic signal of such events. This review summarises and discusses, for the Metazoa, the General aspects of mitochondrial transcription and replication with respect to control regions as well as several proposed models of Gene rearrangements. As whole genome sequencing projects accumulate, more and more observations about mitochondrial Gene transfer to the nucleus are reported. Thus occurrence and phyloGenetic aspects concerning nuclear mitochondrial-like sequences (NUMTS) is another aspect of this review.
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improved systematic trna Gene annotation allows new insights into the evolution of mitochondrial trna structures and into the mechanisms of mitochondrial genome rearrangements
Nucleic Acids Research, 2012Co-Authors: Frank Juhling, Matthias Bernt, Martin Middendorf, Joern Putz, Alexander Donath, Catherine Florentz, Peter F. StadlerAbstract:Transfer RNAs (tRNAs) are present in all types of cells as well as in organelles. tRNAs of animal mitochondria show a low level of primary sequence conservation and exhibit ‘bizarre’ secondary structures, lacking complete domains of the common cloverleaf. Such sequences are hard to detect and hence frequently missed in computational analyses and mitochondrial genome annotation. Here, we introduce an automatic annotation procedure for mitochondrial tRNA Genes in Metazoa based on sequence and structural information in manually curated covariance models. The method, applied to re-annotate 1876 available metazoan mitochondrial RefSeq genomes, allows to distinguish between remaining functional Genes and degrading ‘pseudoGenes’, even at early stages of divergence. The subsequent analysis of a comprehensive set of mitochondrial tRNA Genes gives new insights into the evolution of structures of mitochondrial tRNA sequences as well as into the mechanisms of genome rearrangements. We find frequent losses of tRNA Genes concentrated in basal Metazoa, frequent independent losses of individual parts of tRNA Genes, particularly in Arthropoda, and wide-spread conserved overlaps of tRNAs in opposite reading direction. Direct evidence for several recent Tandem Duplication-Random Loss events is gained, demonstrating that this mechanism has an impact on the appearance of new mitochondrial Gene Orders.
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Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: insights in phyloGenetic relationships of Echinodermata.
Molecular phylogenetics and evolution, 2010Co-Authors: Marleen Perseke, Peter F. Stadler, Guido Fritzsch, Detlef Bernhard, Franz Brümmer, Martin SchlegelAbstract:Abstract The genome architecture and amino acid sequences of six new complete mitochondrial genomes were determined from representatives of Hemichordata (1), Ophiuroidea (3), Echinoidea (1) and Holothuroidea (1) and were analysed together with previously known sequences. PhyloGenetic analyses recovered three lineages within echinoderms, Crinoidea, Ophiuroidea and a group comprising Holothuroidea, Echinoidea, and Asteroidea. In contrast to previous analyses of mitochondrial genomes the increased data set recovered the classical echinoderm phylogeny of Eleutherozoa and Echinozoa in Maximum Likelihood and Bayesian analyses using hemichordate out-group representatives. However, an inconsistent ramification appeared with vertebrate out-groups and in Maximum Parsimony and Neighbour Joining reconstructions. The basal (consensus) Gene Orders of all three lineages could be derived from a hypothetical ancestral crinoid Gene order by one single rearrangement in each lineage. The genome architecture was highly conserved in Echinoidea, whereas the highest Gene order differences and large amounts of unassigned sequences (UAS) were detected in Ophiuroidea, supporting a higher evolutionary rate than in any other echinoderm lineage. The variability in Gene order and UAS regions in ophiuroid genomes suggest dominating rearrangement mechanisms by duplication events.
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evolution of mitochondrial Gene Orders in echinoderms
Molecular Phylogenetics and Evolution, 2008Co-Authors: Marleen Perseke, Peter F. Stadler, Guido Fritzsch, Detlef Bernhard, Kai Ramsch, Matthias Bernt, Daniel Merkle, Martin Middendorf, Martin SchlegelAbstract:A comprehensive analysis of the mitochondrial Gene Orders of all previously published and two novel Antedon mediterranea (Crinoidea) and Ophiura albida (Ophiuroidea) complete echinoderm mitochondrial genomes shows that all major types of rearrangement operations are necessary to explain the evolution of mitochondrial genomes. In addition to protein coding Genes we include all tRNA Genes as well as the control region in our analysis. Surprisingly, 7 of the 16 genomes published in the GenBank database contain misannotations, mostly unannotated tRNAs and/or mistakes in the orientation of tRNAs, which we have corrected here. Although the Gene Orders of mt genomes appear very different, only 8 events are necessary to explain the evolutionary history of echinoderms with the exception of the ophiuroids. Only two of these rearrangements are inversions, while we identify three tandem-duplication-random-loss events and three transpositions.