The Experts below are selected from a list of 2406 Experts worldwide ranked by ideXlab platform
Dominik R Laetsch - One of the best experts on this subject based on the ideXlab platform.
-
comparative genomics of the tardigrades hypsibius dujardini and ramazzottius varieornatus
PLOS Biology, 2017Co-Authors: Yuki Yoshida, Dominik R Laetsch, Lewis Stevens, Sujai Kumar, Georgios Koutsovoulos, Daiki D. Horikawa, Kyoko Ishino, Shiori Komine, Takekazu KuniedaAbstract:Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Panarthropoda by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups. Limnoterrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis and cryobiosis, as do bdelloid rotifers, nematodes, and other animals of the water film. These extremophile behaviors challenge understanding of normal, aqueous physiology: how does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species have been reported to have elevated levels of horizontal gene transfer (HGT) events, but how important this is in evolution, and particularly in the evolution of extremophile physiology, is unclear. To address these questions, we resequenced and reassembled the genome of H. dujardini, a limnoterrestrial tardigrade that can undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the genome of R. varieornatus, a related species with tolerance to rapid desiccation. The 2 species had contrasting gene expression responses to anhydrobiosis, with major transcriptional change in H. dujardini but limited regulation in R. varieornatus. We identified few horizontally transferred genes, but some of these were shown to be involved in entry into anhydrobiosis. Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda.
-
comparative genomics of the tardigrades hypsibius dujardini and ramazzottius varieornatus
bioRxiv, 2017Co-Authors: Yuki Yoshida, Dominik R Laetsch, Lewis Stevens, Sujai Kumar, Georgios Koutsovoulos, Daiki D. Horikawa, Kyoko Ishino, Shiori Komine, Takekazu Kunieda, Masaru TomitaAbstract:Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Panarthropoda by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups. Limno-terrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis and cryobiosis, as do bdelloid rotifers, nematodes and other animals of the water film. These extremophile behaviors challenge understanding of normal, aqueous physiology: how does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species have been reported to have elevated levels of HGT events, but how important this is in evolution, and particularly in the evolution of extremophile physiology, is unclear. To address these questions, we resequenced and reassembled the genome of Hypsibius dujardini, a limno-terrestrial tardigrade that can undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the genome of Ramazzottius varieornatus, a related species with tolerance to rapid desiccation. The two species had contrasting gene expression responses to anhydrobiosis, with major transcriptional change in H. dujardini but limited regulation in R. varieornatus. We identified few horizontally transferred genes, but some of these were shown to be involved in entry into anhydrobiosis. Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda.
-
The position of Tardigrada in Ecdysozoa.
2017Co-Authors: Yuki Yoshida, Dominik R Laetsch, Lewis Stevens, Sujai Kumar, Georgios Koutsovoulos, Daiki D. Horikawa, Kyoko Ishino, Shiori Komine, Takekazu Kunieda, Masaru TomitaAbstract:(A) HOX genes in tardigrades and other Ecdysozoa. HOX gene losses in Tardigrada and Nematoda. HOX gene catalogues of tardigrades and other Ecdysozoa were collated by screening ENSEMBL Genomes and WormBase Parasite. HOX orthology groups are indicated by different colors. Some “missing” HOX loci were identified by Basic Local Alignment Search Tool (BLAST) search of target genomes (indicated by vertical striping of the affected HOX). “?” indicates that presence/absence could not be confirmed because the species was surveyed by PCR or transcriptomics; loci identified by PCR or transcriptomics are indicated by a dotted outline. “X” indicates that orthologous HOX loci were not present in the genome of that species. Some species have duplications of loci mapping to 1 HOX group, and these are indicated by boxes with dashed outlines. The relationships of the species are indicated by the cladogram to the left, and circles on this cladogram indicate Dollo parsimony mapping of events of HOX group loss on this cladogram. Circles are colored congruently with the HOX loci. (B) Evolution of gene families under different hypotheses of tardigrade relationships. Tardigrades share more gene families with Arthropoda than with Nematoda. In this network, derived from the OrthoFinder clustering at inflation value 1.5, nodes represent species (0: Anopheles gambiae, 1: Apis mellifera, 2: Acyrthosiphon pisum, 3: Ascaris suum, 4: Brugia malayi, 5: Bursaphelenchus xylophilus, 6: Caenorhabditis elegans, 7: Cimex lectularius, 8: Capitella teleta, 9: Dendroctonus ponderosae, 10: Daphnia pulex, 11: Hypsibius dujardini, 12: Ixodes scapularis, 13: Meloidogyne hapla, 14: Nasonia vitripennis, 15: Octopus bimaculoides, 16: Priapulus caudatus, 17: Pediculus humanus, 18: Plectus murrayi, 19: Pristionchus pacificus, 20: Plutella xylostella, 37: Ramazzottius varieornatus, 22: Solenopsis invicta, 23: Strigamia maritima, 24: Tribolium castaneum, 25: Trichuris muris, 26: Trichinella spiralis, 27: Tetranychus urticae, 38: Drosophila melanogaster). The thickness of the edge connecting 2 nodes is weighted by the count of shared occurrences of both nodes in OrthoFinder-clusters. Links involving H. dujardini (red) and R. varieornatus (orange) are colored. The inset box on the lower right shows the average weight of edges between each phylum and both Tardigrades, normalized by the maximum weight (i.e., count of co-occurrences of Tardigrades and the annelid C. teleta)" (C) Gene family birth synapomorphies at key nodes in Ecdysozoa under 2 hypotheses: Tardigrada+Nematoda versus Tardigrada+Arthropoda. Each graph shows the number of gene families at the specified node inferred using Dollo parsimony from OrthoFinder clustering at inflation value 1.5. Gene families are grouped by the proportion of taxa above that node that contain a member. Note that to be included as a synapomorphy of a node, a gene family must contain proteins of at least 1 species of each child node of the node in question, and thus, there are no synapomorphies with
-
Gene family births that support different relationships of Tardigrada.
2017Co-Authors: Yuki Yoshida, Dominik R Laetsch, Lewis Stevens, Sujai Kumar, Georgios Koutsovoulos, Daiki D. Horikawa, Kyoko Ishino, Shiori Komine, Takekazu Kunieda, Masaru TomitaAbstract:Gene family births that support different relationships of Tardigrada.
-
no evidence for extensive horizontal gene transfer in the genome of the tardigrade hypsibius dujardini
Proceedings of the National Academy of Sciences of the United States of America, 2016Co-Authors: Georgios Koutsovoulos, Dominik R Laetsch, Jennifer Daub, Claire Conlon, Habib Maroon, Fran Thomas, Lewis Stevens, Sujai Kumar, A. Aziz AboobakerAbstract:Tardigrades are meiofaunal ecdysozoans that are key to understanding the origins of Arthropoda. Many species of Tardigrada can survive extreme conditions through cryptobiosis. In a recent paper [Boothby TC, et al. (2015) Proc Natl Acad Sci USA 112(52):15976–15981], the authors concluded that the tardigrade Hypsibius dujardini had an unprecedented proportion (17%) of genes originating through functional horizontal gene transfer (fHGT) and speculated that fHGT was likely formative in the evolution of cryptobiosis. We independently sequenced the genome of H. dujardini. As expected from whole-organism DNA sampling, our raw data contained reads from nontarget genomes. Filtering using metagenomics approaches generated a draft H. dujardini genome assembly of 135 Mb with superior assembly metrics to the previously published assembly. Additional microbial contamination likely remains. We found no support for extensive fHGT. Among 23,021 gene predictions we identified 0.2% strong candidates for fHGT from bacteria and 0.2% strong candidates for fHGT from nonmetazoan eukaryotes. Cross-comparison of assemblies showed that the overwhelming majority of HGT candidates in the Boothby et al. genome derived from contaminants. We conclude that fHGT into H. dujardini accounts for at most 1–2% of genes and that the proposal that one-sixth of tardigrade genes originate from functional HGT events is an artifact of undetected contamination.
Sandra J. Mcinnes - One of the best experts on this subject based on the ideXlab platform.
-
Research presented at the 14th International Symposium on Tardigrada: progress in studies on water bears
Zoological Journal of the Linnean Society, 2020Co-Authors: Nadja Møbjerg, Łukasz Michalczyk, Sandra J. Mcinnes, Maarten J.m. ChristenhuszAbstract:Abstract The 14th International Symposium on Tardigrada took place in Copenhagen, Denmark from 30 July to 3 August 2018. Approximately 140 participants, representing 28 countries from five continents attended the meeting, and there were 58 talks and 74 posters of which 20 were selected for the Symposium Proceedings published in this special issue. The studies span phylogenomics, systematics, anatomy, morphology, reproductive biology, cryobiology, ecology, diet, microbial interactions and biogeography, taking the next step forward in broadening and deepening our understanding of tardigrade biology.
-
Preliminary description of tardigrade species diversity and distribution pattern around coastal Syowa Station and inland Sør Rondane Mountains, Dronning Maud Land, East Antarctica
Polar Biology, 2014Co-Authors: Megumu Tsujimoto, Sandra J. Mcinnes, Peter Convey, Satoshi ImuraAbstract:Tardigrades are important members of the simple terrestrial ecosystems in the extreme environments in Antarctica. This study provides a baseline description of tardigrade species diversity and distribution pattern within the terrestrial and lake environments of the coastal regions around Syowa Station and the neighbouring inland Sør Rondane Mountains, Dronning Maud Land. We combined data obtained from new and previously described collections and updated data available in the existing literature. We recorded five tardigrade species, three of which ( Echiniscus pseudowendti Dastych 1984 , Hebesuncus ryani Dastych and Harris 1994 , Pseudechiniscus sp.) have not previously been reported from the area, increasing the total recorded tardigrade diversity for this region of continental Antarctica to ten species. The results of our study indicate that tardigrades have been and are major components of the lake environment community in continental Antarctica, with Acutuncus antarcticus (Richters 1904) the most common and dominant species. Our data confirm that the tardigrade species diversity in the vicinity of Syowa Station is very low and suggest potential relationships between individual tardigrade species and terrestrial moss species and depth in freshwater ecosystems.
-
Phylum Tardigrada: an “individual” approach
Cladistics, 2008Co-Authors: Chester J. Sands, Nigel J. Marley, Sandra J. Mcinnes, W.p. Goodall-copestake, Peter Convey, Katrin LinseAbstract:Phylum Tardigrada consists of similar to 1000 tiny, hardy metazoan species distributed throughout terrestrial, limno-terrestrial and oceanic habitats. Their phylogenetic status has been debated, with current evidence placing them in the Ecdysozoa. Although there have been efforts to explore tardigrade phylogeny using both morphological and molecular data, limitations such as their few morphological characters and low genomic DNA concentrations have resulted in restricted taxonomic coverage. Using a protocol that allows us to identify and extract DNA from individuals, we have sequenced 18S rDNA from 343 tardigrades from across the globe. Using maximum parsimony and Bayesian analyses we have found support for dividing Order Parachela into three super-families and further evidence that indicates the traditional taxonomic perspective of families in the class EuTardigrada are nonmonophyletic and require re-working. It appears that conserved morphology within Tardigrada has resulted in conservative taxonomy as we have found cases of several discrete lineages grouped into single genera. Although this work substantially adds to the understanding of the evolution and taxonomy of the phylum, we highlight that inferences gained from this work are likely to be refined with the inclusion of further taxa-specifically representatives of the nine families yet to be sampled.
-
Tardigrade remains from lake sediments
Journal of Paleolimnology, 2008Co-Authors: Louise Cromer, Sandra J. Mcinnes, John A. E. Gibson, Janelle T. AgiusAbstract:Remains of tardigrades have rarely been reported to preserve in sediments, resulting in the absence of important ecological and biogeographic information that they could provide. However, a study of faunal microfossils in Antarctic lake sediment cores has shown that tardigrade eggs and occasionally exuvia can be abundant. Eggs from at least five tardigrade species were identified in sediment cores from six lakes from across the continent, with abundances up to 6,000 (g^−1 dry wt.). It is likely that the cold temperatures and absence of benthic grazers in Antarctic lakes results in particularly good preservation conditions, though it may also be a function of population density. The conservation of tardigrade eggs and exuvia in lake sediments enables a better understanding of paleodistributions and effects of environmental changes for this phylum that cannot otherwise be obtained.
-
Global diversity of tardigrades (Tardigrada) in freshwater
Hydrobiologia, 2007Co-Authors: James R. Garey, Sandra J. Mcinnes, P. Brent NicholsAbstract:Tardigrada is a phylum closely allied with the arthropods. They are usually less than 0.5 mm in length, have four pairs of lobe-like legs and are either carnivorous or feed on plant material. Most of the 900+ described tardigrade species are limnoterrestrial and live in the thin film of water on the surface of moss, lichens, algae, and other plants and depend on water to remain active and complete their life cycle. In this review of 910 tardigrade species, only 62 species representing13 genera are truly aquatic and not found in limnoterrestrial habitats although many other genera contain limnoterrestrial species occasionally found in freshwater.
Georgios Koutsovoulos - One of the best experts on this subject based on the ideXlab platform.
-
comparative genomics of the tardigrades hypsibius dujardini and ramazzottius varieornatus
PLOS Biology, 2017Co-Authors: Yuki Yoshida, Dominik R Laetsch, Lewis Stevens, Sujai Kumar, Georgios Koutsovoulos, Daiki D. Horikawa, Kyoko Ishino, Shiori Komine, Takekazu KuniedaAbstract:Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Panarthropoda by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups. Limnoterrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis and cryobiosis, as do bdelloid rotifers, nematodes, and other animals of the water film. These extremophile behaviors challenge understanding of normal, aqueous physiology: how does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species have been reported to have elevated levels of horizontal gene transfer (HGT) events, but how important this is in evolution, and particularly in the evolution of extremophile physiology, is unclear. To address these questions, we resequenced and reassembled the genome of H. dujardini, a limnoterrestrial tardigrade that can undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the genome of R. varieornatus, a related species with tolerance to rapid desiccation. The 2 species had contrasting gene expression responses to anhydrobiosis, with major transcriptional change in H. dujardini but limited regulation in R. varieornatus. We identified few horizontally transferred genes, but some of these were shown to be involved in entry into anhydrobiosis. Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda.
-
comparative genomics of the tardigrades hypsibius dujardini and ramazzottius varieornatus
bioRxiv, 2017Co-Authors: Yuki Yoshida, Dominik R Laetsch, Lewis Stevens, Sujai Kumar, Georgios Koutsovoulos, Daiki D. Horikawa, Kyoko Ishino, Shiori Komine, Takekazu Kunieda, Masaru TomitaAbstract:Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Panarthropoda by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups. Limno-terrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis and cryobiosis, as do bdelloid rotifers, nematodes and other animals of the water film. These extremophile behaviors challenge understanding of normal, aqueous physiology: how does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species have been reported to have elevated levels of HGT events, but how important this is in evolution, and particularly in the evolution of extremophile physiology, is unclear. To address these questions, we resequenced and reassembled the genome of Hypsibius dujardini, a limno-terrestrial tardigrade that can undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the genome of Ramazzottius varieornatus, a related species with tolerance to rapid desiccation. The two species had contrasting gene expression responses to anhydrobiosis, with major transcriptional change in H. dujardini but limited regulation in R. varieornatus. We identified few horizontally transferred genes, but some of these were shown to be involved in entry into anhydrobiosis. Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda.
-
The position of Tardigrada in Ecdysozoa.
2017Co-Authors: Yuki Yoshida, Dominik R Laetsch, Lewis Stevens, Sujai Kumar, Georgios Koutsovoulos, Daiki D. Horikawa, Kyoko Ishino, Shiori Komine, Takekazu Kunieda, Masaru TomitaAbstract:(A) HOX genes in tardigrades and other Ecdysozoa. HOX gene losses in Tardigrada and Nematoda. HOX gene catalogues of tardigrades and other Ecdysozoa were collated by screening ENSEMBL Genomes and WormBase Parasite. HOX orthology groups are indicated by different colors. Some “missing” HOX loci were identified by Basic Local Alignment Search Tool (BLAST) search of target genomes (indicated by vertical striping of the affected HOX). “?” indicates that presence/absence could not be confirmed because the species was surveyed by PCR or transcriptomics; loci identified by PCR or transcriptomics are indicated by a dotted outline. “X” indicates that orthologous HOX loci were not present in the genome of that species. Some species have duplications of loci mapping to 1 HOX group, and these are indicated by boxes with dashed outlines. The relationships of the species are indicated by the cladogram to the left, and circles on this cladogram indicate Dollo parsimony mapping of events of HOX group loss on this cladogram. Circles are colored congruently with the HOX loci. (B) Evolution of gene families under different hypotheses of tardigrade relationships. Tardigrades share more gene families with Arthropoda than with Nematoda. In this network, derived from the OrthoFinder clustering at inflation value 1.5, nodes represent species (0: Anopheles gambiae, 1: Apis mellifera, 2: Acyrthosiphon pisum, 3: Ascaris suum, 4: Brugia malayi, 5: Bursaphelenchus xylophilus, 6: Caenorhabditis elegans, 7: Cimex lectularius, 8: Capitella teleta, 9: Dendroctonus ponderosae, 10: Daphnia pulex, 11: Hypsibius dujardini, 12: Ixodes scapularis, 13: Meloidogyne hapla, 14: Nasonia vitripennis, 15: Octopus bimaculoides, 16: Priapulus caudatus, 17: Pediculus humanus, 18: Plectus murrayi, 19: Pristionchus pacificus, 20: Plutella xylostella, 37: Ramazzottius varieornatus, 22: Solenopsis invicta, 23: Strigamia maritima, 24: Tribolium castaneum, 25: Trichuris muris, 26: Trichinella spiralis, 27: Tetranychus urticae, 38: Drosophila melanogaster). The thickness of the edge connecting 2 nodes is weighted by the count of shared occurrences of both nodes in OrthoFinder-clusters. Links involving H. dujardini (red) and R. varieornatus (orange) are colored. The inset box on the lower right shows the average weight of edges between each phylum and both Tardigrades, normalized by the maximum weight (i.e., count of co-occurrences of Tardigrades and the annelid C. teleta)" (C) Gene family birth synapomorphies at key nodes in Ecdysozoa under 2 hypotheses: Tardigrada+Nematoda versus Tardigrada+Arthropoda. Each graph shows the number of gene families at the specified node inferred using Dollo parsimony from OrthoFinder clustering at inflation value 1.5. Gene families are grouped by the proportion of taxa above that node that contain a member. Note that to be included as a synapomorphy of a node, a gene family must contain proteins of at least 1 species of each child node of the node in question, and thus, there are no synapomorphies with
-
Gene family births that support different relationships of Tardigrada.
2017Co-Authors: Yuki Yoshida, Dominik R Laetsch, Lewis Stevens, Sujai Kumar, Georgios Koutsovoulos, Daiki D. Horikawa, Kyoko Ishino, Shiori Komine, Takekazu Kunieda, Masaru TomitaAbstract:Gene family births that support different relationships of Tardigrada.
-
no evidence for extensive horizontal gene transfer in the genome of the tardigrade hypsibius dujardini
Proceedings of the National Academy of Sciences of the United States of America, 2016Co-Authors: Georgios Koutsovoulos, Dominik R Laetsch, Jennifer Daub, Claire Conlon, Habib Maroon, Fran Thomas, Lewis Stevens, Sujai Kumar, A. Aziz AboobakerAbstract:Tardigrades are meiofaunal ecdysozoans that are key to understanding the origins of Arthropoda. Many species of Tardigrada can survive extreme conditions through cryptobiosis. In a recent paper [Boothby TC, et al. (2015) Proc Natl Acad Sci USA 112(52):15976–15981], the authors concluded that the tardigrade Hypsibius dujardini had an unprecedented proportion (17%) of genes originating through functional horizontal gene transfer (fHGT) and speculated that fHGT was likely formative in the evolution of cryptobiosis. We independently sequenced the genome of H. dujardini. As expected from whole-organism DNA sampling, our raw data contained reads from nontarget genomes. Filtering using metagenomics approaches generated a draft H. dujardini genome assembly of 135 Mb with superior assembly metrics to the previously published assembly. Additional microbial contamination likely remains. We found no support for extensive fHGT. Among 23,021 gene predictions we identified 0.2% strong candidates for fHGT from bacteria and 0.2% strong candidates for fHGT from nonmetazoan eukaryotes. Cross-comparison of assemblies showed that the overwhelming majority of HGT candidates in the Boothby et al. genome derived from contaminants. We conclude that fHGT into H. dujardini accounts for at most 1–2% of genes and that the proposal that one-sixth of tardigrade genes originate from functional HGT events is an artifact of undetected contamination.
Davide Pisani - One of the best experts on this subject based on the ideXlab platform.
-
MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda
Proceedings of the National Academy of Sciences of the United States of America, 2011Co-Authors: Lahcen I. Campbell, Omar Rota-stabelli, Kevin J Peterson, Stuart J Longhorn, Maximilian J. Telford, Trevor Marchioro, Herve Philippe, Lorena Rebecchi, Gregory D. Edgecombe, Davide PisaniAbstract:Morphological data traditionally group Tardigrada (water bears), Onychophora (velvet worms), and Arthropoda (e.g., spiders, insects, and their allies) into a monophyletic group of invertebrates with walking appendages known as the Panarthropoda. However, molecular data generally do not support the inclusion of tardigrades within the Panarthropoda, but instead place them closer to Nematoda (roundworms). Here we present results from the analyses of two independent genomic datasets, expressed sequence tags (ESTs) and microRNAs (miRNAs), which congruently resolve the phylogenetic relationships of Tardigrada. Our EST analyses, based on 49,023 amino acid sites from 255 proteins, significantly support a monophyletic Panarthropoda including Tardigrada and suggest a sister group relationship between Arthropoda and Onychophora. Using careful experimental manipulations—comparisons of model fit, signal dissection, and taxonomic pruning—we show that support for a Tardigrada + Nematoda group derives from the phylogenetic artifact of long-branch attraction. Our small RNA libraries fully support our EST results; no miRNAs were found to link Tardigrada and Nematoda, whereas all panarthropods were found to share one unique miRNA (miR-276). In addition, Onychophora and Arthropoda were found to share a second miRNA (miR-305). Our study confirms the monophyly of the legged ecdysozoans, shows that past support for a Tardigrada + Nematoda group was due to long-branch attraction, and suggests that the velvet worms are the sister group to the arthropods.
Sujai Kumar - One of the best experts on this subject based on the ideXlab platform.
-
comparative genomics of the tardigrades hypsibius dujardini and ramazzottius varieornatus
PLOS Biology, 2017Co-Authors: Yuki Yoshida, Dominik R Laetsch, Lewis Stevens, Sujai Kumar, Georgios Koutsovoulos, Daiki D. Horikawa, Kyoko Ishino, Shiori Komine, Takekazu KuniedaAbstract:Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Panarthropoda by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups. Limnoterrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis and cryobiosis, as do bdelloid rotifers, nematodes, and other animals of the water film. These extremophile behaviors challenge understanding of normal, aqueous physiology: how does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species have been reported to have elevated levels of horizontal gene transfer (HGT) events, but how important this is in evolution, and particularly in the evolution of extremophile physiology, is unclear. To address these questions, we resequenced and reassembled the genome of H. dujardini, a limnoterrestrial tardigrade that can undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the genome of R. varieornatus, a related species with tolerance to rapid desiccation. The 2 species had contrasting gene expression responses to anhydrobiosis, with major transcriptional change in H. dujardini but limited regulation in R. varieornatus. We identified few horizontally transferred genes, but some of these were shown to be involved in entry into anhydrobiosis. Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda.
-
comparative genomics of the tardigrades hypsibius dujardini and ramazzottius varieornatus
bioRxiv, 2017Co-Authors: Yuki Yoshida, Dominik R Laetsch, Lewis Stevens, Sujai Kumar, Georgios Koutsovoulos, Daiki D. Horikawa, Kyoko Ishino, Shiori Komine, Takekazu Kunieda, Masaru TomitaAbstract:Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Panarthropoda by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups. Limno-terrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis and cryobiosis, as do bdelloid rotifers, nematodes and other animals of the water film. These extremophile behaviors challenge understanding of normal, aqueous physiology: how does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species have been reported to have elevated levels of HGT events, but how important this is in evolution, and particularly in the evolution of extremophile physiology, is unclear. To address these questions, we resequenced and reassembled the genome of Hypsibius dujardini, a limno-terrestrial tardigrade that can undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the genome of Ramazzottius varieornatus, a related species with tolerance to rapid desiccation. The two species had contrasting gene expression responses to anhydrobiosis, with major transcriptional change in H. dujardini but limited regulation in R. varieornatus. We identified few horizontally transferred genes, but some of these were shown to be involved in entry into anhydrobiosis. Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda.
-
The position of Tardigrada in Ecdysozoa.
2017Co-Authors: Yuki Yoshida, Dominik R Laetsch, Lewis Stevens, Sujai Kumar, Georgios Koutsovoulos, Daiki D. Horikawa, Kyoko Ishino, Shiori Komine, Takekazu Kunieda, Masaru TomitaAbstract:(A) HOX genes in tardigrades and other Ecdysozoa. HOX gene losses in Tardigrada and Nematoda. HOX gene catalogues of tardigrades and other Ecdysozoa were collated by screening ENSEMBL Genomes and WormBase Parasite. HOX orthology groups are indicated by different colors. Some “missing” HOX loci were identified by Basic Local Alignment Search Tool (BLAST) search of target genomes (indicated by vertical striping of the affected HOX). “?” indicates that presence/absence could not be confirmed because the species was surveyed by PCR or transcriptomics; loci identified by PCR or transcriptomics are indicated by a dotted outline. “X” indicates that orthologous HOX loci were not present in the genome of that species. Some species have duplications of loci mapping to 1 HOX group, and these are indicated by boxes with dashed outlines. The relationships of the species are indicated by the cladogram to the left, and circles on this cladogram indicate Dollo parsimony mapping of events of HOX group loss on this cladogram. Circles are colored congruently with the HOX loci. (B) Evolution of gene families under different hypotheses of tardigrade relationships. Tardigrades share more gene families with Arthropoda than with Nematoda. In this network, derived from the OrthoFinder clustering at inflation value 1.5, nodes represent species (0: Anopheles gambiae, 1: Apis mellifera, 2: Acyrthosiphon pisum, 3: Ascaris suum, 4: Brugia malayi, 5: Bursaphelenchus xylophilus, 6: Caenorhabditis elegans, 7: Cimex lectularius, 8: Capitella teleta, 9: Dendroctonus ponderosae, 10: Daphnia pulex, 11: Hypsibius dujardini, 12: Ixodes scapularis, 13: Meloidogyne hapla, 14: Nasonia vitripennis, 15: Octopus bimaculoides, 16: Priapulus caudatus, 17: Pediculus humanus, 18: Plectus murrayi, 19: Pristionchus pacificus, 20: Plutella xylostella, 37: Ramazzottius varieornatus, 22: Solenopsis invicta, 23: Strigamia maritima, 24: Tribolium castaneum, 25: Trichuris muris, 26: Trichinella spiralis, 27: Tetranychus urticae, 38: Drosophila melanogaster). The thickness of the edge connecting 2 nodes is weighted by the count of shared occurrences of both nodes in OrthoFinder-clusters. Links involving H. dujardini (red) and R. varieornatus (orange) are colored. The inset box on the lower right shows the average weight of edges between each phylum and both Tardigrades, normalized by the maximum weight (i.e., count of co-occurrences of Tardigrades and the annelid C. teleta)" (C) Gene family birth synapomorphies at key nodes in Ecdysozoa under 2 hypotheses: Tardigrada+Nematoda versus Tardigrada+Arthropoda. Each graph shows the number of gene families at the specified node inferred using Dollo parsimony from OrthoFinder clustering at inflation value 1.5. Gene families are grouped by the proportion of taxa above that node that contain a member. Note that to be included as a synapomorphy of a node, a gene family must contain proteins of at least 1 species of each child node of the node in question, and thus, there are no synapomorphies with
-
Gene family births that support different relationships of Tardigrada.
2017Co-Authors: Yuki Yoshida, Dominik R Laetsch, Lewis Stevens, Sujai Kumar, Georgios Koutsovoulos, Daiki D. Horikawa, Kyoko Ishino, Shiori Komine, Takekazu Kunieda, Masaru TomitaAbstract:Gene family births that support different relationships of Tardigrada.
-
no evidence for extensive horizontal gene transfer in the genome of the tardigrade hypsibius dujardini
Proceedings of the National Academy of Sciences of the United States of America, 2016Co-Authors: Georgios Koutsovoulos, Dominik R Laetsch, Jennifer Daub, Claire Conlon, Habib Maroon, Fran Thomas, Lewis Stevens, Sujai Kumar, A. Aziz AboobakerAbstract:Tardigrades are meiofaunal ecdysozoans that are key to understanding the origins of Arthropoda. Many species of Tardigrada can survive extreme conditions through cryptobiosis. In a recent paper [Boothby TC, et al. (2015) Proc Natl Acad Sci USA 112(52):15976–15981], the authors concluded that the tardigrade Hypsibius dujardini had an unprecedented proportion (17%) of genes originating through functional horizontal gene transfer (fHGT) and speculated that fHGT was likely formative in the evolution of cryptobiosis. We independently sequenced the genome of H. dujardini. As expected from whole-organism DNA sampling, our raw data contained reads from nontarget genomes. Filtering using metagenomics approaches generated a draft H. dujardini genome assembly of 135 Mb with superior assembly metrics to the previously published assembly. Additional microbial contamination likely remains. We found no support for extensive fHGT. Among 23,021 gene predictions we identified 0.2% strong candidates for fHGT from bacteria and 0.2% strong candidates for fHGT from nonmetazoan eukaryotes. Cross-comparison of assemblies showed that the overwhelming majority of HGT candidates in the Boothby et al. genome derived from contaminants. We conclude that fHGT into H. dujardini accounts for at most 1–2% of genes and that the proposal that one-sixth of tardigrade genes originate from functional HGT events is an artifact of undetected contamination.
