Reply to Bemm et al. and Arakawa: Identifying foreign genes in independent
            <i>Hypsibius dujardini</i>
            genome assemblies

Boothby, Thomas E.; Goldstein, Bob

doi:10.1073/pnas.1601149113

Cited by 11 publications

(8 citation statements)

References 16 publications

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“…varieornatus are likely to have been overestimated in these initial, uncurated gene predictions, even after sequence contamination has been removed, as seen in the H . dujardini assembly of Boothby et al [ 41 ].…”

Section: Resultsmentioning

confidence: 99%

“…dujardini genome was published alongside a claim of extensive horizontal gene transfer (HGT) from bacteria and other taxa into the tardigrade genome and a suggestion that HGT might have contributed to the evolution of cryptobiosis [ 19 ]. The extensive HGT claim has been robustly challenged [ 20 , 21 , 39 – 41 ], but the debate as to the contribution of HGT to cryptobiosis remains open. The genomes of these species could be exploited for understanding the mechanisms of rapid-desiccation versus slow-desiccation strategies in tardigrades, the importance of HGT, and the resolution of the deep structure of the Ecdysozoa.…”

Section: Introductionmentioning

confidence: 99%

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Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

et al. 2017

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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.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

et al. 2017

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show abstract

“…The initial, low quality H. dujardini genome was published alongside a claim of extensive horizontal gene transfer (HGT) from bacteria and other taxa into the tardigrade genome, and a suggestion that HGT might have contributed to the evolution of cryptobiosis [19]. The "extensive" HGT claim has been robustly challenged [20,21,[39][40][41], but the debate as to the contribution of HGT to cryptobiosis remains open. The genomes of these species could be exploited for understanding of rapid-desiccation versus slow-desiccation strategies in tardigrades, the importance of HGT, and the resolution of the deep structure of the Ecdysozoa.…”

Section: Introductionmentioning

confidence: 99%

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

Yoshida

Koutsovoulos

Laetsch

et al. 2017

Preprint

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Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of 26 Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal 27 evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the 28 superphylum Ecdysozoa by morphological analyses, but many molecular phylogenies fail to recover this 29 relationship. This tension between molecular and morphological understanding may be very revealing of the 30 mode and patterns of evolution of major groups. Similar to bdelloid rotifers, nematodes and other animals 31 of the water film, limno-terrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis 32 and cryobiosis. These extremophile behaviors challenge understanding of normal, aqueous physiology: how 33 does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species 34 have been reported to have elevated levels of HGT events, but how important this is in evolution, and in 35 particular in the evolution of extremophile physiology, is unclear. To address these questions, we 36 resequenced and reassembled the genome of Hypsibius dujardini, a limno-terrestrial tardigrade that can 37 undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the 38 genome of Ramazzottius varieornatus, a related species with tolerance to rapid desiccation.

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“…Radiation tolerance may have come about not through the evolution of novel biosynthetic pathways, but through a breakdown or disruption of existing pathways, leading to the accumulation of antioxidant intermediates [14]. Horizontal gene transfer, genomic incorporation of DNA from other organisms, has been implicated in the acquisition of novel stress tolerant traits [35, 36, 75–77]. In other cases, hypoxia for example, evolution of regulatory control over existing metabolic and physiological processes has given rise to tolerance [6].…”

Section: Evolutionary Paths To Stress Tolerancementioning

confidence: 99%

Mechanisms and evolution of resistance to environmental extremes in animals

Boothby

2019

EvoDevo

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When animals are exposed to an extreme environmental stress, one of three possible outcomes takes place: the animal dies, the animal avoids the environmental stress and survives, or the animal tolerates the environmental stress and survives. This review is concerned with the third possibility, and will look at mechanisms that rare animals use to survive extreme environmental stresses including freezing, desiccation, intense heat, irradiation, and low-oxygen conditions (hypoxia). In addition, an increasing understanding of the molecular mechanisms involved in environmental stress tolerance allows us to speculate on how these tolerances arose. Uncovering the mechanisms of extreme environmental stress tolerance and how they evolve has broad implications for our understanding of the evolution of early life on this planet, colonization of new environments, and the search for novel forms of life both on Earth and elsewhere, as well as a number of agricultural and health-related applications.

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Reply to Bemm et al. and Arakawa: Identifying foreign genes in independent Hypsibius dujardini genome assemblies

Cited by 11 publications

References 16 publications

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

Mechanisms and evolution of resistance to environmental extremes in animals

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