A chromosome-scale assembly of the axolotl genome

Smith, Jeramiah J.; Timoshevskaya, Nataliya; Timoshevskiy, Vladimir A.; Keinath, Melissa C.; Hardy, Drew; Voss, S. Randal

doi:10.1101/gr.241901.118

Cited by 114 publications

(125 citation statements)

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“…Tissue-specific gene expression data for axolotl (available on the UCSC Genome Browser) revealed high transcription levels of mtnr1b gene in the ovary suggesting that the axolotl genome does encode a functional Mtnr1b receptor. The exon inversion observed for both mtnr1a and mtnr1b genes might be an assembly artifact caused by the presence of large introns and high number of a large repetitive sequences in the very large axolotl genome (78,79). We did identify the four mtnr chromosomal regions in the Gabon caecilian (Geotrypetes seraphini) genome assembly, but both mtnr1c and mtnr1d genes are lacking.…”

Section: Evolution Of Melatonin Receptor Repertoire In Sarcopterygiimentioning

confidence: 79%

New Insights Into the Evolutionary History of Melatonin Receptors in Vertebrates, With Particular Focus on Teleosts

2020

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In order to improve our understanding of melatonin signaling, we have reviewed and revised the evolutionary history of melatonin receptor genes (mtnr) in vertebrates. All gnathostome mtnr genes have a conserved gene organization with two exons, except for mtnr1b paralogs of some teleosts that show intron gains. Phylogeny and synteny analyses demonstrate the presence of four mtnr subtypes, MTNR1A, MTNR1B, MTNR1C, MTNR1D that arose from duplication of an ancestral mtnr during the vertebrate tetraploidizations (1R and 2R). In tetrapods, mtnr1d was lost, independently, in mammals, in archosaurs and in caecilian amphibians. All four mtnr subtypes were found in two non-teleost actinopterygian species, the spotted gar and the reedfish. As a result of teleost tetraploidization (3R), up to seven functional mtnr genes could be identified in teleosts. Conservation of the mtnr 3R-duplicated paralogs differs among the teleost lineages. Synteny analysis showed that the mtnr1d was conserved as a singleton in all teleosts resulting from an early loss after tetraploidization of one of the teleost 3R and salmonid 4R paralogs. Several teleosts including the eels and the piranha have conserved both 3R-paralogs of mtnr1a, mtnr1b, and mtnr1c. Loss of one of the 3R-paralogs depends on the lineage: mtnr1ca was lost in euteleosts whereas mtnr1cb was lost in osteoglossomorphs and several ostariophysians including the zebrafish. We investigated the tissue distribution of mtnr expression in a large range of tissues in medaka. The medaka has conserved the four vertebrate paralogs, and these are expressed in brain and retina, and, differentially, in peripheral tissues. Photoperiod affects mtnr expression levels in a gene-specific and tissue-specific manner. This study provides new insights into the repertoire diversification and functional evolution of the mtnr gene family in vertebrates.

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Section: Evolution Of Melatonin Receptor Repertoire In Sarcopterygiimentioning

confidence: 79%

New Insights Into the Evolutionary History of Melatonin Receptors in Vertebrates, With Particular Focus on Teleosts

2020

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“…This has also been aided by the feasibility of germline transgenesis in axolotls, which has enabled germline mutagenesis and Cre-loxP reporter-mediated lineage tracking (Bryant et al, 2017;Fei et al, 2018Fei et al, , 2017Flowers et al, 2017;Leigh et al, 2018;Nowoshilow et al, 2018). In addition, although the axolotl genome is gigantic (32 Gb, discussed below), it is now assembled and annotated with impressive contiguity (Nowoshilow et al, 2018;Smith et al, 2019). While these technological advantages (transgenesis and genomic resources) have been a major driving force for focusing on the axolotl, a conceptual consideration is whether it is truly possible to examine the 'adult mode' of regeneration in axolotls, given their paedomorphic nature.…”

Section: Life Cycle and Experimental Accessibilitymentioning

confidence: 99%

Model systems for regeneration: salamanders

2019

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Salamanders have been hailed as champions of regeneration, exhibiting a remarkable ability to regrow tissues, organs and even whole body parts, e.g. their limbs. As such, salamanders have provided key insights into the mechanisms by which cells, tissues and organs sense and regenerate missing or damaged parts. In this Primer, we cover the evolutionary context in which salamanders emerged. We outline the varieties of mechanisms deployed during salamander regeneration, and discuss how these mechanisms are currently being explored and how they have advanced our understanding of animal regeneration. We also present arguments about why it is important to study closely related species in regeneration research.

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“…A major advance in salamander research during recent years is the extension of the genetic toolbox. Genome and transcriptomes of several salamander species have been sequenced and annotated (e.g., [56][57][58][59][60][61][62]). Among salamanders, the Mexican axolotl (Ambystoma mexicanum) and the Iberian newt (Pleurodeles waltl) are currently the two most commonly used species with significant genomic information and several genetically modified lines available.…”

Section: Genetic Tools For Salamander Researchmentioning

confidence: 99%

Walking with Salamanders: From Molecules to Biorobotics

Ryczko

Simon

Ijspeert

2020

Trends in Neurosciences

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How do four-legged animals adapt their locomotion to the environment? How do central and peripheral mechanisms interact within the spinal cord to produce adaptive locomotion and how is locomotion recovered when spinal circuits are perturbed? Salamanders are the only tetrapods that regenerate voluntary locomotion after full spinal transection. Given their evolutionary position, they provide a unique opportunity to bridge discoveries made in fish and mammalian models. Genetic dissection of salamander neural circuits is becoming feasible with new methods for precise manipulation, elimination, and visualisation of cells. These approaches can be combined with classical tools in neuroscience and with modelling and a robotic environment. We propose that salamanders provide a blueprint of the function, evolution, and regeneration of tetrapod locomotor circuits. Salamanders as a Model Organism for Studying Locomotion Two major challenges in neuroscience are to decipher how the interplay between central and peripheral mechanisms controls locomotion in four-legged animals (tetrapods) and to delineate the reorganisation of motor circuits after spinal lesion. In this review, we outline the reasons why salamanders are ideally suited to address these two problems. First, salamanders are the only tetrapods capable of regenerating their locomotor circuits after full transection at adult stage [1-3]. Second, they are the closest extant representatives of the first tetrapods that transitioned from aquatic to terrestrial life [4]. This key evolutionary position makes salamanders ideal to provide a bridge between discoveries in fish (such as zebrafish) and mammals (such as mouse). Salamanders swim underwater and walk on ground [4], allowing researchers to investigate to what extent body dynamics and sensory feedback shape these locomotor patterns. Third, high precision dissection of their neural circuits is becoming possible thanks to new tools that will allow visualisation and optogenetic and chemogenetic manipulations that can be combined with classical neuroscience tools and advanced modelling and robotic environments. It is thus timely to highlight the recent advances in salamander research at the intersection of genomics, systems neuroscience, modelling, and robotics, which altogether provide a unique opportunity to decode locomotor control in the intact and regenerated tetrapod nervous system. In this review, we systematically place these approaches and recent results into a cross-species comparative setting, with a special focus on zebrafish and mouse as comparative models for which most data on the genetic identity of locomotor circuits are available. For closer examination of the locomotor circuitries of other related animal models such as lamprey, cat, and Xenopus embryo, we refer readers to prior reviews (lamprey: [5], cat: [6], Xenopus embryo: [7]). The Salamander Nervous System: A Bridge between Fish and Mammalian Models Salamander locomotor circuits include the main features found in all vertebrates (Figure 1A,C). Their...

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A chromosome-scale assembly of the axolotl genome

Cited by 114 publications

References 58 publications

New Insights Into the Evolutionary History of Melatonin Receptors in Vertebrates, With Particular Focus on Teleosts

New Insights Into the Evolutionary History of Melatonin Receptors in Vertebrates, With Particular Focus on Teleosts

Model systems for regeneration: salamanders

Walking with Salamanders: From Molecules to Biorobotics

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