Brown, Thomas and Elewa, Ahmed and Iarovenko, Svetlana and Subramanian, Elaiyaraja and Joven Araus, Alberto and Petzold, Andreas and Susuki, Miyuki and Suzuki, Ken-ichi T. and Hayashi, Toshinori and Toyoda, Atsushi and Oliveira, Catarina and Osipova, Ekaterina and Leigh, Nicholas D. and Simon, Andras and Yun, Maximina H. (2022) Sequencing and chromosome-scale assembly of the giant Pleurodeles waltl genome. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20230322-101534000.13
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Abstract
The Iberian ribbed newt (Pleurodeles waltl) constitutes a central model for probing the basis of regeneration. Here, we present the sequencing and chromosome-scale assembly of the 20.3Gb P.waltl genome, which exhibits the highest level of contiguity and completeness among giant genomes. We uncover that DNA transposable elements are the major contributors to its expansion, with hAT transposons comprising a large portion of repeats. Several hATs are actively transcribed and differentially expressed during adult P. waltl limb regeneration, along with domesticated hAT transposons of the ZBED transcription factor family. Despite its size, syntenic relationships are conserved across the genome. As an example we show the high degree of conservation of the regeneration-associated Tig1 locus with several neighbouring genes. Together, the P. waltl genome provides a fundamental resource for the study of regenerative, developmental and evolutionary principles.
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| Additional Information: | The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. Storage and handling of sequencing data was enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC) at UPPMAX -partially funded by the Swedish Research Council through grant agreement no. 2018-05973-, the DRESDEN Concept Genome Center -part of the technology platform of the CMCB at the TU Dresden, supported by DFG (INST 269/768-1)-, the MPICBG computing cloud, and the Center for Information Services and High-Performance Computing (ZIH) at Technische Universität Dresden. Work performed at NGI/Uppsala Genome Center has been funded by RFI/VR and Science for Life Laboratory, Sweden. We thank Miho Kiyooka and Wei Chen for blastema Iso-seq library preparation and Sequel sequencing in the National Institute for Genetics, Japan. TB supported by DFG (INST 269/768-1). AE is supported by grant PID2020-115672RJ-I00 type JIN from Ministerio de Ciencia y Innovación (Spain). K.T.S is supported by JSPS KAKENHI, Grant-in Aid for Scientific Research(C), 18K06257 and 16H06279 (PAGS). NDL receives funding from the Knut and Alice Wallenberg Foundation and the Swedish Research Council (Registration # 2020-01486). AS is supported by ERC (951477), Swedish Research Council (2018-02443), KAW (2018.0040), Cancerfonden (20 0417). MHY is supported by Deutsche Forschungsgemeinschaft grants (DFG 22137416, 450807335 & 497658823) and TUD-CRTD core and seed funds. Author contributions. TB performed genome assembly and chromosome scaffolding. AE and TB performed genome annotation, with input and scripts from EO. SI performed computational genomic analysis, with input from MHY, TB, AE, AP and NDL. ES optimized and generated tissue samples for genomic and Iso-seq sequencing. AJA analysed 2n DNA content prior to tissue collection. ES, AJA and NDL coordinated sample extraction. MS, KS, TH, AT generated limb blastema Iso-seq. CO analysed data. TB performed macrosynteny comparisons. NDL developed microsynteny pipeline. MHY and AS provided scientific coordination. MHY, AS and NDL supervised the project. AS and MHY provided funding (AS: genome and Iso-seq sequencing except for limb blastema, staff; MHY: computational capacity, staff). AS and MHY edited the manuscript. MHY wrote the manuscript with contributions from all authors. Data Availability. Genome and annotation files are available through the Max Planck Digital Library at the following location: https://doi.org/10.17617/3.90C1ND and NCBI under the BioProject: PRJNA847026. PacBio HiFi, Hi-C and Iso-seq data will also be available under the same BioProject. The authors have declared no competing interest. | ||||||||||||||||||||||||||||||||
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| DOI: | 10.1101/2022.10.19.512763 | ||||||||||||||||||||||||||||||||
| Record Number: | CaltechAUTHORS:20230322-101534000.13 | ||||||||||||||||||||||||||||||||
| Persistent URL: | https://resolver.caltech.edu/CaltechAUTHORS:20230322-101534000.13 | ||||||||||||||||||||||||||||||||
| Usage Policy: | No commercial reproduction, distribution, display or performance rights in this work are provided. | ||||||||||||||||||||||||||||||||
| ID Code: | 120309 | ||||||||||||||||||||||||||||||||
| Collection: | CaltechAUTHORS | ||||||||||||||||||||||||||||||||
| Deposited By: | George Porter | ||||||||||||||||||||||||||||||||
| Deposited On: | 22 Mar 2023 23:20 | ||||||||||||||||||||||||||||||||
| Last Modified: | 22 Mar 2023 23:20 |
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