Published October 31, 2024
| Version v1
Journal article
Open
Mitogenome of a new Ramazzottius species (Tardigrada: Eutardigrada: Ramazzottiidae) discovered in rock pools along with its temperature and desiccation-related proteins repertoire
Authors/Creators
- 1. Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016, Kraków, Poland
Description
Vecchi, Matteo, Stec, Daniel (2025): Mitogenome of a new Ramazzottius species (Tardigrada: Eutardigrada: Ramazzottiidae) discovered in rock pools along with its temperature and desiccation-related proteins repertoire. Organisms Diversity & Evolution 25 (1): 119-135, DOI: 10.1007/s13127-024-00662-x, URL: https://doi.org/10.1007/s13127-024-00662-x
Files
source.pdf
Files
(2.3 MB)
| Name | Size | Download all |
|---|---|---|
|
md5:82243999e7b8da1b4133c2bdaaaebbce
|
2.3 MB | Preview Download |
Linked records
Additional details
Identifiers
- URL
- https://www.checklistbank.org/dataset/313130
- LSID
- urn:lsid:plazi.org:pub:8224FF99FFB8DA1B4133FFBDFFAEFFCE
- URL
- http://publication.plazi.org/id/8224FF99FFB8DA1B4133FFBDFFAEFFCE
References
- Bartels, P. J., Nelson, D. R., Kaczmarek, L, & Michalczyk, L. (2011). Ramazzottius belubellus, a new species of Tardigrada (Eutardigrada: Parachela: Hypsibiidae) from the Great Smoky Mountains National Park (North Carolina, U.S.A.). Proceedings of the Biological Society of Washington, 124(1), 23-27. https://doi.org/10. 2988/10-13.1
- Bernt, M., Donath, A., Juhling, F., Externbrink, F., Florentz, C., Fritzsch, G., Putz, J., Middendorf, M., & Stadler, P. F. (2013). MITOS: Improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution, 69(2), 313- 319. https://doi.org/10.1016/j.ympev.2012.08.023
- Bertolani, R., & Kinchin, I. M. (1993). A new species of Ramazzottius (Tardigrada, Hypsibiidae) in a rain gutter sediment from England. Zoological Journal of the Linnean Society, 109(3), 327-333. https://doi.org/10.1111/j.1096-3642.1993.tb02538.x
- Binda, M. G., & Pilato, G. (1986). Ramazzottius, nuovo genere di Eutardigrado (Hypsibiidae). Animalia, 13, 159-166.
- Binda, M., & Pilato, G. (1994). Notizie sui Tardigradi delle Isole Hawaii con descrizione di due specie nuove. Animalia, 21(1/3), 57-62.
- Biserov, V. (1997). Tardigrades of the Caucasus with a taxonomic analysis of the genus Ramazzottius (Parachela: Hypsibiidae). Zoologischer Anzeiger, 236, 139-159.
- Biserov, V., & Tumanov, D. (1993). Ramazzottius valaamis sp. n. (Tardigrada, Gypsibiidae), a new species of tardigrads from Valaam Island, Karelia. Russia. Zoologiceskij Zurnal, 72(11), 35-39.
- Buchfink, B., Xie, C., & Huson, D. H. (2015). Fast and sensitive protein alignment using DIAMOND. Nature Methods, 12(1), 59-60. https://doi.org/10.1038/nmeth.3176
- Camarda, D., Massa, E., Guidetti, R., & Lisi, O. (2023). A new, simplified, drying protocol to prepare tardigrades for scanning electron microscopy. Microscopy Research and Technique, jemt.24460. https://doi.org/10.1002/jemt.24460
- Casquet, J., Thebaud, C., & Gillespie, R. G. (2012). Chelex without boiling, a rapid and easy technique to obtain stable amplifiable DNA from small amounts of ethanol-stored spiders. Molecular Ecology Resources, 12(1), Article 1. https://doi.org/10.1111/j. 1755-0998.2011.03073.x
- Claps, M. C., & Rossi, G. C. (1984). Contribucion al conocimiento de los tardi ´grados de Argentina. IV. Acta Zoologica Lilloana,38(1), 45-50.
- Dastych, H. (1980). Hypsibius szeptycki sp. mov., a new species of Tardigrada from South Africa. Bull Bulletin de L'Academie Polonaise des Sciences Serie des Sciences Biologiques, 26(6), 505-508.
- Dastych, H. (1983). Two new eutardigrada species from West Spitsbergen and the Tatra mts. Bulletin De La Societe Des Amis Des Sciences Et Des Lettres De Poznan, 23, 195-200.
- Dastych, H. (1993). A new genus and four new species of semiterrestrial water-bears from South Africa (Tardigrada). Mitteilungen Aus Dem Naturhistorischen Museum in Hamburg, 90, 175-186.
- De Coster, W., & Rademakers, R. (2023). NanoPack2: Population-scale evaluation of long-read sequencing data. Bioinformatics, 39(5), btad311. https://doi.org/10.1093/bioinformatics/btad311
- Dey, P. K., Lopez-Lopez, A., Morek, W., & Michalczyk, L. (2024). Tardigrade Augean stables -A challenging phylogeny and taxonomy of the family Ramazzottiidae (Eutardigrada: Hypsibioidea). Zoological Journal of the Linnean Society, 200(1), 95-110. https:// doi.org/10.1093/zoolinnean/zlad161
- Donath, A., Juhling, F., Al-Arab, M., Bernhart, S. H., Reinhardt, F., Stadler, P. F., Middendorf, M., & Bernt, M. (2019). Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes. Nucleic Acids Research, 47(20), 10543- 10552. https://doi.org/10.1093/nar/gkz833
- Edgar, R. C. (2004). MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5), 1792-1797. https://doi.org/10.1093/nar/gkh340
- Emdee, N., Mobjerg, A., Grollmann, M. M., & Mobjerg, N. (2024). Osmotic stress tolerance and transcriptomic response of Ramazzottius varieornatus (Eutardigrada: Ramazzottiidae) following tun formation. Zoological Journal of the Linnean Society, 200(1), 220-229. https://doi.org/10.1093/zoolinnean/zlad046
- Faurby, S., Jonsson, K. I., Rebecchi, L., & Funch, P. (2008). Variation in anhydrobiotic survival of two eutardigrade morphospecies: A story of cryptic species and their dispersal. Journal of Zoology, 275(2), Article 2. https://doi.org/10.1111/j.1469-7998. 2008.00420.x
- Fleming, J. F., Pisani, D., & Arakawa, K. (2024). The evolution of temperature and desiccation-related protein families in Tardigrada reveals a complex acquisition of extremotolerance. Genome Biology and Evolution, 16(1), evad217. https://doi. org/10.1093/gbe/evad217
- GIMP Development Team. (2019). GIMP. https://www.gimp.org
- Greiner, S., Lehwark, P., & Bock, R. (2019). OrganellarGenome-DRAW (OGDRAW) version 1.3.1: Expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Research, 47(W1), W59-W64. https://doi.org/10.1093/nar/ gkz238
- Guidetti, R., Cesari, M., Giovannini, I., Ebel, C., Forschler, M. I., Rebecchi, L., & Schill, R. O. (2022). Morphology and taxonomy of the genus Ramazzottius (Eutardigrada; Ramazzottiidae) with the integrative description of Ramazzottius kretschmanni sp. nov. European Zoological Journal, 89(1), 346-370. https://doi. org/10.1080/24750263.2022.2043468
- Guidetti, R., Massa, E., Bertolani, R., Rebecchi, L., & Cesari, M. (2019). Increasing knowledge of Antarctic biodiversity: New endemic taxa of tardigrades (Eutardigrada; Ramazzottiidae) and their evolutionary relationships. Systematics and Biodiversity, 17(6), 573-593. https://doi.org/10.1080/14772000.2019.1649737
- Guil, N., & Giribet, G. (2012). A comprehensive molecular phylogeny of tardigrades-adding genes and taxa to a poorly resolved phylum-level phylogeny. Cladistics, 28(1), 21-49. https://doi.org/ 10.1111/j.1096-0031.2011.00364.x
- Guy, L., Roat Kultima, J., & Andersson, S. G. E. (2010). genoPlotR: Comparative gene and genome visualization in R. Bioinformatics (Oxford, England), 26(18), 2334-2335. https://doi.org/10.1093/ bioinformatics/btq413
- Hashimoto, T., Horikawa, D. D., Saito, Y., Kuwahara, H., Kozuka-Hata, H., Shin-i, T., et al. (2016). Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein. Nature Communications, 7(1), 12808. https://doi.org/10.1038/ncomms12808
- Hengherr, S., & Schill, R. O. (2018). Environmental adaptations: Cryobiosis. In Schill, R (Eds), Water bears: The biology of Tardigrades. (Vol. 2, pp. 295-310). Springer. https://doi.org/10.1007/ 978-3-319-95702-9_11
- Hoff, K. J., & Stanke, M. (2013). WebAUGUSTUS -A web service for training AUGUSTUS and predicting genes in eukaryotes. Nucleic Acids Research, 41(W1), 123-128. https://doi.org/10.1093/nar/ gkt418
- Horikawa, D. D. (2008). The Tardigrade Ramazzottius varieornatus as a model animal for astrobiological studies. Biological Sciences in Space, 22(3), 93-98. https://doi.org/10.2187/bss.22.93
- Horikawa, D. D., Cumbers, J., Sakakibara, I., Rogoff, D., Leuko, S., Harnoto, R., Arakawa, K., Katayama, T., Kunieda, T., Toyoda, A., Fujiyama, A., & Rothschild, L. J. (2013). Analysis of DNA repair and protection in the Tardigrade Ramazzottius varieornatus and Hypsibius dujardini after exposure to UVC radiation. PLoS ONE, 8(6), Article 6. https://doi.org/10.1371/journal.pone.0064793
- Horikawa, D. D., Kunieda, T., Abe, W., Watanabe, M., Nakahara, Y., Yukuhiro, F., Sakashita, T., Hamada, N., Wada, S., Funayama, T., Katagiri, C., Kobayashi, Y., Higashi, S., & Okuda, T. (2008). Establishment of a rearing system of the extremotolerant tardigrade Ramazzottius varieornatus: A new model animal for astrobiology. Astrobiology, 8(3), 549-556. https://doi.org/10.1089/ast.2007.0139
- Inkscape Project. (2020). Inkscape. https://inkscape.org
- Katoh, K. (2002). MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30(14), Article 14. https://doi.org/10.1093/nar/gkf436
- Katoh, K., & Toh, H. (2008). Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics, 9(4), Article 4. https://doi.org/10.1093/bib/bbn013
- Kihm, J.-H., Zawierucha, K., Rho, H. S., & Park, T.-Y.S. (2023). Homology of the head sensory structures between Heterotardigrada and Eutardigrada supported in a new species of water bear (Ramazzottiidae: Ramazzottius). Zoological Letters, 9(1), 22. https://doi.org/10.1186/s40851-023-00221-w
- Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019). Assembly of long, error-prone reads using repeat graphs. Nature Biotechnology, 37(5), 540-546. https://doi.org/10.1038/s41587-019-0072-8
- Lanfear, R., Frandsen, P. B., Wright, A. M., Senfeld, T., & Calcott, B. (2016). PartitionFinder 2: New methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular Biology and Evolution, msw260. https:// doi.org/10.1093/molbev/msw260
- Lin, Y., Yuan, J., Kolmogorov, M., Shen, M. W., Chaisson, M., & Pevzner, P. A. (2016). Assembly of long error-prone reads using de Bruijn graphs. Proceedings of the National Academy of Sciences, 113(52), E8396-E8405. https://doi.org/10.1073/pnas. 1604560113
- Michalczyk, L, & Kaczmarek, L. (2013). The Tardigrada Register: A comprehensive online data repository for tardigrade taxonomy. Journal of Limnology, 72(s1), 175-181. https://doi.org/10.4081/ jlimnol.2013.s1.e22
- Mobjerg, N., Jorgensen, A., Eibye-Jacobsen, J., Agerlin Halberg, K., Persson, D. K., & Mobjerg Kristensen, R. (2007). New records on cyclomorphosis in the marine eutardigrade Halobiotus crispae (Eutardigrada: Hypsibiidae). Journal of Limnology, 66(s 1), 132- 140. https://doi.org/10.4081/jlimnol.2007.s1.132
- Mutterer, J., & Zinck, E. (2013). Quick-and-clean article figures with FigureJ. Journal of Microscopy, 252(1), 89-91. https://doi.org/ 10.1111/jmi.12069
- Nelson, D. R., Bartels, P. J., & Guil, N. (2018). Tardigrade ecology. In Schill, R (Eds), Water Bears: The Biology of Tardigrades. (Vol. 2, pp. 163-210). Springer. https://doi.org/10.1007/ 978-3-319-95702-9_7
- Neves, R. C., Hvidepil, L. K. B., Sorensen-Hygum, T. L., Stuart, R. M., & Mobjerg, N. (2020). Thermotolerance experiments on active and desiccated states of Ramazzottius varieornatus emphasize that tardigrades are sensitive to high temperatures. Scientific Reports, 10(1), Article 94. https://doi.org/10.1038/s41598-019-56965-z
- Nishimura, O., Hara, Y., & Kuraku, S. (2017). gVolante for standardizing completeness assessment of genome and transcriptome assemblies. Bioinformatics, 33(22), 3635-3637. https://doi.org/ 10.1093/bioinformatics/btx445
- Pedersen, T. L. (2023). patchwork: The composer of plots. https:// CRAN.R-project.org/package=patchwork. Accessed 10 June 2024.
- Pilato, G. (1981). Analisi di nuovi caratteri nello studio degli Eutardigradi. Animalia, 8, 51-57.
- Ramazzotti, G. (1962). Tardigradi del Cile, con descrizione di quattro nuove specifiee di una nuova varieta. Atti Della Societa Italiana Di Scienze Naturali e Del Museo Civico Di Storia Naturale in Milano, 101, 275-287.
- Rambaut, A. (2007). FigTree, a graphical viewer of phylogenetic trees. http://tree.bio.ed.ac.uk/software/figtree/. Accessed 10 June 2024.
- Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A. (2018). Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Systematic Biology, 67(5), Article 5. https://doi.org/ 10.1093/sysbio/syy032
- Rebecchi, L., Altiero, T., & Guidetti, R. (2007). Anhydrobiosis: The extreme limit of desiccation tolerance. Invertebrate Survival Journal, 4(2), 65-81.
- Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Hohna, S., Larget, B., Liu, L., Suchard, M. A., & Huelsenbeck, J. P. (2012). MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61(3), Article 3. https://doi.org/10.1093/sysbio/sys029
- Schill, R. O. (Ed.). (2018). Water bears: The biology of Tardigrades (Vol. 2). Springer. https://doi.org/10.1007/978-3-319-95702-9
- Schill, R. O., & Hengherr, S. (2018). Environmental adaptations: Desiccation tolerance. In Schill, R (Eds), Water Bears: The Biology of Tardigrades. (pp. 273-293). Springer. https://doi.org/10.1007/ 978-3-319-95702-9_10
- Simao, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015). BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31(19), 3210-3212. https://doi.org/10.1093/bioinforma tics/btv351
- Stanke, M., Diekhans, M., Baertsch, R., & Haussler, D. (2008). Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics, 24(5), 637-644. https://doi. org/10.1093/bioinformatics/btn013
- Stec, D., Kristensen, R. M., & Michalczyk, L. (2020). An integrative description of Minibiotus ioculator sp. nov. from the Republic of South Africa with notes on Minibiotus pentannulatus Londono et al., 2017 (Tardigrada: Macrobiotidae). Zoologischer Anzeiger, 286, 117-134. https://doi.org/10.1016/j.jcz.2020.03.007
- Stec, D., Morek, W., Gasiorek, P., Kaczmarek, L, & Michalczyk, L. (2016). Determinants and taxonomic consequences of extreme egg shell variability in Ramazzottius subanomalus (Biserov, 1985)(Tardigrada). Zootaxa, 4208(2), 176-188. https://doi.org/ 10.11646/zootaxa.4208.2.5
- Stec, D., Morek, W., Gasiorek, P., & Michalczyk, L. (2018). Unmasking hidden species diversity within the Ramazzottius oberhaeuseri complex, with an integrative redescription of the nominal species for the family Ramazzottiidae (Tardigrada: Eutardigrada: Parachela). Systematics and Biodiversity, 16(4), 357-376. https://doi. org/10.1080/14772000.2018.1424267
- Stec, D., Zawierucha, K., & Michalczyk, L. (2017). An integrative description of Ramazzottius subanomalus (Biserov, 1985 (Tardigrada) from Poland. Zootaxa, 4300(3), 403-420. https://doi.org/ 10.11646/zootaxa.4300.3.4
- Sugiura, K., Yoshida, Y., Hayashi, K., Arakawa, K., Kunieda, T., & Matsumoto, M. (2024). Sexual dimorphism in the tardigrade Paramacrobiotus metropolitanus transcriptome. Zoological Letters, 10(1), 11. https://doi.org/10.1186/s40851-024-00233-0
- Thulin, G. (1911). Beitrage zur kenntnis der tardigradenfauna schwedens. Arkiv For Zoology, 7, 1-60.
- Trifinopoulos, J., Nguyen, L. T., von Haeseler, A., & Minh, B. Q. (2016). W-IQ-TREE: A fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research, 44(1), 232-235. https://doi.org/10.1093/nar/gkw256
- Troell, S., & Jonsson, K. I. (2023). Occurrence of tardigrades and morphometric and chemical conditions in rock pools by the Baltic Sea. Scientific Reports, 13(1), 19776. https://doi.org/10.1038/ s41598-023-46697-6
- Vecchi, M., & Bruneaux, M. (2021). concatipede: An R package to concatenate fasta sequences easily. . https://doi.org/10.5281/ zenodo.5130604
- Vecchi, M., Ferrari, C., Stec, D., & Calhim, S. (2022). Desiccation risk favours prevalence and diversity of tardigrade communities and influences their trophic structure in alpine ephemeral rock pools. Hydrobiologia, 849(9), 1995-2007. https://doi.org/10. 1007/s10750-022-04820-0
- Vecchi, M., McDaniel, J. L., Chartrain, J., Vuori, T., Walsh, E. J., & Calhim, S. (2023a). Morphology, phylogenetic position, and mating behaviour of a new Mesobiotus (Tardigrada) species from a rock pool in the Socorro Box Canyon (New Mexico, USA). The European Zoological Journal, 90(2), 708-725. https://doi.org/10. 1080/24750263.2023.2263033
- Vecchi, M., Tsvetkova, A., Stec, D., Ferrari, C., Calhim, S., & Tumanov, D. (2023b). Expanding Acutuncus: Phylogenetics and morphological analyses reveal a considerably wider distribution for this tardigrade genus. Molecular Phylogenetics and Evolution, 180, 107707. https://doi.org/10.1016/j.ympev.2023.107707
- Wick, R. R., Schultz, M. B., Zobel, J., & Holt, K. E. (2015). Bandage: Interactive visualization of de novo genome assemblies. Bioinformatics, 31(20), 3350-3352. https://doi.org/10.1093/bioinforma tics/btv383
- Wickham, H. (2016). ggplot2: Elegant graphics for data analysis. Springer-Verlag New York. https://ggplot2.tidyverse.org. Accessed 10 June 2024.
- Wilkins, D. (2024). gggenes: Draw gene arrow maps in 'ggplot2'. https://wilkox.org/gggenes/. Accessed 10 June 2024.
- Zawierucha, K., Ostrowska, M., Vonnahme, T. R., Devetter, M., Nawrot, A. P., Lehmann, S., & Kolicka, M. (2016). Diversity and distribution of Tardigrada in Arctic cryoconite holes. Journal of Limnology, 75(3), 545-559. https://doi.org/10.4081/jlimnol.2016. 1453
- Zawierucha, K., Stec, D., Lachowska-Cierlik, D., Takeuchi, N., Li, Z., & Michalczyk, L. (2018). High Mitochondrial Diversity in a New Water Bear Species (Tardigrada: Eutardigrada) from Mountain Glaciers in Central Asia, with the Erection of a New Genus Cryoconicus. Annales Zoologici, 68(1), 179-201. https://doi.org/ 10.3161/00034541anz2018.68.1.007
- Zawierucha, K., Vecchi, M., Takeuchi, N., Ono, M., & Calhim, S. (2023). Negative impact of freeze -thaw cycles on the survival of tardigrades. Ecological Indicators, 154, 110460. https://doi.org/ 10.1016/j.ecolind.2023.110460
- Zeglinski, K., Hsu, A., Alhamdoosh, M., & Koutsakis, C. (2021). gmoviz: Seamless visualization of complex genomic variations in GMOs and edited cell lines. https://github.com/malhamdoosh/ gmoviz. Accessed 10 June 2024.