The polymorphism of Hydra microsatellite sequences provides strain-specific signatures

Abstract

Hydra are freshwater polyps widely studied for their amazing regenerative capacity, adult stem cell populations, low senescence and value as ecotoxicological marker. Many wildtype strains of H. vulgaris have been collected worldwide and maintained effectively under laboratory conditions by asexual reproduction, while stable transgenic lines have been continuously produced since 2006. Efforts are now needed to ensure the genetic characterization of all these strains, which despite similar morphologies, show significant variability in their response to gene expression silencing procedures, pharmacological treatments or environmental conditions. Here, we established a rapid and reliable procedure at the single polyp level to produce via PCR amplification of three distinct microsatellite sequences molecular signatures that distinguish between Hydra strains and species. The TG-rich region of an uncharacterized gene (ms-c25145) helps to distinguish between Eurasian H. vulgaris-Pallas strains (Hm-105, Basel1, Basel2 and reg-16), between Eurasian and North American H. vulgaris strains (H. carnea, AEP), and between the H. vulgaris and H. oligactis species. The AT-rich microsatellite sequences located in the AIP gene (Aryl Hydrocarbon Receptor Interaction Protein, ms-AIP) also differ between Eurasian and North American H. vulgaris strains. Finally, the AT-rich microsatellite located in the Myb-Like cyclin D-binding transcription factor1 gene (ms-DMTF1) gene helps to distinguish certain transgenic AEP lines. This study shows that the analysis of microsatellite sequences, which is capable of tracing genomic variations between closely related lineages of Hydra, provides a sensitive and robust tool for characterizing the Hydra strains.

A chromosome-scale epigenetic map of theHydragenome reveals conserved regulators of cell state

“…Specifically, the currently available and recently improved reference genome ( Simakov et al 2022 ) was generated using strain 105 of Hydra vulgaris (formerly H. magnipapillata ), whereas all transgenic Hydra lines and the single-cell expression atlas were generated using the AEP strain. The AEP and 105 strains belong to two distinct lineages that split ∼16 million years ago, leading to significant sequence divergence that markedly reduces cross-strain mapping efficiencies ( Martínez et al 2010 ; Schwentner and Bosch 2015 ; Siebert et al 2019 ; Wong et al 2019 ; Schenkelaars et al 2020 ). This highlights the need for an AEP strain reference genome that would allow researchers to more effectively leverage transgenesis and the single-cell expression atlas.…”

TheWnt/β-catenin/TCF/Sp5/Zic4gene network that regulates head organizer activity inHydrais differentially regulated in epidermis and gastrodermis

“…Hydra vulgaris (Hv) from the Basel (Hv_Basel), magnipapillata ( Hm-105 ) or AEP2 (Hv_AEP2) strains [36] were cultured in Hydra Medium (HM: 1 mM NaCl, 1 mM CaCl2, 0.1 mM KCl, 0.1 mM MgSO4, 1 mM Tris pH 7.6) at 18°C and fed two to three times a week with freshly hatched Artemia nauplii (Sanders, Aqua Schwarz). For regeneration experiments, animals were starved for four days, then bisected at mid-gastric bisection.…”

The transcription factor Zic4 promotes tentacle formation and prevents epithelial transdifferentiation in Hydra

“…All experiments were performed with strains of Hydra vulgari s ( Hv ) either Basel1 , AEP2 (kindly provided by R. Steele), or Hm-105 ( 53 ), and the cultures were maintained in Hydra medium (HM) [1 mM NaCl, 1 mM CaCl 2 , 0.1 mM KCl, 0.1 mM MgSO 4 , and 1 mM tris (pH 7.6)]. The animals were fed two to three times per week with freshly hatched Artemia nauplii and starved for 4 days before starting the experiments.…”