Asexual bdelloid rotifer Adineta vaga submitted to desiccation

: gateway to genetic exchanges and mechanisms of extreme resistance.

Abstract

Desiccation resistant bdelloid rotifers are remarkable because of their resistance to a variety of stresses. In addition, they constitute a major scandal in evolutionary biology due to the putative absence of sexual reproduction for at least 60 million years.
Neither male sex organs nor meiosis have ever been observed in these microscopic animals. However, it was not excluded that they may engage in sex on rare occasions. This Phd contributed to the genome equencing project of the first bdelloid genome. The genome sequencing of the bdelloid rotifer Adineta vagashowed that its structure is incompatible with conventional meiosis. In contrast to sexual species, the allelic regions are rearranged and sometimes even found on the same chromosome. Such structure does not allow meiotic pairing (See chapter 2).
Besides, the genome sequencing of A. vagarevealed that around 8 % of genes are of apparent non-metazoan origin, a percentage much higher than observed in most eukaryotes. It remained obscure when bdelloids started to acquire such genes and how it shapes the diversification of bdelloid clade. In this thesis, a preliminary comparative genomic study focusing mainly on HGT acquisition between two bdelloid species was conducted. R
esults highlighted that a significant part of the HGT occurred before the separation of A. vaga and Adineta ricciae. In addition, when comparing with the monogonont rotifer Brachionus plicatilis,it was found that some non-metazoan genes were acquired by rotifers before the separation of
bdelloids and monogononts. Based on the function of HGT orthologs ighlighted in the present research, it was hypothesized that these acquisitions may have contributed to the adaptation to multiple food sources and to the enhanced resistance against desiccation of bdelloid rotifers (See chapter 3).
Adineta vaga inhabits temporary habitats subjected to frequent episodes of drought. It was hypothesized that DNA damage induced by desiccation may have reshaped the genomic structure of these organisms and to be involved in mechanism of horizontal gene transfer. However, the causative link between DNA damage and desiccation has never been proven in rotifers. Using Pulsed-Field Gel Electrophoresis (PFGE), the occurrence of DSB in dried A. vagaand the accumulation of these breaks with time spent in dehydrated state were reported. DSB were gradually repaired upon rehydration. Even when the genome was entirely
shattered into small DNA fragments by proton radiation, A. vaga
individuals were able to efficiently recover from desiccation and repair a large amount of DSBs. Curiously, small DNA fragments remained in sample rehydrated for up to one week 10posing the question of which kinds of DNA repair process is present in rehydrated A. vaga. In addition, no modification in the genomic architecture was observed in irradiated A. vaga
individuals or their F1 descendants despite massive DNA damage induced by proton radiations. Preliminary results suggest therefore that A. vaga may
contain an efficient DNA repair machinery, at least, in their germline (See chapter 4 and 5).
Extreme desiccation and radiation tolerance of A. vagaindividuals made them good candidates to study their resistance mechanisms. During this thesis, the genome was screened for genes putatively involved in desiccation resistance (i.e “the desiccome”). One of the critical components of the desicco
me is the disaccharide trehalose. In this thesis, we highlighted for the first time the presence of trehalose-6-phosphate synthases (TPS) in bdelloids rotifers. Interestingly, A. vagalikely acquired its trehalose biosynthesis and hydrolysis genes by horizontal gene transfers. A strong overexpression of their TPS genes was observed when bdelloids enter desiccation, suggesting a possible signaling role of trehalose-6-phosphate or
trehalose in this process (See chapter 6).
Finally, RNA sequencing was used to investigate the transcriptomic response of hydrated, desiccated and rehydrated A. vaga. In particular, we focused on genetic processes modulated by desiccation and rehydration in
A. vaga, with a particular focus on their DNA DSB repair. Using RNA-seq, the transcriptomic response of early desiccated and rehydrated A. vaga
individuals submitted to 2 weeks of desiccation was compared to hydrated individuals in order to shed some light in this process. Through mechanisms affected by desiccation, we noticed constitutive expression of multiple genes involved in oxidation-reduction processes and an over-expression of antioxidant genes was reported in desiccated and rehydrated A. vaga. Unexpec
tedly, genes related to DNA topological change followed by DNA
replication processes were found to be up-regulated in early desiccated bdelloids. Bdelloids have complete gene repertories to face multiple DNA damage induced by desiccation. Preliminary results noticed up-regulation of key genes involved in Non-Homologous End-Joining (NHEJ) in rehydrated bdelloids. The present study provides a complete list of candidate genes involved in desiccation resistance in bdelloid rotifers that could be used for future functional studies (See Chapte7).

Date of Award	21 Oct 2016
Original language	English
Awarding Institution	University of Namur
Supervisor	Karine Van Doninck (Supervisor), Etienne Danchin (Jury), Isa Schön (Jury), Xavier De Bolle (Jury) & Eric Depiereux (President)