Comparative HaplotypOmics of Parthenogenetic Plectus nEmatodes

Project Information

CHOPPE

Grant agreement ID: 101110569

DOI

10.3030/101110569

Project closed

EC signature date 17 March 2023

Start date 1 May 2023

End date 30 April 2025

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 173 847,36

Coordinated by

UNIVERSITAT ZU KOLN
Germany

Periodic Reporting for period 1 - CHOPPE (Comparative HaplotypOmics of Parthenogenetic Plectus nEmatodes)

Reporting period: 2023-05-01 to 2025-04-30

Summary of the context and overall objectives of the project

Plectus is a genus of nematodes known for its exclusive parthenogenesis (asexual reproduction). The general predominance of sexual reproduction in metazoans, despite its significant energetic costs compared to asexual modes, represents a long-standing question in evolutionary biology. While parthenogenesis offers advantages such as rapid replication and independence from mate finding, it is predicted to lead to the accumulation of deleterious mutations and slower adaptation due to the lack of meiotic recombination. However, the frequent occurrence of parthenogenetic taxa in extreme environments suggests adaptive benefits. To further adapt to arduous habitats, Plectus has a remarkable ability to enter cryptobiosis (a state of suspended metabolism also observed in tardigrades and rotifers) to survive desiccation or freezing. This phenomenon is expected to damage the genome sequence and to be only sustainable along accrued DNA repair machineries.
The lack of high-quality genomic resources for Plectus, with only few fragmented genome assemblies previously published, has severely hindered in-depth analysis of how parthenogenesis and cryptobiosis impact their genome structure and evolution in the context of parthenogenesis and cryptobiosis.
CHOPPE first aimed to develop robust methodologies for sequencing and assembling non-model nematode genomes, like Plectus, into collapsed or phased, chromosome-level or highly contiguous sequences. This included utilizing advanced long-read sequencing technologies (PacBio HiFi, Nanopore) and Hi-C reads. Following the application of these methods to several Plectus species, and the closely related sexual species Anaplectus granulosus, the project sought to understand the adaptation and evolution of Plectus, using comparative genomic approaches addressing gene content, repetitive content, and chromosome structure. We additionally aimed to investigate the origin of asexuality in Plectus and test reversal to asexuality. The project also addressed chromosomal adaptations in cryptobiotic nematodes by analyzing chromosome structure conservation in Plectus and Panagrolaimus nematodes, a phylogenetically distant but phenotypically similar cryptobiotic genus.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Through the course of the project, we developed and applied cutting-edge genomic methodologies and gained knowledge into genomic adaptations along parthenogenesis and cryptobiosis in nematodes. Protocols for high-molecular-weight DNA extraction, sequencing and genome assembly were optimized to yield high-quality collapsed and phased assemblies of non-model nematode species. Heterogeneous sequencing datasets were employed to generate reference assemblies for Plectus sambesii and new lab cultures of Plectus species. Benchmarking of multiple high-accuracy long-read assemblers highlighted the most efficient strategies for haplotype reconstruction, which can be applied to other non-model animal species. Reference genome assemblies, repeat and gene annotations of Plectus species were compared at species and haplotype-level, and macrosyntenic analyses were conducted to investigate the impact of cryptobiosis on chromosome structure. To further study the obligatory nature of parthenogenesis in Plectus, male phenotypes were induced. The results obtained for the genus Plectus were then put in perspective with a similar comparison conducted for the cryptobiotic and partially parthenogenetic genus Panagrolaimus.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

By leveraging recent development in sequencing technologies, CHOPPE made significant strides in understanding the genomic adaptations of Plectus nematodes, in parallel with the genus Panagrolaimus, to decipher the impact of parthenogenesis and cryptobiosis. Versatile methodologies were developed and implemented for non-model nematode species to leverage different long-read sequencing technologies for collapsed and haplotype assemblies. The project further explored the advantages and limitations of multiple sequencing strategies, experimenting with large inputs and single individuals. Several reference genome assemblies and haplotype assemblies of Plectus and Panagrolaimus species were generated and made available on European Nucleotide Archive to serve as a basis for future projects focusing on these genera. Comparative genomics and haplotypomics of Plectus and Anaplectus species brought insight into Plectus’ transition to asexuality, as low and high levels of heterozygosity do not support the hypothesis of a hybridization event at the origin of their parthenogenetic reproductive mode. In addition, Plectus genomes displayed variable genome sizes and repetitive content, suggesting distinct adaptation strategies. Finally, we conducted an unprecedented study of the genomic impact of cryptobiosis in animals through a combined analysis of Plectus and Panagrolaimus, which revealed contrasting patterns between the two genera. While Plectus has mostly conserved chromosome structures, Panagrolaimus species showed remarkable inter- and intrachromosomal rearrangements. These divergent observations hint at distinct DNA repair mechanisms underlying adaptation to extreme environments and open new hypotheses on chromosome evolution in novel habitats.