Schmidtea mediterranea (Freshwater planarian, S2F18) Assembly and Gene Annotation

About Schmidtea mediterranea

The genus Schmidtea comprises four species of freshwater planarians, predominantly found in Europe, with some populations also present in north Africa, Asia and introduced in regions of America [2, 11]. Among these, Schmidtea mediterranea is the most extensively studied species and serves as a well-established model organism for research in regeneration and stem cell biology [13, 7].

The life cycle of S. mediterranea features two distinct reproductive strategies observed in geographically separated wild populations [10]:

• Sexual reproduction: Diploid (2n = 8) sexually reproducing populations are found in the eastern part of the range of the species, including Corsica, Sardinia, Sicily, and one locality in Tunisia. Notably, a triploid (3n = 12) egg-laying population has been identified in Sardinia [4].

• Asexual reproduction by fission: Predominantly diploid (2n = 8) fissiparous forms are located in two localities in Catalunya and the Balearic Islands. These individuals exhibit a heteromorphic translocation between the first and third chromosomes, visible in metaphase spreads, with only one chromosome of each homologous pair affected [12, 1]. A triploid (3n = 12) asexual population has also been reported in Menorca [12]. Today, the presence of S. mediterranea in continental Europe is limited to a few artificial ponds at the "Viver dels Tres Pins" in the mountain of Montjuïc, Barcelona [14]. The diploid laboratory strain C4 originates from a nearby spring in Montjuïc.

This is an assembly of the sexual laboratory strain S2F2 of S. mediterranea originally collected in Sardinia that was extensively inbred over 16 generations to a total of 18 inbreeding generations total, including 2 rounds of regeneration-induced self-fertilization of the same individual.

For the alternative haplotype see schMedS3h1.

Picture credit (Creative Commons BY 4.0): Miquel Vila-Farré, Dept. of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences

Taxonomy ID 79327

Assembly

The assembly presented here has been imported from INSDC and is linked to the assembly accession [GCA_045838255.1].

PacBio Circular consensus sequencing reads were called using pbccs (v6.0.0) and reads with quality > 0.99 (Q20) were taken forward as “HiFi” reads. 44x PacBio HiFi reads (SRA:SRR27325393) and 1 billion Hi-C (SRA: SRR27325345, SRR27325347) reads were used to assemble phased contigs with hifiasm (v0.7). Hi-C reads with mapping quality >=10 were further utilized to scaffold the contigs from each haplotype by SALSA (v2) following the hic- pipeline (https://github.com/esrice/hic-pipeline). Four chromosome-level scaffolds were obtained in both haplotypes after scaffolding, consistent with the karyology of the species. The remaining scaffolding errors were manually curated based on the interaction frequency indicated by the intensity of Hi-C signals.

The assembly was produced by "Max Planck Institute for Multidisciplinary Sciences" and reported in [8].

The total length of the assembly is 819865861 bp contained within 432 scaffolds. The scaffold N50 value is 268961546, the scaffold L50 value is 2. The GC% content of the assembly is 29.5%.

Annotation

Genomic annotation was provided by "Max Planck Institute for Multidisciplinary Sciences".

The genome was annotated using a hybrid genome-guided transcriptome approach. Extensive RNA-seq data both from the sexual laboratory strain (S2F18, internal ID: GOE00500) and the asexual laboratory strain (CIW4, internal ID: GOE00071) were used. Total RNA was extracted from snap-frozen planarian tissue using the protocol described in [6] and [8].

RNA-seq data for the sexual strain included: - Nanopore direct RNA-seq from pooled whole animals sampled at various feeding and regeneration stages (SRR27325410) - Nanopore cDNA RNA-seq from two regeneration series (SRR27325336, SRR27325337), whole animals (SRR27325339), and freshly cut heads and tails (SRR27325338) - Illumina RNA-seq covering various life stages and regeneration stages (SRX2700685; [6])

For the asexual strain this included: - Nanopore direct RNA-seq of heads & tails (SRR27325406) - Nanopore cDNA RNA-seq of heads & tails (SRR27325407, SRR27325409), a regeneration series (SRR27325408), whole animals (SRR27325405), and FACS-sorted stem cells (SRR27325404) - Illumina RNA-seq of wild-type whole animals (SRR27325340, SRR27325341) - 3P-seq (SRP070102; [9])

After read quality trimming, deduplication, filtering, and mapping (using HISAT2 and minimap2 for short and long reads, respectively), a draft transcriptome was generated using Stringtie2 then it was further refined using FLAIR and a collection of custom scripts to filter high- confidence isoforms. For details of the procedure and a step-by-step guide to the genome annotation analysis, see the Supporting Information of [8].

Small RNA features, protein features, BLAST hits and cross-references have been computed by metazoa.

References

1. Baguñà J, Saló E, Auladell C. 1989. Regeneration and pattern formation in planarians: III. Evidence that neoblasts are totipotent stem cells and the source of blastema cells. Development 1 September 1989; 107 (1): 77–86. doi: https://doi.org/10.1242/dev.107.1.77.

2. Ball IR. 1969. Dugesia lugubris (Tricladida: Paludicola) a European immigrant into North American fresh waters. Journal of the Fisheries Research Board of Canada 26, 221–228.

3. Benazzi M, Bagunà J, Ballester R, Puccinelli I, Papa RD. 1975. Further contribution 
 to the taxonomy of the Dugesia lugubris-polychroa group with description of Dugesia mediterranea n. sp. (Tricladida, Paludicola). Bolletino di Zoologia 1975, 42: 81-89.

4. Casu S, Pala M, Vacca RA. 1982. Distribuzione geografica in Sardegna di planarie d’acqua dolce appartenenti alla specie “Dugesia (S.) polychroa“ e “Dugesia (S.) mediterranea“. Bollettino della Società Sarda di Scienze Naturali 21, 177-184.

5. Guo, L., S. Zhang, B. Rubinstein, E. Ross, and A. S. Alvarado. 2016. Widespread maintenance of genome heterozygosity in Schmidtea mediterranea. Nature Ecology & Evolution 1:1–10.

6. Grohme M. A., S. Schloissnig, A. Rozanski, M. Pippel, G. R. Young, S. Winkler, H. Brandl, I. Henry, A. Dahl, S. Powell, M. Hiller, E. Myers, and J. C. Rink. 2018. The genome of Schmidtea mediterranea and the evolution of core cellular mechanisms. Nature 554:56–61.

7. Ivanković M, Haneckova R, Thommen A, Grohme MA, Vila-Farré M, Werner S, Rink JC. 2019. Model systems for regeneration: planarians. Development 146(17):dev167684.

8. Ivanković M., J. N. Brand, L. Pandolfini, T. Brown, M. Pippel, A. Rozanski, T. Schubert, M. A. Grohme, S. Winkler, L. Robledillo, M. Zhang, A. Codino, S. Gustincich, M. Vila-Farré, S. Zhang, A. Papantonis, A. Marques, and J. C. Rink.

9. A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence. Nat Commun 15:8215.

10. Lakshmanan, V., D. Bansal, J. Kulkarni, D. Poduval, S. Krishna, V. Sasidharan, P. Anand, A. Seshasayee, and D. Palakodeti. 2016. Genome-Wide Analysis of Polyadenylation Events in Schmidtea mediterranea. G3 6:3035–3048.

11. Lázaro, E.M., Harrath, A.H., Stocchino, G.A. et al. 2011. Schmidtea mediterranea phylogeography: an old species surviving on a few Mediterranean islands? BMC Evol Biol 11, 274.

12. Leria, L., et al. 2018. Diversification and biogeographic history of the Western Palearctic freshwater flatworm genus Schmidtea (Tricladida: Dugesiidae), with a redescription of Schmidtea nova. Journal of Zoological Systematics and Evolutionary Research 56(3): 335-351.

13. Ribas M. 1990. Cariologia, sistemàtica i biogeografia de les planàries d'aigües dolces al Països Catalans. Barcelona. PhD Thesis, University of Barcelona 1990.

14. Reddien, P. W. 2018. The cellular and molecular basis for planarian regeneration. Cell 175(2): 327-345.

15. Vila-Farré M, Sluys R, Almagro Í, Handberg-Thorsager M, Romero R. 2011. Freshwater planarians (Platyhelminthes, Tricladida) from the Iberian Peninsula and Greece: diversity and notes on ecology. Zootaxa 2779, 1-38.