Schmidtea mediterranea Chromosome Assembly (smed_chr_ref_v1)

Methods From Guo et. al., 2021

Chromosome sequencing

Chromosomes were collected from multiple animals of one clonal line, S2, maintained in the lab by amputation and regeneration. Chromosome spreads were prepared on nuclease-free Membrane Slides (Zeiss) according to a previously developed protocol, except that at the last step, the tissues were dissociated into single nuclei and dropped onto the slides without squashing with a coverslip (39). Single chromosomes were identified under a 40x lens and collected into caps of single PCR tubes by PALM MicroBeam laser microdissection (Zeiss). Collected chromosomes were spun down with a tabletop spinner in 4ul of PBS, and the DNA in the pellets was amplified with REPLI-g Single Cell kit (QIAGEN) for sequencing on the MiSeq or HiSeq 3000 sequencing system (Illumina).

Chromosome-scale genome assembly

A Hi-C sequencing library was prepared from multiple animals of the S2 strain using the enzyme DpnII, following the instructions of Phase Genomics Proximo Animal kit version 3.0 with few modifications. Sequenced reads were aligned to dd_Smes_g4.fasta (16) with bwa mem (version 0.7.17) (40). An assembly file was prepared from the SALSA (21) output FINAL.fasta with juicebox_scripts (Phase Genomics). The assembly and .hic files were loaded into Juicebox (23) for scaffold manipulation (i.e., split, merge, order, orient) and chromosome assembly. The modified assembly file (chromosome-scale) was converted to fasta (Smed_chr_ref_v1) with juicebox_assembly_converter.py.

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smed_chr_ref_v1 Genome Assembly FASTA