PacBio whole-genome sequencing and draft assembly of Stentor coeruleus

Stentor coeruleus is a giant, regenerating unicellular ciliate. These cells reach lengths upwards of 1 mm in length, and the compartmentalized macronucleus extends along the anterior-posterior axis of the cell. The reference genome for this species (Slabodnick et al 2017) was sequenced using short-read Illumina sequencing. Here, we are sharing raw PacBio sequencing data as well as a draft genome assembly. These data will be used to update the Stentor coeruleus reference genome and aid in future studies.

Methods
Stentor husbandry

Stentor coeruleus cultures are kept in glass Pyrex tupperware dishes in approximately 200 mL of Pasteurized Spring Water (Carolina Biological), hereafter referred to as ciliate water. Cells are fed a lentil-sized amount of solid wild-type Chlamydomonas reinhardtii (Chlamy) two or three times a week as needed. 

DNA extraction 

Several hundred Stentor coeruleus were hand-picked from the culture with a micropipette and transferred to 3 different tissue culture plate wells containing ciliate water to rid the cells of algae and debris. Cells were starved overnight and washed again to ensure that no remaining Chlamy will contaminate the extraction. Cells were transferred into an eppendorf tube, allowed to settle, and as much ciliate water as possible was removed. DNA was phenol-chloroform extracted according to a PacBio protocol: https://www.pacb.com/wp-content/uploads/2015/09/SharedProtocol-Extracting-DNA-usinig-Phenol-Chloroform.pdf

Sequencing

Genewiz (formerly) Azenta prepared libraries for two runs on a PacBio Sequel II. 

Assembly

Flye command: flye combined.fastq --out-dir 20240503_flye_out --genome-size 80m --threads 16