Additional file 1 of Chromosome-level genome assembly of the sacoglossan sea slug Elysia timida (Risso, 1818)
Creators: name: Männer, Lisa
name: Schell, Tilman
name: Spies, Julia
name: Galià-Camps, Carles
name: Baranski, Damian
name: Ben Hamadou, Alexander
name: Gerheim, Charlotte
name: Neveling, Kornelia
name: Helfrich, Eric J. N.
name: Greve, Carola
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Supplementary Material 1: Supplemental Figure S1. Climate chamber in which the E. timida slugs were kept in artificial sea water in plastic cups as aquariums. The green tubes provided the air supply. Supplemental Table S1.Databases and tools which were used while operating InterProScan version 5.64-96.0 [101]. Supplemental Table S2.Table of PKS and fatty acid synthase (FAS) sequences from Torres et al. (2020) [34] including the animal species they were received from and the accession number. Supplemental Figure S2. Genome size estimation of E. timida using flow cytometry. The histogram shows the relative propidium iodide fluorescence intensity obtained after simultaneous analysis of E. timida 2C (in green) and the house cricket A. domesticus 2C as an internal standard reference (in red). The PI fluorescent dyes were excited with a solid-state laser emitting at 488 nm. The y-axis gives the counts of propidium iodide (PI) stained nuclei. The x-axis displays the relative red PI fluorescence signal. To obtain the mean relative red PI fluorescence signals, the peaks were enclosed by line segments. The percentages in brackets are the portions of all events in the histogram enclosed by the respective line segments. Supplemental Table S3. Genome size estimates from two individuals of E. timida. The measured individual is given in brackets. Chopping buffer was prepared as described by Galbraith et al. (1983) [152]. Propidium iodide was used as a fluorescent dye. We used the house cricket A. domesticus as standard reference (genome size: 2000 Mb). Supplemental Figure S3. K-mer profile and estimates based on HiFi reads. Supplemental Table S4. Sacoglossan heterozygosity values. The heterozygosity values from all species except for E. timida, were inferred by Theisen &amp; Jensen (1991) [128]. Supplemental Tables S5. PacBio ultra-low library preparation based on PCR amplification with KOD Xtreme™ Hot Start DNA Polymerase (Merck). Supplemental Table S6. Sequencing output and subread mean length of the PacBio low- and ultra-input libraries. Supplemental Figure S4. HiFi read length distribution and statistics. Standard PacBio ultra-low input libraries are listed as SMRT1 and SMRT2. PacBio ultra-low libraries amplified with KOD polymerase are shown as SMRT3 (Sequel IIe) and SMRT4 (Revio). N50 values are presented in bp. Supplemental Table S7. FCS-GX contamination summary. Supplemental Table S8. FCS-GX action summary. Supplemental Figure S5. Blobplot of the assembly after polishing and purging. At this stage of the assembly process, contamination filtering with FCS was already conducted. Supplemental Table S9. Blobtools taxonomic assignment. The table shows all contigs classified as Chlorophyta by “bestsumorder”, which were filtered out among others. Sequences marked with asterisk were categorized as “HICOV” by purge_dups. Supplemental Figure S6. Blobplot of the final genome assembly. Supplemental Figure S7: Maximum likelihood phylogenetic tree of FAS, PKS1 and PKS2 transcripts from E. timida, E. chlorotica, E. diomedea and P. ocellatus. For the alignment the transcriptomic data from the sequences listed in Table 5 and Supplemental Table S2 were used. The branches are labelled with their length and scaled according to the number of substitutions per site. The percentage of trees in which the associated data clustered together is shown next to the branches. The transcript of EtPKS1 was manually constructed based on sequence homology to EcPKS1, EdPKS1 and PoPKS1 as described previously. The transcripts from E. timida are labelled with an asterisk. Supplemental Table S10. Number of blast hits with taxid of Acetabularia acetabulum or Ulva compressa against contigs of the polished E. timida genome assembly. Supplemental Table S11. Number of blast hits for targets with a taxid of Acetabularia acetabulum or Ulva compressa. All target sequences originate from a chloroplast. Supplemental Table S12. Section of the agp file from scaffolding including the 5 Chlorophyta sequences showing all resulting scaffolds containing these Chlorophyta sequences. Except for splitting one of the sequences, none was linked to other nuclear sequences of the E. timida genome assembly. Supplemental Figure S8. The genes encoding EtFAS, EtPKS1 and EtPKS2 are annotated in the genome of E. timida. The exons are labelled in black on the excerpt of the genomic sequence. The arrows present the transcript of the a) EtFAS, b) EtPKS1 and c) EtPKS2. The domains of the enzymes are presented in bubbles below the arrow. The gene encoding EtPKS1 was annotated manually based on sequence homology with the EcPKS1. The label with an x0 indicates an inactive domain. Supplemental Figure S9. Isotopic patterns of the putative polypropionates produced by E. timida and identified by HPLC-ESI-HRMS analysis. Supplemental Figure S10. HPLC-MS data of E. timida extracts. Base peak chromatogram (BPC) and extracted ion chromatograms (EICs) of polypropionates shown in fig. 4. The BPC shows all detected ions present in the crude extract and the EICs show the peaks corresponding to putative polypropionates. Supplemental Table S13. Result of the polypropionate blast search in the annotations of E. timida,E. chlorotica, E. diomedea and P. ocellatus. Both unfiltered (F-) as well as filtered (F+) blast hits are shown. Supplemental Figure S11. Blobplot of the assembly after removing sequences identified as contamination and before HiC scaffolding.