The nematode family Camacolaimidae from the order Plectida is a relatively small group of marine nematodes (Holovachov, 2014) long thought to be free-living selective deposit feeders and epistrate feeders (Wieser, 1953). Recent studies, however, revealed that some members of this clade are intracellular parasites of foraminiferans (Hope and Tchesunov, 1999; Holovachov, 2015; Miljutin and Miljutina, 2016; Tchesunov et al., 2000) and internal parasites of polychaetes (Tchesunov, 2009), including the recently described
Within the order Plectida itself, the symbiotic lifestyle appears in several other lineages in addition to Camacolaimidae. These include endosymbionts of annelids from the family Ochridiidae, parasites of annelids from the family Creagrocercidae (Holovachov, 2014) and parasites of marine invertebrates from the family Benthimermithidae (Leduc and Zhao, 2019). At the same time, Plectida are a sister clade to Rhabditida (Secernentea in older literature), which includes the majority of currently known nematode diversity, and the majority of animal and plant parasitic species, as well as model species (Smythe et al., 2019). As such, plectids in general, and camacolaimids in particular represent a potentially interesting satellite model for the study of the origin of animal parasitism in the aquatic environment.
Sediment samples were collected near Koster islands with a bottom dredge and processed in the lab. Nematodes were extracted from the Amphioxus sand using a decanting and sieving method (Higgins and Thiel, 1988). Post-parasitic juveniles were fixed immediately in RNAlater solution and stored at −20°C. Total RNA was extracted from a single juvenile using the Ambion RNAqueous Micro Kit following the manufacturer’s protocol. Subsequent library preparation and cDNA synthesis was performed using the Takara Bio SMART-Seq HT Kit following manufacturer’s instructions. Resulting double-stranded cDNA was purified using the AMPure XP for PCR purification kit. Final library preparation and transcriptome sequencing were performed at Macrogen Europe B.V (Amsterdam, the Netherlands) using the Illumina Nextera DNA XT library preparation protocol and an Illumina HiSeq X sequencing technology (150PE). Raw reads were first filtered using fastp (Chen et al., 2018) with default settings (Q-score ≥ 15), and then assembled de novo using Trinity v2.9.1 (Grabherr et al., 2011) installation on the Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX,
Assembled transcripts were filtered using Transrate (Smith-Unna et al., 2016) with default settings. The process inspected contig sequences and mapped filtered reads to the contigs and inspected the alignments. The goal was to remove chimeras, and poorly supported contigs from the assembly. Retained contigs (
The final assembly consists of 19,180 protein-coding sequences (including isoforms) with the following BUSCO scores for Nematoda: 65.38% complete, 9.06% partial, and 25.56% missing (out of 982 reference genes), and for Metazoa: 79.45% complete, 3.17% partial and 17.38% missing (out of 978 reference genes).