The compact genome of Caenorhabditis niphades n. sp., isolated from a wood-boring weevil, Niphades variegatus

Background The first metazoan genome sequenced, that of Caenorhabditis elegans, has motivated animal genome evolution studies. To date > 50 species from the genus Caenorhabditis have been sequenced, allowing research on genome variation. Results In the present study, we describe a new gonochoristic species, Caenorhabditis niphades n. sp., previously referred as C. sp. 36, isolated from adult weevils (Niphades variegatus), with whom they appear to be tightly associated during its life cycle. Along with a species description, we sequenced the genome of C. niphades n. sp. and produced a chromosome-level assembly. A genome comparison highlighted that C. niphades n. sp. has the smallest genome (59 Mbp) so far sequenced in the Elegans supergroup, despite being closely related to a species with an exceptionally large genome, C. japonica. Conclusions The compact genome of C. niphades n. sp. can serve as a key resource for comparative evolutionary studies of genome and gene number expansions in Caenorhabditis species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-09011-8.

2) The gonad length includes reflex part of testis and vas deferens.
3) Curved length from vulval opening to the tip of ovary, i.e., including uterus, oviduct, spermathecal and ovary.
4) Ratio of anus-phasmid distance to anal body diam. 5) Relative position of phasmid to total tail length in %. Figure S1. Phylogenetic relationships of C. niphades n. sp. and the other 26 Caenorhabditis species inferred by near-full-length 18S and D2/D3 region of 28S ribosomal RNA genes.
Nucleotide sequences were aligned before concatenation, and maximum-likelihood trees were generated with RAxML v7.2.8 using the best-fitting empirical model with 1,000 bootstrap resampling replicates with the support percentage shown on the nodes. The scale bar shows nucleotide substitutions per site.

Etymology
The species epithet is derived from the carrier insect, Niphades variegatus from that the nematode was isolated.

Materials examined
Holotype male, four paratype males, and five paratype females were deposited in the USDA

Type and other localities
The type specimens of C. niphades n. sp. were collected from the cultured materials of

Diagnosis and relationship
Based upon the arrangement of bursal rays and bursal velum shape, C. niphades n. sp.
However, C. niphades n. sp. has relatively wide stoma, i.e., width-length ratios are ca. 4.2 and 3.8 for males and females, respectively, and its composition, i.e., the ratio of chailo, gymno and stegostom is 1 : 1 : 2, may be characteristic to the species. Practically, the new species can be characterized only by its molecular phylogenetic status, i.e., C. niphades n.
sp. is basal of the Elegans supergroup, and can be clearly distinguished from all other sequenced species by its phylogenetic status.  (Tanaka et al., 2014), and these dauers mask the C. niphades n. sp. dauers during the dissection. More careful dissection survey is necessary to figure out the carrier utilization of C. niphades n. sp.

Remarks on typological characters
In addition to the common characters of Elegans  (Kiontke et al., 2011;Stevens et al., 2019). Therefore, although the structure could be an adaptation to their habitat and feeding preferences, usefulness for the animals, i.e., functional advantage in their habitat, is not clear at current status.