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ZoologyJournal of Helminthology
Peer-reviewed journal article

Morphogenomic description of Cranifera cranifera (Chitwood, 1932) Kloss, 1960 from captive Blaptica dubia Serville, 1838 cockroach

Jans Morffe RodrígueziD, Nadège GuiglielmoniiD, Nadim WasseyiD, Karim GueddachiD, Anja Schuster, Kerstin BeckeriD, Jens BastiD, Oleksandr V. HolovachoviD

Abstract

Nematodes of the superfamily Thelastomatoidea are found in the digestive system of various arthropods, feeding on their host microbiome. They are sometimes considered to be ecologically intermediate forms between free-living rhabditids and parasitic Spirurina, while phylogenetically they are nested within the latter. In addition to new morphological data on the male morphology, this manuscript presents the first nuclear genome assembly of a thelastomatid species, Cranifera cranifera, using long-read sequencing approach, making a total of three nuclear genomes available for superfamilyThelastomatoidea. The C. cranifera nuclear genome assembly presented here is 246 Mb long, consists of 7563 contigs, has an N50 of 43 kb and includes 94% of the BUSCO nematoda_odb12 genes. The mitochondrial genome is 24646 bases long, includes a complete set of protein coding, rRNA and tRNA genes, and a repetitive region 9731 bases long, which includes multiple copies of tRNA-Asn(gtt) and tRNA-Lys(ttt). The nuclear assembly also contained two sequence variants of the 28S rRNA and two of the 18S rRNA genes, highlighting the presence of intragenomic variation within rRNA operon. The newly generated assemblies (nuclear and organelle) will add to a growing body of genomic resources for underrepresented and understudied animal parasitic nematodes from the Clade 3, enabling comprehensive studies in their phylogeny and trait evolution in the future.

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Claude Opus 5.5 · xhigh effort · 8 Nov 2026 · from the full text of version 2 (10 Oct 2026) · CC BY 4.0

Third nuclear genome for arthropod pinworms (Thelastomatoidea): a PacBio long-read Cranifera cranifera assembly (242 Mb, N50 43 kb, 90.5-94% BUSCO) plus a 24644-base mitogenome and male redescription.

Arthropod pinworms (Thelastomatoidea) sit phylogenetically within parasitic Clade 3 nematodes, yet only two other nuclear genomes existed for the superfamily, both from Illumina short reads with no public assembly or annotation files. This work adds long-read nuclear and mitochondrial assemblies for C. cranifera and illustrates the male anterior end and oesophagus for the first time.

Key results

  1. ShownA long-read draft nuclear genome of C. cranifera, the third for Thelastomatoidea. The two earlier ones used Illumina short reads and have no public assembly or annotation files.

    Final decontaminated assembly: 242 Mb, 7562 contigs, N50 43 kb, longest contig 1.10 Mb. BUSCO v.6.0.0 recovered 90.5-94% of expected genes depending on dataset (nematoda_odb12, 596 genes; nematoda_odb12.1, 1477; chromadorea_odb12, 1126; chromadorea_odb12.1, 2034). The other superfamily genomes (Thelastoma shijiazhuangense, Travassosinema thyropygi) are Illumina-based. · Nuclear genome assembly; Nuclear genome assembly; Discussion

  2. ShownA complete mitogenome with 12 protein-coding genes, two rRNAs and, after manual curation, the standard 22 tRNAs. It contains a repeat-rich region whose duplicated blocks carry extra tRNA-Lys and tRNA-Asn copies.

    24644 bases; atp8 absent. Raw Mitos2/Aragorn output listed eight tRNA-Lys(ttt) and four tRNA-Asn(gtt) copies and truncated rRNAs (rrnS 386 nt, rrnL 666 nt). Curation kept one copy per duplicated tRNA and set rrnS to 677 nt and rrnL to 961 nt. Repeat region spans positions 12653-22383; largest repeat 2975-2977 bases, others 1318 and 688 bases. Gene boundaries match 13 published reference mitogenomes. · Mitochondrial genome assembly; Mitochondrial genome assembly

  3. SuggestedThe assembly holds two distinct 28S and two distinct 18S rDNA variants. One variant of each matches published C. cranifera sequences, and the authors interpret the divergent copies as intragenomic rRNA heterogeneity rather than cryptic species.

    28S D2-D3 (753 bp alignment): QB046966 differs from QB046965 at 8 positions (0.67%), seven of them within one 30-base segment and two of those indels. QB046965 is identical to Cuban ON616698; QB046966 is sister to all other C. cranifera. 18S (1508 bp): QB042151 differs from QB042152 at 24 positions (1.62%); QB042152 is identical to ON616698. · Intragenomic variation of rRNA; Discussion; Intragenomic variation of rRNA

  4. ShownFirst illustrations of the male anterior end and oesophagus. The oesophagus is reinterpreted: of the two corpus subregions described by earlier authors, the anterior one is the true corpus and the posterior one is a long isthmus (earlier authors called the isthmus short).

    19 females and 5 males examined by light microscopy; males also by scanning electron microscopy. Versus Chitwood (1932) and Leibersperger (1960), males are longer (0.873–0.956 mm vs 0.790 mm) and wider (64–76 μm vs 40 μm), with a longer tail (38–44 vs 35 μm). Versus Leibersperger: a = 11.9–14.3 vs 19.8, b = 7.7–8.5 vs 6.9. Eight copulatory papillae (two pre-cloacal, six post-cloacal). · Additional data on male morphology; Discussion; Morphological and morphometric studies

  5. SuggestedMapping reads to competing mitogenome assemblies supports the long repeat region as genuine. The authors argue that short-read mitogenomes may collapse such duplications unless coverage is checked.

    Besides the 24644-base assembly, alternatives of 17888, 22497 and 31115 bases were recovered. Raw-read mapping showed collapse in the 17888 and 22497 base versions and a coverage drop in the 31115 base one. The authors cannot fully exclude an artifact, and the short-read point is not tested here. · Discussion; Mitochondrial genome assembly

Methods, data and reproducibility

Pooled nematodes from captive Blaptica dubia were sequenced (ultra-low-input PacBio Revio library); two Flye assemblies were decontaminated (BlobToolKit), merged (quickmerge) and haplotig-purged (redundans), and the mitogenome was assembled with Canu from reads hit by blastn/Diamond searches. Males were redescribed by light and scanning electron microscopy, and rRNA variants placed in maximum-likelihood trees.

  • C. cranifera from a captive Blaptica dubia colony; slide-mounted vouchers for morphometrics and light microscopy (males also examined by SEM) · Cranifera cranifera (nematode) from Blaptica dubia (cockroach) · n = 19 females, 5 males · SMNH 231508–231518
  • PacBio Revio reads from an ultra-low-input library of pooled worms · Cranifera cranifera · n = several specimens, pooled · PRJEB115782 (ENA); BioSample SAMEA122978875; reads ERR17501394
  • Curated nuclear genome assembly · Cranifera cranifera · ERZ30225045; GCA_986284995
  • Mitochondrial genome assembly · Cranifera cranifera · QB100924 (GenBank)
  • 28S D2-D3 and 18S rDNA variants mined from the nuclear assembly · Cranifera cranifera · n = two 28S and two 18S variants · QB046965, QB046966 (28S); QB042151, QB042152 (18S)
  • Published GenBank 28S/18S sequences of C. cranifera (e.g. from B. discoidalis, Cuba; A. tessellata, Costa Rica) and other Thelastomatidae · nematodes (Thelastomatidae) · e.g. ON616698; ON616693
  • Nematode mitochondrial references: Nematode-Mitochondrial-Database genes, proteins from GenBank mitogenomes, and reference mitogenomes for annotation checks · nematodes (multiple species) · n = 52 species; 13 reference mitogenomes · e.g. KY399989.1 (Hammerschmidtiella sp., MitoHifi reference)
Methods & tools
PacBio Revio, Flye, Hifiasm, BUSCO v.6.0.0, BlobToolKit, quickmerge, redundans, MitoHifi, Canu, pilon, Mitos2, MEGA12
Data & accessions
https://www.ebi.ac.uk/ena/browser/view/GCA_986284995https://github.com/WormsEtAl/Nematode-Mitochondrial-Database
Reagents & environment
Most steps were run on the usegalaxy.eu Galaxy server. Versions are given only for BUSCO v.6.0.0, barrnap (Galaxy version 1.2.2, standalone 0.9) and MEGA12.
Reproducibility gaps
No code repository. The read-depth normalisation script (written with Claude AI) is not shared, and repeat identification and annotation curation relied partly on Claude AI and manual checks. Most tool versions and Galaxy parameters are not listed.
Limitations (6)
  • No protein-coding gene annotation, because no RNA-seq data were generated. · stated by the authors
  • The assembly is highly fragmented (7562 contigs, N50 43 kb) and keeps many duplications after purging. The authors attribute this to population-level heterozygosity in the pooled sample, which purge_dups could not handle. · stated by the authors
  • The authors cannot fully rule out that the mitochondrial repeat region is an assembly artifact, since alternative assemblies of 17888, 22497 and 31115 bases were also produced. · stated by the authors
  • Morphometric differences from earlier records may reflect either intraspecific variation between distant populations or measurement error. · stated by the authors
  • DNA came from several pooled worms, so the paired 28S and 18S variants could come from different individuals rather than from within one genome. No single-worm or PCR check separates these. · noted in this summary
  • Headline numbers differ between abstract and results: 246 Mb and 7563 contigs vs 242 Mb and 7562 contigs; mitogenome 24646 vs 24644 bases; repeat region 9731 vs 9729 bases. · noted in this summary

Who should read:Read this if you study Clade 3 nematode or pinworm evolution and need a long-read reference genome, or you are assembling repeat-rich nematode mitogenomes or interpreting divergent rDNA barcodes.

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