The improved genome of the nematode Parapristionchus giblindavisi provides insights into lineage-specific gene family evolution

Abstract

Nematodes such as Caenorhabditis elegans and Pristionchus pacificus are extremely successful model organisms for comparative biology. Several studies have shown that phenotypic novelty but also conserved processes are controlled by taxon-restricted genes. To trace back the evolution of such new or rapidly evolving genes, a robust phylogenomic framework is indispensable. Here, we present an improved version of the genome of Parapristionchus giblindavisi which is the only known member of the sister group of Pristionchus. Relative to the previous short read assembly, the new genome is based on long reads and displays higher levels of contiguity, completeness, and correctness. Specifically, the number of contigs dropped from over 7303 to 735 resulting in an N50 increase from 112 kb to 791 kb. We made use of the new genome to revisit the evolution of multiple gene families. This revealed Pristionchus-specific expansions of several environmentally responsive gene families and a Pristionchus-specific loss of the de novo purine biosynthesis pathway. Focusing on the evolution of sulfatases and sulfotransferases, which control the mouth form plasticity in P. pacificus, reveals differences in copy number and genomic configurations between the genera Pristionchus and Parapristionchus. Altogether, this demonstrates the utility of the P. giblindavisi genome to date and polarize lineage-specific patterns.

The genome assembly ofRhabditoides inermisfrom a complex microbial community reveals further evidence for parallel gene family expansions across multiple nematodes

“…The completeness of the R. inermis genome was estimated by BUSCO to be 88.8% (single-copy and duplicates) using the nematode ortholog data set (odb9) [38,39]. This value is comparable to recently generated nematode genome assemblies from cultures without large-scale microbial contamination [41,42]. Note that the expected BUSCO completeness value should be around 90%, but will also depend on evolutionary distance from the set of reference species in the ortholog set.…”

“…Previous phylogenetic studies suggested a potential sister taxon relationship between R. inermis and the family Diplogastridae [26,27]. To resolve the phylogenetic relationship between R. inermis and diplogastrid nematodes, we compiled a phylogenomic data set of annotated proteins and transcriptomes from 40 species [41,42,[51][52][53][54][55][56][57][58][59][60][61][62][63][64][65][66][67][68][69]. We employed a previously established phylogenomic pipeline for reconstructing a species tree from this type of data [70].…”

Starvation resistance in the nematodePristionchus pacificusrequires a conserved supplementary nuclear receptor

“…We searched the genomes of ten nematode species for orthologs of Ppa-NHR-1, Ppa-NHR-10, and Ppa-NHR-40, using BLASTP (e < 0.0001). The list of genomes included Brugia malayi (clade III -Spiruromorpha), Bursaphelenchus xylophilus (clade IV -Tylenchida), Panagrellus redivivus (clade IV -Tylenchida), Oscheius tipulae (clade V -Rhabditida), Caenorhabditis briggsae (clade V -Rhabditida), Caenorhabditis elegans (clade V -Rhabditida; wormbase.org WS289), Haemonchus contortus (clade V -Strongylida), Micoletzkya japonica (clade V -Diplogasterida), Parapristionchus giblindavisi (clade V -Diplogasterida), and Pristionchus pacificus (clade V -Diplogasterida) [97][98][99][100][101][102][103][104][105][106] (non-diplogastrids: WormBase ParaSite ver. WBPS18; diplogastrids: pristionchus.org).…”

Developmental small RNA transcriptomics reveals divergent evolution of the conserved microRNAmiR-100and thelet-7-complexin nematodes

“…The 24 basepair region between the genomic coordinates 2633305 and 2633328 on chromosome X of P. pacificus (Rödelsperger et al, 2017) was a perfect and unique match against our query sequence. Next, leveraging the availability of sequenced genomes of other species in the family Diplogastridae (Prabh et al, 2018;Röseler et al, 2022;Wighard et al, 2022;Yoshida et al, 2023), the 24-nucleotide read was queried against and gave perfect matches in eight of the 10 genomes. The two exceptions were Pristionchus fissidentatus, where the match was limited to the first 23 nucleotides, and Pristionchus mayeri, where no match was found.…”