Additional description and genome analyses of Caenorhabditis auriculariae representing the basal lineage of genus Caenorhabditis

Abstract

Caenorhabditis auriculariae, which was morphologically described in 1999, was re-isolated from a Platydema mushroom-associated beetle. Based on the re-isolated materials, some morphological characteristics were re-examined and ascribed to the species. In addition, to clarify phylogenetic relationships with other Caenorhabditis species and biological features of the nematode, the whole genome was sequenced and assembled into 109.5 Mb with 16,279 predicted protein-coding genes. Molecular phylogenetic analyses based on ribosomal RNA and 269 single-copy genes revealed the species is closely related to C. sonorae and C. monodelphis placing them at the most basal clade of the genus. C. auriculariae has morphological characteristics clearly differed from those two species and harbours a number of species-specific gene families, indicating its usefulness as a new outgroup species for Caenorhabditis evolutionary studies. A comparison of carbohydrate-active enzyme (CAZy) repertoires in genomes, which we found useful to speculate about the lifestyle of Caenorhabditis nematodes, suggested that C. auriculariae likely has a life-cycle with tight-association with insects.

Caenorhabditisnematodes colonize ephemeral resource patches in neotropical forests

“…Some Caenorhabditis species occupy a substrate niche as specialists (Dayi et al, 2021 ; Kanzaki et al, 2018 ; Li et al, 2014 ). The majority, however, have no obvious substrate preference.…”

Notch signaling in germ line stem cells controls reproductive aging in C. elegans

“…To determine if rapid reproductive aging is specific to hermaphrodite/male nematode species, we analyzed Caenorhabditis species that are female/male. Caenorhabditis is well suited for comparative studies, since the genus contains approximately 60 described species (Dayi et al, 2021; Stevens et al, 2019). At least three of these are hermaphrodite/male ( C. elegans, C. briggsae , and C. tropicalis ), while the remaining species exhibit the ancestral female/male reproductive strategy (e.g.…”

Chromosome-Level Reference Genomes for Two Strains of Caenorhabditis briggsae: An Improved Platform for Comparative Genomics

“…Although an improved reference genome for C. briggsae is an essential step in our efforts to understand genome evolution in Caenorhabditis , it is only a beginning. In recent years, an improved understanding of the natural ecology of Caenorhabditis nematodes has led to a dramatic increase in the discovery of new species with over 60 species now in laboratory culture, and multiple isolates are available for many species ( Kiontke et al 2011 ; Félix et al 2014 ; Ferrari et al 2017 ; Kanzaki et al 2018 ; Crombie et al 2019 ; Stevens et al 2019 ; Dayi et al 2021 ). Although some species have high-quality reference genomes ( C. elegans Sequencing Consortium 1998 ; Kanzaki et al 2018 ; Yin et al 2018 ; Teterina et al 2020 ; Noble et al 2021 ), the majority has been sequenced using short-reads only and therefore have highly fragmented genome assemblies that obscure the higher-order structure of the genome and complicate downstream analyses ( Stevens et al 2019 ).…”