Comparative genomics of 10 new Caenorhabditis species

Abstract

The nematode Caenorhabditis elegans has been central to the understanding of metazoan biology. However, C. elegans is but one species among millions and the significance of this important model organism will only be fully revealed if it is placed in a rich evolutionary context. Global sampling efforts have led to the discovery of over 50 putative species from the genus Caenorhabditis, many of which await formal species description. Here, we present species descriptions for 10 new Caenorhabditis species. We also present draft genome sequences for nine of these new species, along with a transcriptome assembly for one. We exploit these whole-genome data to reconstruct the Caenorhabditis phylogeny and use this phylogenetic tree to dissect the evolution of morphology in the genus. We reveal extensive variation in genome size and investigate the molecular processes that underlie this variation. We show unexpected complexity in the evolutionary history of key developmental pathway genes. These new species and the associated genomic resources will be essential in our attempts to understand the evolutionary origins of the C. elegans model.

Keywords: C. elegans; genomics; morphology; phylogenomics; species description.

Figure 1

Phylogenetic relationships of 32 Caenorhabditis species and D. coronatus. (A) Phylogeny inferred using Bayesian inference with the CAT‐GTR+Γ substitution model. Species described here are highlighted in bold, with previous species numbers in parentheses. Bayesian posterior probabilities are 1.0 unless noted as branch annotations. Scale is in substitutions per site. (B) Alternative hypotheses and support from each analysis approach. ML, Maximum likelihood inference using GTR+Γ substitution model; BI, Bayesian inference using the CAT‐GTR+Γ substitution model; ST, Supertree approach, using gene trees as input (substitution model selected automatically for each alignment).

Figure 2

Morphology of Caenorhabditis parvicauda sp. n. by scanning electron microscopy (SEM) and Nomarski optics (DIC). (A and B) Mouth of an adult male (A, SEM; B, DIC). (C) Cuticular lateral ridges of a dauer juvenile (SEM). (D) Cuticular lateral ridges of an adult male (SEM). (E) Female tail (DIC). (F) Male tail, ventro‐lateral view (SEM). (G) Genital opening with extruded spicules. (H) Male genital opening. (I) Male tail in ventral view (DIC). Anterior is to the left in (A, B, E–I). The animals are from strain JU2070. a, amphid; ad, anterior dorsal papilla; c, cloaca; cem, male cephalic sensillum (absent in females); ls, labial sensillum; pd, posterior dorsal papilla; pre/post‐cs, pre/post cloacal sensillum; v1, etc.: ventral papilla 1, etc.; sp, spicule. Scale bars: 1 μm, except in (E, F, and I): 5 μm. See also Figure S6.

Figure 3

Scanning electron microscopy of Caenorhabditis uteleia sp. n. (A) Mouth of an adult female. (B) Mouth of an adult male. (C and D) Male tail in ventral view. (C’ and D’) Higher magnification of the corresponding male genital openings. (E) Cuticular lateral ridges, adult male. (F) Male genital opening. The animals are from strain JU2469. Anterior is to the left. a, amphid; cem, male cephalic sensillum (absent in females); lf, lateral fold on either side of the hook; ls, labial sensillum; r1, etc., ray 1, etc.; ph, phasmid; sp, spicule; pre/post‐cs, pre/post cloacal sensillum; g, posterior end of the gubernaculum. Bars: 1 μm, except in (C and D): 5 μm.

Figure 4

Male hook shape in Elegans group species. (A–C) Ventral views of the male tail of Caenorhabditis zanzibari strain JU2161 (A), C. tribulationis strain JU2774 (B), and C. wallacei JU1873 (C), in Nomarski optics. The arrow points to the precloacal hook. Bar: 10 μm. (D–F) Scanning electron micrographs of the hooks and post‐cloacal sensilla (post‐cs) in C. sinica JU727 (D), C. zanzibari JU2161 (E), and C. wallacei JU1873 (F). “gub”: forked posterior end of gubernaculum. G,H: Drawings of hook shape. (G) Refers to the trilobed shape in C. sinica, C. tribulationis, and C. zanzibari sp. n, while (H) refers to the simpler shape in most other Elegans supergroup species such as C. wallacei, C. elegans, C. remanei, and C. sulstoni.

Figure 5

Ancestral state reconstruction of precloacal hook morphology and mating position. (A) Mating position. (B) Precloacal lip in the shape of a hook (with a pointed ventral tip). (C) Precloacal lip in the shape of a trilobed hook. Ancestral state reconstruction was performed by generating 1000 stochastic character maps of each morphological character on the phylogenetic tree in Figure 1A using the equal rates model of evolution. Pie charts on internal nodes represent posterior probabilities of ancestral states.

Figure 6

Genome size and gene structure variation in Caenorhabditis. (A) Genome size variation in the context of the Caenorhabditis phylogeny. Hermaphroditic species are highlighted. Phylogenetic tree is based on Figure 1A, with major clades highlighted. (B) Histogram of the log₂‐transformed ratio of intron span in 8954 genes in C. elegans compared to their orthologues in C. sulstoni. (C) Histogram of the log₂‐transformed ratio of intron count in 8954 genes in C. elegans compared to their orthologues in C. sulstoni.

Figure 7

Maximum likelihood gene tree of Notch‐like receptors in Caenorhabditis. (A) Gene tree of the orthogroup containing C. elegans proteins LIN‐12 (CELEG.R107.8) and GLP‐1 (CELEG.F02A9.6) inferred using maximum likelihood (JCCMut+Γ substitution model). Elegans and Japonica groups are highlighted in red and blue, respectively. Duplication events are denoted by orange circles. Branch lengths represent the number of substitutions per sites; scale is shown. Bootstrap values are displayed as branch annotations, “^*” = 100. (B) Inferred events: (1) Duplication of ancestral Notch‐like receptor gene; (2) Duplication of glp‐1 gene; (3) Loss of one of the two duplicated glp‐1 genes in the Elegans group.