[
International Worm Meeting,
2015]
The sequencing of the genome of Caenorhabditis elegans remains one of the milestones of modern biology, and this genome sequence is the essential backdrop to a vast body of work on this key model organism. "Nothing in biology makes sense except in the light of evolution" (Dobzhansky) and thus it is clear that complete understanding of C. elegans will only be achieved when it is placed in an evolutionary context. While several additional Caenorhabditis genomes have been published or made available, a recent surge in the number of available species in culture makes the determination of the genomes of all the species in the genus a timely and rewarding project.We have initiated the Caenorhabditis Genomes Project. From material supplied by collaborators we have so far generated raw Illumina short-insert data for sixteen species. Where possible we have also generated mixed stage stranded RNASeq data for annotation. The data are being made publicly available as early as possible (warts-and-all) through a dedicated genome website at htttp://caenorhabditis.bio.ed.ac.uk, and completed genomes and annotations will be deposited in WormBase as mature assemblies emerge. We welcome additional collaborators to the CGP, whether to assemble new genomes or to delve into the evolutionary history of favourite gene sets and systems.Species sequenced thus far in Edinburgh: Caenorhabditis afra, Caenorhabditis castelli, Caenorhabditis doughertyi, Caenorhabditis guadeloupensis, Caenorhabditis macrosperma, Caenorhabditis nouraguensis, Caenorhabditis plicata, Caenorhabditis virilis, Caenorhabditis wallacei, Caenorhabditis sp. 1, Caenorhabditis sp. 5, Caenorhabditis sp. 21, Caenorhabditis sp. 26, Caenorhabditis sp. 31, Caenorhabditis sp. 32, Caenorhabditis sp. 38, Caenorhabditis sp. 39, Caenorhabditis sp. 40, Caenorhabditis sp. 43.[Samples have been supplied by Aurelien Richaud, Marie-Anne Felix, Christian Braendle, Michael Alion, Piero Lamelza].
Stevens, Lewis, Schwarz, Erich M., Yin, Da, Chandrasekar, Sinduja, Schartner, Caitlin M., Haag, Eric S., Meyer, Barbara J., Ralston, Edward J., Koutsovoulos, Georgios, Anderson, Erika C., Blaxter, Mark
[
International Worm Meeting,
2019]
Hermaphroditism has independently evolved at least three times within the Caenorhabditis genus, and six times in Pristionchus. This has often coincided with substantial losses of protein-coding genes, which are often implicated in male reproduction. However, the hermaphrodite C. tropicalis challenges this pattern. Although C. tropicalis has a substantially reduced genome (83 Mb in size, versus ~130 Mb in several male-female Caenorhabditis species), its closest male-female relative (C. wallacei) has an almost equally small genome (85 Mb). One explanation might be that genome shrinkage in C. tropicalis arose independently of hermaphroditism; this would fit the recent discovery of male-female Caenorhabditis with remarkably compact genomes, such as C. sulstoni with 65 Mb. An alternative explanation might be that C. wallacei reverted to male-female sexuality after hermaphroditism had already shrunk the genome of its shared tropicalis/wallacei ancestor. To begin testing these hypotheses, we used PacBio, Illumina, and Hi-C sequencing to produce third-generation genome assemblies for C. tropicalis and C. wallacei, each having six complete chromosomal scaffolds. Both assemblies are 98.6%-98.7% complete as scored by BUSCO, which matches the score for C. elegans (98.6%). In hermaphroditic C. briggsae versus its male-female sister species C. nigoni, ~7,000 genes lost in C. briggsae disproportionately include small genes with male-biased gene expression, such as the male secreted short (mss) gene family; the mss family encodes sperm surface glycoproteins, found only in outcrossing species, that are required for sperm competitiveness in mating. In contrast, C. tropicalis has only ~1,400 fewer protein-coding genes than C. wallacei (19,722 versus 21,017), 20% the disparity of C. briggsae vs. C. nigoni. Two clustered multigene families with male-biased expression conserved widely in male-female species (mss and a CAP-domain family that includes CRE28795) are absent not only in C. tropicalis but also in C. wallacei. More generally, gene families with conserved XO- or XX-biased expression have consistently fewer members in C. wallacei than in male-female species C. nigoni, C. remanei, or C. brenneri, and the diminished gene numbers of C. wallacei approach or equal those seen in hermaphrodites (for XO-biased and XX-biased gene families, respectively). These data suggest that C. wallacei might indeed be an atypical male-female Caenorhabditis species that underwent a temporary period of hermaphroditism, and jettisoned male reproductive genes during that period.