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Project Progress

To date, we have sequenced the genome and both the mRNA and miRNA transcriptomes of the chaetognath Parasaggita elegans. Chaeotognaths are relatively complex animals and are the first predators that make their appearance in the fossil record during the Early Cambrian (Vannier et al. 2007). The genome assembly of Parasagitta consists of 866,422 scaffolds with the longest scaffold being 28,090 bp. Our assembled genome is 1.2 Gb, and our calculated N50 value is 750 bp. The mRNA transcriptome assembly of is 44Mb with an N50 of 1738bp. For the small RNA transcriptome, we analyzed 93,829 non-redundant sequences, all of which were expressed four or more times in our library. Using both genomic and mRNA transcriptome sequence we compiled a data set of the amino acid sequences from 186 protein-coding genes, and aligned them to an existing phylogenomics data set (Philippe et al., 2011). Our phylogenetic analysis (Figure 1) strongly suggests that chaetognaths are basal to the two major protostome clades, the lophotrochozoans and the ecydysozoans, similar to what others have recently proposed (e.g., Marlétaz et al., 2008). This phylogenetic position indicates that the chaetognath lineage split from the main protostome lineage ~650 Ma, over 100 Ma before they make their appearance in the fossil record. Our analysis of the microRNAs (Tarver et al. 2013) is consistent with this phylogenetic position as the chaetognath P. elegans shares nine miRNAs with ecdysozoans and lophotrochozoans not present in deuterostomes or in more basal organisms like sponges and jellyfish. However, the lophotrochozoans and ecydysozoans also possess three additional miRNAs not present in either our small RNA library or in the genome of the chaetognath, miR-36, miR-67 and miR-317 (Figure 2), suggesting that these miRNAs evolved in the protostome lineage after the lineage split between chaetognaths and the traditional protostomes.

Because the phylogenetic position of chaetognaths appears to be (finally!) firmly established we can now properly evaluate the taxon’s relative microRNA repertoire. Our data indicate that the chaetognath has lost very few miRNAs – only miR-242 and miR-2001 appear to be secondarily lost, consistent with the observation that chaetognaths are relatively complex animals with no obvious signs of secondary simplification, highlighting the disparity between the origins of morphological complexity versus its manifestation in the fossil record.