The Genome of Medicinal Leech (Whitmania pigra) for Exploration of Bioactive Ingredients

BackgroundLeeches are classic annelids that have a huge diversity and closely related to people, especially medicinal leeches. Medicinal leeches have been widely utilized in medicine based on the pharmacological activities of their bioactive ingredients. The discovery of bioactive ingredients is hindered heavily due to the lack of the genome of medicinal leeches.ResultsTo facilitate this discovery and the research of medicinal leeches, we reported the first genome of the medicinal leech (Whitmania pigra). The assembled genome size of W. pigra is 177 Mbp, close to the estimated genome. Approximately about 23% of the genome was repetitive. A total of 26,743 protein-coding genes were subsequently predicted. There are only 9799 (57%) orthologous genes between W. pigra and Helobdella robusta. And only 16% genes in W. pigra showed syntenic arrangement with H. robusta revealed by gene synteny analysis. Furthermore, W. pigra and H. robusta expanded different gene families enriched in the ‘calcium ion’ and ‘sodium ion’ related functions, respectively. By inspecting genome distribution and gene structure of hirudin, we identified a new hirudin gene g17108 (hirudin_2) with different cysteine pattern. At last, we systematically explored and compared the active substances in the genomes of two leeches. The results showed that W. pigra exceeds H. robusta in both kinds and gene number of active molecules.ConclusionsThis study reported the first genome of the medicinal leech (W. pigra), which provides an important genome resource and new insight into the exploration and development of bioactive molecules of medicinal leeches.

Timing and scope of genomic expansion within Annelida: evidence from homeoboxes in the genome of the earthworm Eisenia fetida

Annelida represents a large and morphologically diverse group of bilaterian organisms. The recently published polychaete and leech genome sequences revealed an equally dynamic range of diversity at the genomic level. The availability of more annelid genomes will allow for the identification of evolutionary genomic events that helped shape the annelid lineage and better understand the diversity within the group. We sequenced and assembled the genome of the common earthworm, Eisenia fetida. As a first pass at understanding the diversity within the group, we classified 440 earthworm homeoboxes and compared them to those of the leech Helobdella robusta and the polychaete Capitella teleta. We inferred many gene expansions occurring in the lineage connecting the most recent common ancestor (MRCA) of Capitella and Eisenia to the Eisenia/Helobdella MRCA. Likewise, the lineage leading from the Eisenia/Helobdella MRCA to the leech Helobdella robusta has experienced substantial gains and losses. However, the lineage leading from Eisenia/Helobdella MRCA to E. fetida is characterized by extraordinary levels of homeobox gain. The evolutionary dynamics observed in the homeoboxes of these lineages are very likely to be generalizable to all genes. These genome expansions and losses have likely contributed to the remarkable biology exhibited in this group. These results provide a new perspective from which to understand the diversity within these lineages, show the utility of sub-draft genome assemblies for understanding genomic evolution, and provide a critical resource from which the biology of these animals can be studied. The genome data can be accessed through the Eisenia fetida Genome Portal: http://ryanlab.whitney.ufl.edu/genomes/Efet/