{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T20:27:42Z","timestamp":1768508862832,"version":"3.49.0"},"posted":{"date-parts":[[2023,11,2]]},"group-title":"Genomics","reference-count":138,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,11,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>\n                    Control and elimination of schistosomiasis is an arduous task, with current strategies proving inadequate to break transmission. Exploration of genetic approaches to interrupt\n                    <jats:italic>Schistosoma mansoni<\/jats:italic>\n                    transmission, the causative agent for human intestinal schistosomiasis in sub-Saharan Africa and South America, has led to genomic research of the snail vector hosts of the genus\n                    <jats:italic>Biomphalaria<\/jats:italic>\n                    . Few complete genomic resources exist, with African\n                    <jats:italic>Biomphalaria<\/jats:italic>\n                    species being particularly underrepresented despite this being where the majority of\n                    <jats:italic>S. mansoni<\/jats:italic>\n                    infections occur. Here we generate and annotate the first genome assembly of\n                    <jats:italic>Biomphalaria sudanica<\/jats:italic>\n                    sensu lato, a species responsible for\n                    <jats:italic>S. mansoni<\/jats:italic>\n                    transmission in lake and marsh habitats of the African Rift Valley. Supported by whole-genome diversity data among five inbred lines, we describe orthologs of immune-relevant gene regions in the South American vector\n                    <jats:italic>B. glabrata<\/jats:italic>\n                    and present a bioinformatic pipeline to identify candidate novel pathogen recognition receptors (PRRs).\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>\n                    <jats:italic>De novo<\/jats:italic>\n                    genome and transcriptome assembly of inbred\n                    <jats:italic>B. sudanica<\/jats:italic>\n                    originating from the shoreline of Lake Victoria (Kisumu, Kenya) resulted in a haploid genome size of \u223c944.2 Mb (6732 fragments, N50=1.067 Mb), comprising 23,598 genes (BUSCO=93.6% complete). The\n                    <jats:italic>B. sudanica<\/jats:italic>\n                    genome contains orthologues to all described immune genes\/regions tied to protection against\n                    <jats:italic>S. mansoni<\/jats:italic>\n                    in\n                    <jats:italic>B. glabrata<\/jats:italic>\n                    . The\n                    <jats:italic>B. sudanica PTC2<\/jats:italic>\n                    candidate immune genomic region contained many PRR-like genes across a much wider genomic region than has been shown in\n                    <jats:italic>B. glabrata<\/jats:italic>\n                    , as well as a large inversion between species. High levels of intra-species nucleotide diversity were seen in\n                    <jats:italic>PTC2<\/jats:italic>\n                    , as well as in regions linked to\n                    <jats:italic>PTC1<\/jats:italic>\n                    and\n                    <jats:italic>RADres<\/jats:italic>\n                    orthologues. Immune related and putative PRR gene families were significantly over-represented in the sub-set of\n                    <jats:italic>B. sudanica<\/jats:italic>\n                    genes determined as hyperdiverse, including high extracellular diversity in transmembrane genes, which could be under pathogen-mediated balancing selection. However, no overall expansion in immunity related genes were seen in African compared to South American lineages.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>\n                    The\n                    <jats:italic>B. sudanica<\/jats:italic>\n                    genome and analyses presented here will facilitate future research in vector immune defense mechanisms against pathogens. This genomic\/transcriptomic resource provides necessary data for the future development of molecular snail vector control\/surveillance tools, facilitating schistosome transmission interruption mechanisms in Africa.\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2023.11.01.565203","type":"posted-content","created":{"date-parts":[[2023,11,3]],"date-time":"2023-11-03T02:00:28Z","timestamp":1698976828000},"source":"Crossref","is-referenced-by-count":0,"title":["The genome and transcriptome of the snail\n                  <i>Biomphalaria sudanica s.l.<\/i>\n                  : Immune gene diversification and highly polymorphic genomic regions in an important African vector of\n                  <i>Schistosoma mansoni<\/i>"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4898-462X","authenticated-orcid":false,"given":"Tom","family":"Pennance","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Javier","family":"Calvelo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jacob A.","family":"Tennessen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ryan","family":"Burd","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jared","family":"Cayton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephanie R.","family":"Bollmann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael S.","family":"Blouin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Johannie M.","family":"Spaan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5056-4929","authenticated-orcid":false,"given":"Federico G","family":"Hoffmann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"George","family":"Ogara","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fredrick","family":"Rawago","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kennedy","family":"Andiego","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Boaz","family":"Mulonga","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Meredith","family":"Odhiambo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric S.","family":"Loker","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martina R.","family":"Laidemitt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lijun","family":"Lu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andr\u00e9s","family":"Iriarte","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maurice","family":"Odiere","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michelle L.","family":"Steinauer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"issue":"10","key":"2023110709350540000_2023.11.01.565203v1.1","doi-asserted-by":"crossref","first-page":"e312","DOI":"10.1371\/journal.pntd.0000312","article-title":"The CNCDs and the NTDs: Blurring the Lines Dividing Noncommunicable and Communicable Chronic Diseases","volume":"2","year":"2008","journal-title":"PLoS Negl Trop Dis"},{"key":"2023110709350540000_2023.11.01.565203v1.2","unstructured":"WHO. 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