{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T01:38:50Z","timestamp":1772156330721,"version":"3.50.1"},"posted":{"date-parts":[[2023,1,8]]},"group-title":"Microbiology","reference-count":65,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Malaria causes over 200 million infections and over 600 thousand fatalities each year, with most cases attributed to a human-infectious\n                  <jats:italic>Plasmodium<\/jats:italic>\n                  species,\n                  <jats:italic>Plasmodium falciparum<\/jats:italic>\n                  . Many rodent-infectious\n                  <jats:italic>Plasmodium<\/jats:italic>\n                  species, like\n                  <jats:italic>Plasmodium berghei, Plasmodium chabaudi<\/jats:italic>\n                  , and\n                  <jats:italic>Plasmodium yoelii<\/jats:italic>\n                  , have been used as genetically tractable model species that can expedite studies of this pathogen. In particular,\n                  <jats:italic>P. yoelii<\/jats:italic>\n                  is an especially good model for investigating the mosquito and liver stages of parasite development because key attributes closely resemble those of\n                  <jats:italic>P. falciparum<\/jats:italic>\n                  . Because of its importance to malaria research, in 2002 the 17XNL strain of\n                  <jats:italic>P. yoelii<\/jats:italic>\n                  was the first rodent malaria parasite to be sequenced. While sequencing and assembling this genome was a breakthrough effort, the final assembly consisted of &gt;5000 contiguous sequences that impacted the creation of annotated gene models. While other important rodent malaria parasite genomes have been sequenced and annotated since then, including the related\n                  <jats:italic>P. yoelii<\/jats:italic>\n                  17X strain, the 17XNL strain has not. As a result, genomic data for 17X has become the\n                  <jats:italic>de facto<\/jats:italic>\n                  reference genome for the 17XNL strain while leaving open questions surrounding possible differences between the 17XNL and 17X genomes. In this work, we present a high-quality genome assembly for\n                  <jats:italic>P. yoelii<\/jats:italic>\n                  17XNL using HiFi PacBio long-read DNA sequencing. In addition, we use Nanopore long-read direct RNA-seq and Illumina short-read sequencing of mixed blood stages to create complete gene models that include not only coding sequences but also alternate transcript isoforms, and 5\u2019 and 3\u2019 UTR designations. A comparison of the 17X and this new 17XNL assembly revealed biologically meaningful differences between the strains due to the presence of coding sequence variants. Taken together, our work provides a new genomic and gene expression framework for studies with this commonly used rodent malaria model species.\n                <\/jats:p>","DOI":"10.1101\/2023.01.06.523040","type":"posted-content","created":{"date-parts":[[2023,1,8]],"date-time":"2023-01-08T10:35:12Z","timestamp":1673174112000},"source":"Crossref","is-referenced-by-count":1,"title":["Long-Read Genome Assembly and Gene Model Annotations for the Rodent Malaria Parasite\n                  <i>Plasmodium yoelii<\/i>\n                  17XNL"],"prefix":"10.64898","author":[{"given":"Mitchell J.","family":"Godin","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aswathy","family":"Sebastian","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8366-984X","authenticated-orcid":false,"given":"Istvan","family":"Albert","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1799-3726","authenticated-orcid":false,"given":"Scott E.","family":"Lindner","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2023011002550760000_2023.01.06.523040v1.1","unstructured":"Organization WH. 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