{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T06:07:53Z","timestamp":1792649273014,"version":"4.5.0"},"posted":{"date-parts":[[2025,3,17]]},"group-title":"Genomics","reference-count":63,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,3,17]],"date-time":"2025-03-17T00:00:00Z","timestamp":1742169600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,3,17]]},"abstract":"<jats:label>1<\/jats:label>\n                <jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  The American cockroach,\n                  <jats:italic>Periplaneta americana<\/jats:italic>\n                  , is a cosmopolitan insect notorious for thriving among humans undeterred by attempts to eliminate it. The traits that contribute to its ubiquity as an opportunistic pest, such as long lifespan, expansive neurosensory capacity, and nutritional flexibility, also make\n                  <jats:italic>P. americana<\/jats:italic>\n                  an excellent invertebrate model organism with a long history in neuroscience and physiological research. Current genetic resources available for\n                  <jats:italic>P. americana<\/jats:italic>\n                  highlight its large, complex genome and richly diverse transcriptional capabilities, but fall short of producing a complete, chromosome-level genome. Here, we present a high-quality\n                  <jats:italic>de novo<\/jats:italic>\n                  genome assembly of a laboratory-raised adult female\n                  <jats:italic>P. americana<\/jats:italic>\n                  using a combination of high fidelity PacBio long reads and Hi-C sequencing. The final 3.23 Gb genome was assembled with chromosomal resolution into 17 scaffolds, consistent with previous karyotype analysis, and has a scaffold N50 of 188.1 Mb and genome BUSCO score of 99.7%. This assembly includes a chromosome that was missing from the previous reference genome for this species. Protein prediction and annotation were performed via the NCBI Eukaryotic Genome Annotation Pipeline, which identified 16,780 protein-coding genes and generated an annotation BUSCO score of 97.8%. Ortholog comparisons with available Blattodea assemblies highlight the expanded chemosensory and immune capabilities of\n                  <jats:italic>P. americana<\/jats:italic>\n                  compared to termite relatives. This genome assembly is a valuable tool for facilitating future research on the biology and evolution of this remarkable insect.\n                <\/jats:p>","DOI":"10.1101\/2025.03.14.643325","type":"posted-content","created":{"date-parts":[[2025,3,19]],"date-time":"2025-03-19T16:30:58Z","timestamp":1742401858000},"source":"Crossref","is-referenced-by-count":0,"title":["Genome Report: Improved chromosome-level genome assembly of the American cockroach,\n                  <i>Periplaneta americana<\/i>"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7422-6868","authenticated-orcid":false,"given":"Rachel L.","family":"Dockman","sequence":"first","affiliation":[{"name":"Department of Microbiology, University of Georgia, Athens, GA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tyler J.","family":"Simmonds","sequence":"additional","affiliation":[{"name":"USDA-ARS, Hilo, HI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2612-109X","authenticated-orcid":false,"given":"Kevin J.","family":"Vogel","sequence":"additional","affiliation":[{"name":"Department of Entomology, University of Georgia, Athens, GA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott M.","family":"Geib","sequence":"additional","affiliation":[{"name":"USDA-ARS, Hilo, HI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth A.","family":"Ottesen","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of Georgia, Athens, GA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"issue":"4-5","key":"2026041200010422000_2025.03.14.643325v1.1","first-page":"127409","article-title":"The External Anatomy of the Head and Abdomen of the Roach, Periplaneta americana","volume":"32","year":"1925","journal-title":"Psyche: A Journal of Entomology"},{"key":"2026041200010422000_2025.03.14.643325v1.2","unstructured":"Guthrie, D.M. and A.R. Tindall , The biology of the cockroach. 1968, London: Edward Arnold. 408."},{"key":"2026041200010422000_2025.03.14.643325v1.3","unstructured":"Cornwell, P.B. , The cockroach: a laboratory insect and an industrial pest. 1968, United Kingdom: Huthinson."},{"key":"2026041200010422000_2025.03.14.643325v1.4","unstructured":"The American Cockroach. 1982, London: Chapman and Hall."},{"key":"2026041200010422000_2025.03.14.643325v1.5","doi-asserted-by":"publisher","DOI":"10.1126\/science.156.3782.1640"},{"issue":"1","key":"2026041200010422000_2025.03.14.643325v1.6","doi-asserted-by":"crossref","first-page":"6582","DOI":"10.1038\/s41598-021-85341-z","article-title":"Electromagnetic field and TGF-\u03b2 enhance the compensatory plasticity after sensory nerve injury in cockroach Periplaneta americana","volume":"11","year":"2021","journal-title":"Scientific Reports"},{"issue":"4652","key":"2026041200010422000_2025.03.14.643325v1.7","doi-asserted-by":"crossref","first-page":"1805","DOI":"10.1038\/1821805b0","article-title":"Synaptic Transmission in the Cockroach","volume":"182","year":"1958","journal-title":"Nature"},{"issue":"3","key":"2026041200010422000_2025.03.14.643325v1.8","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1016\/0742-8413(92)90161-Y","article-title":"Receptors for L-glutamate and GABA in the nervous system of an insect (Periplaneta americana)","volume":"103","year":"1992","journal-title":"Comp Biochem Physiol C Comp Pharmacol Toxicol"},{"issue":"3","key":"2026041200010422000_2025.03.14.643325v1.9","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1002\/jcp.1030310308","article-title":"The effect of potassium and calcium on the nervous system of the cockroach, Periplaneta americana","volume":"31","year":"1948","journal-title":"J Cell Comp Physiol"},{"key":"2026041200010422000_2025.03.14.643325v1.10","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0200512"},{"key":"2026041200010422000_2025.03.14.643325v1.11","doi-asserted-by":"publisher","DOI":"10.1093\/aesa\/72.2.197"},{"key":"2026041200010422000_2025.03.14.643325v1.12","doi-asserted-by":"crossref","unstructured":"Arumugam, G. , et al., Purification and functional characterization of lectin with phenoloxidase activity from the hemolymph of cockroach, Periplaneta americana. Arch Insect Biochem Physiol, 2017. 95(2).","DOI":"10.1002\/arch.21390"},{"key":"2026041200010422000_2025.03.14.643325v1.13","doi-asserted-by":"publisher","DOI":"10.1111\/all.15531"},{"issue":"6","key":"2026041200010422000_2025.03.14.643325v1.14","doi-asserted-by":"crossref","first-page":"978","DOI":"10.1111\/1744-7917.12486","article-title":"New insight into foregut functions of xenobiotic detoxification in the cockroach Periplaneta americana","volume":"25","year":"2018","journal-title":"Insect Sci"},{"key":"2026041200010422000_2025.03.14.643325v1.15","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0155254"},{"key":"2026041200010422000_2025.03.14.643325v1.16","doi-asserted-by":"crossref","first-page":"106013","DOI":"10.1016\/j.pestbp.2024.106013","article-title":"Elucidating the detoxification efficacy of Periplaneta americana delta glutathione S-transferase 1 (PaGSTd1) against organophosphates","volume":"203","year":"2024","journal-title":"Pesticide Biochemistry and Physiology"},{"key":"2026041200010422000_2025.03.14.643325v1.17","doi-asserted-by":"crossref","first-page":"1125600","DOI":"10.3389\/fphar.2023.1125600","article-title":"A minireview of the medicinal and edible insects from the traditional Chinese medicine (TCM)","volume":"14","year":"2023","journal-title":"Front Pharmacol"},{"key":"2026041200010422000_2025.03.14.643325v1.18","doi-asserted-by":"publisher","DOI":"10.1016\/0378-8741(88)90157-2"},{"key":"2026041200010422000_2025.03.14.643325v1.19","doi-asserted-by":"crossref","unstructured":"Li, L. , et al., Applications of RNA Interference in American Cockroach. J Vis Exp, 2021(178).","DOI":"10.3791\/63380-v"},{"key":"2026041200010422000_2025.03.14.643325v1.20","doi-asserted-by":"crossref","unstructured":"Huang, J.H. , et al., Practical Use of RNA Interference: Oral Delivery of Double-stranded RNA in Liposome Carriers for Cockroaches. J Vis Exp, 2018(135).","DOI":"10.3791\/57385"},{"key":"2026041200010422000_2025.03.14.643325v1.21","doi-asserted-by":"publisher","DOI":"10.3389\/fphys.2015.00207"},{"key":"2026041200010422000_2025.03.14.643325v1.22","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01837-16"},{"key":"2026041200010422000_2025.03.14.643325v1.23","doi-asserted-by":"crossref","unstructured":"Dockman, R.L. and E.A. Ottesen , Purified fibers in chemically defined synthetic diets destabilize the gut microbiome of an omnivorous insect model. Frontiers in Microbiomes, 2024. 3(1477521).","DOI":"10.3389\/frmbi.2024.1477521"},{"key":"2026041200010422000_2025.03.14.643325v1.24","doi-asserted-by":"publisher","DOI":"10.1016\/0022-1910(96)00028-5"},{"key":"2026041200010422000_2025.03.14.643325v1.25","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.4717"},{"key":"2026041200010422000_2025.03.14.643325v1.26","doi-asserted-by":"crossref","unstructured":"Dukes, H.E. , J.E. Dyer , and E.A. Ottesen , Establishment and Maintenance of Gnotobiotic American Cockroaches (Periplaneta americana). JoVE, 2021(171): p. e61316.","DOI":"10.3791\/61316"},{"key":"2026041200010422000_2025.03.14.643325v1.27","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.03130-15"},{"key":"2026041200010422000_2025.03.14.643325v1.28","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00802-21"},{"key":"2026041200010422000_2025.03.14.643325v1.29","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.03700-15"},{"issue":"1","key":"2026041200010422000_2025.03.14.643325v1.30","doi-asserted-by":"crossref","first-page":"1008","DOI":"10.1038\/s41467-018-03281-1","article-title":"The genomic and functional landscapes of developmental plasticity in the American cockroach","volume":"9","year":"2018","journal-title":"Nature Communications"},{"issue":"1","key":"2026041200010422000_2025.03.14.643325v1.31","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1038\/hdy.1960.56","article-title":"Chromosome structure in Periplaneta americana","volume":"15","year":"1960","journal-title":"Heredity"},{"key":"2026041200010422000_2025.03.14.643325v1.32","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts611"},{"key":"2026041200010422000_2025.03.14.643325v1.33","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-020-01056-5"},{"key":"2026041200010422000_2025.03.14.643325v1.34","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1006277"},{"key":"2026041200010422000_2025.03.14.643325v1.35","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0163962"},{"key":"2026041200010422000_2025.03.14.643325v1.36","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1891-0"},{"key":"2026041200010422000_2025.03.14.643325v1.37","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-019-0201-4"},{"key":"2026041200010422000_2025.03.14.643325v1.38","doi-asserted-by":"publisher","DOI":"10.1186\/s13100-020-00230-y"},{"key":"2026041200010422000_2025.03.14.643325v1.39","unstructured":"Li, H. , Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM arXiv q-bio.GN, 2013."},{"key":"2026041200010422000_2025.03.14.643325v1.40","doi-asserted-by":"crossref","unstructured":"Danecek, P. , et al., Twelve years of SAMtools and BCFtools. Gigascience, 2021. 10(2).","DOI":"10.1093\/gigascience\/giab008"},{"key":"2026041200010422000_2025.03.14.643325v1.41","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2015.07.012"},{"key":"2026041200010422000_2025.03.14.643325v1.42","doi-asserted-by":"crossref","unstructured":"Zhou, C. , S.A. McCarthy , and R. Durbin , YaHS: yet another Hi-C scaffolding tool. Bioinformatics, 2023. 39(1).","DOI":"10.1093\/bioinformatics\/btac808"},{"key":"2026041200010422000_2025.03.14.643325v1.43","unstructured":"Brown, M. , P.M. Gonz\u00e1lez De la Rosa , and B. Mark , A Telomere Identification Toolkit. Zenodo, 2023."},{"key":"2026041200010422000_2025.03.14.643325v1.44","doi-asserted-by":"publisher","DOI":"10.1093\/mol-bev\/msab199"},{"key":"2026041200010422000_2025.03.14.643325v1.45","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-023-05385-y"},{"key":"2026041200010422000_2025.03.14.643325v1.46","doi-asserted-by":"publisher","DOI":"10.1007\/s00294-012-0365-7"},{"key":"2026041200010422000_2025.03.14.643325v1.47","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1921046117"},{"key":"2026041200010422000_2025.03.14.643325v1.48","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms4636"},{"key":"2026041200010422000_2025.03.14.643325v1.49","doi-asserted-by":"publisher","DOI":"10.1038\/s41559-017-0459-1"},{"issue":"10","key":"2026041200010422000_2025.03.14.643325v1.50","doi-asserted-by":"crossref","first-page":"107832","DOI":"10.1016\/j.isci.2023.107832","article-title":"Live-bearing cockroach genome reveals convergent evolutionary mechanisms linked to viviparity in insects and beyond","volume":"26","year":"2023","journal-title":"iScience"},{"key":"2026041200010422000_2025.03.14.643325v1.51","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1832-y"},{"key":"2026041200010422000_2025.03.14.643325v1.52","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.78526"},{"key":"2026041200010422000_2025.03.14.643325v1.53","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-015-0721-2"},{"key":"2026041200010422000_2025.03.14.643325v1.54","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx364"},{"key":"2026041200010422000_2025.03.14.643325v1.55","doi-asserted-by":"publisher","DOI":"10.1089\/omi.2011.0118"},{"key":"2026041200010422000_2025.03.14.643325v1.56","doi-asserted-by":"crossref","unstructured":"Wu, T. , et al., clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation, 2021. 2(3).","DOI":"10.1016\/j.xinn.2021.100141"},{"issue":"1","key":"2026041200010422000_2025.03.14.643325v1.57","first-page":"192","article-title":"Blattodea Karyotype Database","volume":"118","year":"2021","journal-title":"EJE"},{"key":"2026041200010422000_2025.03.14.643325v1.58","doi-asserted-by":"publisher","DOI":"10.1007\/s10577-011-9231-6"},{"key":"2026041200010422000_2025.03.14.643325v1.59","doi-asserted-by":"publisher","DOI":"10.1101\/gr.277387.122"},{"key":"2026041200010422000_2025.03.14.643325v1.60","doi-asserted-by":"crossref","first-page":"22","DOI":"10.12688\/wellcomeopenres.23463.1","article-title":"The genome sequence of the tawny cockroach, Ectobius (Ectobius) pallidus (Olivier, 1789)","volume":"10","year":"2025","journal-title":"Wellcome Open Res"},{"key":"2026041200010422000_2025.03.14.643325v1.61","unstructured":"Ewart, K. , S. Ho , and A.-A. Chowdhury , Annotated genome assemblies for Geoscapheus dilatatus, Panesthia cribrata and Neogeoscapheus hanni 2024: Dryad."},{"key":"2026041200010422000_2025.03.14.643325v1.62","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2110361119"},{"key":"2026041200010422000_2025.03.14.643325v1.63","doi-asserted-by":"publisher","DOI":"10.1111\/imb.1281832"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.03.14.643325","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T07:01:18Z","timestamp":1775977278000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.03.14.643325"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,17]]},"references-count":63,"URL":"https:\/\/doi.org\/10.1101\/2025.03.14.643325","relation":{},"subject":[],"published":{"date-parts":[[2025,3,17]]},"subtype":"preprint"}}