{"doi":"10.1101/2021.07.05.451071","title":"Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, <i>Mesocricetus auratus</i>","abstract":"Abstract Background The Syrian hamster ( Mesocricetus auratus ) has been suggested as a useful mammalian model for a variety of diseases and infections, including infection with respiratory viruses such as SARS-CoV-2. The MesAur1.0 genome assembly was generated in 2013 using whole-genome shotgun sequencing with short-read sequence data. Current more advanced sequencing technologies and assembly methods now permit the generation of near-complete genome assemblies with higher quality and greater continuity. Findings Here, we report an improved assembly of the M. auratus genome (BCM_Maur_2.0) using Oxford Nanopore Technologies long-read sequencing to produce a chromosome-scale assembly. The total length of the new assembly is 2.46 Gbp, similar to the 2.50 Gbp length of a previous assembly of this genome, MesAur1.0. BCM_Maur_2.0 exhibits significantly improved continuity with a scaffold N50 that is 6.7 times greater than MesAur1.0. Furthermore, 21,616 protein coding genes and 10,459 noncoding genes are annotated in BCM_Maur_2.0 compared to 20,495 protein coding genes and 4,168 noncoding genes in MesAur1.0. This new assembly also improves the unresolved regions as measured by nucleotide ambiguities, where approximately 17.11% of bases in MesAur1.0 were unresolved compared to BCM_Maur_2.0 in which the number of unresolved bases is reduced to 3.00%. Conclusions Access to a more complete reference genome with improved accuracy and continuity will facilitate more detailed, comprehensive, and meaningful research results for a wide variety of future studies using Syrian hamsters as models.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2021,"id":217649,"datarank":0.2478512582368962,"base_score":1.3862943611198906,"endowment":1.3862943611198906,"self_citation_contribution":0.20794415416798362,"citation_network_contribution":0.03990710406891256,"self_endowment_contribution":0.20794415416798362,"citer_contribution":0.03990710406891256,"corpus_percentile":40.001547149377274,"corpus_rank":7757,"citation_count":3,"citer_count":2,"citers_with_citation_signal":2,"citers_with_endowment":2,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9139,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":246455,"name":"Muthuswamy Raveendran","orcid":"0000-0001-6185-4059","position":1,"is_corresponding":false},{"id":814578,"name":"Dustin T. Lyfoung","orcid":"0000-0002-2494-5266","position":2,"is_corresponding":false},{"id":49032,"name":"Fritz J. Sedlazeck","orcid":"0000-0001-6040-2691","position":3,"is_corresponding":false},{"id":77521,"name":"Medhat Mahmoud","orcid":"0000-0002-2553-4231","position":4,"is_corresponding":false},{"id":333885,"name":"Trent M. Prall","orcid":"0000-0003-0635-4152","position":5,"is_corresponding":false},{"id":381204,"name":"Julie A. Karl","orcid":"0000-0002-4447-4721","position":6,"is_corresponding":false},{"id":13411,"name":"HarshaVardhan Doddapaneni","orcid":"0000-0002-2433-633X","position":7,"is_corresponding":false},{"id":364152,"name":"Qingchang Meng","orcid":"0000-0001-9783-6610","position":8,"is_corresponding":false},{"id":52124,"name":"Yi Han","orcid":"0000-0001-7605-8979","position":9,"is_corresponding":false},{"id":1751,"name":"Donna M. Muzny","orcid":"0000-0002-3055-0359","position":10,"is_corresponding":false},{"id":246477,"name":"Roger W. Wiseman","orcid":"0000-0002-7682-7085","position":11,"is_corresponding":false},{"id":246460,"name":"David H. O’Connor","orcid":"0000-0003-2139-470X","position":12,"is_corresponding":false},{"id":246479,"name":"Jeffrey Rogers","orcid":"0000-0002-7374-6490","position":13,"is_corresponding":false},{"id":63735,"name":"R. Alan Harris","orcid":"0000-0002-7333-4752","position":0,"is_corresponding":true}],"reference_count":33,"raw_metadata":null,"created_at":"2026-07-18T23:53:20.374789Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}