{"doi":"10.3390/genes12050692","title":"Nanopore Sequencing and Hi-C Based De Novo Assembly of Trachidermus fasciatus Genome","abstract":"<jats:p>Trachidermus fasciatus is a roughskin sculpin fish widespread across the coastal areas of East Asia. Due to environmental destruction and overfishing, the population of this species is under threat. In order to protect this endangered species, it is important to have the genome sequenced. Reference genomes are essential for studying population genetics, domestic farming, and genetic resource protection. However, currently, no reference genome is available for Trachidermus fasciatus, and this has greatly hindered the research on this species. In this study, we integrated nanopore long-read sequencing, Illumina short-read sequencing, and Hi-C methods to thoroughly assemble the Trachidermus fasciatus genome. Our results provided a chromosome-level high-quality genome assembly with a predicted genome size of 542.6 Mbp (2n = 40) and a scaffold N50 of 24.9 Mbp. The BUSCO value for genome assembly completeness was higher than 96%, and the single-base accuracy was 99.997%. Based on EVM-StringTie genome annotation, a total of 19,147 protein-coding genes were identified, including 35,093 mRNA transcripts. In addition, a novel gene-finding strategy named RNR was introduced, and in total, 51 (82) novel genes (transcripts) were identified. Lastly, we present here the first reference genome for Trachidermus fasciatus; this sequence is expected to greatly facilitate future research on this species.</jats:p>","journal":"Genes","year":2021,"id":45269,"datarank":0.3691007784959274,"base_score":1.791759469228055,"endowment":1.791759469228055,"self_citation_contribution":0.26876392038420827,"citation_network_contribution":0.1003368581117191,"self_endowment_contribution":0.26876392038420827,"citer_contribution":0.1003368581117191,"corpus_percentile":null,"corpus_rank":null,"citation_count":5,"citer_count":5,"citers_with_citation_signal":5,"citers_with_endowment":5,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":51844,"name":"Xu Zhang","orcid":null,"position":1,"is_corresponding":false},{"id":211731,"name":"Feng Lv","orcid":null,"position":2,"is_corresponding":false},{"id":211732,"name":"Mengmeng Sang","orcid":null,"position":3,"is_corresponding":false},{"id":211733,"name":"Hairong Hu","orcid":null,"position":4,"is_corresponding":false},{"id":211734,"name":"Jinqiu Wang","orcid":null,"position":5,"is_corresponding":false},{"id":88375,"name":"Dong Liu","orcid":"0000-0003-4154-8286","position":6,"is_corresponding":false},{"id":211730,"name":"Gangcai Xie","orcid":"0000-0002-8286-2987","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":1.791759469228055,"endowment":1.791759469228055,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"34066304","pmcid":"PMC8148166","openalex_id":"https://openalex.org/W3159742829","authors":[],"funders":[{"funder_name":"National Natural Science Foundation of China","grant_id":"31900484","title":null},{"funder_name":"National Natural Science Foundation of China","grant_id":"2018YFA0801004","title":null},{"funder_name":"Natural Science Foundation of Jiangsu Province","grant_id":"BK20190924","title":null},{"funder_name":"Natural Science Foundation of Jiangsu Province","grant_id":"BK20180048","title":null},{"funder_name":"Natural Science Foundation of Jiangsu Province","grant_id":"BRA2019278","title":null}],"total_grants":5,"fwci":0.3256,"citation_percentile":0.55565805,"influential_citations":0,"citation_trend":[{"year":2023,"count":2},{"year":2024,"count":2},{"year":2025,"count":1}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://www.mdpi.com/2073-4425/12/5/692/pdf","host_type":"journal"},{"url":"https://www.mdpi.com/2073-4425/12/5/692/pdf","host_type":"GOLD"},{"url":"https://www.mdpi.com/2073-4425/12/5/692/pdf","host_type":"publisher"},{"url":"https://doi.org/10.3390/genes12050692","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/34066304","host_type":"repository"},{"url":"https://doaj.org/article/e43837b5e2e84a6cbfb10da6e019619b","host_type":"repository"},{"url":"https://dx.doi.org/10.3390/genes12050692","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8148166","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC8148166","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC8148166?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Genomics and Phylogenetic Studies","Aquaculture disease management and microbiota","MicroRNA in disease regulation","Medicine","Environmental Science","Biology","Animals","Contig Mapping","Fish Proteins","Fishes","Genome","Nanopore Sequencing","RNA, Messenger","Whole Genome Sequencing"],"mesh_terms":["Whole Genome Sequencing","Nanopore Sequencing","Animals","Fishes","RNA, Messenger","Genome","Contig Mapping","Fish Proteins"],"keywords":["Genome","Biology","Reference genome","Sequence assembly","Genetics","Genome project","Population","Gene","Nanopore sequencing","Whole genome sequencing","DNA sequencing","Cancer genome sequencing","Computational biology","Evolutionary biology","Gene expression","Novel gene","Trachidermus fasciatus","Nanopore","Genome Assembly","Hi-c"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life below 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