{"doi":"10.3389/fpls.2022.1012277","title":"A chromosome-scale genome assembly of Quercus gilva: Insights into the evolution of Quercus section Cyclobalanopsis (Fagaceae)","abstract":"<jats:p><jats:italic>Quercus gilva</jats:italic> is an ecologically and economically important species of <jats:italic>Quercus</jats:italic> section <jats:italic>Cyclobalanopsis</jats:italic> and is a dominant species in evergreen broad-leaved forests in subtropical regions of East Asia. In the present study, we reported a high-quality chromosome-scale genome assembly of <jats:italic>Q. gilva</jats:italic>, the first reference genome for section <jats:italic>Cyclobalanopsis</jats:italic>, using the combination of Illumina and PacBio sequencing with Hi-C technologies. The assembled genome size of <jats:italic>Q. gilva</jats:italic> was 889.71 Mb, with a contig number of 773 and a contig N50 of 28.32 Mb. Hi-C scaffolding anchored 859.07 Mb contigs (96.54% of the assembled genome) onto 12 pseudochromosomes, with a scaffold N50 of 70.35 Mb. A combination of <jats:italic>de novo</jats:italic>, homology-based, and transcript-based predictions predicted a final set of 36,442 protein-coding genes distributed on 12 pseudochromosomes, and 97.73% of them were functionally annotated. A total of 535.64 Mb (60.20%) of repetitive sequences were identified. Genome evolution analysis revealed that <jats:italic>Q. gilva</jats:italic> was most closely related to <jats:italic>Q. suber</jats:italic> and they diverged at 40.35 Ma, and <jats:italic>Q. gilva</jats:italic> did not experience species-specific whole-genome duplication in addition to the ancient <jats:italic>gamma</jats:italic> (γ) whole-genome triplication event shared by core eudicot plants. <jats:italic>Q. gilva</jats:italic> underwent considerable gene family expansion and contraction, with 598 expanded and 6,509 contracted gene families detected. The first chromosome-scale genome of <jats:italic>Q. gilva</jats:italic> will promote its germplasm conservation and genetic improvement and provide essential resources for better studying the evolution of <jats:italic>Quercus</jats:italic> section <jats:italic>Cyclobalanopsis</jats:italic>.</jats:p>","journal":"Frontiers in Plant Science","year":2022,"id":617988,"datarank":0.47670807455219194,"base_score":3.1780538303479458,"endowment":3.1780538303479458,"self_citation_contribution":0.47670807455219194,"citation_network_contribution":0.0,"self_endowment_contribution":0.47670807455219194,"citer_contribution":0.0,"corpus_percentile":60.0,"corpus_rank":5317,"citation_count":23,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"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":592221,"name":"Na Liu","orcid":"0000-0003-3832-5591","position":1,"is_corresponding":false},{"id":229159,"name":"Xiaolong Jiang","orcid":"0000-0001-8066-1383","position":2,"is_corresponding":false},{"id":1593945,"name":"Zhikuang Qin","orcid":null,"position":3,"is_corresponding":false},{"id":1593948,"name":"Taimoor Hassan Farooq","orcid":null,"position":4,"is_corresponding":false},{"id":1593950,"name":"Fuliang Cao","orcid":null,"position":5,"is_corresponding":false},{"id":15943,"name":"He Li","orcid":"0009-0003-9885-1865","position":6,"is_corresponding":false},{"id":478691,"name":"Xia Zhou","orcid":"0009-0008-6364-1530","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"A chromosome-scale genome assembly of Quercus gilva: Insights into the evolution of Quercus section Cyclobalanopsis (Fagaceae)","abstract":"<jats:p><jats:italic>Quercus gilva</jats:italic> is an ecologically and economically important species of <jats:italic>Quercus</jats:italic> section <jats:italic>Cyclobalanopsis</jats:italic> and is a dominant species in evergreen broad-leaved forests in subtropical regions of East Asia. In the present study, we reported a high-quality chromosome-scale genome assembly of <jats:italic>Q. gilva</jats:italic>, the first reference genome for section <jats:italic>Cyclobalanopsis</jats:italic>, using the combination of Illumina and PacBio sequencing with Hi-C technologies. The assembled genome size of <jats:italic>Q. gilva</jats:italic> was 889.71 Mb, with a contig number of 773 and a contig N50 of 28.32 Mb. Hi-C scaffolding anchored 859.07 Mb contigs (96.54% of the assembled genome) onto 12 pseudochromosomes, with a scaffold N50 of 70.35 Mb. A combination of <jats:italic>de novo</jats:italic>, homology-based, and transcript-based predictions predicted a final set of 36,442 protein-coding genes distributed on 12 pseudochromosomes, and 97.73% of them were functionally annotated. A total of 535.64 Mb (60.20%) of repetitive sequences were identified. Genome evolution analysis revealed that <jats:italic>Q. gilva</jats:italic> was most closely related to <jats:italic>Q. suber</jats:italic> and they diverged at 40.35 Ma, and <jats:italic>Q. gilva</jats:italic> did not experience species-specific whole-genome duplication in addition to the ancient <jats:italic>gamma</jats:italic> (γ) whole-genome triplication event shared by core eudicot plants. <jats:italic>Q. gilva</jats:italic> underwent considerable gene family expansion and contraction, with 598 expanded and 6,509 contracted gene families detected. 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