Jing Fang, Mei Wu, Xinyi Zhang, Yang Chen, Lingjuan Tou, Jinjing Xu, Xiangjun Kong, Yingxiong Qiu
{"title":"同源四倍体金仙莲凤梨染色体水平的基因组组装。","authors":"Jing Fang, Mei Wu, Xinyi Zhang, Yang Chen, Lingjuan Tou, Jinjing Xu, Xiangjun Kong, Yingxiong Qiu","doi":"10.1038/s41597-025-05916-7","DOIUrl":null,"url":null,"abstract":"<p><p>Anoectochilus roxburghii (Orchidaceae), commonly known as Jinxianlian, is a highly valued traditional Chinese herbal medicine. Here, we present a high-quality chromosome-level genome assembly of the cultivar 'Jinkang No.1'. Genome survey analyses suggest that the cultivar is an autotetraploid. The assembled genome spans 5.17 Gb, with a contig N50 of 24.90 Mb, and 93.4% (4.82 Gb) is anchored onto 80 pseudo-chromosomes across 20 homologous groups. Annotation of the genome assembly identifies 76.42% repetitive elements and 88,106 protein-coding genes, with 94.6% of these genes functionally annotated. Ks analysis of collinear gene pairs indicates a recent species-specific polyploidization event, likely resulting in autotetraploidization. This reference genome provides a valuable resource for functional genomics, evolutionary biology, and molecular breeding studies of A. roxburghii and its related species.</p>","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"12 1","pages":"1623"},"PeriodicalIF":6.9000,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Chromosomal-level genome assembly of the autotetraploid Anoectochilus roxburghii (Jinxianlian, Orchidaceae).\",\"authors\":\"Jing Fang, Mei Wu, Xinyi Zhang, Yang Chen, Lingjuan Tou, Jinjing Xu, Xiangjun Kong, Yingxiong Qiu\",\"doi\":\"10.1038/s41597-025-05916-7\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Anoectochilus roxburghii (Orchidaceae), commonly known as Jinxianlian, is a highly valued traditional Chinese herbal medicine. Here, we present a high-quality chromosome-level genome assembly of the cultivar 'Jinkang No.1'. Genome survey analyses suggest that the cultivar is an autotetraploid. The assembled genome spans 5.17 Gb, with a contig N50 of 24.90 Mb, and 93.4% (4.82 Gb) is anchored onto 80 pseudo-chromosomes across 20 homologous groups. Annotation of the genome assembly identifies 76.42% repetitive elements and 88,106 protein-coding genes, with 94.6% of these genes functionally annotated. Ks analysis of collinear gene pairs indicates a recent species-specific polyploidization event, likely resulting in autotetraploidization. This reference genome provides a valuable resource for functional genomics, evolutionary biology, and molecular breeding studies of A. roxburghii and its related species.</p>\",\"PeriodicalId\":21597,\"journal\":{\"name\":\"Scientific Data\",\"volume\":\"12 1\",\"pages\":\"1623\"},\"PeriodicalIF\":6.9000,\"publicationDate\":\"2025-10-08\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Scientific Data\",\"FirstCategoryId\":\"103\",\"ListUrlMain\":\"https://doi.org/10.1038/s41597-025-05916-7\",\"RegionNum\":2,\"RegionCategory\":\"综合性期刊\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"MULTIDISCIPLINARY SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Scientific Data","FirstCategoryId":"103","ListUrlMain":"https://doi.org/10.1038/s41597-025-05916-7","RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MULTIDISCIPLINARY SCIENCES","Score":null,"Total":0}
Chromosomal-level genome assembly of the autotetraploid Anoectochilus roxburghii (Jinxianlian, Orchidaceae).
Anoectochilus roxburghii (Orchidaceae), commonly known as Jinxianlian, is a highly valued traditional Chinese herbal medicine. Here, we present a high-quality chromosome-level genome assembly of the cultivar 'Jinkang No.1'. Genome survey analyses suggest that the cultivar is an autotetraploid. The assembled genome spans 5.17 Gb, with a contig N50 of 24.90 Mb, and 93.4% (4.82 Gb) is anchored onto 80 pseudo-chromosomes across 20 homologous groups. Annotation of the genome assembly identifies 76.42% repetitive elements and 88,106 protein-coding genes, with 94.6% of these genes functionally annotated. Ks analysis of collinear gene pairs indicates a recent species-specific polyploidization event, likely resulting in autotetraploidization. This reference genome provides a valuable resource for functional genomics, evolutionary biology, and molecular breeding studies of A. roxburghii and its related species.
期刊介绍：
Scientific Data is an open-access journal focused on data, publishing descriptions of research datasets and articles on data sharing across natural sciences, medicine, engineering, and social sciences. Its goal is to enhance the sharing and reuse of scientific data, encourage broader data sharing, and acknowledge those who share their data.
The journal primarily publishes Data Descriptors, which offer detailed descriptions of research datasets, including data collection methods and technical analyses validating data quality. These descriptors aim to facilitate data reuse rather than testing hypotheses or presenting new interpretations, methods, or in-depth analyses.
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