Jason Johns, Merly Escalona, Courtney Miller, Noravit Chumchim, Oanh Nguyen, Mohan P A Marimuthu, Samuel Sacco, Colin Fairbairn, Eric Beraut, Erin Toffelmier, H Bradley Shaffer, Scott Hodges
{"title":"特有的蛇形耧菜,Aquilegia eximia的近染色体水平组装。","authors":"Jason Johns, Merly Escalona, Courtney Miller, Noravit Chumchim, Oanh Nguyen, Mohan P A Marimuthu, Samuel Sacco, Colin Fairbairn, Eric Beraut, Erin Toffelmier, H Bradley Shaffer, Scott Hodges","doi":"10.1093/jhered/esaf035","DOIUrl":null,"url":null,"abstract":"<p><p>The flowering plant genus Aquilegia (columbine) is an important contributor to biodiversity and an example of both biotic and abiotic niche adaptation across much of the Northern Hemisphere, and especially in California. Here we report a near chromosome level draft genome assembly for A. eximia, a California endemic species. A. eximia is a serpentine-soil specialist and is very closely related to two columbine species also being studied for the California Conservation Genomics Project (CCGP), A. formosa (widespread) and A. pubescens (high alpine). Utilizing high throughput, long reads (PacBio) and chromatin capture (Omni-C), the A. eximia genome makes marked contiguity improvements compared to the existing reference genome for another North American columbine, A. coerulea 'Goldsmith'. The A. eximia genome will also be more useful for aligning whole genome resequencing data from California columbines than the genomes for more distantly related columbine species, the Asian A. oxysepala var. kansuensis and the European A. vulgaris. Notably we found evidence that A. eximia, A. coerulea 'Goldsmith' and A. vulgaris all share the same overall genome structure and differ from A. oxysepala var. kansuensis by the same reciprocal translocation. The A. eximia reference genome will be a valuable tool for identifying patterns of plant biodiversity across California for the CCGP, as well as for future population genomic and trait mapping studies.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5000,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"\\\"A near chromosome-level assembly of the serpentine endemic columbine, Aquilegia eximia\\\".\",\"authors\":\"Jason Johns, Merly Escalona, Courtney Miller, Noravit Chumchim, Oanh Nguyen, Mohan P A Marimuthu, Samuel Sacco, Colin Fairbairn, Eric Beraut, Erin Toffelmier, H Bradley Shaffer, Scott Hodges\",\"doi\":\"10.1093/jhered/esaf035\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The flowering plant genus Aquilegia (columbine) is an important contributor to biodiversity and an example of both biotic and abiotic niche adaptation across much of the Northern Hemisphere, and especially in California. Here we report a near chromosome level draft genome assembly for A. eximia, a California endemic species. A. eximia is a serpentine-soil specialist and is very closely related to two columbine species also being studied for the California Conservation Genomics Project (CCGP), A. formosa (widespread) and A. pubescens (high alpine). Utilizing high throughput, long reads (PacBio) and chromatin capture (Omni-C), the A. eximia genome makes marked contiguity improvements compared to the existing reference genome for another North American columbine, A. coerulea 'Goldsmith'. The A. eximia genome will also be more useful for aligning whole genome resequencing data from California columbines than the genomes for more distantly related columbine species, the Asian A. oxysepala var. kansuensis and the European A. vulgaris. Notably we found evidence that A. eximia, A. coerulea 'Goldsmith' and A. vulgaris all share the same overall genome structure and differ from A. oxysepala var. kansuensis by the same reciprocal translocation. The A. eximia reference genome will be a valuable tool for identifying patterns of plant biodiversity across California for the CCGP, as well as for future population genomic and trait mapping studies.</p>\",\"PeriodicalId\":54811,\"journal\":{\"name\":\"Journal of Heredity\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":2.5000,\"publicationDate\":\"2025-06-10\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Heredity\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/jhered/esaf035\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"EVOLUTIONARY BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Heredity","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/jhered/esaf035","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"EVOLUTIONARY BIOLOGY","Score":null,"Total":0}
引用次数: 0
摘要
开花植物耧菜属(耧菜属)是生物多样性的重要贡献者,也是北半球大部分地区(尤其是加利福尼亚)生物和非生物生态位适应的一个例子。在这里,我们报告了一个接近染色体水平的草图基因组组装为a . eximia,加州特有的物种。a . eximia是蛇形土壤的专家,与加州保护基因组计划(CCGP)正在研究的两种耧菜非常接近,a . formosa(广泛分布)和a . pubescens(高山)。利用高通量,长读取(PacBio)和染色质捕获(Omni-C),与另一种北美耧菜A. coerulea ‘Goldsmith’的现有参考基因组相比,A. eximia基因组具有显着的邻近性改善。对于比对来自加利福尼亚耧属植物的全基因组重测序数据,eximia耧属植物的基因组也比亲缘关系较远的耧属植物、亚洲的A. oxysepala var. kansuensis和欧洲的A. vulgaris的基因组更有用。值得注意的是,我们发现A. eximia, A. coerulea ‘Goldsmith’和A. vulgaris都具有相同的总体基因组结构,而与A. oxysepala var. kansuensis存在相同的反向易位差异。该参考基因组将为CCGP确定加州植物生物多样性模式以及未来的种群基因组和性状定位研究提供有价值的工具。
"A near chromosome-level assembly of the serpentine endemic columbine, Aquilegia eximia".
The flowering plant genus Aquilegia (columbine) is an important contributor to biodiversity and an example of both biotic and abiotic niche adaptation across much of the Northern Hemisphere, and especially in California. Here we report a near chromosome level draft genome assembly for A. eximia, a California endemic species. A. eximia is a serpentine-soil specialist and is very closely related to two columbine species also being studied for the California Conservation Genomics Project (CCGP), A. formosa (widespread) and A. pubescens (high alpine). Utilizing high throughput, long reads (PacBio) and chromatin capture (Omni-C), the A. eximia genome makes marked contiguity improvements compared to the existing reference genome for another North American columbine, A. coerulea 'Goldsmith'. The A. eximia genome will also be more useful for aligning whole genome resequencing data from California columbines than the genomes for more distantly related columbine species, the Asian A. oxysepala var. kansuensis and the European A. vulgaris. Notably we found evidence that A. eximia, A. coerulea 'Goldsmith' and A. vulgaris all share the same overall genome structure and differ from A. oxysepala var. kansuensis by the same reciprocal translocation. The A. eximia reference genome will be a valuable tool for identifying patterns of plant biodiversity across California for the CCGP, as well as for future population genomic and trait mapping studies.
期刊介绍:
Over the last 100 years, the Journal of Heredity has established and maintained a tradition of scholarly excellence in the publication of genetics research. Virtually every major figure in the field has contributed to the journal.
Established in 1903, Journal of Heredity covers organismal genetics across a wide range of disciplines and taxa. Articles include such rapidly advancing fields as conservation genetics of endangered species, population structure and phylogeography, molecular evolution and speciation, molecular genetics of disease resistance in plants and animals, genetic biodiversity and relevant computer programs.