八倍体草莓的端粒到端粒相基因组揭示了一种赋予炭疽病抗性的受体激酶。

IF 11.8 2区 生物学 Q1 MULTIDISCIPLINARY SCIENCES
Hyeondae Han, Natalia Salinas, Christopher R Barbey, Yoon Jeong Jang, Zhen Fan, Sujeet Verma, Vance M Whitaker, Seonghee Lee
{"title":"八倍体草莓的端粒到端粒相基因组揭示了一种赋予炭疽病抗性的受体激酶。","authors":"Hyeondae Han, Natalia Salinas, Christopher R Barbey, Yoon Jeong Jang, Zhen Fan, Sujeet Verma, Vance M Whitaker, Seonghee Lee","doi":"10.1093/gigascience/giaf005","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Cultivated strawberry (Fragaria xananassa Duch.), an allo-octoploid species arising from at least 3 diploid progenitors, poses a challenge for genomic analysis due to its high levels of heterozygosity and the complex nature of its polyploid genome.</p><p><strong>Results: </strong>This study developed the complete haplotype-phased genome sequence from a short-day strawberry, 'Florida Brilliance' without parental data, assembling 56 chromosomes from telomere to telomere. This assembly was achieved with high-fidelity long reads and high-throughput chromatic capture sequencing (Hi-C). The centromere core regions and 96,104 genes were annotated using long-read isoform RNA sequencing. Using the high quality of the haplotype-phased reference genome, FaFB1, we identified the causal mutation within the gene encoding Leaf Rust 10 Disease-Resistance Locus Receptor-like Protein Kinase (LRK10) that confers resistance to anthracnose fruit rot (AFR). This disease is caused by the Colletotrichum acutatum species complex and results in significant economic losses in strawberry production. Comparison of resistant and susceptible haplotype assemblies and full-length transcript data revealed a 29-bp insertion at the first exon of the susceptible allele, leading to a premature stop codon and loss of gene function. The functional role of LRK10 in resistance to AFR was validated using a simplified Agrobacterium-based transformation method for transient gene expression analysis in strawberry fruits. Transient knockdown and overexpression of LRK10 in fruit indicate a key role for LRK10 in AFR resistance in strawberry.</p><p><strong>Conclusions: </strong>The FaFB1 assembly along with other resources will be valuable for the discovery of additional candidate genes associated with disease resistance and fruit quality, which will not only advance our understanding of genes and their functions but also facilitate advancements in genome editing in strawberry.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8000,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11899574/pdf/","citationCount":"0","resultStr":"{\"title\":\"A telomere-to-telomere phased genome of an octoploid strawberry reveals a receptor kinase conferring anthracnose resistance.\",\"authors\":\"Hyeondae Han, Natalia Salinas, Christopher R Barbey, Yoon Jeong Jang, Zhen Fan, Sujeet Verma, Vance M Whitaker, Seonghee Lee\",\"doi\":\"10.1093/gigascience/giaf005\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Cultivated strawberry (Fragaria xananassa Duch.), an allo-octoploid species arising from at least 3 diploid progenitors, poses a challenge for genomic analysis due to its high levels of heterozygosity and the complex nature of its polyploid genome.</p><p><strong>Results: </strong>This study developed the complete haplotype-phased genome sequence from a short-day strawberry, 'Florida Brilliance' without parental data, assembling 56 chromosomes from telomere to telomere. This assembly was achieved with high-fidelity long reads and high-throughput chromatic capture sequencing (Hi-C). The centromere core regions and 96,104 genes were annotated using long-read isoform RNA sequencing. Using the high quality of the haplotype-phased reference genome, FaFB1, we identified the causal mutation within the gene encoding Leaf Rust 10 Disease-Resistance Locus Receptor-like Protein Kinase (LRK10) that confers resistance to anthracnose fruit rot (AFR). This disease is caused by the Colletotrichum acutatum species complex and results in significant economic losses in strawberry production. Comparison of resistant and susceptible haplotype assemblies and full-length transcript data revealed a 29-bp insertion at the first exon of the susceptible allele, leading to a premature stop codon and loss of gene function. The functional role of LRK10 in resistance to AFR was validated using a simplified Agrobacterium-based transformation method for transient gene expression analysis in strawberry fruits. Transient knockdown and overexpression of LRK10 in fruit indicate a key role for LRK10 in AFR resistance in strawberry.</p><p><strong>Conclusions: </strong>The FaFB1 assembly along with other resources will be valuable for the discovery of additional candidate genes associated with disease resistance and fruit quality, which will not only advance our understanding of genes and their functions but also facilitate advancements in genome editing in strawberry.</p>\",\"PeriodicalId\":12581,\"journal\":{\"name\":\"GigaScience\",\"volume\":\"14 \",\"pages\":\"\"},\"PeriodicalIF\":11.8000,\"publicationDate\":\"2025-01-06\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11899574/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"GigaScience\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/gigascience/giaf005\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"MULTIDISCIPLINARY SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"GigaScience","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/gigascience/giaf005","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MULTIDISCIPLINARY SCIENCES","Score":null,"Total":0}
引用次数: 0

摘要

背景:栽培草莓(Fragaria xananassa Duch.)是一种由至少3个二倍体祖细胞产生的异源八倍体物种,由于其高水平的杂合性和多倍体基因组的复杂性,对基因组分析提出了挑战。结果:本研究从无亲本数据的短日照草莓“Florida Brilliance”中获得了完整的单倍型阶段基因组序列,从端粒到端粒组装了56条染色体。该组装是通过高保真长读取和高通量染色捕获测序(Hi-C)实现的。利用长读异构体RNA测序对着丝粒核心区和96104个基因进行了注释。利用高质量的单倍型阶段参考基因组FaFB1,我们确定了在编码叶锈病10抗病位点受体样蛋白激酶(LRK10)基因内的因果突变,该基因具有对炭疽病果腐病(AFR)的抗性。该病害是由急性炭疽病菌(Colletotrichum acutatum)种复合体引起的,对草莓生产造成重大经济损失。抗性和易感单倍型组合和全长转录数据的比较显示,易感等位基因的第一个外显子插入29 bp,导致过早终止密码子和基因功能丧失。利用简化农杆菌转化法对草莓果实进行瞬时基因表达分析,验证了LRK10在抗AFR中的功能作用。果实中LRK10的瞬时敲低和过表达表明LRK10在草莓抗AFR中起关键作用。结论:FaFB1组装和其他资源将对发现与抗病和果实品质相关的其他候选基因有价值,这不仅将促进我们对基因及其功能的理解,而且还将促进草莓基因组编辑的进展。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
A telomere-to-telomere phased genome of an octoploid strawberry reveals a receptor kinase conferring anthracnose resistance.

Background: Cultivated strawberry (Fragaria xananassa Duch.), an allo-octoploid species arising from at least 3 diploid progenitors, poses a challenge for genomic analysis due to its high levels of heterozygosity and the complex nature of its polyploid genome.

Results: This study developed the complete haplotype-phased genome sequence from a short-day strawberry, 'Florida Brilliance' without parental data, assembling 56 chromosomes from telomere to telomere. This assembly was achieved with high-fidelity long reads and high-throughput chromatic capture sequencing (Hi-C). The centromere core regions and 96,104 genes were annotated using long-read isoform RNA sequencing. Using the high quality of the haplotype-phased reference genome, FaFB1, we identified the causal mutation within the gene encoding Leaf Rust 10 Disease-Resistance Locus Receptor-like Protein Kinase (LRK10) that confers resistance to anthracnose fruit rot (AFR). This disease is caused by the Colletotrichum acutatum species complex and results in significant economic losses in strawberry production. Comparison of resistant and susceptible haplotype assemblies and full-length transcript data revealed a 29-bp insertion at the first exon of the susceptible allele, leading to a premature stop codon and loss of gene function. The functional role of LRK10 in resistance to AFR was validated using a simplified Agrobacterium-based transformation method for transient gene expression analysis in strawberry fruits. Transient knockdown and overexpression of LRK10 in fruit indicate a key role for LRK10 in AFR resistance in strawberry.

Conclusions: The FaFB1 assembly along with other resources will be valuable for the discovery of additional candidate genes associated with disease resistance and fruit quality, which will not only advance our understanding of genes and their functions but also facilitate advancements in genome editing in strawberry.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
GigaScience
GigaScience MULTIDISCIPLINARY SCIENCES-
CiteScore
15.50
自引率
1.10%
发文量
119
审稿时长
1 weeks
期刊介绍: GigaScience seeks to transform data dissemination and utilization in the life and biomedical sciences. As an online open-access open-data journal, it specializes in publishing "big-data" studies encompassing various fields. Its scope includes not only "omic" type data and the fields of high-throughput biology currently serviced by large public repositories, but also the growing range of more difficult-to-access data, such as imaging, neuroscience, ecology, cohort data, systems biology and other new types of large-scale shareable data.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信