豚草科联盟的祖先核型、除草剂抗性和人类过敏原:普通豚草和巨型豚草基因组的启示。

IF 3.9 2区 生物学 Q1 GENETICS & HEREDITY
Plant Genome Pub Date : 2024-06-01 Epub Date: 2024-03-13 DOI:10.1002/tpg2.20442
Martin Laforest, Sara L Martin, Katherine Bisaillon, Brahim Soufiane, Sydney Meloche, François J Tardif, Eric Page
{"title":"豚草科联盟的祖先核型、除草剂抗性和人类过敏原:普通豚草和巨型豚草基因组的启示。","authors":"Martin Laforest, Sara L Martin, Katherine Bisaillon, Brahim Soufiane, Sydney Meloche, François J Tardif, Eric Page","doi":"10.1002/tpg2.20442","DOIUrl":null,"url":null,"abstract":"<p><p>Ambrosia artemisiifolia and Ambrosia trifida (Asteraceae) are important pest species and the two greatest sources of aeroallergens globally. Here, we took advantage of a hybrid to simplify genome assembly and present chromosome-level assemblies for both species. These assemblies show high levels of completeness with Benchmarking Universal Single-Copy Ortholog (BUSCO) scores of 94.5% for A. artemisiifolia and 96.1% for A. trifida and long terminal repeat (LTR) Assembly Index values of 26.6 and 23.6, respectively. The genomes were annotated using RNA data identifying 41,642 genes in A. artemisiifolia and 50,203 in A. trifida. More than half of the genome is composed of repetitive elements, with 62% in A. artemisiifolia and 69% in A. trifida. Single copies of herbicide resistance-associated genes PPX2L, HPPD, and ALS were found, while two copies of the EPSPS gene were identified; this latter observation may reveal a possible mechanism of resistance to the herbicide glyphosate. Ten of the 12 main allergenicity genes were also localized, some forming clusters with several copies, especially in A. artemisiifolia. The evolution of genome structure has differed among these two species. The genome of A. trifida has undergone greater rearrangement, possibly the result of chromoplexy. In contrast, the genome of A. artemisiifolia retains a structure that makes the allotetraploidization of the most recent common ancestor of the Heliantheae Alliance the clearest feature of its genome. When compared to other Heliantheae Alliance species, this allowed us to reconstruct the common ancestor's karyotype-a key step for furthering of our understanding of the evolution and diversification of this economically and allergenically important group.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":3.9000,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed.\",\"authors\":\"Martin Laforest, Sara L Martin, Katherine Bisaillon, Brahim Soufiane, Sydney Meloche, François J Tardif, Eric Page\",\"doi\":\"10.1002/tpg2.20442\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Ambrosia artemisiifolia and Ambrosia trifida (Asteraceae) are important pest species and the two greatest sources of aeroallergens globally. Here, we took advantage of a hybrid to simplify genome assembly and present chromosome-level assemblies for both species. These assemblies show high levels of completeness with Benchmarking Universal Single-Copy Ortholog (BUSCO) scores of 94.5% for A. artemisiifolia and 96.1% for A. trifida and long terminal repeat (LTR) Assembly Index values of 26.6 and 23.6, respectively. The genomes were annotated using RNA data identifying 41,642 genes in A. artemisiifolia and 50,203 in A. trifida. More than half of the genome is composed of repetitive elements, with 62% in A. artemisiifolia and 69% in A. trifida. Single copies of herbicide resistance-associated genes PPX2L, HPPD, and ALS were found, while two copies of the EPSPS gene were identified; this latter observation may reveal a possible mechanism of resistance to the herbicide glyphosate. Ten of the 12 main allergenicity genes were also localized, some forming clusters with several copies, especially in A. artemisiifolia. The evolution of genome structure has differed among these two species. The genome of A. trifida has undergone greater rearrangement, possibly the result of chromoplexy. In contrast, the genome of A. artemisiifolia retains a structure that makes the allotetraploidization of the most recent common ancestor of the Heliantheae Alliance the clearest feature of its genome. When compared to other Heliantheae Alliance species, this allowed us to reconstruct the common ancestor's karyotype-a key step for furthering of our understanding of the evolution and diversification of this economically and allergenically important group.</p>\",\"PeriodicalId\":49002,\"journal\":{\"name\":\"Plant Genome\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.9000,\"publicationDate\":\"2024-06-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Plant Genome\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1002/tpg2.20442\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/3/13 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q1\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Plant Genome","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1002/tpg2.20442","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/3/13 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0

摘要

蓟马(Ambrosia artemisiifolia)和三叶伏牛草(Ambrosia trifida)(菊科)是重要的害虫物种,也是全球两大空气过敏源。在这里,我们利用杂交技术简化了基因组组装,并展示了这两个物种的染色体级组装。A. artemisiifolia 的基准通用单拷贝同源物 (BUSCO) 得分为 94.5%,A. trifida 的基准通用单拷贝同源物 (BUSCO) 得分为 96.1%,长末端重复 (LTR) 组装指数值分别为 26.6 和 23.6。利用 RNA 数据对基因组进行了注释,发现 A. artemisiifolia 中有 41,642 个基因,A. trifida 中有 50,203 个基因。超过一半的基因组由重复元件组成,其中 A. artemisiifolia 占 62%,A. trifida 占 69%。发现了单拷贝的抗除草剂相关基因 PPX2L、HPPD 和 ALS,同时还发现了两个拷贝的 EPSPS 基因;后者可能揭示了抗除草剂草甘膦的可能机制。12 个主要过敏性基因中的 10 个也被定位,其中一些形成了具有多个拷贝的基因簇,尤其是在青蒿中。这两个物种的基因组结构演化有所不同。三裂蒿的基因组经历了较大的重排,这可能是染色体变性的结果。相比之下,A. artemisiifolia 的基因组保留了一种结构,这种结构使 Heliantheae Alliance 最近的共同祖先的异源四倍体化成为其基因组最明显的特征。与其他鹤顶红联盟物种相比,这使我们能够重建共同祖先的核型--这是我们进一步了解这一具有重要经济和过敏原意义的群体的进化和多样化的关键一步。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed.

Ambrosia artemisiifolia and Ambrosia trifida (Asteraceae) are important pest species and the two greatest sources of aeroallergens globally. Here, we took advantage of a hybrid to simplify genome assembly and present chromosome-level assemblies for both species. These assemblies show high levels of completeness with Benchmarking Universal Single-Copy Ortholog (BUSCO) scores of 94.5% for A. artemisiifolia and 96.1% for A. trifida and long terminal repeat (LTR) Assembly Index values of 26.6 and 23.6, respectively. The genomes were annotated using RNA data identifying 41,642 genes in A. artemisiifolia and 50,203 in A. trifida. More than half of the genome is composed of repetitive elements, with 62% in A. artemisiifolia and 69% in A. trifida. Single copies of herbicide resistance-associated genes PPX2L, HPPD, and ALS were found, while two copies of the EPSPS gene were identified; this latter observation may reveal a possible mechanism of resistance to the herbicide glyphosate. Ten of the 12 main allergenicity genes were also localized, some forming clusters with several copies, especially in A. artemisiifolia. The evolution of genome structure has differed among these two species. The genome of A. trifida has undergone greater rearrangement, possibly the result of chromoplexy. In contrast, the genome of A. artemisiifolia retains a structure that makes the allotetraploidization of the most recent common ancestor of the Heliantheae Alliance the clearest feature of its genome. When compared to other Heliantheae Alliance species, this allowed us to reconstruct the common ancestor's karyotype-a key step for furthering of our understanding of the evolution and diversification of this economically and allergenically important group.

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
Plant Genome
Plant Genome PLANT SCIENCES-GENETICS & HEREDITY
CiteScore
6.00
自引率
4.80%
发文量
93
审稿时长
>12 weeks
期刊介绍: The Plant Genome publishes original research investigating all aspects of plant genomics. Technical breakthroughs reporting improvements in the efficiency and speed of acquiring and interpreting plant genomics data are welcome. The editorial board gives preference to novel reports that use innovative genomic applications that advance our understanding of plant biology that may have applications to crop improvement. The journal also publishes invited review articles and perspectives that offer insight and commentary on recent advances in genomics and their potential for agronomic improvement.
×
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