High-quality Lindera megaphylla genome analysis provides insights into genome evolution and allows for the exploration of genes involved in terpenoid biosynthesis

IF 8.7 1区农林科学 Q1 Agricultural and Biological Sciences

Horticulture Research Pub Date : 2025-04-27 DOI:10.1093/hr/uhaf116

Hongli Liu, Jing Liu, Yun Bai, Xinran Zhang, Qingzheng Jiao, Peng Chen, Ruimin Li, Yan Li, Wenbin Xu, Yanhong Fu, Jiuxing Lu, Xiaoming Song, Yonghua Li

{"title":"High-quality Lindera megaphylla genome analysis provides insights into genome evolution and allows for the exploration of genes involved in terpenoid biosynthesis","authors":"Hongli Liu, Jing Liu, Yun Bai, Xinran Zhang, Qingzheng Jiao, Peng Chen, Ruimin Li, Yan Li, Wenbin Xu, Yanhong Fu, Jiuxing Lu, Xiaoming Song, Yonghua Li","doi":"10.1093/hr/uhaf116","DOIUrl":null,"url":null,"abstract":"Lindera megaphylla, a Lauraceae species, is valued for timber, horticulture, and traditional medicine. Here, a high-quality genome of L. megaphylla was obtained at the chromosome level. A total of 96.77% of genomic sequences were mapped onto 12 chromosomes, with a total length of 1,309.2 megabase (Mb) and an N50 scaffold of 107.75 Mb. Approximately 75.91% of genome consists of repetitive sequences, and 7,004 ncRNAs were predicted. We identified 29,482 genes, and 28,657 genes were annotated. Gene family analysis showed expanded gene families were mainly involved in energy metabolism and cellular growth, while contracted ones were associated with carbohydrate metabolism and signal transduction. Our analysis revealed that L. megaphylla has undergone two rounds of whole-genome duplication (WGD). Our results revealed that volatile compounds in L. megaphylla leaves inhibited the growth of several fungi and bacteria. Fifty-two terpene synthase (TPS) genes were identified and classified into six subfamilies, with significant expansion observed in the TPS-b, TPS-f, and TPS-g subfamilies in L. megaphylla. Transcriptomic and metabolomic co-analysis revealed that 43 DEGs were correlated with 117 terpenoids. Further analysis revealed that LmTPS1 was significantly correlated with caryophyllene oxide content. The overexpression of LmTPS1 in transgenic tomato lines significantly increased the contents of β-Caryophyllene and humulene, which further improved the resistance of transgenic tomato plants to common fungal and bacterial diseases. The integrated analysis of genome, metabolome, and transcriptome provides comprehensive insights into the evolution of L. megaphylla and clarifies the molecular mechanisms underlying the protective effects of caryophyllene against biotic stress.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"36 1","pages":""},"PeriodicalIF":8.7000,"publicationDate":"2025-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Horticulture Research","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.1093/hr/uhaf116","RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"Agricultural and Biological Sciences","Score":null,"Total":0}

引用次数: 0

Abstract

Lindera megaphylla, a Lauraceae species, is valued for timber, horticulture, and traditional medicine. Here, a high-quality genome of L. megaphylla was obtained at the chromosome level. A total of 96.77% of genomic sequences were mapped onto 12 chromosomes, with a total length of 1,309.2 megabase (Mb) and an N50 scaffold of 107.75 Mb. Approximately 75.91% of genome consists of repetitive sequences, and 7,004 ncRNAs were predicted. We identified 29,482 genes, and 28,657 genes were annotated. Gene family analysis showed expanded gene families were mainly involved in energy metabolism and cellular growth, while contracted ones were associated with carbohydrate metabolism and signal transduction. Our analysis revealed that L. megaphylla has undergone two rounds of whole-genome duplication (WGD). Our results revealed that volatile compounds in L. megaphylla leaves inhibited the growth of several fungi and bacteria. Fifty-two terpene synthase (TPS) genes were identified and classified into six subfamilies, with significant expansion observed in the TPS-b, TPS-f, and TPS-g subfamilies in L. megaphylla. Transcriptomic and metabolomic co-analysis revealed that 43 DEGs were correlated with 117 terpenoids. Further analysis revealed that LmTPS1 was significantly correlated with caryophyllene oxide content. The overexpression of LmTPS1 in transgenic tomato lines significantly increased the contents of β-Caryophyllene and humulene, which further improved the resistance of transgenic tomato plants to common fungal and bacterial diseases. The integrated analysis of genome, metabolome, and transcriptome provides comprehensive insights into the evolution of L. megaphylla and clarifies the molecular mechanisms underlying the protective effects of caryophyllene against biotic stress.

查看原文本刊更多论文

高质量的巨葡萄树基因组分析提供了基因组进化的见解，并允许探索涉及萜类生物合成的基因

巨木林（Lindera megaphylla）是樟科的一种，具有木材、园艺和传统医药价值。在染色体水平上获得了高质量的巨葡萄球菌基因组。共有96.77%的基因组序列被定位到12条染色体上，总长度为1,309.2 Mb， N50支架为107.75 Mb。约75.91%的基因组由重复序列组成，预测有7,004个ncrna。共鉴定出29,482个基因，其中28,657个基因被注释。基因家族分析表明，扩大的基因家族主要参与能量代谢和细胞生长，而缩小的基因家族主要参与碳水化合物代谢和信号转导。我们的分析表明，巨葡萄球菌经历了两轮全基因组复制（WGD）。结果表明，巨葡萄叶中挥发性化合物对几种真菌和细菌的生长有抑制作用。鉴定出52个萜烯合成酶（TPS）基因，并将其划分为6个亚家族，其中在巨葡萄球菌中TPS-b、TPS-f和TPS-g亚家族扩增明显。转录组学和代谢组学分析显示43个deg与117个萜类化合物相关。进一步分析发现，LmTPS1基因与石竹烯氧化物含量显著相关。LmTPS1在转基因番茄系中的过表达显著提高了β-石竹烯和葎草烯的含量，进一步提高了转基因番茄植株对常见真菌和细菌病害的抗性。基因组、代谢组和转录组的综合分析为巨葡萄球菌的进化提供了全面的见解，并阐明了石竹烯对生物胁迫的保护作用的分子机制。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Horticulture Research Biochemistry, Genetics and Molecular Biology-Biochemistry

CiteScore

11.20

自引率

6.90%

发文量

367

审稿时长

20 weeks

期刊介绍： Horticulture Research, an open access journal affiliated with Nanjing Agricultural University, has achieved the prestigious ranking of number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2022. As a leading publication in the field, the journal is dedicated to disseminating original research articles, comprehensive reviews, insightful perspectives, thought-provoking comments, and valuable correspondence articles and letters to the editor. Its scope encompasses all vital aspects of horticultural plants and disciplines, such as biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.