Carex breviculmis 的基因组组装为其系统发育定位和环境适应提供了证据。

IF 3.6 2区 生物学 Q1 PLANT SCIENCES Annals of botany Pub Date : 2024-08-22 DOI:10.1093/aob/mcae085
Tao Yuan, Xiaoman Gao, Niyan Xiang, Pei Wei, Guiyu Zhang
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引用次数: 0

摘要

薹草(Carex breviculmis)是一种多年生草本植物,具有良好的抗性,被广泛用于饲草生产和草坪管理。我们组装了 469.01 Mb 的基因组,发现了 37,372 个基因,BUSCO 完整性评分为 99.0%。基因组中有 52.03% 的重复序列,主要是受近期 LTR 插入的影响,这些插入促成了基因组的扩展。系统发育分析表明,C. breviculmis 与 C. littledalei 的分化时间约为 6.61 Mya。对重复序列和扩展基因家族(EGFs)的研究突出表明,串联重复(TD)基因迅速扩展,尤其是在与糖代谢、各种氨基酸合成和苯丙类生物合成相关的领域。此外,我们的分析还发现了参与糖酵解、苯丙类生物合成和氨基酸代谢等次级代谢途径的关键基因,这些基因都经历了正选择。我们重建了蔗糖代谢途径,发现了显著的基因扩增,其中包括与蔗糖代谢相关的 16 个 INV 基因、9 个 SPS 基因和 12 个 SuSy 基因,这些基因都出现了不同程度的扩增。总之,这些基因的扩增加上随后的正选择,促成了 C. breviculmis 适应环境胁迫的能力。这项研究为今后研究薹草植物的进化、环境适应性和潜在的遗传育种奠定了基础。
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The genome assembly of Carex breviculmis provides evidence for its phylogenetic localization and environmental adaptation.

Background and aims: Carex breviculmis is a perennial herb with good resistance and is widely used for forage production and turf management. It is important in ecology, environmental protection and biodiversity conservation, but faces several challenges due to human activities. However, the absence of genome sequences has limited basic research and the improvement of wild plants.

Methods: We annotated the genome of C. breviculmis and conducted a systematic analysis to explore its resistance to harsh environments. We also conducted a comparative analysis of Achnatherum splendens, which is similarly tolerant to harsh environments.

Key results: The assembled the genome comprises 469.01 Mb, revealing 37 372 genes with a BUSCO completeness score of 99.0 %. The genome has 52.03 % repetitive sequences, primarily influenced by recent LTR insertions that have contributed to its expansion. Phylogenetic analysis suggested that C. breviculmis diverged from C. littledalei ~6.61 million years ago. Investigation of repetitive sequences and expanded gene families highlighted a rapid expansion of tandem duplicate genes, particularly in areas related to sugar metabolism, synthesis of various amino acids, and phenylpropanoid biosynthesis. Additionally, our analysis identified crucial genes involved in secondary metabolic pathways, such as glycolysis, phenylpropanoid biosynthesis and amino acid metabolism, which have undergone positive selection. We reconstructed the sucrose metabolic pathway and identified significant gene expansions, including 16 invertase, 9 sucrose phosphate synthase and 12 sucrose synthase genes associated with sucrose metabolism, which showed varying levels of expansion.

Conclusions: The expansion of these genes, coupled with subsequent positive selection, contributed to the ability of C. breviculmis to adapt to environmental stressors. This study lays the foundation for future research on the evolution of Carex plants, their environmental adaptations, and potential genetic breeding.

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来源期刊
Annals of botany
Annals of botany 生物-植物科学
CiteScore
7.90
自引率
4.80%
发文量
138
审稿时长
3 months
期刊介绍: Annals of Botany is an international plant science journal publishing novel and rigorous research in all areas of plant science. It is published monthly in both electronic and printed forms with at least two extra issues each year that focus on a particular theme in plant biology. The Journal is managed by the Annals of Botany Company, a not-for-profit educational charity established to promote plant science worldwide. The Journal publishes original research papers, invited and submitted review articles, ''Research in Context'' expanding on original work, ''Botanical Briefings'' as short overviews of important topics, and ''Viewpoints'' giving opinions. All papers in each issue are summarized briefly in Content Snapshots , there are topical news items in the Plant Cuttings section and Book Reviews . A rigorous review process ensures that readers are exposed to genuine and novel advances across a wide spectrum of botanical knowledge. All papers aim to advance knowledge and make a difference to our understanding of plant science.
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