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染色体水平基因组组装和群体基因组分析揭示了红脂大小蠹适应进化的奥秘。

Chromosome-level genome assembly and population genomic analyses provide insights into adaptive evolution of the red turpentine beetle, Dendroctonus valens.

机构信息

College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China.

State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 1000101, China.

出版信息

BMC Biol. 2022 Aug 24;20(1):190. doi: 10.1186/s12915-022-01388-y.


DOI:10.1186/s12915-022-01388-y
PMID:36002826
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9400205/
Abstract

BACKGROUND: Biological invasions are responsible for substantial environmental and economic losses. The red turpentine beetle (RTB), Dendroctonus valens LeConte, is an important invasive bark beetle from North America that has caused substantial tree mortality in China. The lack of a high-quality reference genome seriously limits deciphering the extent to which genetic adaptions resulted in a secondary pest becoming so destructive in its invaded area. RESULTS: Here, we present a 322.41 Mb chromosome-scale reference genome of RTB, of which 98% of assembled sequences are anchored onto fourteen linkage groups including the X chromosome with a N50 size of 24.36 Mb, which is significantly greater than other Coleoptera species. Repetitive sequences make up 45.22% of the genome, which is higher than four other Coleoptera species, i.e., Mountain pine beetle Dendroctonus ponderosae, red flour beetle Tribolium castaneum, blister beetle Hycleus cichorii, and Colorado potato beetle Leptinotarsa decemlineata. We identify rapidly expanded gene families and positively selected genes in RTB, which may be responsible for its rapid environmental adaptation. Population genetic structure of RTB was revealed by genome resequencing of geographic populations in native and invaded regions, suggesting substantial divergence of the North American population and illustrates the possible invasion and spread route in China. Selective sweep analysis highlighted the enhanced ability of Chinese populations in environmental adaptation. CONCLUSIONS: Overall, our high-quality reference genome represents an important resource for genomics study of invasive bark beetles, which will facilitate the functional study and decipher mechanism underlying invasion success of RTB by integrating the Pinus tabuliformis genome.

摘要

背景:生物入侵对环境和经济造成了重大损失。红脂大小蠹(Dendroctonus valens LeConte)是一种来自北美的重要入侵性树皮甲虫,在中国已导致大量树木死亡。缺乏高质量的参考基因组严重限制了对遗传适应导致次要害虫在入侵地区变得如此具有破坏性的程度的理解。

结果:在这里,我们提供了红脂大小蠹的 322.41 Mb 染色体级参考基因组,其中 98%的组装序列锚定在包括 X 染色体在内的 14 条连锁群上,N50 大小为 24.36 Mb,明显大于其他鞘翅目物种。重复序列占基因组的 45.22%,高于其他四个鞘翅目物种,即山松甲虫(Dendroctonus ponderosae)、粉斑螟(Tribolium castaneum)、芫菁(Hyeleus cichorii)和马铃薯甲虫(Leptinotarsa decemlineata)。我们鉴定了红脂大小蠹中快速扩张的基因家族和正选择基因,这可能是其快速环境适应的原因。通过对原产和入侵地区地理种群的基因组重测序揭示了红脂大小蠹的种群遗传结构,表明北美种群存在大量分歧,并说明了其在中国的可能入侵和传播途径。选择压力分析突出了中国种群在环境适应方面的增强能力。

结论:总体而言,我们的高质量参考基因组代表了入侵性树皮甲虫基因组学研究的重要资源,通过整合华山松基因组,将促进红脂大小蠹环境适应能力的功能研究和入侵成功机制的解析。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/379d/9400205/5425035d695b/12915_2022_1388_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/379d/9400205/d782196a9bd4/12915_2022_1388_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/379d/9400205/c00fce6d8000/12915_2022_1388_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/379d/9400205/f6ca145ba8dd/12915_2022_1388_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/379d/9400205/67ed3239d057/12915_2022_1388_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/379d/9400205/5425035d695b/12915_2022_1388_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/379d/9400205/d782196a9bd4/12915_2022_1388_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/379d/9400205/c00fce6d8000/12915_2022_1388_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/379d/9400205/f6ca145ba8dd/12915_2022_1388_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/379d/9400205/67ed3239d057/12915_2022_1388_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/379d/9400205/5425035d695b/12915_2022_1388_Fig5_HTML.jpg

相似文献

[1]
Chromosome-level genome assembly and population genomic analyses provide insights into adaptive evolution of the red turpentine beetle, Dendroctonus valens.

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[2]
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[3]
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[4]
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[7]
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[8]
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[1]
Chromosome-Level Genome Assembly of the Leafcutter Bee Megachile rotundata Reveals Its Ecological Adaptation and Pollination Biology.

Adv Sci (Weinh). 2025-6

[2]
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[3]
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R Soc Open Sci. 2024-12-11

[4]
Chromosome Structural Rearrangements in Invasive Haplodiploid Ambrosia Beetles Revealed by the Genomes of Euwallacea fornicatus (Eichhoff) and Euwallacea similis (Ferrari) (Coleoptera, Curculionidae, Scolytinae).

Genome Biol Evol. 2024-11-1

[5]
Chromosomal-level genome assembly of Hylurgus ligniperda: insights into host adaptation and environmental tolerance.

BMC Genomics. 2024-8-20

[6]
Few chemoreceptor genes in the ambrosia beetle Trypodendron lineatum may reflect its specialized ecology.

BMC Genomics. 2024-8-6

[7]
Genome assembly of the southern pine beetle ( Zimmerman) reveals the origins of gene content reduction in .

bioRxiv. 2024-5-10

[8]
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Sci Data. 2024-3-26

[9]
Evolution and functional role prediction of the CYP6DE and CYP6DJ subfamilies in (Curculionidae: Scolytinae) bark beetles.

Front Mol Biosci. 2023-10-9

[10]
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本文引用的文献

[1]
The Chinese pine genome and methylome unveil key features of conifer evolution.

Cell. 2022-1-6

[2]
Chromosome-level genome assembly reveals genomic architecture of northern range expansion in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae).

Mol Ecol Resour. 2022-4

[3]
The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution.

PLoS Genet. 2021-8

[4]
A high-quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation.

Mol Ecol Resour. 2021-8

[5]
High and rising economic costs of biological invasions worldwide.

Nature. 2021-4

[6]
Investigation of the Molecular Mechanisms of Antioxidant Damage and Immune Response Downregulation in Liver of Under Starvation Stress.

Front Endocrinol (Lausanne). 2021

[7]
A chromosome-level assembly of the harlequin ladybird Harmonia axyridis as a genomic resource to study beetle and invasion biology.

Mol Ecol Resour. 2021-5

[8]
Metabolic Characterization and Consequences of Mitochondrial Pyruvate Carrier Deficiency in .

Metabolites. 2020-9-6

[9]
The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest.

BMC Biol. 2020-7-23

[10]
GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes.

Nat Commun. 2020-3-18

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