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通过基因组重新注释和比较分析鉴定辣椒中的新型 PHD-finger 基因。

Identification of novel PHD-finger genes in pepper by genomic re-annotation and comparative analyses.

机构信息

Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea.

出版信息

BMC Plant Biol. 2022 Apr 20;22(1):206. doi: 10.1186/s12870-022-03580-2.

DOI:10.1186/s12870-022-03580-2
PMID:35443608
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9020097/
Abstract

BACKGROUND

The plant homeodomain (PHD)-finger gene family that belongs to zinc-finger genes, plays an important role in epigenetics by regulating gene expression in eukaryotes. However, inaccurate annotation of PHD-finger genes hinders further downstream comparative, evolutionary, and functional studies.

RESULTS

We performed genome-wide re-annotation in Arabidopsis thaliana (Arabidopsis), Oryza sativa (rice), Capsicum annuum (pepper), Solanum tuberosum (potato), and Solanum lycopersicum (tomato) to better understand the role of PHD-finger genes in these species. Our investigation identified 875 PHD-finger genes, of which 225 (26% of total) were newly identified, including 57 (54%) novel PHD-finger genes in pepper. The PHD-finger genes of the five plant species have various integrated domains that may be responsible for the diversification of structures and functions of these genes. Evolutionary analyses suggest that PHD-finger genes were expanded recently by lineage-specific duplication, especially in pepper and potato, resulting in diverse repertoires of PHD-finger genes among the species. We validated the expression of six newly identified PHD-finger genes in pepper with qRT-PCR. Transcriptome analyses suggest potential functions of PHD-finger genes in response to various abiotic stresses in pepper.

CONCLUSIONS

Our data, including the updated annotation of PHD-finger genes, provide useful information for further evolutionary and functional analyses to better understand the roles of the PHD-finger gene family in pepper.

摘要

背景

植物同源结构域（PHD）-手指基因家族属于锌指基因，通过调节真核生物中的基因表达，在表观遗传学中发挥重要作用。然而，PHD-手指基因的注释不准确阻碍了进一步的下游比较、进化和功能研究。

结果

我们在拟南芥（Arabidopsis）、水稻（Oryza sativa）、辣椒（Capsicum annuum）、马铃薯（Solanum tuberosum）和番茄（Solanum lycopersicum）中进行了全基因组重新注释，以更好地了解 PHD-手指基因在这些物种中的作用。我们的研究鉴定了 875 个 PHD-手指基因，其中 225 个（占总数的 26%）是新鉴定的，包括辣椒中的 57 个（54%）新的 PHD-手指基因。这五个植物物种的 PHD-手指基因具有各种整合的结构域，这些结构域可能负责这些基因结构和功能的多样化。进化分析表明，PHD-手指基因最近通过谱系特异性复制扩张，特别是在辣椒和马铃薯中，导致这些物种之间 PHD-手指基因的多样化。我们用 qRT-PCR 验证了辣椒中六个新鉴定的 PHD-手指基因的表达。转录组分析表明 PHD-手指基因在辣椒响应各种非生物胁迫中可能具有潜在的功能。

结论

我们的数据，包括 PHD-手指基因的更新注释，为进一步的进化和功能分析提供了有用的信息，以更好地了解 PHD-手指基因家族在辣椒中的作用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1f44/9020097/1a6fec43fc3c/12870_2022_3580_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1f44/9020097/e614c3da062d/12870_2022_3580_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1f44/9020097/30a892d13bb5/12870_2022_3580_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1f44/9020097/896dfbabe501/12870_2022_3580_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1f44/9020097/15a4097bb29f/12870_2022_3580_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1f44/9020097/e5f5b5f3ca8f/12870_2022_3580_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1f44/9020097/1a6fec43fc3c/12870_2022_3580_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1f44/9020097/e614c3da062d/12870_2022_3580_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1f44/9020097/30a892d13bb5/12870_2022_3580_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1f44/9020097/896dfbabe501/12870_2022_3580_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1f44/9020097/15a4097bb29f/12870_2022_3580_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1f44/9020097/e5f5b5f3ca8f/12870_2022_3580_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1f44/9020097/1a6fec43fc3c/12870_2022_3580_Fig6_HTML.jpg

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本文引用的文献

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2
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3
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4
Genome-Wide Identification and Expression Analysis of the Zinc Finger Protein Gene Subfamilies under Drought Stress in .干旱胁迫下[物种名称未给出]锌指蛋白基因亚家族的全基因组鉴定与表达分析
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5
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Front Plant Sci. 2022 Aug 19;13:967546. doi: 10.3389/fpls.2022.967546. eCollection 2022.
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Nucleic Acids Res. 2021 Nov 18;49(20):11765-11777. doi: 10.1093/nar/gkab932.
4
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