无花果蕨类植物 Dryopteris affinis 配子体的转录组分析。

IF 3.6 3区 生物学 Q1 PLANT SCIENCES
Planta Pub Date : 2024-10-02 DOI:10.1007/s00425-024-04540-w
Sara Ojosnegros, José Manuel Alvarez, Valeria Gagliardini, Luis G Quintanilla, Ueli Grossniklaus, Helena Fernández
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引用次数: 0

摘要

主要结论蕨类植物 Dryopteris affinis 的无配子体的新基因组图谱解开了这一复杂植物类群最古老的障碍,从而对进化-退化方法有了深入的了解。蕨类植物 Dryopteris affinis ssp. affinis 的配子体是探索无性繁殖和生殖发育以及应激反应分子基础的良好模型。具体来说,这种蕨类植物通过无性繁殖(apogamy)进行无性繁殖,这是无性繁殖的一种特殊情况,即孢子体直接由配子体细胞形成,无需受精。此前,我们利用 RNA 测序方法注释了 6000 多个转录本。在此,我们选择了 100 个推断出的与拟南芥同源的蛋白质,对它们的潜在功能、蛋白质间的相互作用和距离树进行了详细研究。不出所料,大量与被子植物配子发生和胚胎发生有关的蛋白质被鉴定出来,如FERONIA(FER)和CHR11(CHROMATING REMODELING 11),还有十多个候选蛋白质可能参与了无性繁殖、如 ARGONAUTE 家族(AGO4、AGO9 和 AGO10)、BABY BOOM(BBM)、FASCIATED STEM4(FAS4)、FERTILIZATION-INDEPENDENT ENDOSPERM(FIE)和 MATERNAL EFFECT EMBRYO ARREST29(MEE29)。此外,正如热休克蛋白的富集所显示的那样,参与生物和非生物胁迫响应的蛋白也有广泛的代表性。利用 String 平台,相互作用组显示,大多数蛋白质-蛋白质相互作用是基于实验、数据库和文本挖掘数据集预测的,其中 MULTICOPY SUPPRESSOR OF IRA4(MSI4)显示的相互作用数量最多:16.最后,通过比较与更远或更近的植物类群的排列,通过距离树研究了一些蛋白质。这项分析发现,DCL4 是与预测的共同祖先距离最远的蛋白质。与配子体发育(包括无性繁殖)有关的新基因组信息可以拓展我们目前的进化-变形方法视野。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Transcriptomic analyses in the gametophytes of the apomictic fern Dryopteris affinis.

Main conclusion: A novel genomic map of the apogamous gametophyte of the fern Dryopteris affinis unlocks oldest hindrance with this complex plant group, to gain insight into evo-devo approaches. The gametophyte of the fern Dryopteris affinis ssp. affinis represents a good model to explore the molecular basis of vegetative and reproductive development, as well as stress responses. Specifically, this fern reproduces asexually by apogamy, a peculiar case of apomixis whereby a sporophyte forms directly from a gametophytic cell without fertilization. Using RNA-sequencing approach, we have previously annotated more than 6000 transcripts. Here, we selected 100 of the inferred proteins homolog to those of Arabidopsis thaliana, which were particularly interesting for a detailed study of their potential functions, protein-protein interactions, and distance trees. As expected, a plethora of proteins associated with gametogenesis and embryogenesis in angiosperms, such as FERONIA (FER) and CHROMATING REMODELING 11 (CHR11) were identified, and more than a dozen candidates potentially involved in apomixis, such as ARGONAUTE family (AGO4, AGO9, and AGO 10), BABY BOOM (BBM), FASCIATED STEM4 (FAS4), FERTILIZATION-INDEPENDENT ENDOSPERM (FIE), and MATERNAL EFFECT EMBRYO ARREST29 (MEE29). In addition, proteins involved in the response to biotic and abiotic stresses were widely represented, as shown by the enrichment of heat-shock proteins. Using the String platform, the interactome revealed that most of the protein-protein interactions were predicted based on experimental, database, and text mining datasets, with MULTICOPY SUPPRESSOR OF IRA4 (MSI4) showing the highest number of interactions: 16. Lastly, some proteins were studied through distance trees by comparing alignments with respect to more distantly or closely related plant groups. This analysis identified DCL4 as the most distant protein to the predicted common ancestor. New genomic information in relation to gametophyte development, including apomictic reproduction, could expand our current vision of evo-devo approaches.

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来源期刊
Planta
Planta 生物-植物科学
CiteScore
7.20
自引率
2.30%
发文量
217
审稿时长
2.3 months
期刊介绍: Planta publishes timely and substantial articles on all aspects of plant biology. We welcome original research papers on any plant species. Areas of interest include biochemistry, bioenergy, biotechnology, cell biology, development, ecological and environmental physiology, growth, metabolism, morphogenesis, molecular biology, new methods, physiology, plant-microbe interactions, structural biology, and systems biology.
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