Applications in Plant Sciences最新文献_第2页

Guidelines for quantifying leaf chlorophyll content via non-destructive spectrometry 通过无损光谱法量化叶片叶绿素含量的指南

IF 2.7 3区生物学 Q2 PLANT SCIENCES

Applications in Plant Sciences

Pub Date : 2024-08-03 DOI: 10.1002/aps3.11610

Giancarlo M. Chiarenza, Eve Slavich, Angela T. Moles

Premise

Leaf chlorophyll is a fundamental bioindicator used in several fields; however, we lack clear guidelines for optimizing sampling efforts and producing comparable studies.

Methods

We estimated the leaf chlorophyll content of 10 plant species using nondestructive spectrometry methods. We stored half of the leaves at 4°C and half at room temperature under similar light levels to assess the role of storage in the chlorophyll degradation rate.

Results

The chilled mature leaves maintained a chlorophyll content within 5% of the original value for ~1.5 d, while the chlorophyll content of unrefrigerated mature leaves decreased rapidly, indicating that their chlorophyll content should be measured within 4 h. When refrigerated, the chlorophyll content of the expanding leaves remained within 5% of the original level for at least 5 d, but we suggest analyzing them within 3 d. In mature leaves, 73% of the variation in chlorophyll content is at the species level, 15% is between individuals, and the variation within leaves is negligible (<1%). Measuring one mature leaf from eight individuals was sufficient to provide a species chlorophyll estimate within 5% of the true value at least 80% of the time.

Discussion

We advise researchers to prioritize sampling more individuals rather than repeating measures within leaves or individuals. Our findings will help researchers to optimize their time and research efforts, and to obtain more robust ecological data.

前言叶片叶绿素是多个领域使用的基本生物指标；然而，我们缺乏明确的指导方针来优化取样工作并进行可比研究。方法我们使用无损光谱法估算了 10 种植物的叶片叶绿素含量。结果冷藏成熟叶片的叶绿素含量在约 1.5 d 内保持在原始值的 5%以内，而未冷藏成熟叶片的叶绿素含量迅速下降，这表明叶绿素含量应在 4 h 内测量。成熟叶片叶绿素含量的变化，73%在物种水平，15%在个体间，叶片内部的变化可以忽略不计（<1%）。我们建议研究人员优先对更多个体进行取样，而不是在叶片或个体内部重复测量。我们的发现将有助于研究人员优化时间和研究工作，并获得更可靠的生态数据。

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引用次数: 0

expowo: An R package for mining global plant diversity and distribution data expowo：用于挖掘全球植物多样性和分布数据的 R 软件包

IF 2.7 3区生物学 Q2 PLANT SCIENCES

Applications in Plant Sciences

Pub Date : 2024-07-30 DOI: 10.1002/aps3.11609

Débora C. Zuanny, Bruno Vilela, Peter W. Moonlight, Tiina E. Särkinen, Domingos Cardoso

Premise

Data on plant distribution and diversity from natural history collections and taxonomic databases are increasingly becoming available online as exemplified by the Royal Botanic Gardens, Kew's Plants of the World Online (POWO) database. This growing accumulation of biodiversity information requires an advance in bioinformatic tools for accessing and processing the massive data for use in downstream science. We present herein expowo, an open-source package that facilitates extracting and using botanical data from POWO.

Methods and Results

The expowo package is implemented in R and designed to handle the entire vascular plant tree of life. It includes functions to readily distill taxonomic and distributional information about all families, genera, or species of vascular plants. It outputs a complete list of species in each genus of any plant family, with the associated original publication, synonyms, and distribution, and plots global maps of species richness at the country and botanical country levels, as well as graphs displaying species-discovery accumulation curves and nomenclatural changes over time. To demonstrate expowo's strengths in producing easy-to-handle outputs, we also show empirical examples from a set of biodiverse countries and representative species-rich and ecologically important angiosperm families.

Conclusions

By harnessing bioinformatic tools that accommodate varying levels of R programming proficiency, expowo functions assist users who have limited R programming expertise in efficiently distilling specific botanical information from online sources and producing maps and graphics for the further interpretation of biogeographic and taxonomic patterns.

前言来自自然历史收藏和分类数据库的植物分布和多样性数据越来越多地在网上提供，英国皇家植物园邱园的世界植物在线（POWO）数据库就是一例。生物多样性信息的不断积累需要生物信息学工具的进步，以便访问和处理海量数据，用于下游科学研究。我们在此介绍一个开源软件包expowo，它有助于从POWO中提取和使用植物学数据。方法与结果expowo软件包由R语言实现，旨在处理整个维管植物生命树。它包含的功能可轻松提炼出维管植物所有科、属或种的分类和分布信息。它可输出任何植物科中每个属的完整物种列表，包括相关的原始出版物、同义词和分布情况，并绘制国家和植物学国家级别的物种丰富度全球地图，以及显示物种发现积累曲线和命名法随时间变化的图表。为了展示 expowo 在生成易于处理的输出结果方面的优势，我们还展示了一组生物多样性国家和具有代表性的物种丰富且在生态学上具有重要意义的被子植物科的经验实例。

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引用次数: 0

A machine learning algorithm for the automatic classification of Phytophthora infestans genotypes into clonal lineages 将 Phytophthora infestans 基因型自动分类为克隆系的机器学习算法

IF 2.7 3区生物学 Q2 PLANT SCIENCES

Applications in Plant Sciences

Pub Date : 2024-07-23 DOI: 10.1002/aps3.11603

Camilo Patarroyo, Stéphane Dupas, Silvia Restrepo

Premise

The prompt categorization of Phytophthora infestans isolates into described clonal lineages is a key tool for the management of its associated disease, potato late blight. New isolates of this pathogen are currently classified by comparing their microsatellite genotypes with characterized clonal lineages, but an automated classification tool would greatly improve this process. Here, we developed a flexible machine learning–based classifier for P. infestans genotypes.

Methods

The performance of different machine learning algorithms in classifying P. infestans genotypes into its clonal lineages was preliminarily evaluated with decreasing amounts of training data. The four best algorithms were then evaluated using all collected genotypes.

Results

mlpML, cforest, nnet, and AdaBag performed best in the preliminary test, correctly classifying almost 100% of the genotypes. AdaBag performed significantly better than the others when tested using the complete data set (Tukey HSD P < 0.001). This algorithm was then implemented in a web application for the automated classification of P. infestans genotypes, which is freely available at https://github.com/cpatarroyo/genotypeclas.

Discussion

We developed a gradient boosting–based tool to automatically classify P. infestans genotypes into its clonal lineages. This could become a valuable resource for the prompt identification of clonal lineages spreading into new regions.

前言将侵染病菌分离物迅速归类到描述的克隆系中是管理其相关病害马铃薯晚疫病的关键工具。目前，这种病原体的新分离物是通过比较其微卫星基因型和特征克隆系来进行分类的，但自动分类工具将大大改进这一过程。在此，我们为 P. infestans 基因型开发了一种灵活的基于机器学习的分类器。方法通过减少训练数据量，初步评估了不同机器学习算法在将 P. infestans 基因型归入其克隆系方面的性能。结果mlpML、cforest、nnet 和 AdaBag 在初步测试中表现最佳，几乎 100% 正确地对基因型进行了分类。在使用完整数据集进行测试时，AdaBag 的表现明显优于其他算法（Tukey HSD P < 0.001）。该算法随后被应用于一个用于自动分类 P. infestans 基因型的网络应用程序中，该程序可在 https://github.com/cpatarroyo/genotypeclas.DiscussionWe 免费获取。该程序开发了一种基于梯度提升的工具，用于将 P. infestans 基因型自动分类为其克隆系。这将成为迅速识别扩散到新地区的克隆系的宝贵资源。

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引用次数: 0

Variant calling in polyploids for population and quantitative genetics 多倍体中的变异调用，用于群体遗传学和数量遗传学

IF 2.7 3区生物学 Q2 PLANT SCIENCES

Applications in Plant Sciences

Pub Date : 2024-07-17 DOI: 10.1002/aps3.11607

Alyssa R. Phillips

Advancements in genome assembly and sequencing technology have made whole genome sequence (WGS) data and reference genomes accessible to study polyploid species. Compared to popular reduced-representation sequencing approaches, the genome-wide coverage and greater marker density provided by WGS data can greatly improve our understanding of polyploid species and polyploid biology. However, biological features that make polyploid species interesting also pose challenges in read mapping, variant identification, and genotype estimation. Accounting for characteristics in variant calling like allelic dosage uncertainty, homology between subgenomes, and variance in chromosome inheritance mode can reduce errors. Here, I discuss the challenges of variant calling in polyploid WGS data and discuss where potential solutions can be integrated into a standard variant calling pipeline.

基因组组装和测序技术的进步使得全基因组序列（WGS）数据和参考基因组可以用于研究多倍体物种。与流行的降低代表性测序方法相比，WGS 数据提供的全基因组覆盖率和更高的标记密度可以大大提高我们对多倍体物种和多倍体生物学的认识。然而，使多倍体物种变得有趣的生物学特征也给读图、变异识别和基因型估计带来了挑战。考虑等位基因剂量的不确定性、亚基因组之间的同源性以及染色体遗传模式的差异等变异调用特征可以减少误差。在此，我将讨论在多倍体 WGS 数据中进行变异调用所面临的挑战，并探讨可将哪些潜在解决方案整合到标准变异调用管道中。

引用次数: 0

Polyploidy and the evolution of phenotypic integration: Network analysis reveals relationships among anatomy, morphology, and physiology 多倍体与表型整合的进化：网络分析揭示解剖学、形态学和生理学之间的关系

IF 2.7 3区生物学 Q2 PLANT SCIENCES

Applications in Plant Sciences

Pub Date : 2024-07-16 DOI: 10.1002/aps3.11605

Robert L. Baker, Grace L. Brock, Eastyn L. Newsome, Meixia Zhao

Premise

Most traits are polygenic and most genes are pleiotropic, resulting in complex, integrated phenotypes. Polyploidy presents an excellent opportunity to explore the evolution of phenotypic integration as entire genomes are duplicated, allowing for new associations among traits and potentially leading to enhanced or reduced phenotypic integration. Despite the multivariate nature of phenotypic evolution, studies often rely on simplistic bivariate correlations that cannot accurately represent complex phenotypes or data reduction techniques that can obscure specific trait relationships.

Methods

We apply network modeling, a common gene co-expression analysis, to the study of phenotypic integration to identify multivariate patterns of phenotypic evolution, including anatomy and morphology (structural) and physiology (functional) traits in response to whole genome duplication in the genus Brassica.

Results

We identify four key structural traits that are overrepresented in the evolution of phenotypic integration. Seeding networks with key traits allowed us to identify structure–function relationships not apparent from bivariate analyses. In general, allopolyploids exhibited larger, more robust networks indicative of increased phenotypic integration compared to diploids.

Discussion

Phenotypic network analysis may provide important insights into the effects of selection on non-target traits, even when they lack direct correlations with the target traits. Network analysis may allow for more nuanced predictions of both natural and artificial selection.

前提大多数性状是多基因性的，而大多数基因是多效的，从而导致复杂的综合表型。多倍体是探索表型整合进化的绝佳机会，因为整个基因组被复制，使性状之间产生新的关联，并可能导致表型整合的增强或减弱。尽管表型进化具有多变量的性质，但研究往往依赖于简单的二变量相关性，而这种相关性不能准确地代表复杂的表型，或者依赖于数据缩减技术，而这种技术可能会掩盖特定的性状关系。方法我们将网络建模（一种常见的基因共表达分析方法）应用于表型整合研究，以确定表型进化的多变量模式，包括芸苔属全基因组复制时的解剖学和形态学（结构）以及生理学（功能）性状。利用关键性状构建网络使我们能够识别双变量分析中不明显的结构-功能关系。一般来说，与二倍体相比，异源多倍体表现出更大、更稳健的网络，表明表型整合程度有所提高。讨论表型网络分析可为了解选择对非目标性状的影响提供重要信息，即使这些性状与目标性状缺乏直接相关性。网络分析可以对自然选择和人工选择进行更细致的预测。

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引用次数: 0

nQuack: An R package for predicting ploidal level from sequence data using site-based heterozygosity nQuack：利用基于位点的杂合度从序列数据预测倍体水平的 R 软件包

IF 2.7 3区生物学 Q2 PLANT SCIENCES

Applications in Plant Sciences

Pub Date : 2024-07-14 DOI: 10.1002/aps3.11606

Michelle L. Gaynor, Jacob B. Landis, Timothy K. O'Connor, Robert G. Laport, Jeff J. Doyle, Douglas E. Soltis, José Miguel Ponciano, Pamela S. Soltis

Premise

Traditional methods of ploidal-level estimation are tedious; using DNA sequence data for cytotype estimation is an ideal alternative. Multiple statistical approaches to leverage sequence data for ploidy inference based on site-based heterozygosity have been developed. However, these approaches may require high-coverage sequence data, use inappropriate probability distributions, or have additional statistical shortcomings that limit inference abilities. We introduce nQuack, an open-source R package that addresses the main shortcomings of current methods.

Methods and Results

nQuack performs model selection for improved ploidy predictions. Here, we implement expectation maximization algorithms with normal, beta, and beta-binomial distributions. Using extensive computer simulations that account for variability in sequencing depth, as well as real data sets, we demonstrate the utility and limitations of nQuack.

Conclusions

Inferring ploidy based on site-based heterozygosity alone is difficult. Even though nQuack is more accurate than similar methods, we suggest caution when relying on any site-based heterozygosity method to infer ploidy.

前提传统的倍性水平估算方法非常繁琐；利用 DNA 序列数据进行细胞型估算是一种理想的替代方法。目前已开发出多种统计方法，利用序列数据进行基于位点杂合度的倍性推断。然而，这些方法可能需要高覆盖率的序列数据、使用不恰当的概率分布，或存在其他限制推断能力的统计缺陷。我们介绍了一个开源 R 软件包 nQuack，它能解决当前方法的主要缺陷。方法与结果nQuack 能进行模型选择以改进倍性预测。在这里，我们使用正态分布、贝塔分布和贝塔二叉分布实现了期望最大化算法。结论仅根据基于位点的杂合度来推测倍性是很困难的。尽管 nQuack 比类似的方法更准确，但我们建议在依赖任何基于位点的杂合度方法来推断倍性时要谨慎。

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引用次数: 0

Bringing genomics to the field: An integrative approach to seed sourcing for forest restoration 将基因组学带入实地：为森林恢复寻找种子的综合方法

IF 2.7 3区生物学 Q2 PLANT SCIENCES

Applications in Plant Sciences

Pub Date : 2024-06-20 DOI: 10.1002/aps3.11600

Anoob Prakash, Thibaut Capblancq, Kathryn Shallows, David Saville, Deborah Landau, Chad Landress, Tal Jacobs, Stephen Keller

Premise

Global anthropogenic change threatens the health and productivity of forest ecosystems. Assisted migration and reforestation are tools to help mitigate these impacts. However, questions remain about how to approach sourcing seeds to ensure high establishment and future adaptability.

Methods

Using exome-capture sequencing, we demonstrate a computational approach to finding the best n-sets from a candidate list of seed sources that collectively achieve high genetic diversity (GD) and minimal genetic load (GL), while also increasing evolvability in quantitative traits. The benefits of this three-part strategy (diversity-load-evolvability) are to increase near-term establishment success while also boosting evolutionary potential to respond to future stressors. Members of The Nature Conservancy and the Central Appalachian Spruce Restoration Initiative planted 58,000 seedlings across 255 acres. A subset of seedlings was monitored for establishment success and variation in growth.

Results

The results show gains in GD relative to GL and increases in quantitative genetic variation in seedling growth for pooled vs. single-source restoration. No single “super source” was observed across planting sites; rather, monitoring results demonstrate that pooling of multiple sources helps achieve higher GD:GL and evolvability.

Discussion

Our study shows the potential for integrating genomics into local-scale restoration and the importance of building partnerships between academic researchers and applied conservation managers.

前提全球人为变化威胁着森林生态系统的健康和生产力。协助迁移和重新造林是帮助减轻这些影响的工具。然而，如何寻找种子以确保高建树率和未来的适应性仍然是个问题。方法利用外显子组捕获测序，我们展示了一种计算方法，从种子来源候选列表中找到最佳的 n 组，这些 n 组共同实现了高遗传多样性（GD）和最小遗传负荷（GL），同时还提高了数量性状的可进化性。这种由三部分组成的策略（多样性-遗传负荷-可进化性）的好处是，既能提高近期的建植成功率，又能增强进化潜力，以应对未来的压力。大自然保护协会和中阿巴拉契亚云杉恢复计划的成员在 255 英亩的土地上种植了 58,000 株树苗。对一部分幼苗的成活率和生长变化进行了监测。结果表明，相对于 GL，集合修复与单一来源修复在幼苗生长方面的 GD 和定量遗传变异都有所增加。在各个种植地点都没有观察到单一的 "超级来源"；相反，监测结果表明，汇集多个来源有助于实现更高的 GD:GL 值和可进化性。讨论我们的研究显示了将基因组学融入地方规模恢复的潜力，以及在学术研究人员和应用保护管理人员之间建立合作关系的重要性。

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引用次数: 0

Developing Asparagaceae1726: An Asparagaceae-specific probe set targeting 1726 loci for Hyb-Seq and phylogenomics in the family 开发天门冬科（Asparagaceae）1726：天门冬科（Asparagaceae）特异性探针集，针对该科的 1726 个位点进行 Hyb-Seq 和系统发生组学研究。

IF 2.7 3区生物学 Q2 PLANT SCIENCES

Applications in Plant Sciences

Pub Date : 2024-06-18 DOI: 10.1002/aps3.11597

Philip C. Bentz, Jim Leebens-Mack

Premise

Target sequence capture (Hyb-Seq) is a cost-effective sequencing strategy that employs RNA probes to enrich for specific genomic sequences. By targeting conserved low-copy orthologs, Hyb-Seq enables efficient phylogenomic investigations. Here, we present Asparagaceae1726—a Hyb-Seq probe set targeting 1726 low-copy nuclear genes for phylogenomics in the angiosperm family Asparagaceae—which will aid the often-challenging delineation and resolution of evolutionary relationships within Asparagaceae.

Methods

Here we describe and validate the Asparagaceae1726 probe set (https://github.com/bentzpc/Asparagaceae1726) in six of the seven subfamilies of Asparagaceae. We perform phylogenomic analyses with these 1726 loci and evaluate how inclusion of paralogs and bycatch plastome sequences can enhance phylogenomic inference with target-enriched data sets.

Results

We recovered at least 82% of target orthologs from all sampled taxa, and phylogenomic analyses resulted in strong support for all subfamilial relationships. Additionally, topology and branch support were congruent between analyses with and without inclusion of target paralogs, suggesting that paralogs had limited effect on phylogenomic inference.

Discussion

Asparagaceae1726 is effective across the family and enables the generation of robust data sets for phylogenomics of any Asparagaceae taxon. Asparagaceae1726 establishes a standardized set of loci for phylogenomic analysis in Asparagaceae, which we hope will be widely used for extensible and reproducible investigations of diversification in the family.

前提：目标序列捕获（Hyb-Seq）是一种具有成本效益的测序策略，它利用 RNA 探针来富集特定的基因组序列。通过靶向保守的低拷贝同源物，Hyb-Seq 可以实现高效的系统发生学研究。方法：本文描述并验证了天门冬科七个亚科中六个亚科的天门冬1726探针集（https://github.com/bentzpc/Asparagaceae1726）。我们利用这 1726 个位点进行了系统发生组分析，并评估了加入旁系亲属和副捕获质粒体序列可如何利用目标富集数据集加强系统发生组推断：我们从所有采样类群中恢复了至少 82% 的目标直向同源物，系统发生组分析结果表明，所有亚科关系都得到了强有力的支持。此外，在纳入和不纳入目标同源物的分析中，拓扑结构和分支支持是一致的，这表明同源物对系统发生组推断的影响有限：讨论：Asparagaceae1726 在整个天南星科中都很有效，能够为任何天南星科类群的系统发生组学生成稳健的数据集。Asparagaceae1726为天门冬科的系统发生组分析建立了一套标准化的位点，我们希望这套位点能被广泛用于天门冬科多样化的可扩展和可重复的研究。

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引用次数: 0

Conservation applications of niche modeling: Native and naturalized ferns may compete for limited Hawaiian dryland habitat 生态位建模在保护方面的应用：本地蕨类植物和归化蕨类植物可能会争夺有限的夏威夷旱地栖息地

IF 2.7 3区生物学 Q2 PLANT SCIENCES

Applications in Plant Sciences

Pub Date : 2024-06-14 DOI: 10.1002/aps3.11598

Krystalyn Edwards-Calma, Laura Jiménez, Rosana Zenil-Ferguson, Karolina Heyduk, Miles K. Thomas, Carrie M. Tribble

Premise

Competition from naturalized species and habitat loss are common threats to native biodiversity and may act synergistically to increase competition for decreasing habitat availability. We use Hawaiian dryland ferns as a model for the interactions between land-use change and competition from naturalized species in determining habitat availability.

Methods

We used fine-resolution climatic variables and carefully curated occurrence data from herbaria and community science repositories to estimate the distributions of Hawaiian dryland ferns. We quantified the degree to which naturalized ferns tend to occupy areas suitable for native species and mapped the remaining available habitat given land-use change.

Results

Of all native species, Doryopteris angelica had the lowest percentage of occurrences of naturalized species in its suitable area while D. decora had the highest. However, all Doryopteris spp. had a higher percentage overlap, while Pellaea ternifolia had a lower percentage overlap, than expected by chance. Doryopteris decora and D. decipiens had the lowest proportions (<20%) of suitable area covering native habitat.

Discussion

Areas characterized by shared environmental preferences of native and naturalized ferns may decrease due to human development and fallowed agricultural lands. Our study demonstrates the value of place-based application of a recently developed correlative ecological niche modeling approach for conservation risk assessment in a rapidly changing and urbanized island ecosystem.

前提归化物种的竞争和栖息地的丧失是本地生物多样性面临的共同威胁，它们可能会协同作用，加剧对栖息地可用性下降的竞争。我们以夏威夷旱地蕨类植物为模型，研究土地利用变化与归化物种竞争在决定栖息地可用性方面的相互作用。方法我们使用精细分辨率的气候变量以及来自标本馆和社区科学资料库的精心整理的出现数据来估计夏威夷旱地蕨类植物的分布。我们对归化蕨类植物倾向于占据适合本地物种生长的区域的程度进行了量化，并绘制了土地利用变化情况下剩余可用栖息地的地图。结果在所有本地物种中，当归蕨（Doryopteris angelica）在其适宜区域内出现归化物种的比例最低，而花蕨蕨（D. decora）的比例最高。然而，所有鲯鳅属植物的重叠百分比都比预期的要高，而蕨类植物的重叠百分比则比预期的要低。Doryopteris decora和D. decipiens的适宜区覆盖原生栖息地的比例最低（20%）。讨论由于人类开发和农田休耕，具有原生和归化蕨类植物共同环境偏好特征的区域可能会减少。我们的研究表明，在一个快速变化和城市化的岛屿生态系统中，基于地点应用最近开发的相关生态位建模方法进行保护风险评估很有价值。

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引用次数: 0

Genome-wide patterns of homoeologous gene flow in allotetraploid coffee 全基因组同源基因在四倍体咖啡中的流动模式

IF 2.7 3区生物学 Q2 PLANT SCIENCES

Applications in Plant Sciences

Pub Date : 2024-06-14 DOI: 10.1002/aps3.11584

Andre J. Ortiz, Joel Sharbrough

Premise

Allopolyploidy—a hybridization-induced whole-genome duplication event—has been a major driver of plant diversification. The extent to which chromosomes pair with their proper homolog vs. with their homoeolog in allopolyploids varies across taxa, and methods to detect homoeologous gene flow (HGF) are needed to understand how HGF has shaped polyploid lineages.

Methods

The ABBA-BABA test represents a classic method for detecting introgression between closely related species, but here we developed a modified use of the ABBA-BABA test to characterize the extent and direction of HGF in allotetraploid Coffea arabica.

Results

We found that HGF is abundant in the C. arabica genome, with both subgenomes serving as donors and recipients of variation. We also found that HGF is highly maternally biased in plastid-targeted—but not mitochondrial-targeted—genes, as would be expected if plastid–nuclear incompatibilities exist between the two parent species.

Discussion

Together, our analyses provide a simple framework for detecting HGF and new evidence consistent with selection favoring overwriting of paternally derived alleles by maternally derived alleles to ameliorate plastid–nuclear incompatibilities. Natural selection therefore appears to shape the direction and intensity of HGF in allopolyploid coffee, indicating that cytoplasmic inheritance has long-term consequences for polyploid lineages.

前提条件异源多倍体--杂交诱导的全基因组复制事件--一直是植物多样化的主要驱动力。在异源多倍体中，染色体与其同源染色体配对与与其同源染色体配对的程度因类群而异，因此需要检测同源基因流（HGF）的方法来了解 HGF 是如何形成多倍体系的。方法 ABBA-BABA 检验是检测近缘物种间引种的经典方法，但在此我们开发了一种经过改良的 ABBA-BABA 检验方法，以确定阿拉伯咖啡（Coffea arabica）异源四倍体中 HGF 的程度和方向。结果我们发现 HGF 在阿拉伯咖啡基因组中含量丰富，两个亚基因组都是变异的供体和受体。我们还发现，HGF 在质粒靶向基因中具有高度的母性偏向，而在线粒体靶向基因中则没有这种偏向，如果两个亲本之间存在质粒-核不相容的情况，就会出现这种情况。讨论总之，我们的分析为检测 HGF 提供了一个简单的框架，并提供了新的证据，证明选择有利于用母本等位基因覆盖父本等位基因，以改善质核不相容性。因此，自然选择似乎决定了全多倍体咖啡中HGF的方向和强度，表明细胞质遗传对多倍体品系具有长期影响。

{"title":"Genome-wide patterns of homoeologous gene flow in allotetraploid coffee","authors":"Andre J. Ortiz, Joel Sharbrough","doi":"10.1002/aps3.11584","DOIUrl":"https://doi.org/10.1002/aps3.11584","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Allopolyploidy—a hybridization-induced whole-genome duplication event—has been a major driver of plant diversification. The extent to which chromosomes pair with their proper homolog vs. with their homoeolog in allopolyploids varies across taxa, and methods to detect homoeologous gene flow (HGF) are needed to understand how HGF has shaped polyploid lineages.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>The ABBA-BABA test represents a classic method for detecting introgression between closely related species, but here we developed a modified use of the ABBA-BABA test to characterize the extent and direction of HGF in allotetraploid <i>Coffea arabica</i>.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We found that HGF is abundant in the <i>C. arabica</i> genome, with both subgenomes serving as donors and recipients of variation. We also found that HGF is highly maternally biased in plastid-targeted—but not mitochondrial-targeted—genes, as would be expected if plastid–nuclear incompatibilities exist between the two parent species.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Together, our analyses provide a simple framework for detecting HGF and new evidence consistent with selection favoring overwriting of paternally derived alleles by maternally derived alleles to ameliorate plastid–nuclear incompatibilities. Natural selection therefore appears to shape the direction and intensity of HGF in allopolyploid coffee, indicating that cytoplasmic inheritance has long-term consequences for polyploid lineages.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 4","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11584","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142045281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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