The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles ...underlying duplicate gene retention.
We survey 141 sequenced plant genomes to elucidate consequences of gene and genome duplication, processes central to the evolution of biodiversity. We develop a pipeline named DupGen_finder to identify different modes of gene duplication in plants. Genes derived from whole-genome, tandem, proximal, transposed, or dispersed duplication differ in abundance, selection pressure, expression divergence, and gene conversion rate among genomes. The number of WGD-derived duplicate genes decreases exponentially with increasing age of duplication events-transposed duplication- and dispersed duplication-derived genes declined in parallel. In contrast, the frequency of tandem and proximal duplications showed no significant decrease over time, providing a continuous supply of variants available for adaptation to continuously changing environments. Moreover, tandem and proximal duplicates experienced stronger selective pressure than genes formed by other modes and evolved toward biased functional roles involved in plant self-defense. The rate of gene conversion among WGD-derived gene pairs declined over time, peaking shortly after polyploidization. To provide a platform for accessing duplicated gene pairs in different plants, we constructed the Plant Duplicate Gene Database.
We identify a comprehensive landscape of different modes of gene duplication across the plant kingdom by comparing 141 genomes, which provides a solid foundation for further investigation of the dynamic evolution of duplicate genes.
Genome duplication (GD) has permanently shaped the architecture and function of many higher eukaryotic genomes. The angiosperms (flowering plants) are outstanding models in which to elucidate ...consequences of GD for higher eukaryotes, owing to their propensity for chromosomal duplication or even triplication in a few cases. Duplicated genome structures often require both intra- and inter-genome alignments to unravel their evolutionary history, also providing the means to deduce both obvious and otherwise-cryptic orthology, paralogy and other relationships among genes. The burgeoning sets of angiosperm genome sequences provide the foundation for a host of investigations into the functional and evolutionary consequences of gene and GD. To provide genome alignments from a single resource based on uniform standards that have been validated by empirical studies, we built the Plant Genome Duplication Database (PGDD; freely available at http://chibba.agtec.uga.edu/duplication/), a web service providing synteny information in terms of colinearity between chromosomes. At present, PGDD contains data for 26 plants including bryophytes and chlorophyta, as well as angiosperms with draft genome sequences. In addition to the inclusion of new genomes as they become available, we are preparing new functions to enhance PGDD.
Phylogenetic trees are widely used for genetic and evolutionary studies in various organisms. Advanced sequencing technology has dramatically enriched data available for constructing phylogenetic ...trees based on single nucleotide polymorphisms (SNPs). However, massive SNP data makes it difficult to perform reliable analysis, and there has been no ready-to-use pipeline to generate phylogenetic trees from these data.
We developed a new pipeline, SNPhylo, to construct phylogenetic trees based on large SNP datasets. The pipeline may enable users to construct a phylogenetic tree from three representative SNP data file formats. In addition, in order to increase reliability of a tree, the pipeline has steps such as removing low quality data and considering linkage disequilibrium. A maximum likelihood method for the inference of phylogeny is also adopted in generation of a tree in our pipeline.
Using SNPhylo, users can easily produce a reliable phylogenetic tree from a large SNP data file. Thus, this pipeline can help a researcher focus more on interpretation of the results of analysis of voluminous data sets, rather than manipulations necessary to accomplish the analysis.
This paper demonstrates the application of aerial multispectral images in cotton plant phenotyping. Four phenotypic traits (plant height, canopy cover, vegetation index, and flower) were measured ...from multispectral images captured by a multispectral camera on an unmanned aerial system. Data were collected on eight different days from two fields. Ortho-mosaic and digital elevation models (DEM) were constructed from the raw images using the structure from motion (SfM) algorithm. A data processing pipeline was developed to calculate plant height using the ortho-mosaic and DEM. Six ground calibration targets (GCTs) were used to correct the error of the calculated plant height caused by the georeferencing error of the DEM. Plant heights were measured manually to validate the heights predicted from the imaging method. The error in estimation of the maximum height of each plot ranged from -40.4 to 13.5 cm among six datasets, all of which showed strong linear relationships with the manual measurement (R2 > 0.89). Plot canopy was separated from the soil based on the DEM and normalized differential vegetation index (NDVI). Canopy cover and mean canopy NDVI were calculated to show canopy growth over time and the correlation between the two indices was investigated. The spectral responses of the ground, leaves, cotton flower, and ground shade were analyzed and detection of cotton flowers was satisfactory using a support vector machine (SVM). This study demonstrated the potential of using aerial multispectral images for high throughput phenotyping of important cotton phenotypic traits in the field.
A LiDAR-based high-throughput phenotyping (HTP) system was developed for cotton plant phenotyping in the field. The HTP system consists of a 2D LiDAR and an RTK-GPS mounted on a high clearance ...tractor. The LiDAR scanned three rows of cotton plots simultaneously from the top and the RTK-GPS was used to provide the spatial coordinates of the point cloud during data collection. Configuration parameters of the system were optimized to ensure the best data quality. A height profile for each plot was extracted from the dense three dimensional point clouds; then the maximum height and height distribution of each plot were derived. In lab tests, single plants were scanned by LiDAR using 0.5° angular resolution and results showed an R2 value of 1.00 (RMSE = 3.46 mm) in comparison to manual measurements. In field tests using the same angular resolution; the LiDAR-based HTP system achieved average R2 values of 0.98 (RMSE = 65 mm) for cotton plot height estimation; compared to manual measurements. This HTP system is particularly useful for large field application because it provides highly accurate measurements; and the efficiency is greatly improved compared to similar studies using the side view scan.
•A system was developed by using the Kinect-v2 for field-based phenotyping of cotton.•The Kinect-v2 can be used to acquire valid depth images under field conditions.•An algorithm was developed to use ...depth images for cotton plant height measurement.•Correlations (adjusted R2) between system and manual measurements were 0.92–0.98.•Mean relative errors of the system height measurements were less than 8%.
Plant height is an important phenotypic trait that can be used not only as an indicator of overall plant growth but also a parameter to calculate advanced traits such as biomass and yield. Currently, cotton plant height is primarily measured manually, which is laborious and has become a bottleneck for cotton research and breeding programs. The goal of this research was to develop and evaluate a high throughput phenotyping (HTP) system using depth images for measuring cotton plant height under field conditions. For this purpose, a Kinect-v2 camera was evaluated in a static configuration to obtain a performance baseline and in a dynamic configuration to measure plant height in the field. In the static configuration, the camera was mounted on a partially covered wooden frame and oriented towards nadir to acquire depth images of potted cotton plants. Regions of interest of plants were manually selected in the depth images to calculate plant height. In the dynamic configuration, the Kinect-v2 camera was installed inside a partially covered metal-frame that was attached to a high-clearance tractor equipped with real time kinematic GPS. A six-step algorithm was developed to measure the maximum and average heights of individual plots by using the depth images acquired by the system. System performance was evaluated on 108 plots of cotton plants. Results showed that the Kinect-v2 camera could acquire valid depth images of cotton plants under field conditions, when a shaded environment was provided. The plot maximum and average heights calculated by the proposed algorithm were strongly correlated (adjusted R2=0.922–0.987) with those measured manually with accuracies of over 92%. The average processing time was 0.01s to calculate the heights of a plot that typically has 34 depth images, indicating that the proposed algorithm was computationally efficient. Therefore, these results confirmed the ability of the HTP system with depth images to measure cotton plant height under field conditions accurately and rapidly. Furthermore, the imaging-based system has great potential for measuring more complicated geometric traits of plants, which can significantly advance field-based HTP system development in general.
Genome organization and botanical diversity Paterson, Andrew H; Queitsch, Christine
The Plant cell,
2024-May-01, 2024-05-01, 20240501, Letnik:
36, Številka:
5
Journal Article
Recenzirano
The rich diversity of angiosperms, both the planet's dominant flora and the cornerstone of agriculture, is integrally intertwined with a distinctive evolutionary history. Here, we explore the ...interplay between angiosperm genome organization and botanical diversity, empowered by genomic approaches ranging from genetic linkage mapping to analysis of gene regulation. Commonality in the genetic hardware of plants has enabled robust comparative genomics that has provided a broad picture of angiosperm evolution and implicated both general processes and specific elements in contributing to botanical diversity. We argue that the hardware of plant genomes-both in content and in dynamics-has been shaped by selection for rather substantial differences in gene regulation between plants and animals such as maize and human, organisms of comparable genome size and gene number. Their distinctive genome content and dynamics may reflect in part the indeterminate development of plants that puts strikingly different demands on gene regulation than in animals. Repeated polyploidization of plant genomes and multiplication of individual genes together with extensive rearrangement and differential retention provide rich raw material for selection of morphological and/or physiological variations conferring fitness in specific niches, whether natural or artificial. These findings exemplify the burgeoning information available to employ in increasing knowledge of plant biology and in modifying selected plants to better meet human needs.
With many plant genomes sequenced, it is now clear that one distinguishing feature of angiosperm (flowering plant) genomes is their high frequency of whole‐genome duplication. Single‐gene duplication ...is also widespread in angiosperm genomes. Following various mechanisms of gene duplication, genes are often retained or lost in a biased manner, which has suggested recent models for gene family evolution, such as functional buffering and the gene balance hypothesis in addition to now‐classical models, including neofunctionalization and subfunctionalization. Evolutionary consequences of gene duplication, often studied through analyzing gene expression divergence, have enhanced understanding of the biological significance of different mechanisms of gene duplication.
MCScan is an algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes as anchors. The MCScanX toolkit ...implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results and additional downstream analyses. Applications of MCScanX to several sequenced plant genomes and gene families are shown as examples. MCScanX can be used to effectively analyze chromosome structural changes, and reveal the history of gene family expansions that might contribute to the adaptation of lineages and taxa. An integrated view of various modes of gene duplication can supplement the traditional gene tree analysis in specific families. The source code and documentation of MCScanX are freely available at http://chibba.pgml.uga.edu/mcscan2/.
Gene duplication occurs via different modes such as segmental and single-gene duplications. Transposed gene duplication, a specific form of single-gene duplication, 'copies' a gene from an ancestral ...chromosomal location to a novel location. MCScanX is a toolkit for detection and evolutionary analysis of gene colinearity. We have developed MCScanX-transposed, a software package to detect transposed gene duplications that occurred within different epochs, based on execution of MCScanX within and between related genomes. MCScanX-transposed can be also used for integrative analysis of gene duplication modes for a genome and to annotate a gene family of interest with gene duplication modes.
MCScanX-transposed is freely available at http://chibba.pgml.uga.edu/mcscan2/transposed/
Supplementary data are available at Bioinformatics online.
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