Distribution Of Ks Research Articles

Evolution of the R2R3-MYB gene family in six Rosaceae species and expression in woodland strawberry

R2R3-MYB gene family play important roles in plants development, metabolism, and responses to various biotic and abiotic stresses. In this study, 838 R2R3-MYB genes were identified from six Rosaceae species, including 105 in woodland strawberry (Fragaria vesca), 173 in European pear (Pyrus communis), 219 in apple (Malus domestica), 121 in peach (Prunus persica), 121 in Chinese rose (Rosa chinensis), and 99 in black raspberry (Rubus occidentalis). All R2R3-MYB genes in the six Rosaceae species were clustered into 51 species-specific duplicated clades with 109 genes and 50 lineage-specific duplicated clades with 242 genes according to phylogenetic analysis. R2R3-MYB genes were distributed on all chromosomes in each of the six species, with a small amount of tandem duplication events. The proportion of tandem repeat genes ranged from 0 to 25.1%. The R2R3-MYB protein was conserved in a clade and likely to share similar functions. The distribution of Ks showed the duplication times of R2R3-MYB genes in six Rosaceae species. Furthermore, most of the R2R3-MYB genes had Ka/Ks values less than 1, which indicated they were driven by purifying selection during the evolutionary processes. The GO term enrichment analysis revealed that R2R3-MYB genes in strawberry and black raspberry were more divergent than in other Rosaceae species. Analysis of transcriptomes of 42 different tissues and development stages of woodland strawberry showed that high expression levels of R2R3-MYB suggested that the R2R3-MYB genes in strawberry played a key role in growth and development of both vegetative tissues and fruits. The strawberry R2R3-MYB genes in sub-group of S1, S2, S11, S20, and S22 had high expression levels both in young leaves (YL) and old leaves (OL) strawberry tissues under drought treatments.

Transcriptome analysis of two radiated Cycas species and the subsequent species delimitation of the Cycas taiwaniana complex.

Premise Cycas is an important gymnosperm genus, and the most diverse of all cycad genera. The C. taiwaniana complex of species are morphologically similar and difficult to distinguish due to a lack of genomic resources.MethodsWe characterized the transcriptomes of two closely related and endangered Cycas species endemic to Hainan, China: C. hainanensis and C. changjiangensis. Three single‐copy nuclear genes in the C. taiwaniana complex were sequenced based on these transcriptomes, enabling us to evaluate the species boundaries using the multispecies coalescent method implemented in the Bayesian Phylogenetics and Phylogeography program.ResultsWe obtained 68,184 and 81,561 unigenes for C. changjiangensis and C. hainanensis, respectively. We identified six positively selected genes that are mainly involved in stimulus responses, suggesting that environmental adaptation may have played an important role in the relatively recent divergence of these species. The similar KS distribution peaks at 1.0 observed for the paralogs in the two species indicate a common whole‐genome duplication event. Our species delimitation analysis indicated that the C. taiwaniana complex consists of three distinct species, which correspond to the previously reported morphological differences.DiscussionOur study provides valuable genetic resources for Cycas species and guidance for the taxonomic treatment of the C. taiwaniana complex, as well as new insights into evolution of species within Cycas.

Estimation of Field‐Scale Variability in Soil Saturated Hydraulic Conductivity From Rainfall‐Runoff experiments

AbstractSaturated hydraulic conductivity (Ks) is among the important soil properties that influence the partitioning of rainfall into surface and subsurface waters. Point estimates of Ks are difficult to determine and exhibit large spatial variability in fields. Often, data from field‐scale rainfall‐runoff experiments are utilized to assess the properties of the Ks random field that are required in the use of field‐scale infiltration models. Standard methods of calibration are confounded by nonuniqueness and identifiability problems associated with experimental data. In this study, a new method that employed a field‐averaged infiltration model and Monte Carlo simulations was used to obtain the possible range of distributions of Ks that would describe experimental observations over a field for a rainfall event. A Shannon information‐theoretic approach was subsequently adopted to consolidate the ranges of Ks distributions over multiple rainfall events to yield the best range of Ks distributions. The method was applied to data from several rainfall‐runoff events observed under natural conditions over an experimental field characterized by a silty loam soil and a small surface slope. Results suggest the existence of numerous parameter combinations that could satisfy the experimental observations over a single rainfall event, and high variability of these combinations among different events, thereby providing insights regarding the identifiable space of Ks distributions from individual rainfall experiments. Validation results showed that the method provides a realistic estimate of our ability to quantify the spatial variability of Ks in natural fields from rainfall‐runoff experiments.

Comparative transcriptomes and development of expressed sequence tag‐simple sequence repeat markers for two closely related oak species

AbstractQuercus species comprise the major genera in the family Fagaceae and they are widely distributed in the Northern Hemisphere. Many Quercus species, including several endemics, are distributed in China. Genetic resources have been established for the important genera but few transcriptomes are available for Quercus species in China. In this study, we used Illumina paired‐end sequencing to obtain the transcriptomes of two oak species, Q. liaotungensis Koidz. and Q. mongolica Fisch. ex Turcz. Approximately 24 million reads were generated and then a total of 103 618 unigenes were obtained after assembly for both species. Comparative transcriptome analyses of both species identified a total of 12 981 orthologous contigs. The Ka/Ks estimation and enrichment analysis indicated that 1179 (9.08%) orthologs showed rapid evolution, and most of these orthologs were related to functions comprising “DNA repair”, “response to cold”, and “response to drought”. This findings could provide some insights into how these two closely related Quercus species adapted to extreme environments characterized by aridity and cold. The divergence time (approximately 4.27–5.93 Mya) between the two Quercus species was estimated according to the Ks distribution. Moreover, 16 608 simple sequence repeat loci were detected and 12 363 primer pairs were designed. Subsequently, 158 of the 12 363 primer pairs were randomly selected to test the polymorphisms and 92 of the primer pairs were successfully amplified in the two oak species. The resultant orthologs and simple sequence repeat markers are valuable for genetic differentiation analyses and evolutionary studies of Quercus.

Wgd-simple command line tools for the analysis of ancient whole-genome duplications.

SummaryAncient whole-genome duplications (WGDs) have been uncovered in almost all major lineages of life on Earth and the search for traces or remnants of such events has become standard practice in most genome analyses. This is especially true for plants, where ancient WGDs are abundant. Common approaches to find evidence for ancient WGDs include the construction of KS distributions and the analysis of intragenomic colinearity. Despite the increased interest in WGDs and the acknowledgment of their evolutionary importance, user-friendly and comprehensive tools for their analysis are lacking. Here, we present an easy to use command-line tool for KS distribution construction named wgd. The wgd suite provides commonly used KS and colinearity analysis workflows together with tools for modeling and visualization, rendering these analyses accessible to genomics researchers in a convenient manner.Availability and implementationwgd is free and open source software implemented in Python and is available at https://github.com/arzwa/wgd.Supplementary information Supplementary data are available at Bioinformatics online.

Assessing the Performance of Ks Plots for Detecting Ancient Whole Genome Duplications.

Genomic data have provided evidence of previously unknown ancient whole genome duplications (WGDs) and highlighted the role of WGDs in the evolution of many eukaryotic lineages. Ancient WGDs often are detected by examining distributions of synonymous substitutions per site (Ks) within a genome, or “Ks plots.” For example, WGDs can be detected from Ks plots by using univariate mixture models to identify peaks in Ks distributions. We performed gene family simulation experiments to evaluate the effects of different Ks estimation methods and mixture models on our ability to detect ancient WGDs from Ks plots. The simulation experiments, which accounted for variation in substitution rates and gene duplication and loss rates across gene families, tested the effects of WGD age and gene retention rates following WGD on inferring WGDs from Ks plots. Our simulations reveal limitations of Ks plot analyses. Strict interpretations of mixture model analyses often overestimate the number of WGD events, and Ks plot analyses typically fail to detect WGDs when ≤10% of the duplicated genes are retained following the WGD. However, WGDs can accurately be characterized over an intermediate range of Ks. The simulation results are supported by empirical analyses of transcriptomic data, which also suggest that biases in gene retention likely affect our ability to detect ancient WGDs. Although our results indicate mixture model results should be interpreted with great caution, using node-averaged Ks estimates and applying more appropriate mixture models can improve the accuracy of detecting WGDs.

Estimating Saturated Hydraulic Conductivity along a South‐North Transect in the Loess Plateau of China

Core Ideas Ks was estimated using MLR‐type PTFs, ANN‐type PTFs and state‐space analysis. State‐space modeling was scale‐sensitive in estimating Ks in Loess Plateau. Spatial correlations revealed in state‐space analyses were consistent with wavelet coherency. Bulk density, clay content and topography dominated Ks spatial distribution. A precise description of saturated hydraulic conductivity (Ks) and its spatial variability is required for modeling soil and water transport in the vadose zone. Nevertheless, the direct measurement of Ks is expensive and laborious especially for large domains crossing hundreds of kilometers. The objective was to estimate Ks from easily accessible soil properties and environmental factors using pedotransfer functions (PTFs) and state‐space analysis. Along an 860‐km south–north transect in the Loess Plateau of China, soil cores for Ks measurements were collected at depths of 0 to 10, 10 to 20, and 20 to 40 cm at 10‐km intervals from 15 Apr. to 15 May 2013. Multiple linear regression (MLR) and artificial neural network (ANN) were used to derive PTFs for Ks estimation. Based on the eight factors of bulk density, soil organic carbon, sand content, clay content, mean annual precipitation and temperature, slope gradient and elevation, the state‐space analysis appeared to outperform the PTFs in calibrating Ks over the entire transect. The adjusted coefficients of determination (R2adj) for the state‐space models were all greater than 0.9, whereas the corresponding R2adj were much lower for the MLR‐ and ANN‐type PTFs (ranging from 0.398 to 0.880). However, the state‐space approach is quite scale‐sensitive, and overfitting occurred when it was cross‐validated with a leave‐one‐out procedure. It performed almost perfectly in calibration as implied in the R2adj of ∼1 but rather poorly in validation with R2adj typically >0.4. The ANN method exhibited the best Ks estimations at all depths. Both wavelet coherency and state‐space modeling quantified the spatial correlations of Ks with the eight factors investigated and manifested consistent results, that is, bulk density, clay content, and topography were the primary properties controlling Ks distribution. These findings are critical for hydrological modeling and irrigation management in the Loess Plateau of China and possibly other arid and semi‐arid regions.

Variability of streambed hydraulic conductivity in an intermittent stream reach regulated by Vented Dams: A case study

The hydro-geological properties of streambed together with the hydraulic gradients determine the fluxes of water, energy and solutes between the stream and underlying aquifer system. Dam induced sedimentation affects hyporheic processes and alters substrate pore space geometries in the course of progressive stabilization of the sediment layers. Uncertainty in stream-aquifer interactions arises from the inherent complex-nested flow paths and spatio-temporal variability of streambed hydraulic properties. A detailed field investigation of streambed hydraulic conductivity (Ks) using Guelph Permeameter was carried out in an intermittent stream reach of the Pavanje river basin located in the mountainous, forested tract of western ghats of India. The present study reports the spatial and temporal variability of streambed hydraulic conductivity along the stream reach obstructed by two Vented Dams in sequence. Statistical tests such as Levene’s and Welch’s t-tests were employed to check for various variability measures. The strength of spatial dependence and the presence of spatial autocorrelation among the streambed Ks samples were tested by using Moran’s I statistic. The measures of central tendency and dispersion pointed out reasonable spatial variability in Ks distribution throughout the study reach during two consecutive years 2016 and 2017. The streambed was heterogeneous with regard to hydraulic conductivity distribution with high-Ks zones near the backwater areas of the vented dam and low-Ks zones particularly at the tail water section of vented dams. Dam operational strategies were responsible for seasonal fluctuations in sedimentation and modifications to streambed substrate characteristics (such as porosity, grain size, packing etc.), resulting in heterogeneous streambed Ks profiles. The channel downstream of vented dams contained significantly more cohesive deposits of fine sediment due to the overflow of surplus suspended sediment-laden water at low velocity and pressure head. The statistical test results accept the hypothesis of significant spatial variability of streambed Ks but refuse to accept the temporal variations. The deterministic and geo-statistical approaches of spatial interpolation provided virtuous surface maps of streambed Ks distribution.

Impact of soil surface and subsurface properties on soil saturated hydraulic conductivity in the semi-arid Walnut Gulch Experimental Watershed, Arizona, USA

The estimation of saturated hydraulic conductivity (Ks) is of high relevance to correctly reproduce water fluxes, such as infiltration rates or surface runoff in hydrological simulations. Yet, estimation of Ks is challenging especially in semi-arid regions with particular soil surface characteristics like crusting and sealing. This study presents results of a field campaign in the semi-arid Walnut Gulch Experimental Watershed, Arizona (US), where surface and subsurface Ks measurements were undertaken across the watershed. Data of saturated hydraulic conductivity on crust covered and crust-free surfaces was collected and compared to results of commonly used methods to retrieve spatially distributed Ks data. Results reveal that methods typically used for estimating Ks, such as exponential decay functions or pedo-transfer functions (PTFs), can be inadequate in such regions. The analysis shows that in our study area the presence of surface crust is the dominating factor for determining the spatial distribution of Ks. Furthermore, the results reveal that remote sensing data can provide useful information for estimating surface Ks values as it could be successfully applied for the spatial detection of surface crust characteristics.

Scale‐dependency of effective hydraulic conductivity on fire‐affected hillslopes

AbstractEffective hydraulic conductivity (Ke) for Hortonian overland flow modeling has been defined as a function of rainfall intensity and runon infiltration assuming a distribution of saturated hydraulic conductivities (Ks). But surface boundary condition during infiltration and its interactions with the distribution of Ks are not well represented in models. As a result, the mean value of the Ks distribution ( ), which is the central parameter for Ke, varies between scales. Here we quantify this discrepancy with a large infiltration data set comprising four different methods and scales from fire‐affected hillslopes in SE Australia using a relatively simple yet widely used conceptual model of Ke. Ponded disk (0.002 m2) and ring infiltrometers (0.07 m2) were used at the small scales and rainfall simulations (3 m2) and small catchments (ca 3000 m2) at the larger scales. We compared between methods measured at the same time and place. Disk and ring infiltrometer measurements had on average 4.8 times higher values of than rainfall simulations and catchment‐scale estimates. Furthermore, the distribution of Ks was not clearly log‐normal and scale‐independent, as supposed in the conceptual model. In our interpretation, water repellency and preferential flow paths increase the variance of the measured distribution of Ks and bias ponding toward areas of very low Ks during rainfall simulations and small catchment runoff events while areas with high preferential flow capacity remain water supply‐limited more than the conceptual model of Ke predicts. The study highlights problems in the current theory of scaling runoff generation.

Effects of heterogeneity distribution on hillslope stability during rainfalls

The objective of this study was to investigate the spatial relationship between the most likely distribution of saturated hydraulic conductivity (Ks) and the observed pressure head (P) distribution within a hillslope. The cross-correlation analysis method was used to investigate the effects of the variance of lnKs, spatial structure anisotropy of lnKs, and vertical infiltration flux (q) on P at some selected locations within the hillslope. The cross-correlation analysis shows that, in the unsaturated region with a uniform flux boundary, the dominant correlation between P and Ks is negative and mainly occurs around the observation location of P. A relatively high P value is located in a relatively low Ks zone, while a relatively low P value is located in a relatively high Ks zone. Generally speaking, P is positively correlated with q/Ks at the same location in the unsaturated region. In the saturated region, the spatial distribution of Ks can significantly affect the position and shape of the phreatic surface. We therefore conclude that heterogeneity can cause some parts of the hillslope to be sensitive to external hydraulic stimuli (e.g., rainfall and reservoir level change), and other parts of the hillslope to be insensitive. This is crucial to explaining why slopes with similar geometries would show different responses to the same hydraulic stimuli, which is significant to hillslope stability analysis.

Transcriptome analysis of the Holly mangrove Acanthus ilicifolius and its terrestrial relative, Acanthus leucostachyus, provides insights into adaptation to intertidal zones.

BackgroundAcanthus is a unique genus consisting of both true mangrove and terrestrial species; thus, it represents an ideal system for studying the origin and adaptive evolution of mangrove plants to intertidal environments. However, little is known regarding the two respects of mangrove species in Acanthus. In this study, we sequenced the transcriptomes of the pooled roots and leaves tissues for a mangrove species, Acanthus ilicifolius, and its terrestrial congener, A. leucostachyus, to illustrate the origin of the mangrove species in this genus and their adaptive evolution to harsh habitats.ResultsWe obtained 73,039 and 69,580 contigs with N50 values of 741 and 1557 bp for A. ilicifolius and A. leucostachyus, respectively. Phylogenetic analyses based on four nuclear segments and three chloroplast fragments revealed that mangroves and terrestrial species in Acanthus fell into different clades, indicating a single origin of the mangrove species in Acanthus. Based on 6634 orthologs, A. ilicifolius and A. leucostachyus were found to be highly divergent, with a peak of synonymous substitution rate (Ks) distribution of 0.145 and an estimated divergence time of approximately 16.8 million years ago (MYA). The transgression in the Early to Middle Miocene may be the major reason for the entry of the mangrove lineage of Acanthus into intertidal environments. Gene ontology (GO) classifications of the full transcriptomes did not show any apparent differences between A. ilicifolius and A. leucostachyus, suggesting the absence of gene components specific to the mangrove transcriptomes. A total of 99 genes in A. ilicifolius were identified with signals of positive selection. Twenty-three of the 99 positively selected genes (PSGs) were found to be involved in salt, heat and ultraviolet stress tolerance, seed germination and embryo development under periodic inundation. These stress-tolerance related PSGs may be crucial for the adaptation of the mangrove species in this genus to stressful marine environments and may contribute to speciation in Acanthus.ConclusionsWe characterized the transcriptomes of one mangrove species of Acanthus, A. ilicifolius, and its terrestrial relative, A. leucostachyus, and provided insights into the origin of the mangrove Acanthus species and their adaptive evolution to abiotic stresses in intertidal environments.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1813-9) contains supplementary material, which is available to authorized users.

Identification and analysis of retrogenes in the East Asian nematode Caenorhabditis sp. 5 genome.

Retroposition, a molecular mechanism generating new genes, helps the formation of retrogenes and new functions, contributing to the evolution of genomes. The completed genome sequence of Caenorhabditis sp. 5 presents an excellent opportunity to identify retrogenes within C. sp. 5. We identified a total of 43 retrogenes and their corresponding chimeric genes. Among these, 29 were found to be intact retrogenes and 14 to be retropseudogenes. Unexpectedly, a high number of retrogenes appear to be functional and possibly involved in catalysis. Also, the proportion of the retrogenes forming chimeric structure is the highest among Caenorhabditis nematodes. In addition, the Ks distribution shows that C. sp. 5 has more retrogenes with high Ks, which may explain the high functionality of them among Caenorhabditis species. Our study will be helpful in the understanding of the functional and evolutionary impact of retroposition on C. sp. 5 genome.

De novo assembly of the transcriptomes of two yellow mangroves, Ceriops tagal and C. zippeliana, and one of their terrestrial relatives, Pellacalyx yunnanensis

Mangroves are dominant woody plants in the intertidal zones and are of both ecological and economic importance. Species of Ceriops, also called yellow mangroves, have many adaptive traits (including vivipary) for coping with the harsh marine environments. However, little is known about the origination and evolutionary history of this genus. In this study, we aim to provide clues to these two questions by sequencing the transcriptomes of two Ceriops species, Ceriops tagal and Ceriops zippeliana, and one of their terrestrial relatives, Pellacalyx yunnanensis. 48.19, 10.50 and 35.37 million high-quality reads that were generated by Illumina sequencing were assembled into 50,807, 40,543 and 64,147 contigs for the three species, respectively. After removing redundancy and contigs with low coverage, 39,361, 34,362, and 51,668 contigs with the N50 values of 1553, 772 and 1833bp, respectively, were retained for further analysis. Of them, 17,348, 16,484 and 18,038 contigs were successfully annotated with the known gene ontology (GO) terms. GO classifications of the transcriptome profiles for the three species are similar. Most of the contigs were assigned to the cell and organelle related GO terms in the cellular component category, “binding” in the molecular function category, and “cellular process”, “metabolic process” and “biological regulation” in the biological process category. We identified more than 6000 pairs of orthologs for each pair of the three species, with the peak of synonymous substitution rate (Ks) distribution of 0.03 between the two Ceriops species and 0.23 between each Ceriops species and P. yunnanensis. Our transcriptomic data provide a great amount of genomic resources for yellow mangroves and can be used for studying the origination and adaptive evolution of mangroves.

Vertical distribution of soil saturated hydraulic conductivity and its influencing factors in a small karst catchment in Southwest China.

Saturated hydraulic conductivity (Ks) is one of the most important soil hydraulic parameters influencing hydrological processes. This paper aims to investigate the vertical distribution of Ks and to analyze its influencing factors in a small karst catchment in Southwest China. Ks was measured in 23 soil profiles for six soil horizons using a constant head method. These profiles were chosen in different topographical locations (upslope, downslope, and depression) and different land-use types (forestland, shrubland, shrub-grassland, and farmland). The influencing factors of Ks, including rock fragment content (RC), bulk density (BD), capillary porosity (CP), non-capillary porosity (NCP), and soil organic carbon (SOC), were analyzed by partial correlation analysis. The mean Ks value was higher in the entire profile in the upslope and downslope, but lower value, acting as a water-resisting layer, was found in the 10-20 cm soil depth in the depression. Higher mean Ks values were found in the soil profiles in the forestland, shrubland, and shrub-grassland, but lower in the farmland. These results indicated that saturation-excess runoff could occur primarily in the hillslopes but infiltration-excess runoff in the depression. Compared with other land-use types, surface runoff is more likely to occur in the farmlands. RC had higher correlation coefficients with Ks in all categories concerned except in the forestland and farmland with little or no rock fragments, indicating that RC was the dominant influencing factor of Ks. These results suggested that the vertical distributions of Ks and RC should be considered for hydrological modeling in karst areas.

Sequencing of transcriptomes from two Miscanthus species reveals functional specificity in rhizomes, and clarifies evolutionary relationships.

BackgroundMiscanthus is a promising biomass crop for temperate regions. Despite the increasing interest in this plant, limited sequence information has constrained research into its biology, physiology, and breeding. The whole genome transcriptomes of M. sinensis and M. sacchariflorus presented in this study may provide good resources to understand functional compositions of two important Miscanthus genomes and their evolutionary relationships.ResultsFor M. sinensis, a total of 457,891 and 512,950 expressed sequence tags (ESTs) were produced from leaf and rhizome tissues, respectively, which were assembled into 12,166 contigs and 89,648 singletons for leaf, and 13,170 contigs and 112,138 singletons for rhizome. For M. sacchariflorus, a total of 288,806 and 267,952 ESTs from leaf and rhizome tissues, respectively, were assembled into 8,732 contigs and 66,881 singletons for leaf, and 8,104 contigs and 63,212 singletons for rhizome. Based on the distributions of synonymous nucleotide substitution (Ks), sorghum and Miscanthus diverged about 6.2 million years ago (MYA), Saccharum and Miscanthus diverged 4.6 MYA, and M. sinensis and M. sacchariflorus diverged 1.5 MYA. The pairwise alignment of predicted protein sequences from sorghum-Miscanthus and two Miscanthus species found a total of 43,770 and 35,818 nsSNPs, respectively. The impacts of striking mutations found by nsSNPs were much lower between sorghum and Miscanthus than those between the two Miscanthus species, perhaps as a consequence of the much higher level of gene duplication in Miscanthus and resulting ability to buffer essential functions against disturbance.ConclusionsThe ESTs generated in the present study represent a significant addition to Miscanthus functional genomics resources, permitting us to discover some candidate genes associated with enhanced biomass production. Ks distributions based on orthologous ESTs may serve as a guideline for future research into the evolution of Miscanthus species as well as its close relatives sorghum and Saccharum.

Whole Genome Duplication of Intra- and Inter-chromosomes in the Tomato Genome

Whole genome duplication (WGD) events have been proven to occur in the evolutionary history of most angiosperms. Tomato is considered a model species of the Solanaceae family. In this study, we describe the details of the evolutionary process of the tomato genome by detecting collinearity blocks and dating the WGD events on the tree of life by combining two different methods: synonymous substitution rates (Ks) and phylogenetic trees. In total, 593 collinearity blocks were discovered out of 12 pseudo-chromosomes constructed. It was evident that chromosome 2 had experienced an intra-chromosomal duplication event. Major inter-chromosomal duplication occurred among all the pseudo-chromosome. We calculated the Ks value of these collinearity blocks. Two peaks of Ks distribution were found, corresponding to two WGD events occurring approximately 36-82 million years ago (MYA) and 148-205 MYA. Additionally, the results of phylogenetic trees suggested that the more recent WGD event may have occurred after the divergence of the rosid-asterid clade, but before the major diversification in Solanaceae. The older WGD event was shown to have occurred before the divergence of the rosid-asterid clade and after the divergence of rice-Arabidopsis (monocot-dicot).

Profiling of gene duplication patterns of sequenced teleost genomes: evidence for rapid lineage-specific genome expansion mediated by recent tandem duplications

BackgroundGene duplication has had a major impact on genome evolution. Localized (or tandem) duplication resulting from unequal crossing over and whole genome duplication are believed to be the two dominant mechanisms contributing to vertebrate genome evolution. While much scrutiny has been directed toward discerning patterns indicative of whole-genome duplication events in teleost species, less attention has been paid to the continuous nature of gene duplications and their impact on the size, gene content, functional diversity, and overall architecture of teleost genomes.ResultsHere, using a Markov clustering algorithm directed approach we catalogue and analyze patterns of gene duplication in the four model teleost species with chromosomal coordinates: zebrafish, medaka, stickleback, and Tetraodon. Our analyses based on set size, duplication type, synonymous substitution rate (Ks), and gene ontology emphasize shared and lineage-specific patterns of genome evolution via gene duplication. Most strikingly, our analyses highlight the extraordinary duplication and retention rate of recent duplicates in zebrafish and their likely role in the structural and functional expansion of the zebrafish genome. We find that the zebrafish genome is remarkable in its large number of duplicated genes, small duplicate set size, biased Ks distribution toward minimal mutational divergence, and proportion of tandem and intra-chromosomal duplicates when compared with the other teleost model genomes. The observed gene duplication patterns have played significant roles in shaping the architecture of teleost genomes and appear to have contributed to the recent functional diversification and divergence of important physiological processes in zebrafish.ConclusionsWe have analyzed gene duplication patterns and duplication types among the available teleost genomes and found that a large number of genes were tandemly and intrachromosomally duplicated, suggesting their origin of independent and continuous duplication. This is particularly true for the zebrafish genome. Further analysis of the duplicated gene sets indicated that a significant portion of duplicated genes in the zebrafish genome were of recent, lineage-specific duplication events. Most strikingly, a subset of duplicated genes is enriched among the recently duplicated genes involved in immune or sensory response pathways. Such findings demonstrated the significance of continuous gene duplication as well as that of whole genome duplication in the course of genome evolution.

Effects of Measurement Method, Scale, and Landscape Features on Variability of Saturated Hydraulic Conductivity

Knowledge of soil saturated hydraulic conductivity (Ks) and its spatial variation is important to characterize hydrological proc- esses. The objective was to quantify three important variability components, i.e., measurement technique, spatial arrangement in sampling, and differing landscape features (sloped surfaces and gullies), to map Ks distribution in eroded watersheds, such as the Chinese Loess Plateau. Classic and geostatistics were employed to explore the effects of measurement method, sampling scale, and landscape position on the Ks and its spatial variation. In a small watershed with an area of 0.2 km 2 , three techniques, including the soil core (SC), tension infiltration (TI), and Guelph permeameter (GP) methods, were employed to determine the surface Ks at 124 positions on the sloped landscape (minimum sampling space of approximately 10 m). Furthermore, the SC method was applied at 204 positions along four 100-m transects (minimum sampling space of 2 m), and 200 positions along four 10-m transects (minimum sampling space of 0.2 m) on the sloped landscape and 45 positions in the gully areas to determine the surface Ks. The results showed that no significant differences of mean logarithmic value of Ks (Log10 Ks) existed for SC and GP, and the spatial patterns behaved the same for TI and GP. The spatial dependence decreased with a decrease in sampling extent. Structured variability was not observed at the 10-m transect scale. When the minimum sampling space changed from 10 to 2 m, the nugget variance decreased, whereas the structured variance, sill variance, and spatial dependence increased. When minimum sampling space changed from 2 to 0.2 m, the changes in spatial pattern of Ks were negligible, implying that a minimum sampling space of 2 m is needed to capture the spatial pattern of Ks. Ks in the gully areas was significantly less than on the sloped positions. The spatial pattern of Ks changed when the gully positions were included. Gully areas, therefore, should be considered for characterizing the spatial pattern of Ks for watersheds in the Chinese Loess Plateau. DOI: 10.1061/(ASCE)HE.1943-5584.0000630. © 2013 American Society of Civil Engineers. CE Database subject headings: Spatial analysis; Infiltration; Hydraulic conductivity; Measurement. Author keywords: Spatial variability; Gully; Scale; Soil core method; Tension infiltration method; Guelph permeameter method.

Geographic Heterogeneity of Prevalence of the Human Herpesvirus 8 in Sub-Saharan Africa: Clues About Etiology

Human herpesvirus 8 (HHV-8, or Kaposi sarcoma [KS]-associated herpesvirus, KSHV) is a necessary but insufficient cause of KS, as KS develops in few HHV-8-infected persons. In sub-Saharan Africa, marked differences in the geographic distribution of HHV-8 and KS suggest that environmental cofactors influence HHV-8 transmission, control, and progression to KS. However, a direct comparison of HHV-8 prevalence estimates is complicated because studies used different serologic assays and analytic methods. We assessed HHV-8 seropositivity in several African countries with heterogeneous environments and varying KS incidence using a unified approach. HHV-8 antibodies were measured among 3196 adults (aged 20+ years) and 2404 children (aged <20 years) from five studies in four sub-Saharan countries in Africa. Serum samples were tested by the same laboratory using K8.1 and orf73 enzyme immunoassays. Children's HHV-8-seropositivity ranged from 18.1% in Kampala, Uganda, to 33.8% in North Mara, Tanzania, increasing steeply with age in all populations. Among adults, HHV-8-seropositivity ranged from 23.5% in Nigeria to 70.6% in rural West Nile, Uganda. It was higher in males and rural areas. Our data indicate that geographical exposures, gender, age, and factors correlated with rural residence impact HHV-8 seropositivity in sub-Saharan Africa.