Algal genes in aplastidic eukaryotes are not necessarily derived from historical plastids

In photosynthetic eukaryotes, many genes were transferred from plastids or algal endosymbionts to nuclear genomes of host cells. These transferred genes are often considered genetic footprints of plastids. However, genes of algal origin have also been detected in some plastid-lacking eukaryotes, and these genes are often cited as evidence of historical plastids. In this paper, we discuss two recent publications about algal genes in plastid-lacking eukaryotes. Both studies highlight the point that algal genes are not exclusively derived from historical plastids. Instead, the findings show that gene acquisition through feeding activities is a plausible explanation

Concerted gene recruitment in early plant evolution

Analyses of the red algal Cyanidioschyzon genome identified 37 genes that were acquired from non-organellar sources prior to the split of red algae and green plants

Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids?

© 2007 Huang and Gogarten. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Genome Biology 8 (2007): R99, doi:10.1186/gb-2007-8-6-r99.Ancient endosymbioses are responsible for the origins of mitochondria and plastids, and they contribute to the divergence of several major eukaryotic groups. Although chlamydiae, a group of obligate intracellular bacteria, are not found in plants, an unexpected number of chlamydial genes are most similar to plant homologs, which, interestingly, often contain a plastid-targeting signal. This observation has prompted several hypotheses, including gene transfer between chlamydiae and plant-related groups and an ancestral relationship between chlamydiae and cyanobacteria. We conducted phylogenomic analyses of the red alga Cyanidioschyzon merolae to identify genes specifically related to chlamydial homologs. We show that at least 21 genes were transferred between chlamydiae and primary photosynthetic eukaryotes, with the donor most similar to the environmental Protochlamydia. Such an unusually high number of transferred genes suggests an ancient chlamydial endosymbiosis with the ancestral primary photosynthetic eukaryote. We hypothesize that three organisms were involved in establishing the primary photosynthetic lineage: the eukaryotic host cell, the cyanobacterial endosymbiont that provided photosynthetic capability, and a chlamydial endosymbiont or parasite that facilitated the establishment of the cyanobacterial endosymbiont. Our findings provide a glimpse into the complex interactions that were necessary to establish the primary endosymbiotic relationship between plastid and host cytoplasms, and thereby explain the rarity with which long-term successful endosymbiotic relationships between heterotrophs and photoautotrophs were established. Our data also provide strong and independent support for a common origin of all primary photosynthetic eukaryotes and of the plastids they harbor.This work was performed while JH held a National Research Council Associateship Award at the NASA Astrobiology Institute at the Marine Biological Laboratory in Woods Hole, Massachusetts (NCC2-1054). Additional support was provided through NSF (MCB-0237197) and NASA AISR (NNG04GP90G) grants to JPG

The scale and evolutionary significance of horizontal gene transfer in the choanoflagellate

Background It is generally agreed that horizontal gene transfer (HGT) is common in phagotrophic protists. However, the overall scale of HGT and the cumulative impact of acquired genes on the evolution of these organisms remain largely unknown. Results Choanoflagellates are phagotrophs and the closest living relatives of animals. In this study, we performed phylogenomic analyses to investigate the scale of HGT and the evolutionary importance of horizontally acquired genes in the choanoflagellate Monosiga brevicollis. Our analyses identified 405 genes that are likely derived from algae and prokaryotes, accounting for approximately 4.4% of the Monosiga nuclear genome. Many of the horizontally acquired genes identified in Monosiga were probably acquired from food sources, rather than by endosymbiotic gene transfer (EGT) from obsolete endosymbionts or plastids. Of 193 genes identified in our analyses with functional information, 84 (43.5%) are involved in carbohydrate or amino acid metabolism, and 45 (23.3%) are transporters and/or involved in response to oxidative, osmotic, antibiotic, or heavy metal stresses. Some identified genes may also participate in biosynthesis of important metabolites such as vitamins C and K12, porphyrins and phospholipids. Conclusions Our results suggest that HGT is frequent in Monosiga brevicollis and might have contributed substantially to its adaptation and evolution. This finding also highlights the importance of HGT in the genome and organismal evolution of phagotrophic eukaryotes

Air pollution associated with hospital visits for mental and behavioral disorders in Northeast China

BackgroundRelated studies have found that air pollution is an important factor affecting mental and behavioral disorders. Thus, we performed this time-series study to evaluate the relationship between short-term exposure to ambient air pollutants and visits to hospital by patients with mental and behavioral disorders in northeastern China.MethodsWe used quasi-Poisson regression models and generalized additive models to probe the links between air pollution and mental and behavioral disorders. The possible influences were also explored stratified by season, age and gender.ResultsWe found that sulfur dioxide (SO2) had a cumulative effect on mental and behavioral disorders at lag04–lag07 and had the greatest effect at lag07 [Relative risk (RR) = 1.068, 95%CI = 1.021–1.117]. Particulate matter of size 2.5 μm (PM2.5) and SO2 had a cumulative effect on depression and both had the largest effect at lag07 (RR = 1.021, 95%CI = 1.002–1.041; RR = 1.103, 95%CI = 1.032–1.178); SO2 also had a cumulative effect on anxiety disorders, with the largest effect at lag06 (RR = 1.058, 95%CI = 1.009–1.110). In the stratified analysis, people are more susceptible in the cold season compared to the warm season and females and the 18–60-year age group are more sensitive to air pollutants. It is suggested to strengthen management and preventive measures to decrease air pollution exposure.ConclusionThis study found an association between increased concentrations of air pollutants and increased outpatient visits for mental and behavioral disorders. We recommend that preventive and protective measures should be strengthened in an effort to reduce exposure to air pollution in order to maintain physical and mental health

Analyses of the oligopeptide transporter gene family in poplar and grape

<p>Abstract</p> <p>Background</p> <p>Oligopeptide transporters (OPTs) are a group of membrane-localized proteins that have a broad range of substrate transport capabilities and that are thought to contribute to many biological processes. The OPT proteins belong to a small gene family in plants, which includes about 25 members in Arabidopsis and rice. However, no comprehensive study incorporating phylogeny, chromosomal location, gene structure, expression profiling, functional divergence and selective pressure analysis has been reported thus far for Populus and Vitis.</p> <p>Results</p> <p>In the present study, a comprehensive analysis of the OPT gene family in Populus (<it>P. trichocarpa</it>) and Vitis (<it>V. vinifera</it>) was performed. A total of 20 and 18 full-length OPT genes have been identified in Populus and Vitis, respectively. Phylogenetic analyses indicate that these OPT genes consist of two classes that can be further subdivided into 11 groups. Gene structures are considerably conserved among the groups. The distribution of OPT genes was found to be non-random across chromosomes. A high proportion of the genes are preferentially clustered, indicating that tandem duplications may have contributed significantly to the expansion of the OPT gene family. Expression patterns based on our analyses of microarray data suggest that many OPT genes may be important in stress response and functional development of plants. Further analyses of functional divergence and adaptive evolution show that, while purifying selection may have been the main force driving the evolution of the OPTs, some of critical sites responsible for the functional divergence may have been under positive selection.</p> <p>Conclusions</p> <p>Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the Populus and Vitis OPT gene family and of the function and evolution of the OPT gene family in higher plants.</p

Recovery of Outliers in Water Environment Monitoring Data

The water environment monitoring data are time sequences with outliers which depress the data quality, so outlier detection and recovery play an important role in the applications such as knowledge acquisition and prediction modelling of water environment indicators. To detect the outliers, the short-term chain comparison with the sliding window based on the time sequence characteristics is adopted. To recover outliers closer to the real data at that time, the sub-sequences are divided dynamically according to the change characteristics of the dataset, then the similarity between sub-sequences is measured by the shape distance and the outliers are recovered according to the change trend of the corresponding data in the most similar sub-sequences. The monitoring data of a water station are selected in the study. The experimental results show that the recovery method is superior to the commonly used prediction recovery method and fitting recovery method, the recovered data is smoother and the short-term trend is more obvious

Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses?

<p>Abstract</p> <p>Background</p> <p>How photosynthetic organelles, or plastids, were acquired by diverse eukaryotes is among the most hotly debated topics in broad scale eukaryotic evolution. The history of plastid endosymbioses commonly is interpreted under the "chromalveolate" hypothesis, which requires numerous plastid losses from certain heterotrophic groups that now are entirely aplastidic. In this context, discoveries of putatively algal genes in plastid-lacking protists have been cited as evidence of gene transfer from a photosynthetic endosymbiont that subsequently was lost completely. Here we examine this evidence, as it pertains to the chromalveolate hypothesis, through genome-level statistical analyses of similarity scores from queries with two diatoms, <it>Phaeodactylum tricornutum </it>and <it>Thalassiosira pseudonana</it>, and two aplastidic sister taxa, <it>Phytophthora ramorum </it>and <it>P. sojae</it>.</p> <p>Results</p> <p>Contingency tests of specific predictions of the chromalveolate model find no evidence for an unusual red algal contribution to <it>Phytophthora </it>genomes, nor that putative cyanobacterial sequences that are present entered these genomes through a red algal endosymbiosis. Examination of genes unrelated to plastid function provide extraordinarily significant support for both of these predictions in diatoms, the control group where a red endosymbiosis is known to have occurred, but none of that support is present in genes specifically conserved between diatoms and oomycetes. In addition, we uncovered a strong association between overall sequence similarities among taxa and relative sizes of genomic data sets in numbers of genes.</p> <p>Conclusion</p> <p>Signal from "algal" genes in oomycete genomes is inconsistent with the chromalveolate hypothesis, and better explained by alternative models of sequence and genome evolution. Combined with the numerous sources of intragenomic phylogenetic conflict characterized previously, our results underscore the potential to be mislead by <it>a posteriori </it>interpretations of variable phylogenetic signals contained in complex genome-level data. They argue strongly for explicit testing of the different <it>a priori </it>assumptions inherent in competing evolutionary hypotheses.</p

Water Quality Prediction Method Based on OVMD and Spatio-Temporal Dependence

Water quality changes at one monitoring spot are not only related to local historical data but also spatially to the water quality of the adjacent spots. Additionally, the non-linear and non-stationary nature of water quality data has a significant impact on prediction results. To improve the accuracy of water quality prediction models, a comprehensive water quality prediction model has been initially established that takes into account both data complexity and spatio-temporal dependencies. The Optimal Variational Mode Decomposition (OVMD) technology is used to effectively decompose water quality data into several simple and stable time series, highlighting short-term and long-term features and enhancing the model\u27s learning ability. The component sequence and spot adjacency matrix are used as the input of Graph Convolutional Network (GCN) to extract the spatial characteristics of the data, and the spatio-temporal dependencies of water quality data at different spots are obtained by combining GCN into the neurons of Gated Recurrent Unit (GRU). The attention model is added to automatically adjust the importance of each time node to further improve the accuracy of the training model and obtain a multi-step prediction output that more closely aligns with the characteristics of water quality change. The proposed model has been validated with real monitoring data for ammonia nitrogen (NH3-N) and total phosphorus (TP), and the results show that the proposed model is better than ARIMA, GRU and GCN+GRU models in terms of prediction results and it shows obvious advantages in the benchmark comparison experiment, which can provide reliable evidence for water pollution source traceability or early warning