Phylogenetic comparison of 5' splice site determination in central spliceosomal proteins of the U1-70K gene family, in response to developmental cues and stress conditions.

Intron-containing genes have the ability to generate multiple transcript isoforms by splicing, thereby greatly expanding the eukaryotic transcriptome and proteome. In eukaryotic cells, precursor mRNA (pre-mRNA) splicing is performed by a mega-macromolecular complex defined as a spliceosome. Among its splicing components, U1 small nuclear ribonucleoprotein (U1 snRNP) is the smallest subcomplex involved in early spliceosome assembly and 5'-splice site recognition. Its central component, named U1-70K, has been extensively characterized in animals and yeast. Very few investigations on U1-70K genes have been conducted in plants, however. To this end, we performed a comprehensive study to systematically identify 115 U1-70K genes from 67 plant species, ranging from algae to angiosperms. Phylogenetic analysis suggested that the expansion of the plant U1-70K gene family was likely to have been driven by whole-genome duplications. Subsequent comparisons of gene structures, protein domains, promoter regions and conserved splicing patterns indicated that plant U1-70Ks are likely to preserve their conserved molecular function across plant lineages and play an important functional role in response to environmental stresses. Furthermore, genetic analysis using T-DNA insertion mutants suggested that Arabidopsis U1-70K may be involved in response to osmotic stress. Our results provide a general overview of this gene family in Viridiplantae and will act as a reference source for future mechanistic studies on this U1 snRNP-specific splicing factor.

Systematic characterization of the branch point binding protein, splicing factor 1, gene family in plant development and stress responses.

BACKGROUND: Among eukaryotic organisms, alternative splicing is an important process that can generate multiple transcripts from one same precursor messenger RNA, which greatly increase transcriptome and proteome diversity. This process is carried out by a super-protein complex defined as the spliceosome. Specifically, splicing factor 1/branchpoint binding protein (SF1/BBP) is a single protein that can bind to the intronic branchpoint sequence (BPS), connecting the 5' and 3' splice site binding complexes during early spliceosome assembly. The molecular function of this protein has been extensively investigated in yeast, metazoa and mammals. However, its counterpart in plants has been seldomly reported. RESULTS: To this end, we conducted a systematic characterization of the SF1 gene family across plant lineages. In this work, a total of 92 sequences from 59 plant species were identified. Phylogenetic relationships of these sequences were constructed, and subsequent bioinformatic analysis suggested that this family likely originated from an ancient gene transposition duplication event. Most plant species were shown to maintain a single copy of this gene. Furthermore, an additional RNA binding motif (RRM) existed in most members of this gene family in comparison to their animal and yeast counterparts, indicating that their potential role was preserved in the plant lineage. CONCLUSION: Our analysis presents general features of the gene and protein structure of this splicing factor family and will provide fundamental information for further functional studies in plants.

The defense system for Bidens pilosa root exudate treatments in Pteris multifida gametophyte.

According to the novel weapons hypothesis, root exudates are the inhibition factors for native species growth and development through invasive plants. It is hypothesized that antioxidant system (AOS) presents an effective role in plant defense system. The allelopathy indexes of P. multifida gametophyte biomass and sporogonium conversions rates turn negative with the dose and time effects, and the synthetical allelopathic effect index was -55.07% at 100% treatments under root exudates treatments. Under transmission electron microscopy, the cell structures turn burry. Next, AOS and programmed cell death (PCD) were tested in this study. In AOS, strong activities of superoxide dismutase, catalase, glutathione reductase and glutathione S-transferase (GST) were identified in gametophyte cells under the treatments, as well as the contents of glutathione, ascorbic acid and reduced ascorbate, while GPX activity decreased. Based on the input (SOD activity) and the output (GST activity) of antioxidant system, and the decreasing system control would be a reason leading gametophyte death under root exudates. At day 10, PCD would get its peak of 46.93% at 100% root exudates. We found a dynamic balance of PCD and AOS under the exudates treatments. We detected hexadecanoic acid, ethylene glycol and undecane are three major chemicals in root exudates. Our results provide a reference of AOS and PCD working under root exudates treatments in plants and offer novel strategy for the native species protection and invasion plants control in environment science.

Atmospheric deposition of heavy metals in Wuxi, China: estimation based on native moss analysis.

We studied atmospheric deposition of heavy metals in Wuxi, China, using moss (Haplocladium microphyllum and H. angustifolium) as a biomonitoring agent. Moss samples were collected from 49 sites determined by a systematic sampling method. The top layer of soil on each site was also sampled. No significant correlation (P < 0.05) was observed between the moss and soil concentrations for any of the six heavy metal elements (Cd, Cr, Cu, Ni, Pb, and Zn), indicating that the soil substrate had little effect on the heavy metal concentrations in the moss materials. The metal enrichment capacity of the moss material, characterized by the concentration ratio between the moss and soil samples for each heavy metal, was topped by Cd and then followed by Zn, Pb, Cu, Cr, and Ni, respectively. Significant (P < 0.05) correlations were found among the six elements in mosses, suggesting potential anthropogenic inputs of these heavy metal pollutants. Based on concentrations of the heavy metals in mosses and the calculated contamination factors, we evaluated the contamination level of each heavy metal on the 49 sampling sites. Spatial distribution maps of heavy metal deposition for each element were interpolated using ArcGIS 9.0. A total pollution coefficient was calculated for each sampling site to identify the seriously polluted areas in the region.

The chromosome-level holly (Ilex latifolia) genome reveals key enzymes in triterpenoid saponin biosynthesis and fruit color change.

The Ilex L. (hollies) genus of Aquifoliaceae shows high species diversity in tropical and subtropical regions of Asia and South America. Throughout the range of the genus, Ilex species have been widely used in beverage and medicine production and as ornamentals. Here, we assembled a high-quality, chromosome-level genome of Ilex latifolia, which has extremely high economic value because of its useful secondary metabolite production and the high ornamental value of its decorative red berries. The 99.8% genome sequence was anchored to 20 pseudochromosomes, with a total length of 766.02 Mb and a scaffold N50 of 33.45 Mb. Based on the comparative genomic analysis of 14 angiosperm species, we recovered I. latifolia as the sister group to all other campanulids. Two whole-genome duplication (WGD) events were identified in hollies: one shared ancient WGD in the ancestor of all eudicots and a recent and independent WGD in hollies. We performed a genome-wide search to screen candidate genes involved in the biosynthesis of pentacyclic triterpenoid saponins in I. latifolia. Three subfamilies of CYP450 (CYP71A, CYP72A, and CYP716A) appear to have expanded. The transcriptomic analysis of I. latifolia leaves at five developmental stages revealed that two CYP716A genes and one CYP72A gene probably play important roles in this biosynthetic pathway. In addition, we totally identified 12 genes in the biosynthesis pathways of pelargonidin and cyanidin and observed their differential expression in green and red fruit pericarps, suggesting an association between pelargonidin and cyanidin biosynthesis and fruit pericarp color change. The accumulation of pelargonidin and cyanidin is expected to play an important role in the ornamental value of I. latifolia. Altogether, this study elucidated the molecular basis of the medicinal and ornamental value of I. latifolia, providing a data basis and promising clues for further applications.

Selaginellawuyishanensis (sect. Tetragonostachyae, Selaginellaceae), a new species from East China and its phylogenetic position based on molecular data.

A new spikemoss species, Selaginellawuyishanensis, is described and illustrated based on materials collected from Fujian Province, East China. The new species can be distinguished from S.lutchuensis Koidzumi and S.albociliata P. S. Wang by its leaves with extremely long cilia (up to 8 mm) and distinctly white margins, ovate ventral sporophylls, and sporophyll-pteryx completely inverted on dorsal sporophylls. In the present work, a molecular phylogeny, taxonomic description, distribution information, line drawing, and photographs of this new species are presented. A morphological comparison is also given to distinguish it from morphologically similar species in Selaginellasect.Tetragonostachyae (Hook. & Grev.) Hieron. & Sadeb.

Alternative splicing and its regulatory role in woody plants.

Alternative splicing (AS) is an important post-transcriptional process to enhance proteome diversity in eukaryotic organisms. In plants, numerous reports have primarily focused on AS analysis in model plant species or herbaceous plants, leading to a notable lack of research on AS in woody plants. More importantly, emerging evidence indicates that many important traits, including wood formation and stress resistance, in woody plants are controlled by AS. In this review article, we summarize the current progress of all kinds of AS studies in different tree species at various stages of development and in response to various stresses, revealing the significant role played by AS in woody plants, as well as the similar properties and differential regulation within their herbaceous counterparts. Furthermore, we propose several potential strategies to facilitate the functional characterization of splicing factors in woody plants and evaluate a general pipeline for the systematic characterization of splicing isoforms in a complex AS regulatory network. The utilization of genetic studies and high-throughput omics integration approaches to analyze AS genes and splicing factors is likely to further advance our understanding of AS modulation in woody plants.

[Elevational Distribution Characteristics of Soil Bacterial Community and Enzyme Activities in Mount Huangshan].

Mount Huangshan has a well-preserved ecosystem and obvious differences in vertical geography, which provide a natural laboratory for studying the altitudinal distribution patterns of soil microbial communities in a mid-subtropical forest ecosystem. The soil bacterial community structure and diversity of the samples collected every 100 m from 670 to 1870 m on the south slope of Mount Huangshan were examined using Illumina MiSeq high-throughput sequencing technology. The soil physicochemical properties and soil enzyme activities of the samples were also measured to explore the relationship between bacterial communities and soil properties as well as enzyme activities. The results showed that ① The contents of soil total nitrogen, available nitrogen, total potassium, and total organic carbon were significantly different across the altitudes (P<0.01) and generally increased as altitude increased. The soil sucrase activities across altitudes were significantly different (P<0.01), and generally increased as altitude increased. However, there was no significant difference in acid phosphatase and urease activities between different altitudes (P>0.05). ② The 12 elevational gradients were divided into three groups:low altitude (670-875 m), medium altitude (1080-1370 m), and high altitude (1460-1780 m). The OTUs in low altitude sites were greater than in high altitude sites but lower compared to medium altitude sites. However, the differences in OTUs across altitude sites were not significant. ③ The soil bacterial community diversity showed a unimodal pattern in a small range of altitudes from 875-1370 m, although no apparent trend was observed at the altitudes from 670-1780 m. ④ There were 7 dominant phyla and 15 dominant orders with a relative abundance of more than 3% in all soil samples. ⑤ Correlation heat map analysis between the top 15 bacterial phyla and soil physicochemical properties as well as enzyme activities showed that soil pH had the greatest effect on the differences in soil bacterial community structure across the different altitudes. Pearson correlation analysis and Partial Mantel test also showed that bacterial community α-diversity (P<0.01) and ß-diversity (Partial Mantel r=0.560, P=0.001) were mainly affected by soil pH. Consequently, soil pH was the key environmental factor determining the soil bacterial community structure and diversity across the different altitudes on Mount Huangshan.

Changes in gametophyte physiology of Pteris multifida induced by the leaf leachate treatment of the invasive Bidens pilosa.

In recent years, the response of fern gametophytes to environment has raised much attention. However, studies on the influence of plant invasion to fern gametophytes are scarce. Allelopathy plays an important role in biological invasion. Hence, it is necessary to study the allelopathic effects of invasive plants on fern gametophytes and elucidate the mechanisms by which invasive plants cause phytotoxicity. As one of the main invasive plants in China, Bidens pilosa exhibits allelopathic effects on spermatophyte growth. Field investigation shows that many ferns are threatened by the invasion of B. pilosa. The distribution of Pteris multifida overlaps with that of B. pilosa in China. To examine the potential involvement of allelopathic mechanisms of B. pilosa leaves, changes in the physiology in P. multifida gametophytes are analyzed. We found that cell membrane and antioxidant enzyme activities as well as photosynthesis pigment contents of the gametophytes were affected by B. pilosa leachates. Gametophytes of P. multifida exposed to B. pilosa had increased damages to cell membranes, expressed in thiobarbituric acid reacting substance (TBARS) concentrations, malondialdehyde (MDA), electrolyte leakage (membrane permeability), and degree of injury. Enzyme activities, assessed by superoxide dismutase (SOD) and catalase (CAT) as well as guaiacol peroxidase (GPX) enhanced with the increase in leachate concentration after 2-day exposure. Meanwhile, lower chlorophyll a (Chl a), chlorophyll b (Chl b), carotenoid (Car), and the total chlorophyll were measured as leachate concentrations increased. At day 10, leaf leachates of B. pilosa exhibited the greatest inhibition. These results suggest that the observed inhibitory or stimulatory effects on the physiology studied can have an adverse effect on P. multifida and that allelopathic interference seems to have involved in this process.

Photosynthetic electron-transfer reactions in the gametophyte of Pteris multifida reveal the presence of allelopathic interference from the invasive plant species Bidens pilosa.

To date, the response of the fern gametophyte to its environment has received considerable attention. However, studies on the influence of plant invasion on the fern gametophyte are fewer. Allelopathy has been hypothesized to play an important role in biological invasion. Hence, it is necessary to study the allelopathy of invasive plant species to the fern gametophyte and elucidate the mechanisms by which invasive plants cause phytotoxicity. As one of the main invasive plants in China, Bidens pilosa exhibits allelopathic effects on the gametophytic growth of Pteris multifida. The root exudate plays an important role among various allelochemical delivery mechanisms in B. pilosa. The effect invasive plant species has on photosynthesis in native species is poorly understood. To elucidate this effect, the changes in photosynthesis in the gametophytes of P. multifida are analyzed to examine the mechanisms of the root exudates of B. pilosa. Meanwhile, a non-invasive plant, Coreopsis basalis, was also applied to investigate the effects on fluorescence and pigments in P. multifida gametophytes. We found that gametophytes exposed to both B. pilosa and C. basalis had decreased fluorescence parameters in comparison with the control, except for non-photochemical quenching. Furthermore, it was found that these parameters were markedly affected from day 2 to day 10 in the presence of both exudates at a concentration of 25% or above. B. pilosa exudate had a negative dose-dependent effect on chlorophyll a, chlorophyll b, carotenoid, and the total chlorophyll in the gametophyte. The inhibitory effects increased with increasing exudate concentrations of both species, exhibiting the greatest inhibition at day 10. In conclusion, B. pilosa irreversibly affected the photosynthesis of P. multifida on both PS I and PS II. Root exudates caused the primary damage with respect to the decrease of the acceptors and donors of photon and electron in photosynthetic units and the production and the relative yield of photochemical quantum in PS II. With the effects of exudates, part of the energy is released as heat in chloroplasts. The comparison of invasive and non-invasive plants in allelopathic experiments demonstrated that invasive plants were responsible for the critical damage to the photosynthetic process in local species.

[Predicting the impact of global warming on the geographical distribution pattern of Quercus variabilis in China].

The geographical distribution of Quercus variabilis in China with its climate characteristics was analyzed based on DIVA-GIS which was also used to estimate the response of future potential distribution to global warming by Bioclim and Domain models. Analysis results showed the geographical distribution of Q. variabilis could be divided into 7 subregions: Henduan Mountains, Yunnan-Guizhou Plateau, North China, East China, Liaodong-Shandong Peninsula, Taiwan Island, and Qinling-Daba Mountains. These subregions are across 7 temperature zones, 2 moisture regions and 17 climatic subregions, including 8 climate types. The modern abundance center of Q. variabilis is Qinling, Daba and Funiu mountains. The condition of mean annual temperature 7.5-19.8 degrees C annual precipitation 471-1511 mm, is suitable for Q. variabilis. Areas under the receiver operating characteristic curve (AUC values), of Domain and Boiclim models were 0.910, 0.779; the former predicted that the potential regions of high suitability for Q. variabilis are Qinling, Daba, Funiu, Tongbai, and Dabie mountains, eastern and western Yunnan-Guizhou Plateau, hills of southern Jiangsu and Anhui, part of the mountains in North China. Global warming might lead to the shrinking in suitable region and retreating from the south for Q. variabilis.

[Assessment of heavy metal contamination by moss-bag method and road-dust method for Taizhou urban area].

The aims of this study were to examine the contents and distribution character of heavy metals in urban areas of Taizhou, Jiangsu Province. Contents of 8 kinds of metals, including As, Cd, Cr, Cu, Mn, Ph, V and Zn, in the moss-bags and road dusts were determined, and the method of potential ecological risk index was used to assess the heavy metal contamination. The results indicated that the current situation of heavy metal contamination was serious in Taizhou, and the ecological risks of heavy metals were high. The mean concentrations of Cd, Zn, Pb in the air near the ground were 8.41 , 6.94 and 5. 85 times higher than the soil background values, respectively; and the mean concentrations of Zn, Cd, Pb, and Cu in the road dusts were 22. 63, 6. 58, 5. 13 and 4. 45 times higher than the soil background values, respectively. The results of potential ecological risk index showed that Cd was the main ecological risk factor both in the air near the ground and the road soils, its contribution rates in ecological risks accounted for 92.43% in the air near the ground and 72. 46% in the road soils. The Pearson correlation coefficients of heavy metals showed that there was a significant correlation among the heavy metals in the air near the ground, which implied the sources of pollution in the air were fewer than those of the road dust. Analysis indicated that traffic emission was the major anthropogenic source and the key influencing factor for heavy metal contamination of Taizhou, and that the potential ecological risk of bus stations were the highest.

[Analysis and assessment of atmospheric pollution based on accumulation characterization of heavy metals in Platanus acerifolia leaves].

The present work was aimed to evaluate the heavy metal pollution in the atmosphere of Huainan City. We measured and clustered the accumulation of six heavy metals in Platanus acerifolia leaves in 20 sampling fields with six types of environmental conditions, and analyzed the EF value of heavy metal enrichment in the leaves. The results showed that the accumulations in Platanus acerifolia leaves varied according to different types of metals, following the order of Zn > Cu > Cr > Ni > Pb > Cd. Environmental conditions also had great influence on the accumulation of heavy metals. Cd and Cu were mostly found in cement plant and mine, respectively, and Cr, Ni, Pb and Zn were significant higher in main road, compared with other environmental conditions. The average values of EF for all the metals expect Cr in scenic and village area were over 1. The average values of EF for all the metals in mine, power plant, main road and cement plant were above 3. The overall pollution condition of heavy metals in Huainan City followed the order of Cd > Cu > Zn > Ni > Pb > Cr.

[Leaf micro-morphology and features in adsorbing air suspended particulate matter and accumulating heavy metals in seven trees species].

The purpose of this study was to assess the relationship between tree leaf micro-morphology and features in adsorbing air suspended particulate matter and accumulating heavy metals. Seven tree species, including Ginkgo biloba, at heavy traffic density site in Huainan were selected to analyze the frequency of air particulate matter retained by leaves, the particle amount of different sizes per unit leaf area retained by leaves and its related micro-morphology structure, and the relationship between particle amount of different sizes per unit leaf area retained by leaves and its related accumulation of heavy metals. We found that the species characterized by small leaf area, special epidemis with abundant fax, and highly uneven cell wall, as well as big and dense stomata and without trichomes mainly absorbed fine particulate matter; while those species with many trichomes mainly retained coarse particulate matter. Accumulation of heavy metals in leaves of the seven species was significantly different except for Ph. Tree species with high capacities in heavy metal accumulation were Ginkgo biloba, Ligustrum lucidum, and Cinnamomum camphora. Accumulation of Cd, Cr, Ni, Zn, Cu and total heavy metal concentration for seven tree species was positively related to the amount of particulate matter absorbed. Correlation coefficients of d10 vs d2.5, d10 vs d1.0, d2.5 vs d1.0 were 0.987, 0.971, 0.996, respective, and the correlate level was significant. The ratios of d2.5/d10, d1.0/d10, d1.0/d2.5 were 0.844, 0.763, 0.822, indicating that the particulate matter from traffic was mainly fine particulates.

[Effects of shading on photosynthesis characteristics of Photinia x frasery and Aucuba japonica var. variegata].

This paper studied the effects of different shading (light transmittance 20%, 40%, 60%, and 100%) on the photosynthesis characteristics of two ornamental foliage plants Photinia x frasery and Aucuba japonica var. variegata. After shading for six weeks, the net photosynthesis rates of two plants measured ex situ under natural light enhanced, compared to those measured in situ, and, with the increase of shading degree, the net photosynthetic rates had an increasing trend, with the maximum being 9.7 micromol x m(-2) x s(-1) for Photinia x frasery and 8.3 micromol x m(-2) x s(-1) for Aucuba japonica var. variegata. In the meantime, the transpiration rates of the two plants increased significantly. Shading increased the chlorophyll a, b, and a+b contents and the chlorophyll/carotenoids ratio, decreased the chlorophyll a/b, but less affected the carotenoids content. The phenotypic plasticity index (PPI) of net photosynthesis rate and transpiration rate of Photinia x frasery and Aucuba japonica var. variegate was 2.08 and 3.21, and 0.55 and 1.60, respectively. The chlorophyll and carotenoids contents of the two plants were relatively stable, indicating the minor influence of external environment factors on pigments. Aucuba japonica var. variegata had a higher shading tolerance than Photinia x frasery.

[Photosynthetic characters of Quercus acutissima from different provenances under effects of salt stress].

The photosynthetic characteristics of Quercus acutissima from Feixian, Chuzhou and Wanyuan provenances were investigated under NaCl stress at 5 concentrations. For the three provenances, their leaf chlorophyll a (Chl a) and chlorophyll b (Chl b) contents and net photosynthetic rate (Pn) decreased with increasing salt stress, among which, the maximal decrement of Chl a content was 21.5%-36.1% for Feixian provenance, and 3.5%-19.8% for Wanyuan provenance. The diurnal variation of Pn, in control groups had a single peak, and no midday photosynthetic depression was observed. Under high salt stress, all the provenances presented midday photosynthetic depression. Path analysis indicated that the major factors affecting Pn were vapor pressure deficit (VPD) and leaf temperature (Tl) , while the minor factors were stomatal conductance (Gs) , intercellular CO2 concentration (Ci), and photosynthetically active radiation (PARi). In the control groups, the photosynthetic characteristics mainly depended on the climate factors of provenance location. Based on the variations of leaf chlorophyll contents and Pn among the provenances under different salt stress, Wanyuan provenance had the highest salt tolerance, followed by Chuzhou provenance, and Feixian provenance.