Guishui Xie

Genome-Wide Identification of Jatropha curcas Aquaporin Genes and the Comparative Analysis Provides Insights into the Gene Family Expansion and Evolution in Hevea brasiliensis

Aquaporins (AQPs) are channel-forming integral membrane proteins that transport water and other small solutes across biological membranes. Despite the vital role of AQPs, to date, little is known in physic nut (Jatropha curcas L., Euphorbiaceae), an important non-edible oilseed crop with great potential for the production of biodiesel. In this study, 32 AQP genes were identified from the physic nut genome and the family number is relatively small in comparison to 51 in another Euphorbiaceae plant, rubber tree (Hevea brasiliensis Muell. Arg.). Based on the phylogenetic analysis, the JcAQPs were assigned to five subfamilies, i.e., nine plasma membrane intrinsic proteins (PIPs), nine tonoplast intrinsic proteins (TIPs), eight NOD26-like intrinsic proteins (NIPs), two X intrinsic proteins (XIPs), and four small basic intrinsic proteins (SIPs). Like rubber tree and other plant species, functional prediction based on the aromatic/arginine selectivity filter, Frogers positions, and specificity-determining positions showed a remarkable difference in substrate specificity among subfamilies of JcAQPs. Genome-wide comparative analysis revealed the specific expansion of PIP and TIP subfamilies in rubber tree and the specific gene loss of the XIP subfamily in physic nut. Furthermore, by analyzing deep transcriptome sequencing data, the expression evolution especially the expression divergence of duplicated HbAQP genes was also investigated and discussed. Results obtained from this study not only provide valuable information for future functional analysis and utilization of Jc/HbAQP genes, but also provide a useful reference to survey the gene family expansion and evolution in Euphorbiaceae plants and other plant species.

Species Diversity in a Naturally Managed Rubber Plantation in Hainan Island, South China:

Due to production activities, species richness in rubber plantations varies considerably. To answer the question of how many species could potentially survive rubber plantation, we established a dynamic plot with an area of 1 hm2 in a rubber plantation in Danzhou, Hainan Island, south China. We surveyed and analyzed plant species diversity and spatial distribution patterns of dominant species in the plot. The results showed that (a) there are a total of 183 species belonging to 155 genera and 69 families in the 1 hm2 plot of the plantation. This level of species richness is slightly lower than a typical tropical rainforest of the same size. (b) Subplots as small as 4,000 m2 already contain at least 90% of species, genus, and family, respectively, which indicates that 1 hm2 plot may be large enough for the dynamic monitoring of species diversity in rubber plantations, in our region at least. (c) All of the 20 dominant species have a clumping distribution at Scale 0 to 5 m, which is similar to the finding in tropical rain forests. In conclusion, many plant species grow back in rubber plantations that are minimally managed or called naturally managed. Such a management approach could be useful in maintaining species diversity in rubber plantations.

Papain-like cysteine protease encoding genes in rubber ( Hevea brasiliensis ): comparative genomics, phylogenetic, and transcriptional profiling analysis

AbstractMain conclusion43HbPLCPsrepresenting nine subfamilies or 20 orthologous groups were found in rubber, where paralogs were resulted from the recent WGD and local duplication. Several senescence-associated genes were also identified. Papain-like cysteine proteases (PLCPs) comprise a large family of proteolytic enzymes involved in plant growth and development, seed germination, organ senescence, immunity, and stress response. Despite their importance and the extensive research in the model plant Arabidopsis thaliana, little information is available on rubber tree (Hevea brasiliensis), a rubber-producing plant of the Euphorbiaceae family. This study performed a genome-wide identification of PLCP family genes in rubber, resulting in a relatively high number of 43 members. The phylogenetic analysis assigned these genes into nine subfamilies, i.e., RD21 (6), CEP (4), XCP (4), XBCP3 (2), THI (1), SAG12 (18), RD19 (4), ALP (2), and CTB (2). Most of them were shown to have orthologs in Arabidopsis; however, several members in SAG12, CEP and XBCP3 subfamilies form new groups as observed in other core eudicots such as Manihot esculenta, Ricinus communis, Populus trichocarpa, and Vitis vinifera. Based on an expert sequence comparison, 20 orthologous groups (OGs) were proposed for core eudicots, and rubber paralogs were shown to be resulted from the recent whole-genome duplication (WGD) as well as local duplication. Transcriptional profiling showed distinct expression pattern of different members across various tissues, e.g., root, leaf, bark, laticifer, flower, and seed. By using the senescence-specific HbSAG12H1 as the indicator, the transcriptome of senescent rubber leaves was deeply sequenced and several senescence-associated PLCP genes were identified. Results obtained from this study provide valuable information for future functional analysis and utilization of PLCP genes in Hevea and other species.

Components of Soil Respiration and Its Monthly Dynamics in Rubber Plantation Ecosystems

Our objective was to quantify four components and study effect factors of soil respiration in rubber plantation ecosystems. Providing the basic data support for the establishment of the trade of rubber plantation ecosystem carbon source/sink. We used Li-6400 (IRGA, Li-COR) to quantitate four components of soil respiration in rubber plantation ecosystems at different ages. Soil respiration can be separated as four components: heterotrophic respiration (Rh), respiration of roots (Rr), respiration of litter layer (Rl) and respiration of mineral soil (Rm). The soil respiration rate (Rs) showed significant seasonal variation. The maximum soil respiration rate of the whole year appeared in August, and the minimum in November or December. The components of soil respiration rate order showed as: heterotrophic respiration>respiration of roots>respiration of litter layer>respiration of mineral soil. The soil respiration rate was highly significant correlation (p<;0.01, Q10=1.13~2.37) with 0~10 cm soil temperature in dry season, and significant correlation (p<;0.05, Q10=1.10~1.77) with 0~10cm soil temperature in wet season. And soil respiration rate was not significant correlation with soil water content of 5 cm (p≥0.05). The soil respiration components of four kinds forest ages accounted for the percentage contribution to the flux of annual carbon emissions (Rs) as: Rh: 35.28~52.75%, Rr: 21.73~39.97%, Rl: 17.13~19.63%, Rm: 6.605~10.27%%, respectively. The soil respiration rate carbon flux of 5a, 10a, 19a and 33a respectively were 10.03, 10.34, 11.96 and 11.09 t·hm-2·a-1. And the annual carbon flux of soil respiration increased with stand ages increasing in rubber plantation ecosystems.

Seasonal changes impact soil bacterial communities in a rubber plantation on Hainan Island, China

Rubber plantations have expanded rapidly over the past 20 years in tropical Asia and their impacts on regional ecosystems have garnered much concern. While much attention has been given to the negative impacts on aboveground diversity and function, the belowground bacterial soil community has received much less attention. Here, we investigated the community composition and diversity of soil bacteria of rubber plantations on Hainan Island in south China. The goals of the study were to describe changes in bacterial compositions and diversity across seasons. We found that seasonality defined by differences in rainfall amount strongly influenced bacterial communities. At both the Phylum and Family levels, we found significant differences in the total number of taxa, as well as the composition of the community as a function of season. Diversity of soil samples in the dry-rainy season was highest of three seasons, suggesting that bacterial structure was more sensitive in alternate periods of season. Diversity in the rainy season was substantial lower than in dry season. Results from a redundancy analysis showed that seasonal changes explained the largest part (31.9%) of the total variance of bacterial community composition. In conclusion, seasonal change had the greatest influence on bacterial communities, which overshadowed the effects of soil nutrient as well as other factors, and controls the bacterial communities in soils of RP in tropical region of Hainan.

Identifying Establishment Year and Pre-Conversion Land Cover of Rubber Plantations on Hainan Island, China Using Landsat Data during 1987–2015

Knowing the stand age of rubber tree (Hevea brasiliensis) plantations is vitally important for best management practices, estimations of rubber latex yields, and carbon cycle studies (e.g., biomass, carbon pools, and fluxes). However, the stand age (as estimated from the establishment year of rubber plantation) is not available across large regions. In this study, we analyzed Landsat time series images from 1987–2015 and developed algorithms to identify (1) the establishment year of rubber plantations; and (2) the pre-conversion land cover types, such as old rubber plantations, evergreen forests, and cropland. Exposed soil during plantation establishment and linear increases in canopy closure during non-production periods (rubber seedling to mature plantation) were used to identify the establishment year of rubber plantations. Based on the rubber plantation map for 2015 (overall accuracy = 97%), and 1981 Landsat images since 1987, we mapped the establishment year of rubber plantations on Hainan Island (R2 = 0.85/0.99, and RMSE = 2.34/0.54 years at pixel/plantation scale). The results show that: (1) significant conversion of croplands and old rubber plantations to new rubber plantations has occurred substantially in the northwest and northern regions of Hainan Island since 2000, while old rubber plantations were mainly distributed in the southeastern inland strip; (2) the pattern of rubber plantation expansion since 1987 consisted of fragmented plantations from smallholders, and there was no tendency to expand towards a higher altitude and steep slope regions; (3) the largest land source for new rubber plantations since 1988 was old rubber plantations (1.26 × 105 ha), followed by cropland (0.95 × 105 ha), and evergreen forests (0.68 × 105 ha). The resultant algorithms and maps of establishment year and pre-conversion land cover types are likely to be useful in plantation management, and ecological assessments of rubber plantation expansion in China. Remote Sens. 2018, 10, 1240; doi:10.3390/rs10081240 www.mdpi.com/journal/remotesensing Remote Sens. 2018, 10, 1240 2 of 23

Change in Soil Microbial Community Compositions and Diversity Following the Conversion of Tropical Forest to Rubber Plantations in Xishuangbanan, Southwest China:

The ecological consequences of converting tropical forests to rubber plantations on the soil microbial compositions and diversity remain unknown. By using an Illumina MiSeq sequencing analysis, we assessed the compositions and diversity of bacterial and fungal community in soils of rubber plantation (or rubber forest, RF), secondary tropical forest (STF), and tropical seasonal rainforest (TSR) in Xishuangbanna, southwest China. Our findings revealed that (a) for bacterial composition, Bacillaceae was the most dominant family (13.60%) in RF soil, while it only accounted for 4.13% in STF and 6.92% in TSR. For fungal composition, the largest family in soils of RF was Basidiomycota_unclassified. However, the largest family in STF and TSR was Russulaceae. (b) Number of operational taxonomic units, Chao index, and Shannon index of bacterial community in soil of RF were significantly higher than those of TSR and STF. However, these diversity indices of fungal community in RF were significantly lower than those of TSR and STF. (c) Soil pH and total phosphorus were very important drivers for bacterial community, whereas soil organic matter and total nitrogen were the most important factors for fungal community. (d) The microbial biomass carbon in RF was relative lower than those in STF and TSR, which suggested that the total microbial biomass decreased after forest conversion. To protect the total diversity of this region, the individual farmers should use herbicides as little as possible to reserve ground vegetation. And the government could outline a land-use policy that prohibits the cultivation in areas of natural vegetation.