Data from: A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate changeYizhen Wan, Heidi R. Schwaninger, Angela M. Baldo, Joanne A. Labate, Gan-Yuan Zhong & Charles J. Simon
Background: Grapes are one of the most economically important fruit crops. There are about 60 species in the genus Vitis. The phylogenetic relationships among these species are of keen interest for the conservation and use of this germplasm. We selected 309 accessions from 48 Vitis species,varieties, and outgroups, examined ~11 kb (~3.4 Mb total) of aligned nuclear DNA sequences from 27 unlinked genes in a phylogenetic context, and estimated divergence times based on fossil calibrations....
Data from: Phosphorus amendment mitigates nitrogen addition-induced phosphorus limitation in two plant species in a desert steppe, ChinaHuang Juying, Hailong Yu, Henry Lin, Yu Zhang, Eric B. Searle, Zhiyou Yuan & Juying Huang
Background and aims: The increasing deposition of atmospheric nitrogen (N) due to anthropogenic activities has significantly enhanced N inputs to ecosystems, resulting in an imbalance in the N: phosphorus (P) ratios in plants and soils. This study aimed to determine whether, and to what extent, P addition alleviates N-induced P limitation in a desert steppe ecosystem. Methods: We conducted a multi-level N:P supply experiment (i.e., constant N with varied P-addition levels) for a grass species,...
Data from: The jujube genome provides insights into genome evolution and the domestication of sweetness/acidity taste in fruit treesJian Huang, Chunmei Zhang, Xing Zhao, Zhangjun Fei, KangKang Wan, Zhong Zhang, Xiaoming Pang, Xiao Yin, Yang Bai, Xiaoqing Sun, Lizhi Gao, Ruiqiang Li, Jinbo Zhang & Xingang Li
Jujube (Ziziphus jujuba Mill.) belongs to the Rhamnaceae family and is a popular fruit tree species with immense economic and nutritional value. Here, we report a draft genome of the dry jujube cultivar 'Junzao' and the genome resequencing of 31 geographically diverse accessions of cultivated and wild jujubes (Ziziphus jujuba var. spinosa). Comparative analysis revealed that the genome of 'Dongzao', a fresh jujube, was ~86.5 Mb larger than that of the 'Junzao', partially due to...
Data from: Rainfall pulse response of carbon fluxes in a temperate grass ecosystem in the semiarid Loess PlateauYakun Tang, Jun Jiang, Chen Chen, Yunming Chen & Xu Wu
Rainfall pulses can significantly influence carbon cycling in water limited ecosystems. The magnitude of carbon flux component responses to precipitation may vary depending on precipitation amount and antecedent soil moisture, associated with nonlinear responses of plants and soil microbes. The present study was carried out in a temperate grass ecosystem during 2013–2015 in the semiarid Loess Plateau of China, to examine the response of carbon fluxes to precipitation using the “threshold-delay” model. The unique contribution...
Poly-lactic electrospun porous fibers have been widely used in tissue engineering scaffolds. However, the application of linear Poly-lactic is limited due to its poor hydrophilicity, which leads to phase separation and has been seldom used in porous fiber preparation. Instead, using of branching Poly-lactic acts as a new effective method to prepare porous fibers because it can increase Poly-lactic polar property and make it easy to be formulated in the following application. In current study,...
Data from: Root elemental composition in Chinese forests: implications for biogeochemical niche differentiationNing Zhao, Hui Liu, Qiufeng Wang, Ruili Wang, Zhiwei Xu, Cui Jiao, Jianxing Zhu, Guirui Yu, Nianpeng He, Huiming Liu & Cuicui Jiao
1. Trait-based community analysis provides a new approach to integrate functional ecology with community ecology. However, our understanding of the linkages between root chemical traits and community chemical diversity and assembly is still in its infancy. 2. Environmental filtering and niche differentiation are two opposite driving forces of community assembly based on deterministic niche processes. We hypothesize that environmental filtering is a strong driver of root chemical assembly at a large spatial scale, whereas biogeochemical...
Data from: Thermal regime drives a latitudinal gradient in morphology and life history in a livebearing fishRüdiger Riesch, Ryan A. Martin, Sarah E. Diamond, Jonas Jourdan, Martin Plath & R. Brian Langerhans
Within-species diversity is often driven by changing selective regimes along environmental gradients. Here, we provide a direct test of the environmental factors underlying phenotypic diversity across the wide native distribution of eastern mosquitofish (Gambusia holbrooki). We investigated life-history and body-shape divergence (including multiple measures of body size) across more than 14 degrees of latitude in North America, and used Akaike’s information criterion-based model selection to determine the relative contributions of thermal regime, population densities and...
Geographical and temporal variation of multiple paternity in invasive mosquitofish (Gambusia holbrooki, Gambusia affinis)Jiancao Gao, Francesco Santi, Linjun Zhou, Xiaoqin Wang, Rüdiger Riesch & Martin Plath
Multiple paternity (MP) increases offspring’s genetic variability, which could be linked to invasive species’ evolvability in novel distribution ranges. Shifts in MP can be adaptive, with greater MP in harsher/colder environments or towards the end of the reproductive season, but climate could also affect MP indirectly via its effect on reproductive life histories. We tested these hypotheses by genotyping N = 2,903 offspring from N = 306 broods of two closely related livebearing fishes, Gambusia...
Data from: Mycorrhizal symbiosis pathway and edaphic fertility frame root economics space among tree speciesHan Yan, Grégoire T. Freschet, Huimin Wang, J. Aaron Hogan, Shenggong Li, Oscar J. Valverde-Barrantes, Xiaoli Fu, Ruili Wang, Xiaoqin Dai, Lei Jiang, Shengwang Meng, Fengting Yang, Miaomiao Zhang & Liang Kou
The root economics space (RES) is multidimensional and largely shaped by belowground biotic and abiotic influences. However, how root-fungal symbioses and edaphic fertility drive this complexity remains unclear. Here, we measured absorptive root traits of 112 tree species in temperate and subtropical forests of China, including traits linked to functional differences between arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) hosts. Our data, from known mycorrhizal tree species, revealed a ‘fungal-symbiosis’ dimension distinguishing AM from ECM species....
Decreasing species richness and positive Rapoport effects of Crambidae (Lepidoptera) on Mount TaibaiYufeng Zheng, Zhaofu Yang, Bolan Yang & Jinyu Zhan
The vertical gradient pattern of species richness has been studied intensively over the past decades. Among these, Rapoport's rule is one of the important hypotheses of the patterns of species richness and macroecology, asserting the latitude or altitude distributional width of animal and plant species gradually narrows from a high latitude or high altitude area to low latitude or low altitude areas. However, altitudinal distributions and Rapoport’s rule have rarely been tested for Asian Lepidopterans....
sj-xlsx-5-tct-10.1177_15330338221124658 - Supplemental material for In Vitro and in Vivo Study of the Effect of Osteogenic Pulsed Electromagnetic Fields on Breast and Lung Cancer CellsMike Y. Chen, Jing Li, Nianli Zhang, Erik I. Waldorff, James T. Ryaby, Philip Fedor, Yongsheng Jia & Yujun Wang
Supplemental material, sj-xlsx-5-tct-10.1177_15330338221124658 for In Vitro and in Vivo Study of the Effect of Osteogenic Pulsed Electromagnetic Fields on Breast and Lung Cancer Cells by Mike Y. Chen, Jing Li, Nianli Zhang and Erik I. Waldorff, James T. Ryaby, Philip Fedor, Yongsheng Jia, Yujun Wang in Technology in Cancer Research & Treatment
Additional file 2 of Comprehensive characterization of ubiquitinome of human colorectal cancer and identification of potential survival-related ubiquitinationWei Zhang, Yan Yang, Liewen Lin, Jingquan He, Jingjing Dong, Bin Yan, Wanxia Cai, Yumei Chen, Lianghong Yin, Donge Tang, Fanna Liu & Yong Dai
Additional file 2. Table S1. Ubiquitination annotation. Table S2. Protein annotation. Table S3. 42 proteins having ten or more than ten ubiquitination modifications. Table S4. 20 ubiquitin-binding motifs. Table S5. 2242 proteins with an upregulated ubiquitination and 1204 proteins with a down-regulated ubiquitination. Table S6. 1172 up-regulated proteins and 1700 down-regulated proteins. Table S7. 646 Secretory proteins. Table S8. 53 proteins having an upregulated expression simultaneously with a down-regulated ubiquitination and 116 proteins having down-regulated...
Numerical investigation of asymmetric weld fusion geometry in laser welding of aluminium alloy with beam oscillationXi Chen, Nan Jiang, Meng Jiang, Yang Du, Shengchong Ma, Yuan Chen, Caiwang Tan, Zhenglong Lei, Sicong Zhao & Yanbin Chen
In this work, the asymmetric weld fusion geometry in oscillating laser beam welding (OLBW) of aluminium alloy was reported and investigated using a numerical approach. A multi-physics heat transfer and fluid flow model of OLBW was developed and validated with the corresponding experimental results. The weld fusion geometry, temperature fields, and fluid flow behaviours for four commonly used oscillation modes, line, circle, eight, and infinity, were calculated to analyse the origin of the asymmetric weld...
Dominant factors of the phosphorus regulatory network differ under various dietary phosphate loads in healthy individualsGuoxin Ye, Jiaying Zhang, Zhaori Bi, Weichen Zhang, Minmin Zhang, Qian Zhang, Mengjing Wang & Jing Chen
The purpose of this study was to explore the contribution of each factor of the phosphorus metabolism network following phosphorus diet intervention via Granger causality analysis. In this study, a total of six healthy male volunteers were enrolled. All participants sequentially received regular, low-, and high-phosphorus diets. Consumption of each diet lasted for five days, with a 5-day washout period between different diets. Blood and urinary samples were collected on the fifth day of consumption...
Additional file 5 of Floral organ transcriptome in Camellia sasanqua provided insight into stamen petaloidMenglong Fan, Xinlei Li, Ying Zhang, Si Wu, Zhixin Song, Hengfu Yin, Weixin Liu, Zhengqi Fan & Jiyuan Li
Additional file 5: Table S5. The GO enrichment analysis of coexpression modules.
Additional file 6 of Floral organ transcriptome in Camellia sasanqua provided insight into stamen petaloidMenglong Fan, Xinlei Li, Ying Zhang, Si Wu, Zhixin Song, Hengfu Yin, Weixin Liu, Zhengqi Fan & Jiyuan Li
Additional file 6: Table S6. The KEGG enrichment analysis of coexpression modules.
Additional file 7 of Floral organ transcriptome in Camellia sasanqua provided insight into stamen petaloidMenglong Fan, Xinlei Li, Ying Zhang, Si Wu, Zhixin Song, Hengfu Yin, Weixin Liu, Zhengqi Fan & Jiyuan Li
Additional file 7: Table S7. The primer of RT-qPCR.
Data from: Unique evolutionary trajectories in repeated adaptation to hydrogen sulphide-toxic habitats of a neotropical fish (Poecilia mexicana)Markus Pfenninger, Simit Patel, Lenin Arias-Rodriguez, Barbara Feldmeyer, Rüdiger Riesch & Martin Plath
Replicated ecological gradients are prime systems to study processes of molecular evolution underlying ecological divergence. Here, we investigated the repeated adaptation of the neotropical fish Poecilia mexicana to habitats containing toxic hydrogen sulphide (H2S) and compared two population pairs of sulphide-adapted and ancestral fish by sequencing population pools of >200 individuals (Pool-Seq). We inferred the evolutionary processes shaping divergence and tested the hypothesis of increase of parallelism from SNPs to molecular pathways. Coalescence analyses showed...
The root economics spectrum (RES), a common hypothesis postulating a tradeoff between resource acquisition and conservation traits, is being challenged by conflicting relationships between root diameter, tissue density (RTD) and root nitrogen concentration (RN). Here, we analyze a global trait dataset of absorptive roots for over 800 plant species. For woody species (but not for non-woody species), we find nonlinear relationships between root diameter and RTD and RN, which stem from the allometric relationship between...
Trade-off between vegetation type, soil erosion control and surface water in global semi-arid regions: A meta-analysisGao-Lin Wu, Yi-Fan Liu, Zeng Cui, Yu Liu, Zhi-Hua Shi, Rui Yin & Paul Kardol
Soil erosion control and water resource protection can closely interact during restoration of terrestrial ecosystems. In semi‐arid ecosystems, an urgent issue is how vegetation restoration can achieve the goal of soil erosion mitigation and water conservation, which in turn, feeds back to ecosystem functioning. We reviewed 78 articles from 22 countries in semi‐arid areas to evaluate the effects of vegetation type (i.e. forest, grassland and scrubland) on runoff and sediment yields across different environmental conditions...
Expression Analysis and Functional Characterization of CER1 Family Genes Involved in Very-LongChain Alkanes Biosynthesis in Brachypodium distachyonLi Quan & Hongqi Wu
Cuticular wax accumulation and composition affects drought resistance in plants. Brachypodium distachyon plants subjected to water deficit and polyethylene glycol treatments resulted in a significant increase in total wax load, in which very-long-chain (VLC) alkanes were more sensitive to these treatments than other wax compounds, implying that VLC alkanes biosynthesis plays a more important role in drought resistance in B. distachyon. ECERIFERUM1 (CER1) has been reported to encode a core enzyme involved in VLC alkanes...
Revealing the roles of DnaA on the biological characteristics of Brucella and the inflammatory response to BrucellaWang Aihua
The Brucella cell cycle, including chromosomal replication and cell division, is coordinated with the virulence of the bacteria. DnaA, a chromosomal replication initiator protein, is an essential regulator of cell cycle progression and is tightly regulated both temporally and spatially because it is activated only once per cell cycle in bacteria. Although DnaA exists in many bacteria, the role of DnaA during Brucella infection, with the exception of its induction of the initiation of chromosome...
Brucellosis is an endemic zoonotic infectious disease in the majority developing country that causes huge economic losses. As immunogenic and protective antigens at the surface of Brucella spp, outer membrance proteins (Omps) are particularly attractive for developing vaccine and could have more relevant role in host-pathogen interactions. Omp16, a homologue to peptidoglycan-associated lipoproteins (pals), is essential for Brucella survival in vitro. At present, the functions of Omp16 has been poorly studies. Here, the gene expression...
Afforestation can lower microbial diversity and functionality in deep soil layers in a semiarid regionXiaorong Wei
Afforestation is an effective approach to rehabilitate degraded ecosystems, but often depletes deep soil moisture. Presently, it is not known how an afforestation-induced decrease in moisture affects soil microbial community and functionality, hindering our ability to understand the sustainability of the rehabilitated ecosystems. To address this issue, we examined the impacts of 20 years of afforestation on soil bacterial community, co-occurrence pattern and functionalities along vertical profile (0-500 cm depth) in a semiarid region of...
Additional file 3 of Comprehensive analysis of alternative polyadenylation regulators concerning CD276 and immune infiltration in bladder cancerMing Xiong, Wencheng Li, Longwang Wang, Liang Chen, Zhaohui Chen, Chengcheng Wei, Futian Zhang, Jiawei Chen, Gallina Kazobinka, Jun Zhao & Teng Hou
Additional file 3: Supplementary Table 2. Correlation statistics between CPSF3 and immune checkpoint-related genes.
North West Agriculture and Forestry University94
Chinese Academy of Sciences54
Capital Medical University42
Sun Yat-sen University37
Wenzhou Medical University35
Chinese Academy of Medical Sciences & Peking Union Medical College35
Central South University33