18 Works

Data from: Addition of nitrogen to canopy versus understory has different effects on leaf traits of understory plants in a subtropical evergreen broad–leaved forest

Songbo Tang, Lingling Zhang, Hans Lambers, Wendan Ren, Xiaofei Lu, Enqing Hou, Shenglei Fu & Yuanwen Kuang
Atmospheric nitrogen (N) deposition has substantial effects on forest ecosystems. The effects of N deposition on understory plants have been simulated by spraying N on the forest floor. Such understory addition of N (UAN) might simulate atmospheric N deposition in a biased manner, because it bypasses the canopy. We compared the effects of UAN and canopy addition of N (CAN) at 0, 25, and 50 kg N ha–1 year–1 on specific leaf area (SLA), leaf...

Additional file 10 of Comparative analyses of three complete Primula mitogenomes with insights into mitogenome size variation in Ericales

Lei Wei, Tong-Jian Liu, Gang Hao, Xue-Jun Ge & Hai-Fei Yan
Additional file 10: Table S1. Assembly information of three Primula taxa. Table S2. The number of protein-coding genes in the three Primula mitogenomes. Table S3. Tandem repeats in the Primula smithiana mitogenome. Table S4. Tandem repeats in the Primula palinuri mitogenome. Table S5. Tandem repeats in the Primula valentiniana mitogenome. Table S6. Information on MTPTs within the three Primula mitogenomes. Table S7. The shared nuclear sequences within the three Primula mitogenomes. Table S8. The nucleotide...

Data from: In situ glacial survival maintains high genetic diversity of Mussaenda kwangtungensis on continental islands in subtropical China

Miaomiao Shi, Yuyuan Wang, Tingting Duan, Xin Qian, Tong Zeng & Dianxiang Zhang
Generally, island populations are predicted to have less genetic variation than their mainland relatives. However, there has been exceptions, indicating that the relationships were impacted by several factors, e.g historical processes. In the present study, we chose a group of subtropical islands located in South China as the study system, which are quite younger and much closer to the mainland than most of the previous studied island systems, to test the hypothesis that in situ...

Data from: Three new synonyms of Rungia stolonifera (Acanthaceae) from China and Vietnam

Zheli Lin, Van Hai Do & Yunfei Deng
Examination of relevant type materials and living plants reveals that Rungia axilliflora, R. densiflora and R. evrardii are conspecific with R. stolonifera. Lectotypes are designated for the names R. evrardii and R. stolonifera.

Data from: Substrate stoichiometry determines nitrogen fixation throughout succession in southern Chinese forests

Mianhai Zheng, Hao Chen, Dejun Li, Yiqi Luo & Jiangming Mo
The traditional view holds that biological nitrogen (N) fixation often peaks in early- or mid-successional ecosystems and declines throughout succession based on the hypothesis that soil N richness and/or phosphorus (P) depletion become disadvantageous to N fixers. This view, however, fails to support the observation that N fixers can remain active in many old-growth forests despite the presence of N-rich and/or P-limiting soils. Here, we found unexpected increases in N fixation rates in the soil,...

Effects of different functional structure parameters of plant communities on slope runoff in different periods of the year in semiarid grasslands

Jian Hou, Yihe Lu, Zongshan Li & Huoxing Zhu
Research on sustainable use of water resources is needed to ensure food security, limit erosion, and prevent land degradation. Owing to the importance of water conservation to ecosystems, further research on the water conservation functions of different ecosystems is needed. Given the influence on water conservation functions, it is critical to identify environmental factors mediating slope runoff. In this study, the focal study area was the Yangjuangou catchment (36°42' N, 109°31' E) of the Loess...

Trivalvaria tomentosa (Annonaceae), a new species from Southeast Yunnan, China

Bine Xue, Jian-Wu Li, Jun-Jie Liao, Ming-Zhong Mo, Yun-Hong Tan & You-Sheng Chen
Trivalvaria tomentosa sp. nov. is herein described from Yunnan Province in China. It is easily distinguished from all previously described Trivalvaria species by having tomentose twigs, petioles, abaxial surface of the leaves, sepals and petals. A detailed description for the new species, along with line drawings, photographs, as well as morphological comparisons with similar species, are provided. A phylogenetic analysis was conducted to confirm the placement of this new species within Trivalvaria.

Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae

Bin-Bin Liu, Zhi-Yao Ma, Chen Ren, Richard Hodel, Miao Sun, Xiu-Qun Liu, Guang-Ning Liu, De-Yuan Hong, Elizabeth Zimmer & Jun Wen
With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In this study, through simulations, we evaluated the optimal (minimum) sequencing depth and performance for recovering single-copy nuclear genes (SCNs) from genome skimming data, by subsampling genome resequencing data and...

Tumour suppressor TET2 safeguards enhancers from aberrant DNA methylation and epigenetic reprogramming in ERα-positive breast cancer cells

Ruitu Lyu, Xuguo Zhu, Yinghui Shen, Lijun Xiong, Lu Liu, Hang Liu, Feizhen Wu, Christian Argueta & Li Tan
Aberrant DNA methylation is an epigenetic hallmark of malignant tumours. The DNA methylation level is regulated by not only DNA methyltransferases (DNMTs) but also Ten-Eleven Translocation (TET) family proteins. However, the exact role of TET genes in breast cancer remains controversial. Here, we uncover that the ERα-positive breast cancer patients with high TET2 mRNA expression had better overall survival rates. Consistently, knockout of TET2 promotes the tumorigenesis of ERα-positive MCF7 breast cancer cells. Mechanistically, TET2...

Tumor suppressor TET2 safeguards enhancers from aberrant DNA methylation and epigenetic reprogramming in ERα-positive breast cancer cells

Ruitu Lyu, Xuguo Zhu, Yinghui Shen, Lijun Xiong, Lu Liu, Hang Liu, Feizhen Wu, Christian Argueta & Li Tan
Aberrant DNA methylation is an epigenetic hallmark of malignant tumors. The DNA methylation level is regulated by not only DNA methyltransferases (DNMTs) but also Ten-Eleven Translocation (TET) family proteins. However, the exact role of TET genes in breast cancer remains controversial. Here, we uncover that the ERα-positive breast cancer patients with high TET2 mRNA expression had better overall survival rates. Consistently, knockout of TET2 promotes the tumorigenesis of ERα-positive MCF7 breast cancer cells. Mechanistically, TET2...

Tumour suppressor TET2 safeguards enhancers from aberrant DNA methylation and epigenetic reprogramming in ERα-positive breast cancer cells

Ruitu Lyu, Xuguo Zhu, Yinghui Shen, Lijun Xiong, Lu Liu, Hang Liu, Feizhen Wu, Christian Argueta & Li Tan
Aberrant DNA methylation is an epigenetic hallmark of malignant tumours. The DNA methylation level is regulated by not only DNA methyltransferases (DNMTs) but also Ten-Eleven Translocation (TET) family proteins. However, the exact role of TET genes in breast cancer remains controversial. Here, we uncover that the ERα-positive breast cancer patients with high TET2 mRNA expression had better overall survival rates. Consistently, knockout of TET2 promotes the tumorigenesis of ERα-positive MCF7 breast cancer cells. Mechanistically, TET2...

Additional file 2 of Quantifying substantial carcinogenesis of genetic and environmental factors from measurement error in the number of stem cell divisions

Xinhui Liu, Jifeng Yang, Hongkai Li, Qing Wang, Yuanyuan Yu, Xiaoru Sun, Shucheng Si, Lei Hou, Lu Liu, Fan Yang, Ran Yan, Yifan Yu, Zhentao Fu, Zilong Lu, Dejin Li, Hao Xue, Xiaolei Guo, Fuzhong Xue & Xiaokang Ji
Additional file 2: Table S1. Ranked matrix of LCR in global scope and the contribution of the genetic and environmental factors on the variation in cancer risk. Table S2. Ranked matrix of LCR in national-wide of China and the contribution of the genetic and environmental factors on the variation in cancer risk. Table S3. Ranked matrix of LCR in counties of Shandong province, China and the contribution of the genetic and environmental factors on the...

Additional file 10 of Comparative analyses of three complete Primula mitogenomes with insights into mitogenome size variation in Ericales

Lei Wei, Tong-Jian Liu, Gang Hao, Xue-Jun Ge & Hai-Fei Yan
Additional file 10: Table S1. Assembly information of three Primula taxa. Table S2. The number of protein-coding genes in the three Primula mitogenomes. Table S3. Tandem repeats in the Primula smithiana mitogenome. Table S4. Tandem repeats in the Primula palinuri mitogenome. Table S5. Tandem repeats in the Primula valentiniana mitogenome. Table S6. Information on MTPTs within the three Primula mitogenomes. Table S7. The shared nuclear sequences within the three Primula mitogenomes. Table S8. The nucleotide...

Data from: Footprints of divergent selection in natural populations of Castanopsis fargesii (Fagaceae)

Ye Sun, Chun Li, Hong Wen Huang & Charles H. Cannon
Given predicted rapid climate change, an understanding of how environmental factors affect genetic diversity in natural populations is important. Future selection pressures are inherently unpredictable, so forest management policies should maintain both overall diversity and identify genetic markers associated with the environmental factors expected to change most rapidly, like temperature and rainfall. In this study, we genotyped 648 individuals in 28 populations of Castanopsis fargesii (Fagaceae) using 32 expressed sequence tag (EST)-derived microsatellite markers. After...

Data from: Genetic architecture of quantitative flower and leaf traits in a pair of sympatric sister species of Primulina

Chen Feng, Chao Feng, Lihua Yang, Ming Kang & Mark D. Rausher
Flowers and leaves each represent suites of functionally interrelated traits that are often involved in species divergence and local adaptation. However, a major unresolved issue is how the individual component traits that make up a complex trait such as a flower evolve in a coordinated fashion to retain a high degree of functionality. We use a quantitative trait loci (QTL) approach to elucidate the genetic architecture of divergence in flower and leaf traits between sister...

The community-level scaling relationship between leaf nitrogen and phosphorus changes with plant growth, climate and nutrient limitation

Yanpei Guo, Zhengbing Yan, Gheyur Gheyret, Guoyi Zhou, Zongqiang Xie & Zhiyao Tang
This dataset contains community-level leaf nitrogen (N) and phosphorus (P) concentration data from an intensive field investigation across China, including 1080 shrub-community sites from shrublands and 2087 tree-community sites from forests. Mean annual temperature and Thornthwaite moisture index, net primary productivity, and soil total N and P concentrations of each site are also included in this dataset.

The dataset of five chloroplast regions used in: A contribution to Gymnosphaera (Cyatheaceae) in mainland Asia: Two new species, reinstatement of Cyathea bonii, and their phylogenetic positions

Shi-Yong Dong, Zheng-Yu Zuo, Yong Xiao, Ling Huang, Van The Pham, Ke Loc Phan & Ming Kang
Gymnosphaera represents a minor lineage within the scaly tree-fern family Cyatheaceae. Tropical and subtropical mainland Asia is a main distribution area of Gymnosphaera. However, the species diversity of Gymnosphaera is currently incompletely known in mainland Asia due to lacking critical revision. Here we present new findings of species diversity and their relationships with mainland Asian Gymnosphaera based on field surveys, the examination of herbarium collections, and phylogenetic analyses of sequences of multiple chloroplast and nuclear...

Additional file 2 of Quantifying substantial carcinogenesis of genetic and environmental factors from measurement error in the number of stem cell divisions

Xinhui Liu, Jifeng Yang, Hongkai Li, Qing Wang, Yuanyuan Yu, Xiaoru Sun, Shucheng Si, Lei Hou, Lu Liu, Fan Yang, Ran Yan, Yifan Yu, Zhentao Fu, Zilong Lu, Dejin Li, Hao Xue, Xiaolei Guo, Fuzhong Xue & Xiaokang Ji
Additional file 2: Table S1. Ranked matrix of LCR in global scope and the contribution of the genetic and environmental factors on the variation in cancer risk. Table S2. Ranked matrix of LCR in national-wide of China and the contribution of the genetic and environmental factors on the variation in cancer risk. Table S3. Ranked matrix of LCR in counties of Shandong province, China and the contribution of the genetic and environmental factors on the...

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