62 Works

Data from: Inferring roles in defense from metabolic allocation of rice diterpenoids

Xuan Lu, Juan Zhang, Benjamin Brown, Riqing Li, Julio Rodríguez-Romero, Aileen Berasategui, Bo Liu, Meimei Xu, Dangping Luo, Zhiqiang Pan, Scott R. Baerson, Jonathan Gershenzon, Zhaohu Li, Ane Sesma, Bing Yang & Reuben J. Peters
Among their responses to microbial infection, plants deploy an arsenal of antibiotic natural products. While these historically have been identified on the basis of their antibiotic activity in vitro, this leaves open the question of their relevance to defense in planta. The vast majority of such natural products from the important crop plant rice (Oryza sativa) are diterpenoids whose biosynthesis proceeds via either ent- or syncopalyl diphosphate (CPP) intermediates, and which were isolated on the...

Tomato Protein Phosphatase 2C (SlPP2C3) influences fruit ripening onset and fruit glossiness

Ping Leng
Abscisic acid (ABA) plays a vital role in coordinating physiological processes during fresh fruit ripening. ABA can bind to ABA receptors which interacts and inhibits their co-receptors type 2C phosphatases (PP2Cs). However, the dissected mechanism of PP2C during fruit ripening is unclear. In this study, we identify the role of SlPP2C3, a tomato type 2C phosphatase, as a negative regulator of ABA signaling and fruit ripening. SlPP2C3 selectively interacted with monomeric ABA receptors and SlSnRK2.8...

Data from: Re-assessing the diversity of negative strand RNA viruses in insects

Simon Käfer, Sofia Paraskevopoulou, Florian Zirkel, Nicolas Wieseke, Alexander Donath, Malte Petersen, Terry C. Jones, Shanlin Liu, Xin Zhou, Martin Middendorf, Sandra Junglen, Bernhard Misof & Christian Drosten
The spectrum of viruses in insects is important for subjects as diverse as public health, veterinary medicine, food production, and biodiversity conservation. The traditional interest in vector-borne diseases of humans and livestock has drawn the attention of virus studies to hematophagous insect species. However, these represent only a tiny fraction of the broad diversity of Hexapoda, the most speciose group of animals. Here, we systematically probed the diversity of negative strand RNA viruses in the...

Data from: Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region

Yi Zhang, Yongfang Lu, Marnoch Yindee, Kuan-Yi Li, Hsiao-Yun Kuo, Yu-Ten Ju, Shaohui Ye, , Qiang Li, Yachun Wang, Vu Chi Cuong, Lan Doan Pham, Bounthong Bouahom, Bingzhuang Yang, Xianwei Liang, Zhihua Cai, Dianne Vankan, Wallaya Manatchaiworakul, Nonglid Kowlim, Somphot Duangchantrasiri, Worawidh Wajjwalku, Ben Colenbrander, Yuan Zhang, Peter Beerli, Johannes A. Lenstra … & J. Stuart F. Barker
The swamp type of the Asian water buffalo is assumed to have been domesticated by about 4000 years BP, following the introduction of rice cultivation. Previous localizations of the domestication site were based on mitochondrial DNA (mtDNA) variation within China, accounting only for the maternal lineage. We carried out a comprehensive sampling of China, Taiwan, Vietnam, Laos, Thailand, Nepal and Bangladesh and sequenced the mtDNA Cytochrome b gene and control region and the Y-chromosomal ZFY,...

Data from: Growth of maize on mixed nitrate and ammonium promotes auxin synthesis and biomass accumulation

Peng Wang, Zhangkui Wang, Qingchun Pan, Xichao Sun, Huan Chen, Fanjun Chen, Lixing Yuan & Guohua Mi
Mixed nitrate (NO3-) and ammonium (NH4+) as nitrogen source can improve plant growth. The underlying mechanism was explored by using metabolomics and transcriptome. Maize plants were grown hydroponically with three nitrogen forms (nitrate, 75/25 nitrate/ammonium and ammonium). Mixed N increased photosynthetic rate compared to nitrate supply, and had the highest leaf area, shoot and root biomass among the three nitrogen treatments. In shoot and root, the concentration of nitrogenous compounds (NH4+, Gln, Asn) and carbohydrates...

Data from: Evolution of interspecies unilateral incompatibility in the relatives of Arabidopsis thaliana

Ling Li, Bo Liu, Xiaomei Deng, Hainan Zhao, Hongyan Li, Shilai Xing, Della D. Fetzer, Mengya Li, Mikhail E. Nasrallah, June B. Nasrallah & Pei Liu
The evolutionary concurrence of intraspecies self-incompatibility (SI) and explosive angiosperm radiation in the Cretaceous has led to the hypothesis that SI was one of the predominant drivers of rapid speciation in angiosperms. Interspecies unilateral incompatibility (UI) usually occurs when pollen from a self-compatible (SC) species is rejected by the pistils of a SI species, while the reciprocal pollination is compatible (UC). Although this SI x SC type UI is most prevalent and viewed as a...

Data from: Extreme polyandry aids the establishment of invasive populations of a social insect

Guiling Ding, Huanli Xu, Benjamin P. Oldroyd & Rosalyn S. Gloag
Although monandry is believed to have facilitated the evolution of eusociality, many highly eusocial insects have since evolved extreme polyandry. The transition to extreme polyandry was likely driven by the benefits of within-colony genetic variance to task specialization and/or disease resistance, but the extent to which it confers secondary benefits, once evolved, is unclear. Here we investigate the consequences of extreme polyandry on the invasive potential of the Asian honey bee, Apis cerana. In honey...

Data from: Temporal dynamics of nutrient uptake by neighboring plant species: evidence from intercropping

Wei-Ping Zhang, Guang-Cai Liu, Jian-Hao Sun, Dario Fornara, Li-Zhen Zhang, Fang-Fang Zhang & Long Li
The productivity of species-diverse plant assemblages strongly depends on the temporal dynamics of nutrient uptake by competing neighbouring plants. Our understanding, however, of how rates of nitrogen (N), phosphorous (P) and potassium (K) uptake might change through time between neighbouring plant species under field conditions is still very limited. Here, we specifically measure the temporal trajectories of N, P and K uptake by staple food plants such as wheat (Triticum aestivum L.), barley (Hordeum vulgare...

Historical rice farming in China linked to contemporary polygenic score differences

Chen Zhu, Thomas Talhelm, Yingxiang Li, Gang Chen, Jiong Zhu & Jun Wang
Following domestication in the lower Yangtze River valley 9,400 years ago, rice farming spread throughout China and changed lifestyle patterns among Neolithic populations. Here we report evidence that the advent of rice domestication and cultivation may have shaped humans not only culturally but also genetically. Leveraging recent findings from molecular genetics, we construct a number of polygenic scores of behavioural traits and examine their associations with rice cultivation based on a sample of 4,101 individuals...

Data from: Phylogenetic niche conservatism and variations in species diversity-climate relationships

Qinggang Wang, Yaoqi Li, Dongting Zou, Xiangyan Su, Hongyu Cai, Ao Luo, Ke Jiang, Xiaoling Zhang, Xiaoting Xu, Nawal Shrestha & Zhiheng Wang
Although contemporary climate has been identified as one of the major determinants of large-scale species diversity patterns, its effect on species diversity greatly varies among clades. Understanding the drivers of the variation in species diversity-climate relationships (DCRs) across clades, which is critical for developing general mechanisms underlying the effects of climate on species diversity patterns, remains a current challenge. Using newly compiled distribution data of 914 Rosaceae species in China and a dated genus-level phylogeny,...

Data from: Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment (SLAF) sequencing

Wenjin Su, Lianjun Wang, Jian Lei, Shasha Chai, Yi Liu, Yuanyuan Yang, Xinsun Yang & Chunhai Jiao
Sweet potato, Ipomoea batatas (L.) Lam., is an important food crop that is cultivated worldwide. However, no genome-wide assessment of the genetic diversity of sweet potato has been reported to date. In the present study, the population structure and genetic diversity of 197 sweet potato accessions most of which were from China were assessed using 62,363 SNPs. A model-based structure analysis divided the accessions into three groups: group 1, group 2 and group 3. The...

Data from: The impact of variable degrees of freedom and scale parameters in Bayesian methods for genomic prediction in Chinese Simmental beef cattle

Bo Zhu, Miao Zhu, Jicai Jiang, Hong Niu, Yanhui Wang, Yan Wu, Lingyang Xu, Yang Chen, Lupei Zhang, Xue Gao, Huijiang Gao, Jianfeng Liu, Junya Li, Yang Wu & Yan Chen
Three conventional Bayesian approaches (BayesA, BayesB and BayesCπ) have been demonstrated to be powerful in predicting genomic merit for complex traits in livestock. A priori, these Bayesian models assume that the non-zero SNP effects (marginally) follow a t-distribution depending on two fixed hyperparameters, degrees of freedom and scale parameters. In this study, we performed genomic prediction in Chinese Simmental beef cattle and treated degrees of freedom and scale parameters as unknown with inappropriate priors. Furthermore,...

Data from: Population structure of a global agricultural invasive pest, Bactrocera dorsalis (Diptera: Tephritidae)

Yu-Jia Qin, Matthew N. Krosch, Mark K. Schutze, Yue Zhang, Xiao-Xue Wang, Chandra S. Prabhakar, Agus Susanto, Alvin K.W. Hee, Sunday Ekesi, Kemo Badji, Mahfuza Khan, Yu-Bing Huang, Jia-Jiao Wu, Qiao-Ling Wang, Ge Yan, Li-Huan Zhu, Zi-Hua Zhao, Li-Jun Liu, Anthony R. Clarke, Zhi-Hong Li & Alvin K. W. Hee
Bactrocera dorsalis, the Oriental fruit fly, is one of the world’s most destructive agricultural insect pests and a major impediment to international fresh commodity trade. The genetic structuring of the species across its entire geographic range has never been undertaken, because under a former taxonomy B. dorsalis was divided into four distinct taxonomic entities, each with their own, largely non-overlapping, distributions. Based on the extensive sampling of six a priori groups from 63 locations, genetic...

Data from: Nutrient addition affects scaling relationship of leaf nitrogen to phosphorus in Arabidopsis thaliana

Zhengbing Yan, Xiuping Li, Di Tian, Wenxuan Han, Xinghui Hou, Haihua Shen, Yalong Guo & Jingyun Fang
1. Ambient nutrient changes influence the coupling of nitrogen (N) and phosphorus (P) in terrestrial ecosystems, but whether it could alter the scaling relationship of plant leaf N to P concentrations remains unclear. 2. Here we conducted experimental manipulations using Arabidopsis thaliana, with five levels of N and P additions and nine repeated experiments, and then evaluated the changes in the scaling relationship of leaf N to P concentrations under nutrient additions. 3. Overall, leaf...

Data from: Old World and New World Phasmatodea: phylogenomics resolve the evolutionary history of stick and leaf insects

Sabrina Simon, Harald Letsch, Sarah Bank, Thomas R. Buckley, Alexander Donath, Shanlin Liu, Ryuichiro Machida, Karen Meusemann, Bernhard Misof, Lars Podsiadlowski, Xin Zhou, Benjamin Wipfler & Sven Bradler
Phasmatodea comprises over 3,000 extant species and stands out as one of the last remaining insect orders for which a robust, higher-level phylogenetic hypothesis is lacking. New research suggests that the extant diversity is the result of a surprisingly recent and rapid radiation that has been difficult to resolve with standard Sanger sequence data. In order to resolve the early branching events of stick and leaf insects, we analyzed transcriptomes from 61 species, including 38...

Role of an ABA receptor SlPYL9 in tomato fruit ripening

Wenbin Kai, Juan Wang, Bin Liang, Ying Fu, Yu Zheng, Wenbo Zhang, Qian Li & Ping Leng
Abstract Abscisic acid (ABA) regulates fruit ripening, yet little is known about the exact roles of ABA receptors in fruit. In this study, we revealed the role of SlPYL9, a tomato PYR (pyrabactin resistance) / PYL (pyrobactin resistance-like) / RCAR (regulatory component of ABA receptors) ABA receptor, as a positive regulator of ABA signaling and fruit ripening. SlPYL9 inhibited protein phosphatase-type 2C (PP2C2/6) in ABA dose-dependent way, and it interacts physically with SlPP2C 2 /...

Data from: Phylogenomics and the evolution of hemipteroid insects

Kevin P. Johnson, Christopher H. Dietrich, Frank Friedrich, Rolf G. Beutel, Benjamin Wipfler, Ralph S. Peters, Julie M. Allen, Malte Petersen, Alexander Donath, Kimberly K. O. Walden, Alexey M. Kozlov, Lars Podsiadlowski, Christoph Mayer, Karen Meusemann, Alexandros Vasilikopoulos, Robert M. Waterhouse, Stephen L. Cameron, Christiane Weirauch, Daniel R. Swanson, Diana M. Percy, Nate B. Hardy, Irene Terry, Shanlin Liu, Xin Zhou, Bernhard Misof … & Kazunori Yoshizawa
Hemipteroid insects (Paraneoptera), with over 10% of all known insect diversity, are a major component of terrestrial and aquatic ecosystems. Previous phylogenetic analyses have not consistently resolved the relationships among major hemipteroid lineages. We provide maximum likelihood-based phylogenomic analyses of a taxonomically comprehensive dataset comprising sequences of 2,395 single-copy, protein-coding genes for 193 samples of hemipteroid insects and outgroups. These analyses yield a well-supported phylogeny for hemipteroid insects. Monophyly of each of the three hemipteroid...

Data from: Symbiotic soil fungi enhance resistance and resilience of an experimental grassland to drought and nitrogen deposition

Yangyang Jia, Marcel Van Der Heijden, Cameron Wagg, Gu Feng & Florian Walder
Ecosystem stability is threatened by multiple global change factors such as drought and elevated nitrogen deposition. Yet, it is still poorly understood whether soil organisms can buffer against such perturbations. Here we focus on arbuscular mycorrhizal fungi (AMF), a common and widespread group of soil fungi. AMF form symbiotic associations with the majority of terrestrial land plants and promote a range of ecosystem services including plant production, diversity and nutrient cycling. We tested whether AMF...

Analysis of RNA-seq, DNA target enrichment, and Sanger nucleotide sequence data resolves deep splits in the phylogeny of cuckoo wasps (Hymenoptera: Chrysididae)

Thomas Pauli, Karen Meusemann, Sandra Kukowka, Manuela Sann, Alexander Donath, Christoph Mayer, Jan Philip Oeyen, Yolanda Ballesteros, Alexander Berg, Eric Van Den Berghe, Hermes Escalona, Adalgisa Guglielmino, Manfred Niehuis, Massimo Olmi, Lars Podsiadlowski, Carlo Polidori, Jeroen De Rond, Paolo Rosa, Thomas Schmitt, Franco Strumia, Mareike Wurdack, Shanlin Liu, Xin Zhou, Bernhard Misof, Ralph Peters … & Oliver Niehuis
The wasp family Chrysididae (cuckoo wasps, gold wasps) comprises exclusively parasitoid and kleptoparasitic species, many of which feature a stunning iridescent coloration and phenotypic adaptations to their parasitic life style. Previous attempts to infer phylogenetic relationships among the family’s major lineages (subfamilies, tribes, genera) based on Sanger sequence data were insufficient to statistically resolve the monophyly and the phylogenetic position of the subfamily Amiseginae and the phylogenetic relationships among the tribes Allocoeliini, Chrysidini, Elampini, and...

Data from: Impacts of environmental heterogeneity on moss diversity and distribution of Didymodon (Pottiaceae) in Tibet, China

Shanshan Song, Xuehua Liu, Xueliang Bai, Yanbin Jiang, Xianzhou Zhang, Chengqun Yu & Xiaoming Shao
Tibet makes up the majority of the Qinghai-Tibet Plateau, often referred to as the roof of the world. Its complex landforms, physiognomy, and climate create a special heterogeneous environment for mosses. Each moss species inhabits its own habitat and ecological niche. This, in combination with its sensitivity to environmental change, makes moss species distribution a useful indicator of vegetation alteration and climate change. This study aimed to characterize the diversity and distribution of Didymodon (Pottiaceae)...

Data from: Is diversification in male reproductive traits driven by evolutionary trade-offs between weapons and nuptial gifts?

Xingyue Liu, Fumio Hayashi, Laura Corley Lavine & Ding Yang
Many male animals have evolved exaggerated traits that they use in combat with rival males to gain access to females and secure their reproductive success. But some male animals invest in nuptial gifts that gains them access to females. Both these reproductive strategies are costly in that resources are needed to produce the weapon or nuptial gift. In closely related species where both weapons and nuptial gifts are present, little is known about the potential...

Data from: Livestock grazing regulates ecosystem multifunctionality in semi‐arid grassland

Haiyan Ren, Valerie T. Eviner, Weiyang Gui, Gail W.T. Wilson, Adam B. Cobb, Gaowen Yang, Yingjun Zhang, Shuijin Hu, Yongfei Bai & Gail W. T. Wilson
1. Ecological theories and experimental evidence indicate that human activity induced losses in biodiversity can have substantial impacts on multiple ecosystem functions. It remains unclear, however, how grazing affects grassland biodiversity and ecosystem multifunctionallity (EMF). 2. Here, we assessed the grazing effects on different dimensions of biodiversity (i.e. plants and soil microbes) and EMF based on a 11-year field experiment in a semi-arid grassland. 3. We found that soil organic C, available nitrogen, and plant...

Data from: Estimating the number of sexual events per generation in a facultatively sexual haploid population

Richard A. Ennos & Xinsheng Hu
In populations of facultatively sexual organisms the proportion of sexually produced offspring contributed each generation is a critical determinant of their evolutionary potential. However, estimating this parameter in natural populations has proved difficult. Here we develop a population genetic model for estimating the number of sexual events occurring per generation for facultatively sexual haploids possessing a biallelic mating type locus (e.g. Chlamydomonas, ascomycete fungi). Our model treats the population as two subpopulations possessing opposite mating...

Data from: Complex disease and phenotype mapping in the domestic dog

Jessica J. Hayward, Marta G. Castelhano, Kyle C. Oliveira, Elizabeth Corey, Cheryl Balkman, Tara L. Baxter, Margret L. Casal, Sharon A. Center, Meiying Fang, Susan J. Garrison, Sara E. Kalla, Pavel Korniliev, Michael I. Kotlikoff, N. Sydney Moise, Laura M. Shannon, Kenneth W. Simpson, Nathan B. Sutter, Rory J. Todhunter & Adam R. Boyko
The domestic dog is becoming an increasingly valuable model species in medical genetics, showing particular promise to advance our understanding of cancer and orthopaedic disease. Here we undertake the largest canine genome-wide association study to date, with a panel of over 4,200 dogs genotyped at 180,000 markers, to accelerate mapping efforts. For complex diseases, we identify loci significantly associated with hip dysplasia, elbow dysplasia, idiopathic epilepsy, lymphoma, mast cell tumour and granulomatous colitis; for morphological...

Data from: Population variation reveals independent selection towards small body size in Chinese Debao pony

Adiljan Kader, Yan Li, Kunzhe Dong, David M. Irwin, Qianjun Zhao, Xiaohong He, Jianfeng Liu, Yabin Pu, Neena Amatya Gorkhali, Xuexue Liu, Lin Jiang, Xiangchen Li, Weijun Guan, Yaping Zhang, Dong-Dong Wu & Yuehui Ma
Body size, one of the most important quantitative traits under evolutionary scrutiny, varies considerably among species and among populations within species. Revealing the genetic basis underlying this variation is very important, particularly in humans where there is a close relationship with diseases and in domestic animals as the selective patterns are associated with improvements in production traits. The Debao pony is a horse breed with small body size that is unique to China; however, it...

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