57 Works

Data from: Genome-wide search for quantitative trait loci controlling important plant and flower traits in petunia using an interspecific recombinant inbred population of Petunia axillaris and Petunia exserta

Zhe Cao, Yufang Guo, Qian Yang, Yanhong He, Mohammed Fetouh, Ryan M. Warner, Zhanao Deng & Mohammed I. Fetouh
A major bottleneck in plant breeding has been the much limited genetic base and much reduced genetic diversity in domesticated, cultivated germplasm. Identification and utilization of favorable gene loci or alleles from wild or progenitor species can serve as an effective approach to increasing genetic diversity and breaking this bottleneck in plant breeding. This study was conducted to identify quantitative trait loci (QTL) in wild or progenitor petunia species that can be used to improve...

Data from: Molecular evolution patterns reveal life history features of mycoplasma-related endobacteria associated with arbuscular mycorrhizal fungi

Kevin H. Toomer, Xiuhua Chen, Mizue Naito, Stephen J. Mondo, Henk C. Den Bakker, Nicholas W. VanKuren, Ylva Lekberg, Joseph B. Morton & Teresa E. Pawlowska
The mycoplasma-related endobacteria (MRE), representing a recently discovered lineage of Mollicutes, are widely distributed across arbuscular mycorrhizal fungi (AMF, Glomeromycota). AMF colonize roots of most terrestrial plants and improve plant mineral nutrient uptake in return for plant-assimilated carbon. The role of MRE in the biology of their fungal hosts is unknown. To start characterizing this association, we assessed partitioning of MRE genetic diversity within AMF individuals and across the AMF phylogeographic range. We further used...

Data from: Contrasting responses of phosphatase kinetic parameters to nitrogen and phosphorus additions in forest soils

Xinyu Zhang, Yang Yang, Chuang Zhang, Shuli Niu, Guirui Yu, Huimin Wang, Evgenia Blagodatskaya, Yakov Kuzyakov, Dashuan Tian, Yuqian Tang, Shuang Liu & Xiaomin Sun
1. Global changes include increasing nitrogen (N) and phosphorus (P) deposition, which affect microbial nutrient demand and biogeochemical cycles. The responses of P-mineralizing enzymes to these global change components are poorly defined and are not specified in forest soils differing in P content. 2. We chose one site in a P-rich and two sites in P-poor forests and established sixteen 20 × 20 m plots at each site. Control, either N only, P only, or...

An invasive plant rapidly increased the similarity of soil fungal pathogen communities

Xinmin Lu
Background and Aims: Plant invasions can change soil microbial communities and affect subsequent invasions directly or indirectly via foliar herbivory. It has been proposed that invaders promote uniform biotic communities that displace diverse, spatially variable communities (“Biotic Homogenization Hypothesis”) but this has not been experimentally tested for soil microbial communities, so the underlying mechanisms and dynamics are unclear. Here, we compared density-dependent impacts of the invasive plant Alternanthera philoxeroides and its native congener A.sessilis on...

Data from: GRF-interacting factor1 regulates shoot architecture and meristem determinacy in maize

Dan Zhang, Wei Sun, Renee Singh, Yuanyuan Zheng, Zheng Cao, Manfei Li, China Lunde, Sarah Hake & Zuxin Zhang
Plant architecture results from a balance of indeterminate and determinate cell fates. Cells with indeterminate fates are located in meristems, comprising groups of pluripotent cells that produce lateral organs. Meristematic cells are also found in intercalary stem tissue, which provides cells for internodes, and at leaf margins to contribute to leaf width. We identified a maize (Zea mays) mutant that has a defect in balancing determinacy and indeterminacy. The mutant has narrow leaves and short...

Data from: Invasive alien plants benefit more from clonal integration in heterogeneous environments than natives

Yong-Jian Wang, Heinz Müller-Schärer, Mark Van Kleunen, Ai-Ming Cai, Ping Zhang, Rong Yan, Bi-Cheng Dong & Fei-Hai Yu
What confers invasive alien plants a competitive advantage over native plants remains open to debate. Many of the world's worst invasive alien plants are clonal and able to share resources within clones (clonal integration), particularly in heterogeneous environments. Here, we tested the hypothesis that clonal integration benefits invasive clonal plants more than natives and thus confers invasives a competitive advantage. We selected five congeneric and naturally co-occurring pairs of invasive alien and native clonal plants...

Data from: Positive selection drives adaptive diversification of the 4-coumarate: CoA ligase (4CL) gene in angiosperms

Haiyan Sun, Liangcai Peng, Kai Guo, Shengqiu Feng, Weihua Zou, Ying Li & Chunfen Fan
Lignin and flavonoids play a vital role in the adaption of plants to a terrestrial environment. 4-Coumarate: coenzyme A ligase (4CL) is a key enzyme of general phenylpropanoid metabolism which provides the precursors for both lignin and flavonoids biosynthesis. However, very little is known about how such essential enzymatic functions evolve and diversify. Here, we analyze 4CL sequence variation patterns in a phylogenetic framework to further identify the evolutionary forces that lead to functional divergence....

Data from: Evolution and phylogeography analysis of diploid and polyploid Misgurnus anguillicaudatus populations across China

Jia Zhong, Shaokui Yi, Laiyan Ma & Weimin Wang
The origin and evolution of polyploid organisms have been extensively studied in plants, but this topic remains only partially understood in vertebrates, where polyploidy is relatively rare. In this study, we used Misgurnus anguillicaudatus, a fish that comprises five ploidy levels in nature, as a model animal to improve our understanding of biogeographic history and evolution of polyploid vertebrates. After collecting samples from different geographical populations in China, their ploidy levels were determined using flow...

Data from: Genetic basis of sRNA quantitative variation analyzed using an experimental population derived from an elite rice hybrid

Jia Wang, Wen Yao, Dan Zhu, Weibo Xie & Qifa Zhang
We performed a genetic analysis of sRNA abundance in flag leaf from an immortalized F2 (IMF2) population in rice. We identified 53,613,739 unique sRNAs and 165,797 sRNA expression traits (s-traits). A total of 66,649 s-traits mapped 40,049 local-sQTLs and 30,809 distant-sQTLs. By defining 80,362 sRNA clusters, 22,263 sRNA cluster QTLs (scQTLs) were recovered for 20,249 of all the 50,139 sRNA cluster expression traits (sc-traits). The expression levels for most of s-traits from the same genes...

Larger males facilitate population expansion in Ophraella communa

Yan Zhang, Zhongshi Zhou, Chenchen Zhao, Weihua Ma, Shaowei Cui, Hongsong Chen, Chao Ma & Jianying Guo
One of the most intriguing concepts in animal ecology is the reproductive advantages offered by larger body size, and the females prefer to mate with larger males in order to gain reproductive advantage. Currently, it is not clear how females recognize signs of male “quality” and what mechanisms are involved in producing offspring with direct or indirect benefits. Our study aims to assess the preferences of females for males in Ophraella communa, determine the reproductive...

Trade-off between vegetation type, soil erosion control and surface water in global semi-arid regions: A meta-analysis

Gao-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...

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...

Ants adjust their tool use strategy in response to foraging risk

Aiming Zhou, Yuzhe Du & Jian Chen
1. Ants are among a few invertebrates that can use certain tools. For example, some ants can use debris and soil grains to transport liquid food. Although there has been evidence showing that ants can select the most efficient tools in transporting liquid food, little is known about their flexibility in using a specific tool under environmental pressure. 2. Black imported fire ants, Solenopsis richteri Forel, can use sands as a tool for foraging. We...

Genome and transcriptome assemblies of TIL11

Lin Li, Zhao Li & Linqian Han
Here, we employed single-molecule long-read sequencing of cDNA libraries from five tissues of the teosinte inbred line TIL11 and identified 70,044 non-redundant transcript isoforms. 23,527 predicted genes were identified using our state-of-the-art, machine learning-based bioinformatics pipeline DenovoAS_Finder without a complete reference genome. Additionally, we constructed a draft TIL11 genome based on a Nanopore sequencing dataset with 16,633 high-quality contigs and a N50 of 112 kb.

Data from: Genome-wide analysis reveals artificial selection on coat colour and reproductive traits in Chinese domestic pigs

Chao Wang, Hongyang Wang, Yu Zhang, Zhonglin Tang, Kui Li & Bang Liu
Pigs from Asia and Europe were independently domesticated from c. 9000 years ago. During this period, strong artificial selection has led to dramatic phenotypic changes in domestic pigs. However, the genetic basis underlying these morphological and behavioural adaptations is relatively unknown, particularly for indigenous Chinese pigs. Here, we performed a genome-wide analysis to screen 196 regions with selective sweep signals in Tongcheng pigs, which are a typical indigenous Chinese breed. Genes located in these regions...

Data from: Comparative transcriptomics uncovers alternative splicing changes and signatures of selection from maize improvement

Jun Huang, Youjun Gao, Haitao Jia, Lei Liu, Dan Zhang & Zuxin Zhang
Background: Alternative splicing (AS) is an important regulatory mechanism that greatly contributes to eukaryotic transcriptome diversity. A substantial amount of evidence has demonstrated that AS complexity is relevant to eukaryotic evolution, development, adaptation, and complexity. In this study, six teosinte and ten maize transcriptomes were sequenced to analyze AS changes and signatures of selection in maize domestication and improvement. Results In maize and teosinte, 13,593 highly conserved genes, including 12,030 multiexonic genes, were detected. By...

Data from: Leaf economics spectrum in rice: Leaf anatomical, biochemical and physiological trait trade-offs

Dongliang Xiong & Jaume Flexas
The leaf economics spectrum (LES) is an eco-physiological concept describing the trade-offs of leaf structural, and physiological traits, that has been widely investigated across multiple scales. However, the effects of the breeding process on the LES in crops, as well as the mechanisms of the trait trade-offs underlying the LES, have not been thoroughly elucidated to date. In this study, a dataset, including leaf anatomical, biochemical and functional traits, was constructed to evaluate the trait...

Data from: Inferring outcrossing in the homothallic fungus Sclerotinia sclerotiorum using linkage disequilibrium decay

Weidong Chen, Renuka N. Attanayake, Vidhura Tennekoon, Dennis A. Johnson, Lyndon D. Porter, Luis Del Río-Mendoza & Daohong Jiang
The occurrence and frequency of outcrossing in homothallic fungal species in nature is an unresolved question. Here we report detection of frequent outcrossing in the homothallic fungus Sclerotinia sclerotiorum. In using multilocus linkage disequilibrium (LD) to infer recombination among microsatellite alleles, high mutation rates confound the estimates of recombination. To distinguish high mutation rates from recombination to infer outcrossing, 8 population samples comprising 268 S. sclerotiorum isolates from widely distributed agricultural fields were genotyped for...

Data from: New locus reveals the genetic architecture of sex reversal in the Chinese tongue sole (Cynoglossus semilaevis)

Yu Cui, Weifeng Wang, Liyong Ma, Jinhua Jie, Yanhong Zhang, Huanling Wang & Hengde Li
Sex reversal in insects, amphibians, reptiles, and fishes is a complicated and interesting biological phenomenon. Sex reversal changes the sex ratio of populations and may complicate breeding schemes. In the Chinese tongue sole (Cynoglossus semilaevis), genetic females may change into pseudomales, thereby increasing aquaculture costs because of the lower growth rate of the males than that of the females. Here, we identify a new locus associated with sex reversal; this single nucleotide polymorphism (SNP) is...

The assembly genome of a wild landrace of tea plant (named as DASZ)

Weiwei Wen
Using Pacbio long reads, Illumina short reads to assemble the genome of a wild landrace of tea plant (named as DASZ).

Land Use Change and Grain Production, Hubei, China

Chengchao Zuo
Observed and modelled land use map, grain production statistics for Hubei province, China

Data from: Modeled and measured ecosystem respiration in maize–soybean systems over 10 years

Ming Zhan, Adam J. Liska, Anthony L. Nguy-Robertson, Andrew E. Suyker, Matthew P. Pelton & Haishun Yang
Crop residue is an abundant resource for the potential production of biofuels, but a better understanding of its use on net carbon emissions must be developed to mitigate climate change. This analysis combines two established crop growth models (Hybrid-Maize and Soysim) with a simple soil and crop residue respiration model to estimate daily ecosystem respiration (ERe) from maize and soybean; ERe was estimated to be the sum of CO2 emissions from the oxidation of the...

Data from: Predicting rice hybrid performance using univariate and multivariate GBLUP models based on North Carolina mating design II

X. Wang, L. Li, Z. Yang, X. Zheng, S. Yu, C. Xu & Z. Hu
Genomic selection (GS) is more efficient than traditional phenotype-based methods in hybrid breeding. The present study investigated the predictive ability of genomic best linear unbiased prediction models for rice hybrids based on the North Carolina mating design II, in which a total of 115 inbred rice lines were crossed with 5 male sterile lines. Using 8 traits of the 575 (115 × 5) hybrids from two environments, both univariate (UV) and multivariate (MV) prediction analyses,...

Data from: Testing reticulate evolution of four Vitis species from East Asia using restriction‐site associated DNA sequencing

Zhi-Yao Ma, Jun Wen, Jing-Pu Tian, Abbas Jamal, Longqing Chen, Xiu-Qun Liu & Long-Qing Chen
Reticulate evolution is an important driving force of angiosperm evolution. It has been proposed as an important evolutionary process in Vitis subgenus Vitis. Events of natural hybridization and introgression of several taxa native to North America have been hypothesized and discussed. However, there is no convincing evidence of reticulate evolution reported for closely related Vitis taxa from East Asia. We aim to explore natural hybridization and introgression among four closely related Vitis taxa from East...

Data from: Past distribution of epiphyllous liverworts in China: the usability of historical data

Yanbin Jiang, Tiejun Wang, Yupeng Wu, Ronggui Hu, Ke Huang & Xiaoming Shao
Epiphyllous liverworts form a special group of bryophytes that primarily grow on the leaves of understory vascular plants in tropical and subtropical evergreen broadleaf forests. Being sensitive to moisture and temperature changes, epiphyllous liverworts are often consider to be good indicators of climate change and forest degradation. However, they are a poorly collected and taxonomically complicated group, with an only partly identified distribution pattern. In this study, we built four models based on 24 environmental...

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