Data from: Positive selection drives adaptive diversification of the 4-coumarate: CoA ligase (4CL) gene in angiospermsHaiyan 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: Genetic basis of sRNA quantitative variation analyzed using an experimental population derived from an elite rice hybridJia 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...
Data from: Molecular evolution patterns reveal life history features of mycoplasma-related endobacteria associated with arbuscular mycorrhizal fungiKevin 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: Comparative transcriptomics uncovers alternative splicing changes and signatures of selection from maize improvementJun 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: Paternal epigenetic effects of population density on locust phase-related characteristics associated with heat-shock protein expressionBing Chen, Shaoqin Li, Qiang Ren, Xiwen Tong, Xia Zhang & Le Kang
Many species exhibit transgenerational plasticity by which environmental cues experienced by either parent can be transmitted to their offspring, resulting in phenotypic variants in offspring to match ancestral environments. However, the manner by which paternal experiences affect offspring plasticity through epigenetic inheritance in animals generally remains unclear. In this study, we examined the transgenerational effects of population density on phase-related traits in the migratory locust Locusta migratoria. Using an experimental design that explicitly controls genetic...
Data from: Identifying litchi (Litchi chinensis Sonn.) cultivars and their genetic relationships using single nucleotide polymorphism (SNP) markersWei Liu, Zhidan Xiao, Xiuli Bao, Xiaoyan Yang, Jing Fang & Xu Xiang
Litchi is an important fruit tree in tropical and subtropical areas of the world. However, there is widespread confusion regarding litchi cultivar nomenclature and detailed information of genetic relationships among litchi germplasm is unclear. In the present study, the potential of single nucleotide polymorphism (SNP) for the identification of 96 representative litchi accessions and their genetic relationships in China was evaluated using 155 SNPs that were evenly spaced across litchi genome. Ninety SNPs with minor...
Data from: Impacts of environmental heterogeneity on moss diversity and distribution of Didymodon (Pottiaceae) in Tibet, ChinaShanshan 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: High-throughput genotyping for species identification and diversity assessment in germplasm collectionsAnnaliese S. Mason, Jing Zhang, Reece Tollenaere, Paula Vasquez Teuber, Jessica Dalton-Morgan, Liyong Hu, Guijun Yan, David Edwards, Robert Redden & Jacqueline Batley
Germplasm collections provide an extremely valuable resource for breeders and researchers. However, misclassification of accessions by species often hinders the effective use of these collections. We propose that use of high-throughput genotyping tools can provide a fast, efficient and cost-effective way of confirming species in germplasm collections, as well as providing valuable genetic diversity data. We genotyped 180 Brassicaceae samples sourced from the Australian Grains Genebank across the recently released Illumina Infinium Brassica 60K SNP...
Huazhong Agricultural University8
University of Montana1
University of Queensland1
Inner Mongolia University1
West Virginia University1
South China Normal University1
Guangdong Academy of Agricultural Sciences1
Department of Environment, Land, Water and Planning1
Zoological Society of London1