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The female‐specifically expressed response regulator (PdFERR) gene in Populus deltoides, a sex determination gene (an orthologous gene of ARR17 in Populus tremula), was found to promote femaleness in heterologous expression lines of Arabidopsis. None of the genes in the Arabidopsis genome seem to be orthologous to PdFERR. Although originating from two evolutionarily distant plants, the dioecious poplar FERR might promote femaleness in the hermaphroditic Arabidopsis through an evolutionary consistent regulatory pathway. However, there is no molecular evidence to support this viewpoint. In this study, to identify the shared downstream orthologous gene of PdFERR, we used yeast two‐hybrid assay to screen potential interactors of PdFERR in Arabidopsis. We identified the ethylene response factor 96 (AtERF96) and confirmed the interaction via in vivo and in vitro assays. The ERF96 orthologous gene in P. deltoides was also experimentally confirmed to interact with PdFERR. PdFERR could then promote femaleness in poplar or Arabidopsis through interactions with ERF96, which provide a new perspective for understanding the PdFERR gene regulating sex differentiation. [ABSTRACT FROM AUTHOR]

Plant roots significantly influence soil microbial diversity, and soil microorganisms play significant roles in both natural and agricultural ecosystems. Although the genetically modified (GM) crops with enhanced insect and herbicide resistance are thought to have unmatched yield and stress resistance advantages, thorough and in‐depth case studies still need to be carried out in a real‐world setting due to the potential effects of GM plants on soil microbial communities. In this study, three treatments were used: a recipient soybean variety Jack, a triple transgenic soybean line JD321, and the glyphosate‐treated JD321 (JD321G). Three sampling stages (flowering, seed filling and maturing), as well as three host niches of soybean rhizosphere [intact roots (RT), rhizospheric soil (RS) and surrounding soil (SS)] were established. In comparison to Jack, the rhizospheric soil of JD321G had higher urease activity and lower nitrite reductase at the flowering stage. Different treatments and different sampling stages existed no significant effects on the compositions of microbial communities at different taxonomic levels. However, at the genus level, the relative abundance of three plant growth‐promoting fungal genera (i.e. Mortierella, Chaetomium and Pseudombrophila) increased while endophytic bacteria Chryseobacterium and pathogenic bacteria Streptomyces decreased from the inside to the outside of the roots (i.e. RT → RS → SS). Moreover, two bacterial genera, Bradyrhizobium and Ensifer were more abundant in RT than in RS and SS, as well as three species, Agrobacterium radiobacter, Ensifer fredii and Ensifer meliloti, which are closely related to nitrogen‐fixation. Furthermore, five clusters of orthologous groups (COGs) associated to nitrogen‐fixation genes were higher in RT than in RS, whereas only one COG annotated as dinitrogenase iron‐molybdenum cofactor biosynthesis protein was lower. Overall, the results imply that the rhizosphere host niches throughout the soil–plant continuum largely control the composition and function of the root‐associated microbiome of triple transgenic soybean. [ABSTRACT FROM AUTHOR]

SUMMARY: Sex differences and evolutionary differences are critical biological issues. Ginkgo is an ancient lineage of dioecious gymnosperms with special value for studying the mechanism of sex determination in plants. However, the major genetic basic underlying sex chromosomes remains to be uncovered. In this study, we identify the sex‐determining region of Ginkgo and locate it to the area from megabases 48 to 75 on chromosome 2. We find that the male sex‐determining region of Ginkgo contains more than 200 genes, including four MADS‐box genes, demonstrating that the Ginkgo sex determination system is of the XY type. We also find that genetic sex differences result in specialized flavonoid metabolism and regulation in each sex. These findings establish a foundation for revealing the molecular mechanism of sexual dimorphism and promoting the development of the Ginkgo industry. [ABSTRACT FROM AUTHOR]

SUMMARY: Acer truncatum (purpleblow maple) is a woody tree species that produces seeds with high levels of valuable fatty acids (especially nervonic acid). However, the lack of a complete genome sequence has limited both basic and applied research on A. truncatum. We describe a high‐quality draft genome assembly comprising 633.28 Mb (contig N50 = 773.17 kb; scaffold N50 = 46.36 Mb) with at least 28 438 predicted genes. The genome underwent an ancient triplication, similar to the core eudicots, but there have been no recent whole‐genome duplication events. Acer yangbiense and A. truncatum are estimated to have diverged about 9.4 million years ago. A combined genomic, transcriptomic, metabonomic, and cell ultrastructural analysis provided new insights into the biosynthesis of very long‐chain monounsaturated fatty acids. In addition, three KCS genes were found that may contribute to regulating nervonic acid biosynthesis. The KCS paralogous gene family expanded to 28 members, with 10 genes clustered together and distributed in the 0.27‐Mb region of pseudochromosome 4. Our chromosome‐scale genomic characterization may facilitate the discovery of agronomically important genes and stimulate functional genetic research on A. truncatum. Furthermore, the data presented also offer important foundations from which to study the molecular mechanisms influencing the production of nervonic acids. Significance Statement: Here, we provide the first report on the Acer truncatum genome. Our work provides extensive genetic resources necessary for very long‐chain monounsaturated fatty acid biosynthesis. [ABSTRACT FROM AUTHOR]

Podophyllotoxin is a potent cytotoxic agent and serves as a useful lead compound for development of anticancer agents. Tubulin is known as an attractive target for drug discovery and cancer therapies. There are few studies on the treatment of breast cancer with podophyllotoxin and its derivatives targeting tubulin. Here, a series of novel aryl 1,3,4‐oxadiazole/1,3,4‐thiadiazole acid podophyllotoxin ester derivatives (D1–D16) were synthesized. Among these compounds, D9 exhibited excellent antiproliferation activity against MCF‐7 cells (IC50=2.46±0.12 μM). Furthermore, D9 caused cell cycle arrest at the G2/M phase and induced cell apoptosis. Confocal microscopy showed that D9 inhibited microtubule polymerization by causing cancer cell growth inhibition. Molecular docking results suggested D9 could bind to the active binding site of tubulin. In a mouse model, compound D9 suppressed malignant growth without causing significant toxicity to normal tissues. Our findings support the utility of D9 as a novel compound for the development of anticancer agent. [ABSTRACT FROM AUTHOR]

Summary: Phylogenetic analysis is complicated by interspecific gene flow and the presence of shared ancestral polymorphisms, particularly those maintained by balancing selection. In this study, we aimed to examine the prevalence of these factors during the diversification of Populus, a model tree genus in the Northern Hemisphere.We constructed phylogenetic trees of 29 Populus taxa using 80 individuals based on re‐sequenced genomes. Our species tree analyses recovered four main clades in the genus based on consensus nuclear phylogenies, but in conflict with the plastome phylogeny. A few interspecific relationships remained unresolved within the multiple‐species clade because of inconsistent gene trees. Our results indicated that gene flow has been widespread within each clade and also occurred among the four clades during their early divergence.We identified 45 candidate genes with ancient polymorphisms maintained by balancing selection. These genes were mainly associated with mating compatibility, growth and stress resistance.Both gene flow and selection‐mediated ancient polymorphisms are prevalent in the genus Populus. These are potentially important contributors to adaptive variation. Our results provide a framework for the diversification of model tree genus that will facilitate future comparative studies. [ABSTRACT FROM AUTHOR]

Many willow species, especially the short-rotation coppice willows, are suitable for development into renewable bioenergy crops. In this study, we conducted high-throughput transcriptome sequencing of a shrub willow, S. suchowensis, to generate expressed sequence tags ( ESTs) for gene discovery and molecular marker development. Totally, 136.1 million clean reads were generated from five different tissues of S. suchowensis using Illumina RNA-seq technology. De novo sequence assembly produced 90 269 unigenes, among which 64 127 unigenes were annotated in one or more of the NR, Swiss-Prot, GO, COG and KEGG databases. A total of 21 052 simple sequence repeats were identified in the expressed sequence assemblies, and a primer database containing 36 912 EST- SSR markers were developed for 12 304 SSR loci. Subsequently, 25 primers were randomly selected for experimental test. Among which, 24 primers succeeded in PCR amplification and 21 produced amplicons in expected sizes, suggesting that the sequence assemblies were of high quality. The established sequence database and marker resource are useful for different aspects of genetic studies on Salix spp., and particularly valuable for marker-assisted breeding of willows. [ABSTRACT FROM AUTHOR]

As part of a larger project to sequence the Populus genome and generate genomic resources for this emerging model tree, we constructed a physical map of the Populus genome, representing one of the few such maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the Populus genome, which has been estimated from the genome sequence assembly to be 485 ± 10 Mb in size. BAC ends were sequenced to assist long-range assembly of whole-genome shotgun sequence scaffolds and to anchor the physical map to the genome sequence. Simple sequence repeat-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. A total of 2411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa, version 1.0). These alignments represent a total coverage of 384 Mb (79%) of the entire poplar sequence assembly and 295 Mb (96%) of linkage group sequence assemblies. A striking result of the physical map contig alignments to the sequence assembly was the co-localization of multiple contigs across numerous regions of the 19 linkage groups. Targeted sequencing of BAC clones and genetic analysis in a small number of representative regions showed that these co-aligning contigs represent distinct haplotypes in the heterozygous individual sequenced, and revealed the nature of these haplotype sequence differences. [ABSTRACT FROM AUTHOR]