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Tree peony (Paeonia Sect. Moutan) is a famous ornamental plant, with huge historical, cultural, and economic significance worldwide. In this study, we reported the ~13.79 Gb draft genome of a wide‐grown Paeonia suffruticosa cultivar “Luo shen xiao chun,” representing the largest sequenced genome in dicots to date. Phylogenetic analyses based on genome sequences demonstrated that P. suffruticosa was placed as sister to Vitales, and they together formed a clade that was sister to Rosids, weakly supporting a relationship of ((Saxifragales and Vitales) and Rosids). The identification and expression analysis of MADS‐box genes based on the genome assembly and de novo transcriptome assembly of P. suffruticosa revealed that the function of C class genes was restricted in flower development, which might be responsible for the stamen petalody in tree peony cultivars. Overall, the first sequenced genome in the family Paeoniaceae provides an important resource for the origin, domestication, and evolutionary study as well as cultivar breeding in tree peony.

Emmer wheat as the progenitor of common wheat, holds the genetic potentiality for improvement of wheat yield, quality and stress tolerance such as drought and salt. To comprehensively evaluate the salt tolerance of emmer wheat, a total of 30 traits including growth, physiology and photosynthesis related as well as K+ and Na+ content of 30 wild emmer and 14 durum wheat accessions were systematically investigated and compared between normal and saline conditions. Salt tolerance index (STI) based on multiple regression analysis of these traits was calculated and five wild emmer accessions showed high salt tolerance, which could be used as valuable resource for wheat salt tolerance improvement. Furthermore, wild emmer genotypes showed wider trait performance variation compared to durum wheat, indicating the higher genetic diversity in wild emmer wheat. Then, shoot Na+ content, shoot K+/Na+ ratio, root length and root surface area were identified as suitable indexes for salt tolerance evaluation. Na+ exclusion mechanism was found to be playing an important role in response to salt stress in emmer wheat. The salt tolerance in emmer wheat was systematically characterized here, which not only provided the elite germplasm for wheat improvement, but also provided the efficient method and some useful indexes for salt tolerance assessing.

High-density genetic maps play a vital role in dissecting genetic components of biologically or agronomically important traits and molecular marker-assisted selection breeding, especially for a species with limited genomic information. Tree Peony (Paeonia suffruticosa Andr. Moutan DC.) is a traditional flowering plant in China, with important ornamental value, which have been spread around the world. However, less genetic and genomic information is available for the tree peony molecular studies. Here, we performed restriction site-associated DNA sequencing (RADseq) of an F1 population, derived from a traditional variety “Qing Long Wo Mo Chi (QL)” and a variety “Mo Zi Lian (MZL)”. High-density genetic maps were developed using RADseq markers for female (1471 markers) and male (793 markers) parents. They covered 965.69 and 870.21 cM, with the average marker intervals of 0.66 and 1.10 cM along the seven and five linkage groups (LGs), respectively. Furthermore, the identified markers were assigned to 1671 bins, representing the unique genetic positions in LGs, and inter-marker distances smaller than 5 cM covered 97.93% of genetic maps. This study suggests that rapid de novo construction of genetic maps in peony could be conducted through RADseq approach, which provides an important tool for further linkage mapping and genomic structure analysis, and enable development of molecular markers for molecular breeding in tree peony.

Tree peony (Paeonia Sect. Moutan) is a famous ornamental plant, with huge historical, cultural, and economic significance worldwide. In this study, we reported the ~13.79 Gb draft genome of a wide‐grown Paeonia suffruticosa cultivar “Luo shen xiao chun,” representing the largest sequenced genome in dicots to date. Phylogenetic analyses based on genome sequences demonstrated that P. suffruticosa was placed as sister to Vitales, and they together formed a clade that was sister to Rosids, weakly supporting a relationship of ((Saxifragales and Vitales) and Rosids). The identification and expression analysis of MADS‐box genes based on the genome assembly and de novo transcriptome assembly of P. suffruticosa revealed that the function of C class genes was restricted in flower development, which might be responsible for the stamen petalody in tree peony cultivars. Overall, the first sequenced genome in the family Paeoniaceae provides an important resource for the origin, domestication, and evolutionary study as well as cultivar breeding in tree peony., Tree peony (Paeonia Sect. Moutan) is a famous ornamental plant, with huge historical, cultural, and economic significance worldwide. The presented genome assembly in this study would serve as an important resource for functional genomic and genetic studies on tree peony, which would be useful for the conservation of endangered wild paeonia species and exploring the mechanisms of plant diversification and adaption under domestication in various environments.

Drought stress is one of the most adverse environmental limiting factors for wheat (Triticum aestivum L.) productivity worldwide. For better understanding of the molecular mechanism of wheat in response to drought, a comparative transcriptome approach was applied to investigate the gene expression change of two wheat cultivars, Jimai No. 47 (drought-tolerant) and Yanzhan No. 4110 (drought-sensitive) in the field under irrigated and drought-stressed conditions. A total of 3754 and 2325 differential expressed genes (DEGs) were found in Jimai No. 47 and Yanzhan No. 4110, respectively, of which 377 genes were overlapped, which could be considered to be the potential drought-responsive genes. GO (Gene Ontology) analysis showed that these DEGs of tolerant genotype were significantly enriched in signaling transduction and MAP (mitogen-activated protein) kinase activity, while that of sensitive genotype was involved in photosynthesis, membrane protein complex, and guard cell differentiation. Furthermore, 32 and 2 RNA editing sites were identified in drought-tolerant and sensitive genotypes under drought compared to irrigation, demonstrating that RNA editing also plays an important role in response to drought in wheat. This study investigated the gene expression pattern and RNA editing sites of two wheat cultivars with contrasting tolerance in field condition, which will contribute to a better understanding of the molecular mechanism of drought tolerance in wheat and beyond.

MicroRNAs (miRNAs) are a class of endogenous RNAs that regulates the gene expression involved in various biological and metabolic processes. Barley is one of the most important cereal crops worldwide and is a model organism for genetic and genomic studies in Triticeae species. However, the miRNA research in barley has lagged behind other model species in grass family. To obtain more information of miRNA genes in barley, we sequenced a small RNA library created from a pool of equal amounts of RNA from four different tissues using Solexa sequencing. In addition to 126 conserved miRNAs (58 families), 133 novel miRNAs belonging to 50 families were identified from this sequence data set. The miRNA* sequences of 15 novel miRNAs were also discovered, suggesting the additional evidence for existence of these miRNAs. qRT-PCR was used to examine the expression pattern of six randomly selected miRNAs. Some miRNAs involved in drought and salt stress response were also identified. Furthermore, the potential targets of these putative miRNAs were predicted using the psRNATarget tools. Our results significantly increased the number of novel miRNAs in barley, which should be useful for further investigation into the biological functions and evolution of miRNAs in barley and other species.

BackgroundCrofton weed (Ageratina adenophora) is one of the most hazardous invasive plant species, which causes serious economic losses and environmental damages worldwide. However, the sequence resource and genome information of A. adenophora are rather limited, making phylogenetic identification and evolutionary studies very difficult. Here, we report the complete sequence of the A. adenophora chloroplast (cp) genome based on Illumina sequencing.Methodology/principal findingsThe A. adenophora cp genome is 150, 689 bp in length including a small single-copy (SSC) region of 18, 358 bp and a large single-copy (LSC) region of 84, 815 bp separated by a pair of inverted repeats (IRs) of 23, 755 bp. The genome contains 130 unique genes and 18 duplicated in the IR regions, with the gene content and organization similar to other Asteraceae cp genomes. Comparative analysis identified five DNA regions (ndhD-ccsA, psbI-trnS, ndhF-ycf1, ndhI-ndhG and atpA-trnR) containing parsimony-informative characters higher than 2%, which may be potential informative markers for barcoding and phylogenetic analysis. Repeat structure, codon usage and contraction of the IR were also investigated to reveal the pattern of evolution. Phylogenetic analysis demonstrated a sister relationship between A. adenophora and Guizotia abyssinica and supported a monophyly of the Asterales.ConclusionWe have assembled and analyzed the chloroplast genome of A. adenophora in this study, which was the first sequenced plastome in the Eupatorieae tribe. The complete chloroplast genome information is useful for plant phylogenetic and evolutionary studies within this invasive species and also within the Asteraceae family.