Human selection has reshaped crop genomes. Here we report an apple genome variation map generated through genome sequencing of 117 diverse accessions. A comprehensive model of apple speciation and domestication along the Silk Road is proposed based on evidence from diverse genomic analyses. Cultivated apples likely originate from Malus sieversii in Kazakhstan, followed by intensive introgressions from M. sylvestris. M. sieversii in Xinjiang of China turns out to be an “ancient” isolated ecotype not directly contributing to apple domestication. We have identified selective sweeps underlying quantitative trait loci/genes of important fruit quality traits including fruit texture and flavor, and provide evidences supporting a model of apple fruit size evolution comprising two major events with one occurring prior to domestication and the other during domestication. This study outlines the genetic basis of apple domestication and evolution, and provides valuable information for facilitating marker-assisted breeding and apple improvement.

Exosomes are secreted by most cell types and circulate in body fluids. Recent studies have revealed that exosomes play a significant role in intercellular communication and are closely associated with the pathogenesis of disease. Therefore, exosomes are considered promising biomarkers for disease diagnosis. However, exosomes are always mixed with other components of body fluids. Consequently, separation methods for exosomes that allow high‐purity and high‐throughput separation with a high recovery rate and detection techniques for exosomes that are rapid, highly sensitive, highly specific, and have a low detection limit are indispensable for diagnostic applications. For decades, many exosome separation and detection techniques have been developed to achieve the aforementioned goals. However, in most cases, these two techniques are performed separately, which increases operation complexity, time consumption, and cost. The emergence of microfluidics offers a promising way to integrate exosome separation and detection functions into a single chip. Herein, an overview of conventional and microfluidics‐based techniques for exosome separation and detection is presented. Moreover, the advantages and drawbacks of these techniques are compared.

With global climate change, water scarcity threatens whole agro/ecosystems. The desert moss Syntrichia caninervis, an extremophile, offers novel insights into surviving desiccation and heat. The sequenced S. caninervis genome consists of 13 chromosomes containing 16 545 protein-coding genes and 2666 unplaced scaffolds. Syntenic relationships within the S. caninervis and Physcomitrella patens genomes indicate the S. caninervis genome has undergone a single whole genome duplication event (compared to two for P. patens) and evidence suggests chromosomal or segmental losses in the evolutionary history of S. caninervis. The genome contains a large sex chromosome composed primarily of repetitive sequences with a large number of Copia and Gypsy elements. Orthogroup analyses revealed an expansion of ELIP genes encoding proteins important in photoprotection. The transcriptomic response to desiccation identified four structural clusters of novel genes. The genomic resources established for this extremophile offer new perspectives for understanding the evolution of desiccation tolerance in plants.

BackgroundSyntrichia caninervis is a desiccation-tolerant moss and the dominant bryophyte of the Biological Soil Crusts (BSCs) found in the Mojave and Gurbantunggut deserts. Next generation high throughput sequencing technologies offer an efficient and economic choice for characterizing non-model organism transcriptomes with little or no prior molecular information available.ResultsIn this study, we employed next generation, high-throughput, Illumina RNA-Seq to analyze the poly-(A) + mRNA from hydrated, dehydrating and desiccated S. caninervis gametophores. Approximately 58.0 million paired-end short reads were obtained and 92,240 unigenes were assembled with an average size of 493 bp, N50 value of 662 bp and a total size of 45.48 Mbp. Sequence similarity searches against five public databases (NR, Swiss-Prot, COSMOSS, KEGG and COG) found 54,125 unigenes (58.7%) with significant similarity to an existing sequence (E-value ≤ 1e-5) and could be annotated. Gene Ontology (GO) annotation assigned 24,183 unigenes to the three GO terms: Biological Process, Cellular Component or Molecular Function. GO comparison between P. patens and S. caninervis demonstrated similar sequence enrichment across all three GO categories. 29,370 deduced polypeptide sequences were assigned Pfam domain information and categorized into 4,212 Pfam domains/families. Using the PlantTFDB, 778 unigenes were predicted to be involved in the regulation of transcription and were classified into 49 transcription factor families. Annotated unigenes were mapped to the KEGG pathways and further annotated using MapMan. Comparative genomics revealed that 44% of protein families are shared in common by S. caninervis, P. patens and Arabidopsis thaliana and that 80% are shared by both moss species.ConclusionsThis study is one of the first comprehensive transcriptome analyses of the moss S. caninervis. Our data extends our knowledge of bryophyte transcriptomes, provides an insight to plants adapted to the arid regions of central Asia, and continues the development of S. caninervis as a model for understanding the molecular aspects of desiccation-tolerance.

Sand burial, persistent seed bank and soil water content (SWC) are three factors that potentially can affect regeneration in sand dune plant populations. To evaluate the effects of these three factors on population regeneration of Eremosparton songoricum, a rare and endangered legume, we investigated seed germination, seedling emergence and seedling survival in greenhouse and controlled field experiments in different sand dunes microsites. Freshly matured seeds are physically dormant, and the highest germination was only 9.3±5.8% at 25/10°C. Seed germination occurred at burial depths from 0 to 10 cm, but the maximum depth from which seedlings emerged was 6 cm; from 1 to 6 cm, the deeper the burial, the lower the percentage of seedling emergence. Only 36.2% of the total soil seed banks occurred at depths of 0-6 cm. For artificially sown seeds at different dune microsites, mean seedling emergence percentage was 6.8%. Of 150 seedlings that emerged in the field investigation at the study site, only those germinating in flat sandy areas survived, and mean survival percentage was only 2.0%. Thus, the proportion of non-dormant seeds in soil seed banks that developed into seedlings and survived to the end of the growing season was only 0.2%. Minimum SWC for seed germination, seedling emergence and seedling survival was 2.0%. During monitoring of emergent seedlings in the field, low seedling recruitment was at least partly due to the rate of root extension (1.6± 0.3 cm day −1 ) into the sandy soil, which was slower than that of the downward movement of plant-available moisture (2.8±0.6 cm day −1 ). Thus, population regeneration under natural conditions rarely occurred via Plant Soil (2011) 345:69-87

BackgroundThe desiccation-tolerant moss Bryum argenteum is an important component of the Biological Soil Crusts (BSCs) found in the Gurbantunggut desert. Desiccation tolerance is defined as the ability to revive from the air dried state. To elucidate the molecular mechanisms related to desiccation tolerance, we employed RNA-Seq and digital gene expression (DGE) technologies to study the genome-wide expression profiles of the dehydration and rehydration processes in this important desert plant.ResultsWe applied a two-step approach to investigate the gene expression profile upon rehydration in the moss Bryum argenteum using Illumina HiSeq2000 sequencing platform. First, a total of 57,247 transcript assembly contigs (TACs) were obtained from 54.79 million reads by de novo assembly, with an average length of 863 bp and N50 of 1,372 bp. Among the reconstructed TACs, 36,916 (64.5 %) revealed similarity with existing protein sequences in the public databases. 23,509 and 21,607 TACs were assigned GO and KEGG annotation information, respectively. Second, samples were taken from 3 hydration stages: desiccated (Dry), rehydrated 2 h (R2) and rehydrated 24 h (R24), and DEG libraries were constructed for Differentially Expressed Genes (DEGs) discovery. 4,081 and 6,709 DEGs were identified in R2 and R24, compared with Dry, respectively. Compared to the desiccated sample, up-regulated genes after two hours of hydration are primarily related to stress responses. GO function enrichment network, EKGG metabolic pathway and MapMan analysis supports the idea of the rapid recovery of photosynthesis after 24 h of rehydration. We identified 770 transcription factors (TFs) which were classified into 50 TF families. 142 TF transcripts were up-regulated upon rehydration including 23 members of the ERF family.ConclusionsIn this study, we constructed a pioneering, high-quality reference transcriptome in B. argenteum and generated three DGE libraries to elucidate the changes of gene expression upon rehydration. Expression profiles consistent with the rapid recovery of photosynthesis (at R2) and the re-establishment of a positive carbon balance following rehydration (at R24) were observed. Our study will extend our knowledge of bryophyte transcriptomes and provide further insight into the molecular mechanisms related to rehydration and desiccation-tolerance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1633-y) contains supplementary material, which is available to authorized users.

Advances in phylogeography are of great value for understanding the population structure and origins of invasive genotypes. Such insights provide constructive information for current or future biological control research efforts. In this study, we investigated a highly variable chloroplast DNA (cpDNA) marker for populations of the weed Lepidium draba (Brassicaceae) in its native Eurasian and invasive US ranges. We sequenced DNA from 684 individuals from Eurasia and the US and found 41 different haplotypes. Our comparative study between the native and invasive ranges showed a 33% reduction in allelic richness (A) and a 7% reduction in haplotype diversity (h) since introduction into the US. Most genetic variation in the native range was observed within geographical regions and populations, not between regions, and this result was similar for the invasive range. Assignment tests indicated the most likely origins of many invasive haplotypes. Some of these occurred in western Europe, supporting an expanded native range that had been proposed for the species. Exact locations were identified for a diverse set of invasive haplotypes which can be used in ongoing host-specificity tests of potential biological control agents.

Summary This paper addresses the problem of output feedback sampled‐data stabilization for upper‐triangular nonlinear systems with improved maximum allowable transmission delay. A class of hybrid systems are firstly introduced. The transmission delay may be larger than the sampling period. Then, sufficient conditions are proposed to guarantee global exponential stability of the hybrid systems. Based on these sufficient conditions and a linear continuous‐discrete observer, an output feedback control law is presented to globally exponentially stabilize the feedforward nonlinear system. The improved maximum allowable transmission delay is also given. The results are also extended to output feedback sampled‐data stabilization for lower‐triangular nonlinear systems. Finally, illustrative examples are used to verify the effectiveness of the proposed design methods. Copyright © 2016 John Wiley & Sons, Ltd.