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Gene expression data for Archaeplastida are accumulating exponentially, with more than 300 000 RNA-sequencing (RNA-seq) experiments available for hundreds of species. The gene expression data stem from thousands of experiments that capture gene expression in various organs, tissues, cell types, (a)biotic perturbations, and genotypes. Advances in software tools make it possible to process all these data in a matter of weeks on modern office computers, giving us the possibility to study gene expression in a kingdom-wide manner for the first time. We discuss how the expression data can be accessed and processed and outline analyses that take advantage of cross-species analyses, allowing us to generate powerful and robust hypotheses about gene function and evolution. Ministry of Education (MOE) Singapore Food Agency Published version I.J. is supported by Nanyang Biologics. M.M. is supported by Singapore Food Agency grant SFS_RND_SUFP_001_05 and Singaporean Ministry of Education grant MOE2018-T2-2-053. Q.W.T. is supported by a Nanyang Technological University PhD stipend.

Plants accumulate a vast array of secondary metabolites, which constitute a natural resource for pharmaceuticals. Oldenlandia corymbosa belongs to the Rubiaceae family, and has been used in traditional medicine to treat different diseases, including cancer. However, the active metabolites of the plant, their biosynthetic pathway and mode of action in cancer are unknown. To fill these gaps, we exposed this plant to eight different stress conditions and combined different omics data capturing gene expression, metabolic profiles, and anti-cancer activity. Our results show that O. corymbosa extracts are active against breast cancer cell lines and that ursolic acid is responsible for this activity. Moreover, we assembled a high-quality genome and uncovered two genes involved in the biosynthesis of ursolic acid. Finally, we also revealed that ursolic acid causes mitotic catastrophe in cancer cells and identified three high-confidence protein binding targets by Cellular Thermal Shift Assay (CETSA) and reverse docking. Altogether, these results constitute a valuable resource to further characterize the biosynthesis of active metabolites in the Oldenlandia group, while the mode of action of ursolic acid will allow us to further develop this valuable compound. Ministry of Education (MOE) Nanyang Technological University Published version I.J. is supported by Nanyang Biologics, M.M. is supported by a NTU Start‐Up Grant and Singaporean Ministry of Education grant MOE2018‐T2‐2‐053. J.M.D (NTU‐PPF‐2019). Y.K. is supported by Natural Product Research Laboratory Biomedical Research Council of A*STAR (Agency for Science, Technology and Research) Transition Fund (H16/99/b0/004), the Singapore Institute of Food and Biotechnology Innovation core fund.

Natural products from traditional medicinal plants are valuable candidates for clinical cancer therapy. Plants from the Oldenlandia-Hedyotis complex are popular ingredients of Traditional Chinese Medicine (TCM), however a major hurdle in the plant bioprospecting process of TCM plants is that the active metabolites, their biosynthetic pathways, and mode of action are often unknown. We show that Oldenlandia corymbosa extracts are active against breast cancer cell lines. To study the genes involved in the biosynthesis of active compounds in this medicinal plant, we assembled a high-quality genome. We show that the main active compound is ursolic acid and that abiotic stresses cause changes in anti-cancer activity, metabolite composition, and gene expression of plants. To reveal the mode of action of ursolic acid, we show that cancer cells undergo mitotic catastrophe, and we identify three high-confidence protein binding targets by Cellular Thermal Shift Assay (CETSA) and reverse docking.

Germ cells provide the cellular basis for sexual reproduction in multicellular animals. In males, germ cells differentiate into sperm, one of the most morphologically diverse eukaryotic cell types. Owing both to this remarkable diversity and to the rapid evolution of reproduction-related genes, the transcriptional program of male germ cells is widely regarded as divergent across species1,2. However, the possibility that these cells retain a distinctive evolutionarily-conserved genetic basis remains largely unexplored. Here we show, using phylostratigraphy, that the complex male germ cell transcriptome has an old evolutionary origin shared between vertebrate and invertebrate species. Through multilayer network analysis of the human, mouse and fruit fly meiotic transcriptome, we establish that old genes serve as a genetic scaffold from which complexity has evolved, and identify a core set of 79 ancient functional interactions at the heart of male germ cell identity. By silencing a cohort of 920 candidate genes likely to affect the acquisition and maintenance of this identity, we uncover 164 previously unknown spermatogenesis genes. Integrating this information with whole-exome sequencing data from azoospermic men reveals three novel genetic causes of human male infertility shared between species that have diverged for more than 600 million years. Our results redefine the importance of evolutionary history on human reproductive disease and illustrate the translational potential of a new synergy between comparative network biology and medical genetics. We anticipate that our open-access and easily-adaptable interdisciplinary research platform will be harnessed in the context of other cell types and diseases.

Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To better understand the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with 20 other sequenced genomes, including the available genomes of five other aphids, along with the transcriptomes of two species belonging to Adelgidae (a closely related clade to the aphids) and Coccoidea. We found that gene duplication has been pervasive throughout the evolution of aphids, including many parallel waves of recent, species-specific duplications. Most notably, we identified a consistent set of very ancestral duplications, originating from a large-scale gene duplication predating the diversification of Aphidomorpha (comprising aphids, phylloxerids, and adelgids). Genes duplicated in this ancestral wave are enriched in functions related to traits shared by Aphidomorpha, such as association with endosymbionts, and adaptation to plant defenses and phloem-sap-based diet. The ancestral nature of this duplication wave (106–227 Ma) and the lack of sufficiently conserved synteny make it difficult to conclude whether it originated from a whole-genome duplication event or, alternatively, from a burst of large-scale segmental duplications. Genome sequencing of other aphid species belonging to different Aphidomorpha and related lineages may clarify these findings., This research was funded by European Regional Development Fund (ERDF) and Ministerio de Economía y Competitividad (Spain) (Grant Nos. PGC2018-099344-B-100 and BFU2015-67107). T.G. group also acknowledges support from the Catalan Research Agency (AGAUR) SGR857, and grants from the European Union’s Horizon 2020 research and innovation program under the grant agreements ERC-2016-724173 and MSC-747607. T.G. also receives support from an INB (Grant No. PT17/0009/0023—ISCIII-SGEFI/ERDF).

Yeast-two-hybrid (Y2H) is widely used as a strategy to detect protein–protein interactions (PPIs). Recent advancements have made it possible to generate and analyse genome-wide PPI networks en masse by coupling Y2H with next-generation sequencing technology. However, one of the major challenges of yeast two-hybrid assay is the large amount of false-positive hits caused by auto-activators (AAs), which are proteins that activate the reporter genes without the presence of an interacting protein partner. Here, we have developed a negative selection to minimize these auto-activators by integrating the pGAL2-URA3 fragment into the yeast genome. Upon activation of the pGAL2 promoter by an AA, yeast cells expressing URA3 cannot grow in media supplemented with 5-Fluoroorotic acid (5-FOA). Hence, we selectively inhibit the growth of yeast cells expressing auto-activators and thus minimizing the amount of false-positive hits. Here, we have demonstrated that auto-activators can be successfully removed from a Marchantia polymorpha cDNA library using pGAL2-URA3 and 5-FOA treatment, in liquid and solid-grown cultures. Furthermore, since URA3 can also serve as a marker for uracil autotrophy, we propose that our approach is a valuable addition to any large-scale Y2H screen. Ministry of Education (MOE) Nanyang Technological University Published version This article was supported by Max Planck Gesellschaft and is funded by NTU Start-Up Grant and Singaporean Ministry of Education grant MOE2018-T2-2-053.

The appearance of plant organs mediated the explosive radiation of land plants, which shaped the biosphere and allowed the establishment of terrestrial animal life. The evolution of organs and immobile gametes required the coordinated acquisition of novel gene functions, the co-option of existing genes and the development of novel regulatory programmes. However, no large-scale analyses of genomic and transcriptomic data have been performed for land plants. To remedy this, we generated gene expression atlases for various organs and gametes of ten plant species comprising bryophytes, vascular plants, gymnosperms and flowering plants. A comparative analysis of the atlases identified hundreds of organ- and gamete-specific orthogroups and revealed that most of the specific transcriptomes are significantly conserved. Interestingly, our results suggest that co-option of existing genes is the main mechanism for evolving new organs. In contrast to female gametes, male gametes showed a high number and conservation of specific genes, which indicates that male reproduction is highly specialized. The expression atlas capturing pollen development revealed numerous transcription factors and kinases essential for pollen biogenesis and function. Ministry of Education (MOE) Nanyang Technological University Submitted/Accepted version I.J. is supported by Singaporean Ministry of Education grant MOE2018-T2-2-053, while M.M. is supported by a NTU Start-Up Grant. ERA-CAPS EVO-REPRO I2163 and FWF grant P30802 were awarded to F.B.; FCT ERA-CAPS-0001-2014 and PTDC-BIA-FBT-28484-2017 to J.D.B.; and ERA-CAPS EVO-REPRO DR 334/12-1 to S.S. and T.D. D. Hackenberg was supported by ERA-CAPS UK Biotechnology and Biological Research Council grant BB/N005090 awarded to D.T.; M.B. was supported through the FWF Lise Meitner fellowship M1818. The Vienna BioCenter Core Facilities GmbH (VBCF) Plant Sciences Facility acknowledges funding from the Austrian Federal Ministry of Education, Science and Research and the City of Vienna. L.S. was supported by CSF grant 17-23183S. C.M. and D. Honys were supported by the Czech Ministry of Education, Youth and Sport (LTC18034 and LTAIN19030) through the European Regional Development Fund-Project “Centre for Experimental Plant Biology” number CZ.02.1.01/0.0/0.0/16_019/0000738. The Genomics Unit of Instituto Gulbenkian de Ciência was partially supported by the ONEIDA Project (LISBOA01-0145-FEDER-016417) co-funded by FEEI–‘Fundos Europeus Estruturais e de Investimento’ from the ‘Programa Operacional Regional Lisboa 2020’ and by national funds from FCT–‘Fundação para a Ciência e a Tecnologia’. C.S.M. acknowledges a doctoral fellowship from the FCT (PD/BD/114362/2016) under the Plants for Life PhD Program. J.D.B. received salary support from the FCT through an ‘Investigador FCT’ position. M.J. and J.G. were supported by a US National Science Foundation grant (IOS1540019).

The evolution of plant organs, including leaves, stems, roots, and flowers, mediated the explosive radiation of land plants, which shaped the biosphere and allowed the establishment of terrestrial animal life. Furthermore, the fertilization products of angiosperms, seeds serve as the basis for most of our food. The evolution of organs and immobile gametes required the coordinated acquisition of novel gene functions, the co-option of existing genes, and the development of novel regulatory programs. However, our knowledge of these events is limited, as no large-scale analyses of genomic and transcriptomic data have been performed for land plants. To remedy this, we have generated gene expression atlases for various organs and gametes of 10 plant species comprising bryophytes, vascular plants, gymnosperms, and flowering plants. Comparative analysis of the atlases identified hundreds of organ- and gamete-specific gene families and revealed that most of the specific transcriptomes are significantly conserved. Interestingly, the appearance of organ-specific gene families does not coincide with the corresponding organ’s appearance, suggesting that co-option of existing genes is the main mechanism for evolving new organs. In contrast to female gametes, male gametes showed a high number and conservation of specific genes, suggesting that male reproduction is highly specialized. The expression atlas capturing pollen development revealed numerous transcription factors and kinases essential for pollen biogenesis and function. To provide easy access to the expression atlases and these comparative analyses, we provide an online database, www.evorepro.plant.tools, that allows the exploration of expression profiles, organ-specific genes, phylogenetic trees, co-expression networks, and others.

Objectives The aim of our study was to determine the incidence of late onset sepsis and the most frequent microorganisms causing it in the Neonatal Unit (Neonatal Intensive Care Unit ie NICU and Level 2 nursery) at Hospital Cayetano Heredia, in Lima, Peru. Methods Descriptive and retrospective study. We reviewed all positive blood cultures and cultures of cerebrospinal fluid drawn from inborn patients beyond 72 hours of life, admitted to the NICU or our Level 2 nursery from January 2015 to December 2019. Results The incidence of late onset sepsis in our unit was 7.4% of admitted patients and 10.04 per 1000 live births. 234 episodes of LOS occurred in 204 patients through our study period. The incidence was higher in very low birth weight infants, reaching 36.2% and even higher in extremely-low birth weight infants (40.7%). The most frequent causative microorganisms were: coagulase-negative Staphylococcus, followed by Klebsiella spp. The most frequent cause of late onset sepsis in very low birth weight infants was gram negative bacteria (Klebsiella spp, being the most frequent microorganism). Conclusions Late onset neonatal sepsis is prevalent in our Neonatal Unit. It is important to know which are the most prevalent causative microorganisms in order to be able to choose an adequate antibiotic coverage and to design strategies to prevent them.

Graphical abstract, The fungi kingdom is composed of eukaryotic heterotrophs, which are responsible for balancing the ecosystem and play a major role as decomposers. They also produce a vast diversity of secondary metabolites, which have antibiotic or pharmacological properties. However, our lack of knowledge of gene function in fungi precludes us from tailoring them to our needs and tapping into their metabolic diversity. To help remedy this, we gathered genomic and gene expression data of 19 most widely-researched fungi to build an online tool, fungi.guru, which contains tools for cross-species identification of conserved pathways, functional gene modules, and gene families. We exemplify how our tool can elucidate the molecular function, biological process and cellular component of genes involved in various biological processes, by identifying a secondary metabolite pathway producing gliotoxin in Aspergillus fumigatus, the catabolic pathway of cellulose in Coprinopsis cinerea and the conserved DNA replication pathway in Fusarium graminearum and Pyricularia oryzae. The tool is available at www.fungi.guru.

Background Olive tree (Olea europaea L. subsp. europaea, Oleaceae) has been the most emblematic perennial crop for Mediterranean countries since its domestication around 6000 years ago in the Levant. Two taxonomic varieties are currently recognized: cultivated (var. europaea) and wild (var. sylvestris) trees. However, it remains unclear whether olive cultivars derive from a single initial domestication event followed by secondary diversification, or whether cultivated lineages are the result of more than a single, independent primary domestication event. To shed light into the recent evolution and domestication of the olive tree, here we analyze a group of newly sequenced and available genomes using a phylogenomics and population genomics framework. Results We improved the assembly and annotation of the reference genome, newly sequenced the genomes of twelve individuals: ten var. europaea, one var. sylvestris, and one outgroup taxon (subsp. cuspidata)—and assembled a dataset comprising whole genome data from 46 var. europaea and 10 var. sylvestris. Phylogenomic and population structure analyses support a continuous process of olive tree domestication, involving a major domestication event, followed by recurrent independent genetic admixture events with wild populations across the Mediterranean Basin. Cultivated olives exhibit only slightly lower levels of genetic diversity than wild forms, which can be partially explained by the occurrence of a mild population bottleneck 3000–14,000 years ago during the primary domestication period, followed by recurrent introgression from wild populations. Genes associated with stress response and developmental processes were positively selected in cultivars, but we did not find evidence that genes involved in fruit size or oil content were under positive selection. This suggests that complex selective processes other than directional selection of a few genes are in place. Conclusions Altogether, our results suggest that a primary domestication area in the eastern Mediterranean basin was followed by numerous secondary events across most countries of southern Europe and northern Africa, often involving genetic admixture with genetically rich wild populations, particularly from the western Mediterranean Basin.

Yeast-two-hybrid (Y2H) is widely used as a strategy to detect protein-protein interactions (PPIs). Recent advancements have made it possible to generate and analyse genome-wide PPI networks en masse by coupling Y2H with next-generation sequencing technology. However, one of the major challenges of yeast two-hybrid assay is the large amount of false-positive hits caused by auto-activators (AAs), which are proteins that activate the reporter genes without the presence of an interacting protein partner. Here, we have developed a negative selection to minimize these auto-activators by integrating the pGAL2-URA3 fragment into the yeast genome. Upon activation of the pGAL2 promoter by an AA, yeast cells expressing URA3 cannot grow in media supplemented with 5-Fluoroorotic acid (5-FOA). Hence, we selectively inhibit the growth of yeast cells expressing auto-activators and thus minimizing the amount of false-positive hits. Here, we have demonstrated that auto-activators can be successfully removed from a Marchantia polymorpha cDNA library using pGAL2-URA3 and 5-FOA treatment, in liquid and solid-grown cultures. Furthermore, since URA3 can also serve as a marker for uracil autotrophy, we propose that our approach is a valuable addition to any large-scale Y2H screen.

BackgroundThe olive tree (Olea europaea L. subsp. europaea, Oleaceae) has been the most economic perennial crop for Mediterranean countries since its domestication around 6,000 years ago. Two taxonomic varieties are currently recognized: cultivated (var. europaea) and wild (var. sylvestris) trees. To shed light into the recent evolution and domestication of the olive tree, we sequenced the genomes of twelve individuals: ten var. europaea, one var. sylvestris, and one outgroup taxon (subsp. cuspidata). All of them were analysed together with an improved assembly of var. europaea reference genome and the available assembly of var. sylvestris.ResultsOur analyses show that cultivated olives exhibit slightly lower levels of overall genetic diversity than wild forms, and that this can be partially explained by the occurrence of a mild population bottleneck 5000-7000 years ago during the primary domestication period. We also provide the first phylogenetic analysis of genome-wide sequences, which supports a continuous process of domestication of the olive tree. This, together with population structure and introgression analyses highlights genetic admixture with wild populations across the Mediterranean Basin in the course of domestication.ConclusionsAltogether, our results suggest that a primary domestication area in the eastern Mediterranean basin was followed by numerous secondary events across most countries of southern Europe and northern Africa, often involving genetic admixture with genetically rich wild populations, particularly from the western Mediterranean Basin. Based on selection tests and a search for selective sweeps, we found that genes associated with stress response and developmental processes were positively selected in cultivars. However, we did not find evidence that genes involved in fruit size or oil content were under positive selection.

We sequenced the genome of the highly heterozygous almond Prunus dulcis cv. Texas combining short and long-read sequencing. We obtained a genome assembly totaling 227.6 Mb of the estimated 238 Mb almond genome size, of which 91% is anchored to eight pseudomolecules corresponding to its haploid chromosome complement, and annotated 27,969 protein-coding genes and 6,747 non-coding transcripts. By phylogenomic comparison with the genomes of 16 additional close and distant species we estimated that almond and peach (P. persica) diverged around 5.88 Mya. These two genomes are highly syntenic and show a high degree of sequence conservation (20 nucleotide substitutions/kb). However, they also exhibit a high number of presence/absence variants, many attributable to the movement of transposable elements (TEs). TEs have generated an important number of presence/absence variants between almond and peach, and we show that the recent history of TE movement seems markedly different between them. TEs may also be at the origin of important phenotypic differences between both species, and in particular, for the sweet kernel phenotype, a key agronomic and domestication character for almond. Here we show that in sweet almond cultivars, highly methylated TE insertions surround a gene involved in the biosynthesis of amygdalin, whose reduced expression has been correlated with the sweet almond phenotype. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond and its close relative peach., This research was supported in part by grants from: the Ministry of Economy and Competitiveness (MINECO/FEDER projects AGL2012-40228-C02-01, AGL2015-68329-R and RTA2015-00050-00-00, Severo Ochoa Program for Centres of Excellence in R&D 201-2019 SEV-2015-0533 and CERCA Programme-Generalitat de Catalunya) from Spain. MW acknowledges grant support from the Waite Research Institute of the University of Adelaide.

Combining both short and long-read sequencing, we have estimated the almondPrunus dulciscv. Texas genome size in 235 Mbp and assembled 227.6 Mb of its sequence. The highly heterozygous compact genome of Texas comprises eight chromosomes, to which we have anchored over 91% of the assembly. We annotated 27,042 protein-coding genes and 6,800 non-coding transcripts. High levels of genetic variability were characterized after resequencing a collection of ten almond accessions. Phylogenomic comparison with the genomes of 16 other close and distant species allowed estimating that almond and peach diverged around 5.88 Mya. Comparison between peach and almond genomes confirmed the high synteny between these close relatives, but also revealed high numbers of presence-absence variants, many attributable to the movement of transposable elements (TEs). The number and distribution of TEs between peach and almond was similar, but the history of TE movement was distinct, with peach having a larger proportion of recent transpositions and almond preserving a higher level of polymorphism in the older TEs. When focusing on specific genes involved in key characters such as the bitter vs. sweet kernel taste and the formation of a fleshy mesocarp, we found that for one gene associated with the biosynthesis of amygdalin that confers the bitter kernel taste, several TEs were inserted in its vicinity only in sweet almond cultivars but not in bitter cultivars andPrunusbitter kernel relatives, includingP. webbii,P. mume, and other species like peach and cherry. TE insertions likely to produce affects in the expression of six more genes involved in the formation of the fleshy mesocarp were also identified. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond with respect to peach.

Melon is an economically important fruit crop that has been cultivated for thousands of years; however, the genetic basis and history of its domestication still remain largely unknown. Here we report a comprehensive map of the genomic variation in melon derived from the resequencing of 1,175 accessions, which represent the global diversity of the species. Our results suggest that three independent domestication events occurred in melon, two in India and one in Africa. We detected two independent sets of domestication sweeps, resulting in diverse characteristics of the two subspecies melo and agrestis during melon breeding. Genome-wide association studies for 16 agronomic traits identified 208 loci significantly associated with fruit mass, quality and morphological characters. This study sheds light on the domestication history of melon and provides a valuable resource for genomics-assisted breeding of this important crop., This work was supported by funding from the Agricultural Science and Technology Innovation Program (to Yongyang Xu, S.H., Z.Z. and H.W.), the China Agriculture Research System (CARS-25 to Yongyang Xu and H.W.), the Leading Talents of Guangdong Province Program (00201515 to S.H.), the Shenzhen Municipal (The Peacock Plan KQTD2016113010482651 to S.H.), the Dapeng district government, National Natural Science Foundation of China (31772304 to Z.Z.), the Science and Technology Program of Guangdong (2018B020202007 to S.H.), the National Natural Science Foundation of China (31530066 to S.H.), the National Key R&D Program of China (2016YFD0101007 to S.H.), USDA National Institute of Food and Agriculture Specialty Crop Research Initiative (2015-51181-24285 to Z.F.), the European Research Council (ERC-SEXYPARTH to A.B.), the Spanish Ministry of Economy and Competitiveness (AGL2015–64625-C2-1-R to J.G.-M.), Severo Ochoa Programme for Centres of Excellence in R&D 2016–2010 (SEV-2015–0533 to J.G.-M.), the CERCA Programme/Generalitat de Catalunya to J.G.-M. and the German Science Foundation (SPP1991 Taxon-OMICS to H.S.).

BackgroundPolyploidization is one of the major evolutionary processes that shape eukaryotic genomes, being particularly common in plants. Polyploids can arise through direct genome doubling within a species (autopolyploidization) or through the merging of genomes from distinct species after hybridization (allopolyploidization). The relative contribution of either mechanism in plant evolution is debated. Here we used phylogenomics to dissect the tempo and mode of duplications in the genome of the olive tree (Olea europaea), one of the first domesticated Mediterranean fruit trees.ResultsOur results depict a complex scenario involving at least three past polyploidization events, of which two -at the bases of the family Oleaceae and the tribe Oleeae, respectively- are likely to be the result of ancient allopolyploidization. A more recent polyploidization involves specifically the olive tree and relatives.ConclusionOur results show the power of phylogenomics to distinguish between allo- and auto- polyplodization events and clarify the conundrum of past duplications in the olive tree lineage.

Background The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a small number of closely related host species. Remarkably, the green peach aphid, Myzus persicae, colonises plant species across 40 families and single M. persicae clonal lineages can colonise distantly related plants. This remarkable ability makes M. persicae a highly destructive pest of many important crop species. Results To investigate the exceptional phenotypic plasticity of M. persicae, we sequenced the M. persicae genome and assessed how one clonal lineage responds to host plant species of different families. We show that genetically identical individuals are able to colonise distantly related host species through the differential regulation of genes belonging to aphid-expanded gene families. Multigene clusters collectively upregulate in single aphids within two days upon host switch. Furthermore, we demonstrate the functional significance of this rapid transcriptional change using RNA interference (RNAi)-mediated knock-down of genes belonging to the cathepsin B gene family. Knock-down of cathepsin B genes reduced aphid fitness, but only on the host that induced upregulation of these genes. Conclusions Previous research has focused on the role of genetic adaptation of parasites to their hosts. Here we show that the generalist aphid pest M. persicae is able to colonise diverse host plant species in the absence of genetic specialisation. This is achieved through rapid transcriptional plasticity of genes that have duplicated during aphid evolution. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1145-3) contains supplementary material, which is available to authorized users.

After publication of this article [1] we noticed that reference 50 was incorrect. The correct reference 50 is as follows: Santamaría S, Gonzalez-Cabrera J, Martinez M, Grbic V, Castanera P, Diaz L, Ortego F. Digestive proteases in bodies and faeces of the two-spotted spider mite, Tetranychus urticae. J Insect Physiol. 2015; 78:69–77 http://www.sciencedirect.com/science/article/pii/S0022191015001018

With the advancement of science and technology, it is crucial to have effective preservation methods for the stable long-term storage of biological material (biomaterials). As an alternative to cryopreservation, various techniques have been developed, which are based on the survival mechanism of anhydrobiotic organisms. In this sense, it has been found that the synthesis of xeroprotectants can effectively stabilize biomaterials in a dry state. The most widely studied xeroprotectant is trehalose, which has excellent properties for the stabilization of certain proteins, bacteria, and biological membranes. There have also been attempts to apply trehalose to the stabilization of eukaryotic cells but without conclusive results. Consequently, a xeroprotectant or method that is useful for the stable drying of a particular biomaterial might not necessarily be suitable for another one. This article provides an overview of recent advances in the use of new techniques to stabilize biomaterials and compare xeroprotectants with other more standard methods.

BackgroundThe prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception, and the majority have evolved to colonise a small number of closely related host species. Remarkably, the green peach aphid,Myzus persicae, colonises plant species across 40 families and singleM. persicaeclonal lineages can colonise distantly related plants. This remarkable ability makesM. persicaea highly destructive pest of many important crop species.ResultsTo investigate the exceptional phenotypic plasticity ofM. persicae, we sequenced theM. persicaegenome and assessed how one clonal lineage responds to host plant species of different families. We show that genetically identical individuals are able to colonise distantly related host species through the differential regulation of genes belonging to aphid-expanded gene families. Multigene clusters collectively up-regulate in single aphids within two days upon host switch. Furthermore, we demonstrate the functional significance of this rapid transcriptional change using RNA interference (RNAi)-mediated knock-down of genes belonging to the cathepsin B gene family. Knock-down of cathepsin B genes reduced aphid fitness, but only on the host that induced up-regulation of these genes.ConclusionsPrevious research has focused on the role of genetic adaptation of parasites to their hosts. Here we show that the generalist aphid pestM. persicaeis able to colonise diverse host plant species in the absence of genetic specialisation. This is achieved through rapid transcriptional plasticity of genes that have duplicated during aphid evolution.

12 p.-6 fig.-5 tab. Fernando Cruz et al., Background: The Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive oil. The molecular bases underlying the phenotypic differences among domesticated cultivars, or between domesticated olive trees and their wild relatives, remain poorly understood. Both wild and cultivated olive trees have 46 chromosomes (2n)., Findings: A total of 543 Gb of raw DNA sequence from whole genome shotgun sequencing, and a fosmid library containing 155,000 clones from a 1,000+ year-old olive tree (cv. Farga) were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 443 kb, and a total length of 1.31 Gb, which represents 95 % of the estimated genome length (1.38 Gb). In addition, the associated fungus Aureobasidium pullulans was partially sequenced. Genome annotation, assisted by RNA sequencing from leaf, root, and fruit tissues at various stages, resulted in 56,349 unique protein coding genes, suggesting recent genomic expansion. Genome completeness, as estimated using the CEGMA pipeline, reached 98.79 %., Conclusions: The assembled draft genome of O. europaea will provide a valuable resource for the study of the evolution and domestication processes of this important tree, and allow determination of the genetic bases of key phenotypic traits. Moreover, it will enhance breeding programs and the formation of new varieties., This project was funded by Banco Santander, which provided plant material and financed whole genome sequencing of the olive tree. The authors especially want to thank the late Mr. Emilio Botín for his support in driving this project. IJ was supported by a grant from the Peruvian Ministry of Education: ‘Beca Presidente de la República’ (2013-III).