Young evolutionary origins of dioecy in the genus Asparagus.

PREMISE: Dioecy (separate sexes) has independently evolved numerous times across the angiosperm phylogeny and is recently derived in many lineages. However, our understanding is limited regarding the evolutionary mechanisms that drive the origins of dioecy in plants. The recent and repeated evolution of dioecy across angiosperms offers an opportunity to make strong inferences about the ecological, developmental, and molecular factors influencing the evolution of dioecy, and thus sex chromosomes. The genus Asparagus (Asparagaceae) is an emerging model taxon for studying dioecy and sex chromosome evolution, yet estimates for the age and origin of dioecy in the genus are lacking. METHODS: We use plastome sequences and fossil time calibrations in phylogenetic analyses to investigate the age and origin of dioecy in the genus Asparagus. We also review the diversity of sexual systems present across the genus to address contradicting reports in the literature. RESULTS: We estimate that dioecy evolved once or twice approximately 2.78-3.78 million years ago in Asparagus, of which roughly 27% of the species are dioecious and the remaining are hermaphroditic with monoclinous flowers. CONCLUSIONS: Our findings support previous work implicating a young age and the possibility of two origins of dioecy in Asparagus, which appear to be associated with rapid radiations and range expansion out of Africa. Lastly, we speculate that paleoclimatic oscillations throughout northern Africa may have helped set the stage for the origin(s) of dioecy in Asparagus approximately 2.78-3.78 million years ago.

Poly(ADP-ribose) Polymerase (PARP) is Critically Involved in Liver Ischemia/Reperfusion-injury.

BACKGROUND: Poly(ADP-ribose) polymerase (PARP) is a DNA-repairing enzyme activated by extreme genomic stress, and therefore is potently activated in the remnant liver suffering from ischemia after surgical resection. However, the impact of PARP on post-ischemic liver injury has not been elucidated yet. MATERIALS AND METHODS: We investigated the impact of PARP on murine hepatocyte/liver injury induced by hypoxia/ischemia, respectively. RESULTS: PJ34, a specific inhibitor of PARP, markedly protected against hypoxia/reoxygenation (H/R)-induced cell death, though z-VAD-fmk, a pan-caspase inhibitor similarly showed the protective effect. PJ34 did not affect H/R-induced caspase activity or caspase-mediated cell death. z-VAD-fmk also did not affect the production of PAR (i.e., PARP activity). Therefore, PARP- and caspase-mediated cell death occurred in a mechanism independent of each other in H/R. H/R immediately induced activation of PARP and cell death afterwards, both of which were suppressed by PJ34 or Trolox, an antioxidant. This suggests that H/R-induced cell death occurred redox-dependently through PARP activation. H/R and OS induced nuclear translocation of apoptosis inducing factor (AIF, a marker of parthanatos) and RIP1-RIP3 interaction (a marker of necroptosis), both of which were suppressed by PJ34. H/R induced PARP-mediated parthanatos and necroptosis redox-dependently. In mouse experiments, PJ34 significantly reduced serum levels of AST, ALT & LDH and areas of hepatic necrosis after liver ischemia/reperfusion, similar to z-VAD-fmk or Trolox. CONCLUSION: PARP, activated by ischemic damage and/or oxidative stress, may play a critical role in post-ischemic liver injury by inducing programmed necrosis (parthanatos and necroptosis). PARP inhibition may be one of the promising strategies against post-ischemic liver injury.

Molecular mechanism underlying pseudopeloria in Habenaria radiata (Orchidaceae).

Habenaria radiata (Orchidaceae) has two whorls of perianth, comprising three greenish sepals, two white petals and one lip (labellum). By contrast, the pseudopeloric (with a decreased degree of zygomorphy) mutant cultivar of H. radiata, 'Hishou', has changes in the identities of the dorsal sepal to a petaloid organ and the two ventral sepals to lip-like organs. Here, we isolated four DEFICIENS-like and two AGL6-like genes from H. radiata, and characterized their expression. Most of these genes revealed similar expression patterns in the wild type and in the 'Hishou' cultivar, except HrDEF-C3. The HrDEF-C3 gene was expressed in petals and lip in the wild type but was ectopically expressed in sepal, petals, lip, leaf, root and bulb in 'Hishou'. Sequence analysis of the HrDEF-C3 loci revealed that the 'Hishou' genome harbored two types of HrDEF-C3 genes: one identical to wild-type HrDEF-C3 and the other carrying a retrotransposon insertion in its promoter. Genetic linkage analysis of the progeny derived from an intraspecific cross between 'Hishou' and the wild type demonstrated that the mutant pseudopeloric trait was dominantly inherited and was linked to the HrDEF-C3 gene carrying the retrotransposon. These results indicate that the pseudopeloric phenotype is caused by retrotransposon insertion in the HrDEF-C3 promoter, resulting in the ectopic expression of HrDEF-C3. As the expression of HrAGL6-C2 was limited to lateral sepals and lip, the overlapping expression of HrDEF-C3 and HrAGL6-C2 is likely to be responsible for the sepal to lip-like identity in the lateral sepals of the 'Hishou' cultivar.

Comparative Metabolome and Transcriptome Analyses of Susceptible Asparagus officinalis and Resistant Wild A. kiusianus Reveal Insights into Stem Blight Disease Resistance.

Phomopsis asparagi is one of the most serious fungal pathogens, which causes stem blight disease in Asparagus officinalis (AO), adversely affecting its production worldwide. Recently, the development of novel asparagus varieties using wild Asparagus genetic resources with natural P. asparagi resistance has become a priority in Japan due to the lack of resistant commercial AO cultivars. In this study, comparative metabolome and transcriptome analyses of susceptible AO and resistant wild Asparagus kiusianus (AK) 24 and 48 h postinoculated (AOI_24 hpi, AOI_48 hpi, AKI_24 hpi and AKI_48 hpi, respectively) with P. asparagi were conducted to gain insights into metabolic and expression changes associated with AK species. Following infection, the resistant wild AK showed rapid metabolic changes with increased levels of flavonoids and steroidal saponins and decreased asparagusic acid glucose ester content, compared with the susceptible AO plants. Transcriptome data revealed a total of 21 differentially expressed genes (DEGs) as the core gene set that displayed upregulation in the resistant AK versus susceptible AO after infection with P. asparagi. Kyoto Encyclopedia of Genes and Genomes pathway analysis of these DEGs identified 11 significantly enriched pathways, including flavonoid biosynthesis and primary metabolite metabolism, in addition to plant signaling and defense-related pathways. In addition, comparative single-nucleotide polymorphism and Indel distributions in susceptible AO and resistant AK plants were evaluated using the latest AO reference genome Aspof.V1. The data generated in this study are important resources for advancing Asparagus breeding programs and for investigations of genetic linkage mapping, phylogenetic diversity and plant defense-related genes.

MYB transcription factor gene involved in sex determination in Asparagus officinalis.

Dioecy is a plant mating system in which individuals of a species are either male or female. Although many flowering plants evolved independently from hermaphroditism to dioecy, the molecular mechanism underlying this transition remains largely unknown. Sex determination in the dioecious plant Asparagus officinalis is controlled by X and Y chromosomes; the male and female karyotypes are XY and XX, respectively. Transcriptome analysis of A. officinalis buds showed that a MYB-like gene, Male Specific Expression 1 (MSE1), is specifically expressed in males. MSE1 exhibits tight linkage with the Y chromosome, specific expression in early anther development and loss of function on the X chromosome. Knockout of the MSE1 orthologue in Arabidopsis induces male sterility. Thus, MSE1 acts in sex determination in A. officinalis.

Bioluminescent Indicator for Highly Sensitive Analysis of Estrogenic Activity in a Cell-Based Format.

Estrogens regulate different physiological systems with wide ranges of concentrations. The rapid analysis of estrogens is crucially important for drug discovery and medical diagnosis, but quantitation of nanomolar estrogens in live cells persists as an important challenge. We herein describe a bioluminescent indicator used to detect low concentrations of estrogens quantitatively with a high signal-to-background ratio. The indicator comprises a ligand-binding domain of an estrogen receptor connected with its binding peptide, which is sandwiched between split fragments of a luciferase mutant. Results show that the indicator recovered its bioluminescence upon binding to 17ß-estradiol at concentrations higher than 1.0 × 10-10 M. The indicator was reactive to agonists but did not respond to antagonists. The indicator is expected to be applicable for rapid screening estrogenic compounds and inhibitors, facilitating the discovery of drug candidates in a high-throughput manner.

Bioluminescent probes to analyze ligand-induced phosphatidylinositol 3,4,5-trisphosphate production with split luciferase complementation.

A lipid second messenger, phosphatidylinositol (3,4,5)-trisphosphate (PIP3), is a signaling molecule that mediates central cellular events, such as growth, motility, and development by activating downstream proteins. Although functions of various PIP3 binding partners have been unveiled, the various roles of PIP3 have not been resolved thoroughly because of limitations of PIP3 analysis. Herein, we describe a novel method for the analysis of relative PIP3 amount based on spontaneous complementation of split luciferase fragments. An N-terminal fragment of a luciferase was located on the plasma membrane (LucN-pm). A C-terminal fragment of a luciferase fused with PIP3 binding units, pleckstrin homology domains (PHDs) of the general receptor for phosphoinositides 1 (GRP1), was expressed in cytosol (PP-LucC). In response to PIP3 production, PP-LucC was brought to the plasma membrane and colocalized with LucN-pm. The LucN-pm and PP-LucC reconstituted spontaneously to form an active luciferase, producing bioluminescence recovery. We obtained bioluminescence signals corresponding to relative PIP3 amounts successfully upon stimulation with an agonist. We also demonstrated that the probes were applied for a high-throughput screening format and for monitoring of PIP3 production on the plasma membrane by bioluminescence. This method enables further study of PIP3 and supports versatile applications related to the PIP3 amount.

Origin of purple asparagus cultivar 'Pacific Purple' based on the sequence of sex determination gene.

Garden asparagus is one of the most important crops worldwide. Since this crop is dioecious and male plants generally have higher yields compared to female plants, several DNA markers for sex identification have been developed for acceleration of asparagus breeding. Among these markers, Asp1-T7sp and MSSTS710 were found to be effective in sex determination for many asparagus cultivars. However, we previously found that these markers were not completely suitable for sex identification in the purple asparagus cultivar 'Pacific Purple'. There are two types of male individuals in this cultivar: One type is PP-m, which is identified the sex type by Asp1-T7sp and MSSTS710 markers, while the other type is PP-m* whose sex type is not identified by these markers. Since the sex identification markers are located on the non-recombining Y region, it was expected that the sequence around this region might be different between PP-m and PP-m*. In this study, the sequence of one of the sex-determining genes, MSE1/AoMYB35/AspTDF1, was analyzed, and a comparative analysis was conducted among PP-m and PP-m* of 'Pacific Purple', A. officinalis and related species A. maritimus. The results revealed that PP-m and PP-m* has the similar sequence of MSE1/AoMYB35/AspTDF1 gene from A. officinalis and A. maritimus, respectively. 'Pacific Purple' is a cultivar developed through polycross hybrid from Italian landrace 'Violetto d'Albenga' (VA), suggesting that VA originated from an interspecific crossing between A. officinalis and A. maritimus and that the pollen parent used in 'Pacific Purple' breeding contained two types of male individuals with different MSE1/AoMYB35/AspTDF1 sequence. As a result, PP-m and PP-m* of 'Pacific Purple' harbors the similar sequences of the MSE1/AoMYB35/AspTDF1 gene from A. officinalis and A. maritimus, respectively.

Molecular phylogeny of the genus Asparagus (Asparagaceae) explains interspecific crossability between the garden asparagus (A. officinalis) and other Asparagus species.

The genus Asparagus comprises approximately 200 species, some of which are commercially cultivated, such as the garden asparagus (A. officinalis). Many Asparagus species, including A. officinalis, are dioecious and have been grouped into a subgenus distinct from that of hermaphroditic species. Although many interspecific crossings have been attempted to introduce useful traits into A. officinalis, only some of the dioecious species were found to be cross-compatible with A. officinalis. Here, molecular phylogenetic analyses were conducted to determine whether interspecific crossability is proportional to the genetic distance between the crossing pairs and to further clarify the evolutionary history of the Asparagus genus. A clade with all cross-compatible species and no cross-incompatible species was recovered in the phylogenetic tree based on analyses of non-coding cpDNA regions. In addition, a sex-linked marker developed for A. officinalis amplified a male-specific region in all cross-compatible species. The phylogenetic analyses also provided some insights about the evolutionary history of Asparagus; for example, by indicating that the genus had its origin in southern Africa, subsequently spreading throughout the old world through intensive speciation and dispersal. The results also suggest that dioecious species were derived from a single evolutionary transition from hermaphroditism in Asparagus. These findings not only contribute towards the understanding of the evolutionary history of the genus but may also facilitate future interspecific hybridization programs involving Asparagus species.

Random BAC FISH of monocot plants reveals differential distribution of repetitive DNA elements in small and large chromosome species.

BAC FISH (fluorescence in situ hybridization using bacterial artificial chromosome probes) is a useful cytogenetic technique for physical mapping, chromosome marker screening, and comparative genomics. As a large genomic fragment with repetitive sequences is inserted in each BAC clone, random BAC FISH without adding competitive DNA can unveil complex chromosome organization of the repetitive elements in plants. Here we performed the comparative analysis of the random BAC FISH in monocot plants including species having small chromosomes (rice and asparagus) and those having large chromosomes (hexaploid wheat, onion, and spider lily) in order to understand a whole view of the repetitive element organization in Poales and Asparagales monocots. More unique and less dense dispersed signals of BAC FISH were observed in species with smaller chromosomes in both the Poales and Asparagales species. In the case of large-chromosome species, 75-85% of the BAC clones were detected as dispersed repetitive FISH signals along entire chromosomes. The BAC FISH of Lycoris did not even show localized repetitive patterns (e.g., centromeric localization) of signals.

[Thrombosis with Thrombocytopenia Syndrome after ChAdOx1 nCoV-19 vaccination].

A 48-year-old Japanese man who had no previous medical history received his first dose of the ChAdOx1 nCoV-19 vaccine. Ten days after the vaccine administration, he developed a headache. Laboratory results indicated throm-bocytopenia and DIC. A head CT revealed microbleeding in the left parietal lobe. Contrast-enhanced CT showed thrombus in the left transverse sinus and left sigmoid sinus. A brain MRI demonstrated venous hemorrhagic infarction and subarachnoid hemorrhages in the left parietal lobe, and whole-body enhanced CT also revealed portal vein embolism and renal infarction. He was diagnosed with thrombosis with thrombocytopenia syndrome, and was treated according to the guideline. He has been recovering with the treatments. This is the first reported case of TTS associated with the ChAdOx1 nCoV-19 vaccine in Japan.

Chromosome-scale haplotype-phased genome assemblies of the male and female lines of wild asparagus (Asparagus kiusianus), a dioecious plant species.

Asparagus kiusianus is a disease-resistant dioecious plant species and a wild relative of garden asparagus (Asparagus officinalis). To enhance A. kiusianus genomic resources, advance plant science, and facilitate asparagus breeding, we determined the genome sequences of the male and female lines of A. kiusianus. Genome sequence reads obtained with a linked-read technology were assembled into four haplotype-phased contig sequences (∼1.6 Gb each) for the male and female lines. The contig sequences were aligned onto the chromosome sequences of garden asparagus to construct pseudomolecule sequences. Approximately 55,000 potential protein-encoding genes were predicted in each genome assembly, and ∼70% of the genome sequence was annotated as repetitive. Comparative analysis of the genomes of the two species revealed structural and sequence variants between the two species as well as between the male and female lines of each species. Genes with high sequence similarity with the male-specific sex determinant gene in A. officinalis, MSE1/AoMYB35/AspTDF1, were presented in the genomes of the male line but absent from the female genome assemblies. Overall, the genome sequence assemblies, gene sequences, and structural and sequence variants determined in this study will reveal the genetic mechanisms underlying sexual differentiation in plants, and will accelerate disease-resistance breeding in garden asparagus.

Prognostic value of cerebrospinal fluid cytokine changes in herpes simplex virus encephalitis.

A recent trial suggested that corticosteroid was beneficial in herpes simplex virus encephalitis (HSVE), but that precise role remains unclear. We assessed the differences of cerebrospinal fluid (CSF) cytokine changes between different outcomes and between patients with and without corticosteroid administration at the acute stage of HSVE. Interleukin (IL)-1beta, IL-2, IL-6, IL-10, interferon (IFN)-gamma, and tumor necrosis factor-alpha were measured in 56 serial CSFs taken from 20 adult HSVE patients. Their outcomes were poor in 7 and good in 13 patients, and corticosteroid was administered in 10. The differences in the initial and maximum cytokine values were assessed among the different outcomes. The decline rate of cytokine values between the initial and second CSF samples was also assessed between patients with and without corticosteroid. The initial IFN-gamma and maximum IL-6 with a poor outcome were higher than those with a good outcome (p=0.019 for IFN-gamma and p=0.013 for IL-6). The decline rate of IL-6 in patients with corticosteroid was higher than that without corticosteroid (p=0.034). The initial IFN-gamma and maximum IL-6 CSF values represented prognostic biomarkers in HSVE. One pharmacological mechanism related to corticosteroid in HSVE is apparently inhibition of pro-inflammatory cytokines such as IL-6.

The Greenish Flower Phenotype of Habenaria radiata (Orchidaceae) Is Caused by a Mutation in the SEPALLATA-Like MADS-Box Gene HrSEP-1.

In Arabidopsis thaliana, the E-class SEPALLATA (SEP) genes are generally expressed across all floral whorls. These genes play fundamental roles in floral organ fate determination during development by interacting with other MADS-box gene products, such as those from A-, B-, and C-class genes. However, the function of SEP genes in orchid remains obscure. Here, we analyzed a mutant orchid cultivar with greenish flowers in Habenaria radiata and found that this phenotype is caused by the absence of SEP function. Wild type H. radiata flowers contain a column and two perianth whorls consisting of three greenish sepals, two white petals, and a lip (labellum). By contrast, the flowers of H. radiata cultivar 'Ryokusei' appear greenish, with three normal sepals in whorl 1, two greenish petals and a lip in whorl 2, and several sepaloid organs and a ventral column in whorls 3 and 4. We isolated two SEP-like genes (HrSEP-1 and HrSEP-2) and two AGAMOUS-like genes (HrAG-1 and HrAG-2) from wild type H. radiata and compared their expression in the wild type vs. the mutant cultivar. HrAG-1 and HrAG-2 were expressed in the column in the wild type, whereas these genes were expressed in the ventral column and in sepaloid organs that had been converted from a column in 'Ryokusei.' HrSEP-1 and HrSEP-2 were expressed in all floral organs in the wild type. However, in the mutant cultivar, HrSEP-2 was expressed in all floral organs, while HrSEP-1 expression was not detected. Thus, we analyzed the genomic structures of HrSEP-1 in the wild type and 'Ryokusei' and identified a retrotransposon-like element in its first exon in 'Ryokusei.' Yeast two-hybrid assays demonstrated that HrSEP-1 interacts with HrDEF, HrAG-1, and HrAG-2. These results indicate that the mutant phenotype of 'Ryokusei' flowers is caused by the loss of function of HrSEP-1. Therefore, this gene plays an important role in column, lip, and petal development in H. radiata flowers.

Detection of Necroptosis in Ligand-Mediated and Hypoxia-Induced Injury of Hepatocytes Using a Novel Optic Probe-Detecting Receptor-Interacting Protein (RIP)1/RIP3 Binding.

Liver injury is often observed in various pathological conditions including posthepatectomy state and cancer chemotherapy. It occurs mainly as a consequence of the combined necrotic and apoptotic types of cell death. In order to study liver/hepatocyte injury by the necrotic type of cell death, we studied signal-regulated necrosis (necroptosis) by developing a new optic probe for detecting receptor-interacting protein kinase 1 (RIP)/RIP3 binding, an essential process for necroptosis induction. In the mouse hepatocyte cell line, TIB-73 cells, TNF-α/cycloheximide (T/C) induced RIP1/3 binding only when caspase activity was suppressed by the caspase-specific inhibitor z-VAD-fmk (zVAD). T/C/zVAD-induced RIP1/3 binding was inhibited by necrostatin-1 (Nec-1), an allosteric inhibitor of RIP1. The reduced cell survival by T/C/zVAD was improved by Nec-1. These facts indicate that T/C induces necroptosis of hepatocytes when the apoptotic pathway is inhibited/unavailable. FasL also induced cell death, which was only partially inhibited by zVAD, indicating the possible involvement of necroptosis rather than apoptosis. FasL activated caspase 3 and, similarly, induced RIP1/3 binding when the caspases were inactivated. Interestingly, FasL-induced RIP1/3 binding was significantly suppressed by the antioxidants Trolox and N-acetyl cysteine (NAC), suggesting the involvement of reactive oxygen species (ROS) in FasL-induced necroptotic cellular processes. H2O2, by itself, induced RIP1/3 binding that was suppressed by Nec-1, but not by zVAD. Hypoxia induced RIP1/3 binding after reoxygenation, which was suppressed by Nec-1 or by the antioxidants. Cell death induced by hypoxia/reoxygenation (H/R) was also improved by Nec-1. Similar to H2O2, H/R did not require caspase inhibition for RIP1/3 binding, suggesting the involvement of a caspase-independent mechanism for non-ligand-induced and/or redox-mediated necroptosis. These data indicate that ROS can induce necroptosis and mediate the FasL- and hypoxia-induced necroptosis via a molecular mechanism that differs from a conventional caspase-dependent pathway. In conclusion, necroptosis is potentially involved in liver/hepatocyte injury induced by oxidative stress and FasL in the absence of apoptosis.

Differential gene expression analysis and SNP/InDel marker discovery in resistant wild Asparagus kiusianus and susceptible A. officinalis in response to Phomopsis asparagi infection.

This data article reports de novo transcriptome analysis of resistant wild Asparagus kiusianus and susceptible A. officinalis plants 24 and 48 h post-inoculation (24 and 48 hpi) with Phomopsis asparagi. Differential gene expression (DGE) analysis demonstrated that several genes involved in secondary metabolites and plant-pathogen interactions are up-regulated in resistant wild A. kiusianus relative to susceptible A. officinalis. The assembled contig sequences generated in this study were used to search single nucleotide polymorphism (SNP) and insertion/deletion (InDel) distribution in A. kiusianus and A. officinalis plants. SNP and InDel data developed from this transcriptome analysis will be used to generate a high-density linkage map to facilitate further development of molecular marker-assisted selection in A. officinalis.

Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome.

The application of a new gene-based strategy for sequencing the wheat mitochondrial genome shows its structure to be a 452 528 bp circular molecule, and provides nucleotide-level evidence of intra-molecular recombination. Single, reciprocal and double recombinant products, and the nucleotide sequences of the repeats that mediate their formation have been identified. The genome has 55 genes with exons, including 35 protein-coding, 3 rRNA and 17 tRNA genes. Nucleotide sequences of seven wheat genes have been determined here for the first time. Nine genes have an exon-intron structure. Gene amplification responsible for the production of multicopy mitochondrial genes, in general, is species-specific, suggesting the recent origin of these genes. About 16, 17, 15, 3.0 and 0.2% of wheat mitochondrial DNA (mtDNA) may be of genic (including introns), open reading frame, repetitive sequence, chloroplast and retro-element origin, respectively. The gene order of the wheat mitochondrial gene map shows little synteny to the rice and maize maps, indicative that thorough gene shuffling occurred during speciation. Almost all unique mtDNA sequences of wheat, as compared with rice and maize mtDNAs, are redundant DNA. Features of the gene-based strategy are discussed, and a mechanistic model of mitochondrial gene amplification is proposed.

Class B gene expression and the modified ABC model in nongrass monocots.

The discovery of the MADS-box genes and the study of model plants such as Arabidopsis thaliana and Antirrhinum majus have greatly improved our understanding of the molecular mechanisms driving the diversity in floral development. The class B genes, which belong to the MADS-box gene family, are important regulators of the development of petals and stamens in flowering plants. Many nongrass monocot flowers have two whorls of petaloid organs, which are called tepals. To explain this floral morphology, the modified ABC model was proposed. This model was exemplified by the tulip, in which expansion and restriction of class B gene expression is linked to the transition of floral morphologies in whorl 1. The expression patterns of class B genes from many monocot species nicely fit this model; however, those from some species, such as asparagus, do not. In this review, we summarize the relationship between class B gene expression and floral morphology in nongrass monocots, such as Liliales (Liliaceae) and Asparagales species, and discuss the applicability of the modified ABC model to monocot flowers.

Comparative de novo transcriptome profiles in Asparagus officinalis and A. kiusianus during the early stage of Phomopsis asparagi infection.

Asparagus kiusianus, an important wild relative of cultivated asparagus (A. officinalis), exhibits resistance to stem blight disease caused by Phomopsis asparagi. However, the mechanisms underlying this resistance are not understood and no transcriptomic or genetic resources are available for this species. De novo transcriptome sequencing of A. officinalis and A. kiusianus stems was performed 24 h after inoculation with P. asparagi. In total, 35,259 and 36,321 transcripts were annotated in A. officinalis and A. kiusianus, respectively. 1,027 up-regulated and 752 down-regulated transcripts were differentially expressed in the two Asparagus species. RNA sequencing data were validated using quantitative real-time reverse transcription PCR. Several defense-related genes including peroxidase 4, cationic peroxidase SPC4-like, pathogenesis-related protein-1-like, and jasmonic acid biosynthesis and signaling-related genes including phospholipase D alpha 1, 12-oxophytodienoate reductase and jasmonate-induced protein 23 KD were up-regulated in A. kiusianus relative to A. officinalis. In addition, infected A. kiusianuns exhibited a substantial increase in jasmonic acid and methyl jasmonate relative to A. officinalis. Peroxidase activity was significantly elevated in infected A. kiusianus compared with infected A. officinalis. Our transcriptomic database provides a resource for identifying novel genes and molecular markers-associated with Phomopsis disease resistance and will facilitate breeding and improvement of cultivated asparagus varieties.

The asparagus genome sheds light on the origin and evolution of a young Y chromosome.

Sex chromosomes evolved from autosomes many times across the eukaryote phylogeny. Several models have been proposed to explain this transition, some involving male and female sterility mutations linked in a region of suppressed recombination between X and Y (or Z/W, U/V) chromosomes. Comparative and experimental analysis of a reference genome assembly for a double haploid YY male garden asparagus (Asparagus officinalis L.) individual implicates separate but linked genes as responsible for sex determination. Dioecy has evolved recently within Asparagus and sex chromosomes are cytogenetically identical with the Y, harboring a megabase segment that is missing from the X. We show that deletion of this entire region results in a male-to-female conversion, whereas loss of a single suppressor of female development drives male-to-hermaphrodite conversion. A single copy anther-specific gene with a male sterile Arabidopsis knockout phenotype is also in the Y-specific region, supporting a two-gene model for sex chromosome evolution.