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Long terminal repeat (LTR)-retrotransposons (LTR-RTs) comprise a major portion of many plant genomes and may exert a profound impact on genome structure, function, and evolution. Although many studies have focused on these elements in an individual species, their dynamics on a family level remains elusive. Here, we investigated the abundance, evolutionary dynamics, and impact on associated genes of LTR-RTs in 16 species in an economically important plant family, Cucurbitaceae. Results showed that full-length LTR-RT numbers and LTR-RT content varied greatly among different species, and they were highly correlated with genome size. Most of the full-length LTR-RTs were amplified after the speciation event, reflecting the ongoing rapid evolution of these genomes. LTR-RTs highly contributed to genome size variation via species-specific distinct proliferations. The Angela and Tekay lineages with a greater evolutionary age were amplified in Trichosanthes anguina, whereas a recent activity burst of Reina and another ancient round of Tekay activity burst were examined in Sechium edule. In addition, Tekay and Retand lineages belonging to the Gypsy superfamily underwent a recent burst in Gynostemma pentaphyllum. Detailed investigation of genes with intronic and promoter LTR-RT insertion showed diverse functions, but the term of metabolism was enriched in most species. Further gene expression analysis in G.pentaphyllum revealed that the LTR-RTs within introns suppress the corresponding gene expression, whereas the LTR-RTs within promoters exert a complex influence on the downstream gene expression, with the main function of promoting gene expression. This study provides novel insights into the organization, evolution, and function of LTR-RTs in Cucurbitaceae genomes.

Background Dioecious spinach (Spinacia oleracea L.), a commercial and nutritional vegetable crop, serves as a model for studying the mechanisms of sex determination and differentiation in plants. However, this mechanism is still unclear. Herein, based on PacBio Iso-seq and Illumina RNA-seq data, comparative transcriptome analysis of male and female flowers were performed to explore the sex differentiation mechanism in spinach. Results Compared with published genome of spinach, 10,800 transcripts were newly annotated; alternative splicing, alternative polyadenylation and lncRNA were analyzed for the first time, increasing the diversity of spinach transcriptome. A total of 2965 differentially expressed genes were identified between female and male flowers at three early development stages. The differential expression of RNA splicing-related genes, polyadenylation-related genes and lncRNAs suggested the involvement of alternative splicing, alternative polyadenylation and lncRNA in sex differentiation. Moreover, 1946 male-biased genes and 961 female-biased genes were found and several candidate genes related to gender development were identified, providing new clues to reveal the mechanism of sex differentiation. In addition, weighted gene co-expression network analysis showed that auxin and gibberellin were the common crucial factors in regulating female or male flower development; however, the closely co-expressed genes of these two factors were different between male and female flower, which may result in spinach sex differentiation. Conclusions In this study, 10,800 transcripts were newly annotated, and the alternative splicing, alternative polyadenylation and long-noncoding RNA were comprehensively analyzed for the first time in spinach, providing valuable information for functional genome study. Moreover, candidate genes related to gender development were identified, shedding new insight on studying the mechanism of sex determination and differentiation in plant.

The transfer of mitochondrial DNA to the nuclear genome gives rise to the nuclear DNA sequences of mitochondrial origin (NUMTs), considered as a driving force in genome evolution. In this study, NUMTs in 23 bat genomes were investigated and compared systematically. The results showed that NUMTs existed in 22 genomes except for Noctilio leporinus, suggesting that mitochondrial fragment insertion in the nuclear genome was a common event in bat genomes. However, remarkable variations in NUMTs number, cumulative length, and proportion in the nuclear genome were discovered across bat species. Further orthologous NUMT loci analysis of the Phyllostomidae family indicated that the NUMTs insertion events in bat genomes were homoplasy-free. The NUMTs were mainly inserted into the intergenic regions, particularly, co-localized with repetitive sequences (especially transposable elements). However, several NUMTs were inserted into genes, some of which were in the exon region of functional genes. One NUMT in the genome of Pteropus alecto surprisingly matched with cDNA of ATP8B3 that provided evidence of NUMTs with coding function. Phylogenic analysis on NUMTs originating from COXI and COXII loci highlighted 2 clusters of Yinpterochiroptera and Yangochiroptera for Chiroptera. Seven NUMTs from Rhinolophus ferrumequinum were amplified, and the sequencing results confirmed the reliability of the NUMT analysis. One of them was polymorphic for the presence or absence of the NUMT insertion, and each genotype of NUMT loci showed a distinct regional distribution pattern. The information obtained in this study provides novel insights into the NUMT organization and features in bat genomes and establishes a basis for further studying of the evolution of bat species.

DNA methylation is a crucial regulatory mechanism in many biological processes. However, limited studies have dissected the contribution of DNA methylation to sexual differentiation in dioecious plants. In this study, we investigated the variances in methylation and transcriptional patterns of male and female flowers of garden asparagus. Compared with male flowers, female flowers at the same stages showed higher levels of DNA methylation. Both male and female flowers gained DNA methylation globally from the premeiotic to meiotic stages. Detailed analysis revealed that the increased DNA methylation was largely due to increased CHH methylation. Correlation analysis of differentially expressed genes and differentially methylated regions suggested that DNA methylation might not have contributed to the expression variation of the sex-determining genes SOFF and TDF1 but probably played important roles in sexual differentiation and flower development of garden asparagus. The upregulated genes AoMS1, AoLAP3, AoAMS, and AoLAP5 with varied methylated CHH regions might have been involved in sexual differentiation and flower development of garden asparagus. Plant hormone signaling genes and transcription factor genes also participated in sexual differentiation and flower development with potential epigenetic regulation. In addition, the CG and CHG methylation levels in the Y chromosome were notably higher than those in the X chromosome, implying that DNA methylation might have been involved in Y chromosome evolution. These data provide insights into the epigenetic modification of sexual differentiation and flower development and improve our understanding of sex chromosome evolution in garden asparagus.

Spinach (Spinacia oleracea Linnaeus, 1753) is an ideal material for studying molecular mechanisms of early-stage sex chromosome evolution in dioecious plants. Degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR) technique facilitates the retrotransposon-relevant studies by enriching specific repetitive DNA sequences from a micro-dissected single chromosome. We conducted genomic subtractive hybridization to screen sex-biased DNA sequences by using the DOP-PCR amplification products of micro-dissected spinach Y chromosome. The screening yielded 55 male-biased DNA sequences with 30 576 bp in length, of which, 32 DNA sequences (12 049 bp) contained repeat DNA sequences, including LTR/Copia, LTR/Gypsy, simple repeats, and DNA/CMC-EnSpm. Among these repetitive DNA sequences, four DNA sequences that contained a fragment of Ty3-gypsy retrotransposons (SP73, SP75, SP76, and SP77) were selected as fluorescence probes to hybridization on male and female spinach karyotypes. Fluorescence in situ hybridization (FISH) signals of SP73 and SP75 were captured mostly on the centromeres and their surrounding area for each homolog. Hybridization signals primarily appeared near the putative centromeres for each homologous chromosome pair by using SP76 and SP77 probes for FISH, and sporadic signals existed on the long arms. Results can be served as a basis to study the function of repetitive DNA sequences in sex chromosome evolution in spinach.

Sex chromosome evolution has mostly been studied in species with heteromorphic sex chromosomes. The Spinacia genus serves as an ideal model for investigating evolutionary mechanisms underlying the transition from homomorphic to heteromorphic sex chromosomes. Among evolutionary factors, repetitive sequences play multiple roles in sex chromosome evolution while their forces have not been fully explored in Spinacia species. Here, we identified major repetitive sequence classes in male and female genomes of Spinacia species and their ancestral relative sugar beet to elucidate the evolutionary processes of sex chromosome evolution using next-generation sequencing (NGS) data. Comparative analysis revealed that the repeat elements of Spinacia species are considerably higher than of sugar beet, especially the Ty3/Gypsy and Ty1/Copia retrotransposons. The long terminal repeat retroelements (LTR) Angela, Athila, and Ogre may be accounted for the higher proportion of repeats in the spinach genome. Comparison of the repeats proportion between female and male genomes of three Spinacia species indicated the different representation in Spinacia tetrandra samples but not in the S. oleracea or S. turkestanica samples. From these results, we speculated that emergence of repetitive DNA sequences may correlate the formation of sex chromosome and the transition from homomorphic sex chromosomes to heteromorphic sex chromosomes as heteromorphic sex chromosomes exclusively existed in Spinacia tetrandra. Three novel sugar beet-specific satellites were identified and confirmed by fluorescence in situ hybridization (FISH); six out of eight new spinach-specific satellites were mapped to the short arm of sex chromosomes. A total of 141 copies of SolSat01-171-s were found in the sex determination region (SDR). Thus, the accumulation of satellite DNA on the short arm of chromosome 1 may be involved in the sex chromosome evolution in Spinacia species. Our study provides a fundamental resource for understanding repeat sequences in Spinacia species and their roles in sex chromosome evolution.

Asparagus setaceus is an important ornamental plant and is important to study the sex chromosome evolution in genus Asparagus. Here the complete chloroplast (cp) genome sequence of A. setaceus was determined. The cpDNA is 156,978 bp in length, contains a large single copy region of 85,311 bp and a small single copy region of 18,641 bp, which was separated by a pair of inverted repeat regions of 26,513 bp each. The cp genome contains 132 genes, including 88 protein-coding genes, 6 ribosomal RNA genes, and 38 transfer RNA genes. Phylogenetic analysis indicates that A. setaceus is closely related to Asparagus officinalis and Asparagus schoberioides.

Asparagus setaceusis a popular ornamental plant cultivated in tropical and subtropical regions globally. Here, we constructed a chromosome-scale reference genome ofA. setaceusto facilitate the investigation of its genome characteristics and evolution. Using a combination of Nanopore long reads, Illumina short reads, 10× Genomics linked reads, and Hi-C data, we generated a high-quality genome assembly ofA. setaceuscovering 710.15 Mb, accounting for 98.63% of the estimated genome size. A total of 96.85% of the sequences were anchored to ten superscaffolds corresponding to the ten chromosomes. The genome ofA. setaceuswas predicted to contain 28,410 genes, 25,649 (90.28%) of which were functionally annotated. A total of 65.59% of the genome was occupied by repetitive sequences, among which long terminal repeats were predominant (42.51% of the whole genome). Evolutionary analysis revealed an estimated divergence time ofA. setaceusfrom its close relativeA. officinalisof ~9.66 million years ago, andA. setaceusunderwent two rounds of whole-genome duplication. In addition, 762 specific gene families, 96 positively selected genes, and 76 resistance (R) genes were detected and functionally predicted inA. setaceus. These findings provide new knowledge about the characteristics and evolution of theA. setaceusgenome, and will facilitate comparative genetic and genomic research on the genusAsparagus.

The transfer of genetic material from the mitochondria and plastid to the nucleus gives rise to nuclear integrants of mitochondrial DNA (NUMTs) and nuclear integrants of plastid DNA (NUPTs). This frequently occurring DNA transfer is ongoing and has important evolutionary implications. In this review, based on previous studies and the analysis of NUMT/NUPT insertions of more than 200 sequenced plant genomes, we analyzed and summarized the general features of NUMTs/NUPTs and highlighted the genetic consequence of organellar DNA insertions. The statistics of organellar DNA integrants among various plant genomes revealed that organellar DNA-derived sequence content is positively correlated with the nuclear genome size. After integration, the nuclear organellar DNA could undergo different fates, including elimination, mutation, rearrangement, fragmentation, and proliferation. The integrated organellar DNAs play important roles in increasing genetic diversity, promoting gene and genome evolution, and are involved in sex chromosome evolution in dioecious plants. The integrating mechanisms, involving non-homologous end joining at double-strand breaks were also discussed.

Spinach is a nutritional leafy green vegetable, and it also serves as a model species for studying sex chromosome evolution. Genetic marker development and genome structure analysis are important in breeding practice and theoretical evolution studies of spinach. In this study, the frequency and distribution of different microsatellites in the recently released draft spinach genome were characterized. A total of 261,002 perfect microsatellites were identified (estimated frequency: ~262.1 loci/Mbp). The most abundant microsatellites were tetranucleotide and trinucleotide, accounting for 33.2% and 27.7% of the total number of microsatellites, respectively. A total of 105 primer pairs were designed and screened, and 34 were polymorphic among the detected spinach cultivars. Combined with seven primer sets developed previously, 41 primer pairs were used to investigate genetic diversity among 43 spinach cultivars in China. The average polymorphism information content value of the 41 markers was 0.43, representing an intermediate level. The spinach cultivars had a low genetic diversity, and no detectable common factors were shared by each group in the UPGMA dendrogram. This study's findings facilitate further investigations on the organization of the microsatellites in spinach genome and provide clues for future breeding applications of spinach in China.

Background The transfer of chloroplast DNA into nuclear genome is a common process in plants. These transfers form nuclear integrants of plastid DNAs (NUPTs), which are thought to be driving forces in genome evolution, including sex chromosome evolution. In this study, NUPTs in the genome of a dioecious plant Asparagus officinalis L. were systematically analyzed, in order to investigate the characteristics of NUPTs in the nuclear genome and the relationship between NUPTs and sex chromosome evolution in this species. Results A total of 3155 NUPT insertions were detected, and they represented approximated 0.06% of the nuclear genome. About 45% of the NUPTs were organized in clusters. These clusters were derived from various evolutionary events. The Y chromosome contained the highest number and largest proportion of NUPTs, suggesting more accumulation of NUPTs on sex chromosomes. NUPTs were distributed widely in all of the chromosomes, and some regions preferred these insertions. The highest density of NUPTs was found in a 47 kb region in the Y chromosome; more than 75% of this region was occupied by NUPTs. Further cytogenetic and sequence alignment analysis revealed that this region was likely the centromeric region of the sex chromosomes. On the other hand, the male-specific region of the Y chromosome (MSY) and the adjacent regions did not have NUPT insertions. Conclusions These results indicated that NUPTs were involved in shaping the genome of A. officinalis through complicated process. NUPTs may play important roles in the centromere shaping of the sex chromosomes of A. officinalis, but were not implicated in MSY formation. Electronic supplementary material The online version of this article (10.1186/s12870-019-1975-8) contains supplementary material, which is available to authorized users.

Background Repetitive sequences, including transposable elements (TEs) and satellite DNAs, occupy a considerable portion of plant genomes. Analysis of the repeat fraction benefits the understanding of genome structure and evolution. Spinach (Spinacia oleracea L.), an important vegetable crop, is also a model dioecious plant species for studying sex determination and sex chromosome evolution. However, the repetitive sequences of the spinach genome have not been fully investigated. Results We extensively analyzed the repetitive components of draft spinach genome, especially TEs and satellites, by different strategies. A total of 16,002 full-length TEs were identified. Among the most abundant long terminal repeat (LTR) retrotransposons (REs), Copia elements were overrepresented compared with Gypsy ones. Angela was the most dominating Copia lineage; Ogre/Tat was the most abundant Gypsy lineage. The mean insertion age of LTR-REs was 1.42 million years; approximately 83.7% of these elements were retrotransposed during the last two million years. RepeatMasker totally masked about 64.05% of the spinach genome, with LTR-REs, non-LTR-REs, and DNA transposons occupying 49.2, 2.4, and 5.6%, respectively. Fluorescence in situ hybridization (FISH) analysis showed that most LTR-REs dispersed all over the chromosomes, by contrast, elements of CRM lineage were distributed at the centromeric region of all chromosomes. In addition, Ogre/Tat lineage mainly accumulated on sex chromosomes, and satellites Spsat2 and Spsat3 were exclusively located at the telomeric region of the short arm of sex chromosomes. Conclusions We reliably annotated the TE fraction of the draft genome of spinach. FISH analysis indicates that Ogre/Tat lineage and the sex chromosome-specific satellites DNAs might participate in sex chromosome formation and evolution. Based on FISH signals of microsatellites, together with 45S rDNA, a fine karyotype of spinach was established. This study improves our knowledge of repetitive sequence organization in spinach genome and aids in accurate spinach karyotype construction. Electronic supplementary material The online version of this article (10.1186/s13100-019-0147-6) contains supplementary material, which is available to authorized users.

The primers used for amplification of the RT sequences of lineages in spinach. (DOC 42 kb)

Table S1. The detailed information of NUPTs in the nuclear genome of A. officinalis. (DOCX 44 kb)

Topological layout and consensus sequence of satellite DNAs. (DOC 1441 kb)

∆(8)-sphingolipid desaturase catalyzes the C8 desaturation of a long chain base, which is the characteristic structure of various complex sphingolipids. The genes of 20 ∆(8)-sphingolipid desaturases from 12 plants were identified and functionally detected by using Saccharomyces cerevisiae system to elucidate the relationship between the biochemical function and evolution of this enzyme. Results showed that the 20 genes all can encode a functional ∆(8)-sphingolipid desaturase, which catalyzes different ratios of two products, namely, 8(Z) and 8(E)-C18-phytosphingenine. The coded enzymes could be divided into two groups on the basis of biochemical functions: ∆(8)-sphingolipid desaturase with a preference for an E-isomer product and ∆(8)-sphingolipid desaturase with a preference for a Z-isomer product. The conversion rate of the latter was generally lower than that of the former. Phylogenetic analysis revealed that the 20 desaturases could also be clustered into two groups, and this grouping is consistent with that of the biochemical functions. Thus, the biochemical function of ∆(8)-sphingolipid desaturase is correlated with its evolution. The two groups of ∆(8)-sphingolipid desaturases could arise from distinct ancestors in higher plants. However, they might have initially evolved from ∆(8)-sphingolipid desaturases in lower organisms, such as yeasts, which can produce E-isomer products only. Furthermore, almost all of the transgenic yeasts harboring ∆(8)-sphingolipid desaturase genes exhibit an improvement in aluminum tolerance. Our study provided new insights into the biochemical function and evolution of ∆(8)-sphingolipid desaturases in plants.

Asparagus setaceus is an important ornamental plant and is important to study the sex chromosome evolution in genus Asparagus. Here the complete chloroplast (cp) genome sequence of A. setac...

Spinach (Spinacia oleracea L.) is a diploid dioecious plant with a pair of homomorphic sex chromosomes X and Y. Plant DNA methylation, a known process for genome epigenetic modification, regulates gene expression in plants. To explore the effects of DNA methylation on spinach growth and sexual development, spinach seeds were treated with the demethylating reagent 5-azaC. The resulting phenotypes were then investigated, including germination percentage, root length, plant height, flowering time, and sexual phenotype. Results showed that 5-azaC at a low concentration (30 µM) only slightly influenced spinach development but promoted seed germination. The germination percentage, root length, and plant height negatively correlated with 5-azaC at 100–1000 µM. The flowering time significantly reduced at all four treatments with 5-azaC. In addition, 5-azaC influenced the sexual phenotype of spinach and remarkably increased the percentage of monoecious individuals. These results may suggest that vegetative and reproductive growth are both epigenetically regulated by DNA methylation.

We prove that there exists a unique quasi-stationary distribution for the minimal birth–death process with exit boundary. A spectral representation for the quasi-stationary distribution is also obtained.

The effects of exposure to heavy metals, copper (Cu) and lead (Pb) in the soil, separately and in combination, were examined in Safflower (Carthamus tinctorius L.). Plant growth and development, GSH level and GSH2 expression at seedling, branching, and flowering stages were studied. Cu at lower concentrations had a stimulating effect on seedling height and root length. A significant positive correlation was observed between heavy metal concentrations and inhibition of plant growth. Plant height, root length and lateral root numbers decreased progressively with increasing concentrations of Cu and Pb. Except at the seedling stage, the metal mixture elicited a synergistic effect on safflower growth and development. The GSH content was significantly reduced in both safflower roots and leaves at increased concentrations of heavy metals, with the exception of the treatment with a low concentration of Cu that resulted in a slightl increase in GSH content at the seedling and branching stages. RT-PCR analysis revealed a negative correlation between GSH2 expression levels and metal concentration. Short exposure to low concentrations of Cu induce an increase in GSH synthesis to preserve normal plant growth, whereas prolonged exposure and large Cu and Pb concentrations affect the GSH metabolic chain, and are severely toxicity. The findings obtained in this study enhance our understanding of the role of the GSH pool in the response of plants to heavy metal-induced stress, and serve as a basis for improved cultivation of safflower.

Classical forward genetic analysis relies on construction of complicated progeny populations and development of many molecular markers for linkage analysis in genetic mapping, which is both time- and cost-consuming. The recently developed MutMap is a new forward genetic approach based on high-throughput next-generation sequencing technologies. It is more efficient and affordable than traditional methods. Moreover, new extended methods based on MutMap have been developed: MutMap+, which is based on self-crossing; MutMap-Gap, which is used to recognize the causative variations occurring in genome gap regions; QTL-seq, a method similar to MutMap for mapping quantitative trait loci. These methods are free from constructing complicated mapping population, genetic hybridization and linkage information. They have greatly accelerated the identification of genetic elements associated with interested phenotypic variation. Here, we review the basic principles of MutMap, and discuss their future applications in next generation sequencing-based forward genetic mapping and crop improvement.

Chromosome evolution is a fundamental aspect of evolutionary biology. The evolution of chromosome size, structure and shape, number, and the change in DNA composition suggest the high plasticity of nuclear genomes at the chromosomal level. Repetitive DNA sequences, which represent a conspicuous fraction of every eukaryotic genome, particularly in plants, are found to be tightly linked with plant chromosome evolution. Different classes of repetitive sequences have distinct distribution patterns on the chromosomes. Mounting evidence shows that repetitive sequences may play multiple generative roles in shaping the chromosome karyotypes in plants. Furthermore, recent development in our understanding of the repetitive sequences and plant chromosome evolution has elucidated the involvement of a spectrum of epigenetic modification. In this review, we focused on the recent evidence relating to the distribution pattern of repetitive sequences in plant chromosomes and highlighted their potential relevance to chromosome evolution in plants. We also discussed the possible connections between evolution and epigenetic alterations in chromosome structure and repatterning, such as heterochromatin formation, centromere function, and epigenetic-associated transposable element inactivation.

Background Garden asparagus (Asparagus officinalis) is a highly valuable vegetable crop of commercial and nutritional interest. It is also commonly used to investigate the mechanisms of sex determination and differentiation in plants. However, the sex expression mechanisms in asparagus remain poorly understood. Results De novo transcriptome sequencing via Illumina paired-end sequencing revealed more than 26 billion bases of high-quality sequence data from male and female asparagus flower buds. A total of 72,626 unigenes with an average length of 979 bp were assembled. In comparative transcriptome analysis, 4876 differentially expressed genes (DEGs) were identified in the possible sex-determining stage of female and male/supermale flower buds. Of these DEGs, 433, including 285 male/supermale-biased and 149 female-biased genes, were annotated as flower related. Of the male/supermale-biased flower-related genes, 102 were probably involved in anther development. In addition, 43 DEGs implicated in hormone response and biosynthesis putatively associated with sex expression and reproduction were discovered. Moreover, 128 transcription factor (TF)-related genes belonging to various families were found to be differentially expressed, and this finding implied the essential roles of TF in sex determination or differentiation in asparagus. Correlation analysis indicated that miRNA-DEG pairs were also implicated in asparagus sexual development. Conclusions Our study identified a large number of DEGs involved in the sex expression and reproduction of asparagus, including known genes participating in plant reproduction, plant hormone signaling, TF encoding, and genes with unclear functions. We also found that miRNAs might be involved in the sex differentiation process. Our study could provide a valuable basis for further investigations on the regulatory networks of sex determination and differentiation in asparagus and facilitate further genetic and genomic studies on this dioecious species. Electronic supplementary material The online version of this article (doi:10.1186/s12870-017-1091-6) contains supplementary material, which is available to authorized users.

In this study, 17 male-specific amplified fragment length polymorphism (AFLP) markers were identified between male and female Humulus scandens plants. BLAST analysis revealed that 7 of the 17 sex-linked sequences were highly similar to retrotransposons. Two stable male-specific sequence-characterized amplified regions (SCAR) markers were developed. These AFLP and SCAR markers are novel molecular probes that can be used efficiently to identify the genetic gender of H. scandens and may provide a basis for further investigations on the evolution of sex chromosomes.

Asparagus officinalis L. is a dioecious plant. A region called the M-locus located on a pair of homomorphic L5 chromosomes controls sexual dimorphism in asparagus. This study aims to conduct microd...

∆8-sphingolipid desaturase is characterized by its ability to catalyze desaturation at the C8 position of the long-chain base of sphingolipids in plants. No previous studies have been conducted on genes encoding Δ8-sphingolipid desaturases in the woody plant Populus tomentosa. In this study, three genes that encode Δ8-sphingolipid desaturase were isolated from P. tomentosa. Among these genes, PtD8A and PtD8B showed high sequence similarity; whereas PtD8C exhibited large sequence divergence. RT-PCR results showed that PtD8A and PtD8B were expressed in all tissues detected, whereas PtD8C was not expressed in roots. Heterologous expression in yeast revealed that PtD8A/B/C were functional Δ8-sphingolipid desaturases, and can catalyze the C18-phytosphingenine desaturation to produce 8(Z)- and 8(E)-C18-phytosphingenine. However, the conversion rate and ratios of the two products differed. Compared with control cells, transgenic yeasts expressing PtD8A/B/C exhibited enhanced aluminum tolerance. Our findings further elucidated the biochemical functions and evolutionary history of Δ8-sphingolipid desaturases in plants. Candidate genes for breeding new poplar germplasm resources with enhanced tolerance ability to aluminium were also provided.

In this paper, we deal with multidimensional backward stochastic equations (BSDES) driven by continuous semi-martingale. We first obtain the existence of solution for this kind of BSDES with locally Lipschitz coefficient, which generalizes the corresponding results in Khaled Bahlali.

Spinach has long been used as a model for genetic and physiological studies of sex determination and expression. Although trisomic analysis from a cross between diploid and triploid plants identified the XY chromosome as the largest chromosome, no direct evidence has been provided to support this at the molecular level. In this study, the largest chromosomes of spinach from mitotic metaphase spreads were microdissected using glass needles. Degenerate oligonucleotide primed polymerase chain reaction was used to amplify the dissected chromosomes. The amplified products from the Y chromosome were identified using the male-specific marker T11A. For the first time, the largest spinach chromosome was confirmed to be a sex chromosome at the molecular level. PCR products from the isolated chromosomes were used in an in situ probe mixture for painting the Y chromosome. The fluorescence signals were mainly distributed on all chromosomes and four pair of weaker punctate fluorescence signal sites were observed on the terminal region of two pair of autosomes. These findings provide a foundation for the study of sex chromosome evolution in spinach.

Dioecious plants usually harbor 'young' sex chromosomes, providing an opportunity to study the early stages of sex chromosome evolution. Transposable elements (TEs) are mobile DNA elements frequently found in plants and are suggested to play important roles in plant sex chromosome evolution. The genomes of several dioecious plants have been sequenced, offering an opportunity to annotate and mine the TE data. However, comprehensive and unified annotation of TEs in these dioecious plants is still lacking. In this study, we constructed a dioecious plant transposable element database (DPTEdb). DPTEdb is a specific, comprehensive and unified relational database and web interface. We used a combination of de novo, structure-based and homology-based approaches to identify TEs from the genome assemblies of previously published data, as well as our own. The database currently integrates eight dioecious plant species and a total of 31 340 TEs along with classification information. DPTEdb provides user-friendly web interfaces to browse, search and download the TE sequences in the database. Users can also use tools, including BLAST, GetORF, HMMER, Cut sequence and JBrowse, to analyze TE data. Given the role of TEs in plant sex chromosome evolution, the database will contribute to the investigation of TEs in structural, functional and evolutionary dynamics of the genome of dioecious plants. In addition, the database will supplement the research of sex diversification and sex chromosome evolution of dioecious plants.Database URL: http://genedenovoweb.ticp.net:81/DPTEdb/index.php.

Garden asparagus (Asparagus officinalis), an important vegetable cultivated worldwide, can also serve as a model dioecious plant species in the study of sex determination and sex chromosome evolution. However, limited DNA marker resources have been developed and used for this species. To expand these resources, we examined the DNA sequences for simple sequence repeats (SSRs) in 163,406 scaffolds representing approximately 400 Mbp of the A. officinalis genome. A total of 87,576 SSRs were identified in 59,565 scaffolds. The most abundant SSR repeats were trinucleotide and tetranucleotide, accounting for 29.2 and 29.1% of the total SSRs, respectively, followed by di-, penta-, hexa-, hepta-, and octanucleotides. The AG motif was most common among dinucleotides and was also the most frequent motif in the entire A. officinalis genome, representing 14.7% of all SSRs. A total of 41,917 SSR primers pairs were designed to amplify SSRs. Twenty-two genomic SSR markers were tested in 39 asparagus accessions belonging to ten cultivars and one accession of Asparagus setaceus for determination of genetic diversity. The intra-species polymorphism information content (PIC) values of the 22 genomic SSR markers were intermediate, with an average of 0.41. The genetic diversity between the ten A. officinalis cultivars was low, and the UPGMA dendrogram was largely unrelated to cultivars. It is here suggested that the sex of individuals is an important factor influencing the clustering results. The information reported here provides new information about the organization of the microsatellites in A. officinalis genome and lays a foundation for further genetic studies and breeding applications of A. officinalis and related species.

Male and female spinach (Spinacia oleracea L, 2n = 12) were karyotyped by chromosome measurements and subjected to fluorescence in situ hybridization with 45s rDNA The chromosome complement comprised two long nearly subtelocentrics, two short subtelocentrics, two acrocentrics, and six submetacentrics. The X and Y chromosomes were not distinguished by morphological analysis; thus, six obvious 45s rDNA sites were labeled with Texas red and clearly observed as red signals on three pairs of chromosomes. Among the three pairs of signal sites, a pair of the largest one was located on the short arms of chromosome 5, which is a satellite chromosome. Another prominent signal site was found on the short arms of chromosomes 2 and 6. However, from single images with 45s rDNA (red) of male or female spinach, weak 45s rDNA sites labeled with Texas red were observed on chromosomes 1 and 3. The weak 45s rDNA signals site were located on the large arm of chromosome 3 of both male and female spinach. Interestingly, differe...

ƒIn this paper, we study the one-dimensional backward stochastic equations driven by continuous local martingale. We establish a generalized the comparison theorem for any solutions where the coefficient is uniformly Lipschitz continuous in z and is equi-continuous in y.

Ion implantation, as a new biophysically mutagenic technique, has shown a great potential for horticultural plant breeding. Up to date, little is known about the mutation mechanism of ion implantation at the DNA level. To reveal the mutation effect of Fe+ ion implantation on Baiyangdian red lotus, the random amplified polymorphic DNA (RAPD) was used, and then the bands of mutants and the control in the radiation-sensitive sites were cloned to be sequenced for comparing their DNA sequences. The results indicated that the total base mutation rate of mutants was 0.87%, and there was different in the six mutants. The types of base changes included base transition, transversion, deletion, and insertion. Among the 159 base changes detected, the frequency of single base substitutions (61.01%) was higher than that of base deletions and insertions (38.99%), and the frequency of base transitions (44.65%) was 2.7 times of that of the base transversions (16.35%). The transitions between C and T accounted for largest proportion, A→G transitions and A→T transversions were also present at high frequency. Adenine, thymine, guanine or cytosine could be replaced by any of other three bases, except that there was no C → G substitution. However, thymine was more sensitive to the irradiation than other bases. In our study, we found many purine bases around the purine mutational sites, and many pyrimidine bases around the pyrimidine mutational sites. These will further help us to understand the mechanism of mutagenesis by ion implantation.

Suppression of recombination is the prerequisite for plant sex chromosome evolution from a pair of autosomes. Recombination suppression around the locus controlling sex determination results in sex chromosome degeneration and differentiation. Important events such as repetitive sequence accumulation, heterochromatize, and DNA methylation have relation to recombination suppression. Accumulation of repetitive DNA sequence, including transposable elements and satellite DNA, leads to primitive sex chromosome differentiated on morphological and molecular structure, and also gives rise to chromosome heterochromatize, and thus recombination between sex chromosomes was suppressed. Here, we re-viewed the advances in this field, meanwhile, the function of DNA methylation in recombination suppression was analyzed.

Garden asparagus (Asparagus officinalis L.) is a dioecious species whose male and female flowers are found in separate unisexual individuals. A region called the M-locus, located on a pair of homomorphic sex chromosomes, controls sexual dimorphism in asparagus. To date, no sex determining gene has been isolated from asparagus. To identify more genes involved in flower development in asparagus, subtractive hybridization library of male flowers in asparagus was constructed by suppression subtraction hybridization. A total of 107 expressed sequence tags (ESTs) were identified. BLASTX analysis showed that the library contained several genes that could be related to flower development. The expression patterns of seven selected genes believed to be involved in the development of asparagus male flower were further analyzed by semi-quantitative or real-time reverse-transcription polymerase chain reaction (RT-PCR). Results showed that AOEST4-5, AOEST12-40, and AOEST13-38 were strongly expressed in the male flower stage, whereas no transcript level of AOEST13-38 was detected in the female flower stage. The expression levels of AOEST13-87, AOEST13-92, AOEST13-40, and AOEST18-87 in the male flower stage were also higher than those in the female flower stage, although these transcripts were also expressed in other tissues. The identified genes can provide a strong starting point for further studies on the underlying molecular differences between the male and female flowers of asparagus.

Asparagus officinalis is an economically and nutritionally important vegetable crop that is widely cultivated and is used as a model dioecious species to study plant sex determination and sex chromosome evolution. To improve our understanding of its genome composition, especially with respect to transposable elements (TEs), which make up the majority of the genome, we performed Illumina HiSeq2000 sequencing of both male and female asparagus genomes followed by bioinformatics analysis. We generated 17 Gb of sequence (12×coverage) and assembled them into 163,406 scaffolds with a total cumulated length of 400 Mbp, which represent about 30% of asparagus genome. Overall, TEs masked about 53% of the A. officinalis assembly. Majority of the identified TEs belonged to LTR retrotransposons, which constitute about 28% of genomic DNA, with Ty1/copia elements being more diverse and accumulated to higher copy numbers than Ty3/gypsy. Compared with LTR retrotransposons, non-LTR retrotransposons and DNA transposons were relatively rare. In addition, comparison of the abundance of the TE groups between male and female genomes showed that the overall TE composition was highly similar, with only slight differences in the abundance of several TE groups, which is consistent with the relatively recent origin of asparagus sex chromosomes. This study greatly improves our knowledge of the repetitive sequence construction of asparagus, which facilitates the identification of TEs responsible for the early evolution of plant sex chromosomes and is helpful for further studies on this dioecious plant.

DNA methylation has been implicated in the regulation of gene expression, genome imprinting, and chromatin remodeling in eukaryotes. In this study, we analyzed possible alterations in levels and patterns of cytosine methylation in male and female spinach plants after treatment with demethylation agent 5-azacytidine (5-azaC) using two methods: (1) direct determination of 5-methylcytidine (5 mC) amounts in genomic DNA by high-performance liquid chromatography (HPLC) separation and quantification of nucleosides and (2) methylation-sensitive inter-simple sequence repeat (MS-ISSR) technique. HPLC analysis revealed that the DNA methylation events in male and female spinach leaves markedly decreased upon 30 μM 5-azaC treatment, and the methylation level gradually decreased with the increase in 5-azaC concentration. To study the altered DNA methylation patterns in spinach after 5-azaC treatment, untreated and 500 μM 5-azaC-treated samples were analyzed by MS-ISSR assay. A total of 385 informative profiles were resolved using 35 ISSR primer sets. MS-ISSR analysis showed various altered methylation patterns between untreated and 5-azaC-treated spinach plants. These alterations were mainly demethylation events, which were largely consistent with the HPLC results. Both HPLC and MS-ISSR analyses showed that the changes in DNA methylation levels and patterns were similar in male and female spinach leaves, which implies that sex was not the main factor influencing DNA methylation levels and patterns in the vegetative organs of spinach. This study could provide a molecular basis of the altered DNA methylation induced by 5-azaC, and lay a foundation for further investigation of the relationship between methylation and sex determination and development in this dioecious plant spinach.

To identify rapidly a number of genes probably involved in sex determination and differentiation of the dioecious plant Asparagus officinalis, gene expression profiles in early flower development for male and female plants were investigated by microarray assay with 8,665 probes. In total, 638 male-biased and 543 female-biased genes were identified. These genes with biased-expression for male and female were involved in a variety of processes associated with molecular functions, cellular components, and biological processes, suggesting that a complex mechanism underlies the sex development of asparagus. Among the differentially expressed genes involved in the reproductive process, a number of genes associated with floral development were identified. Reverse transcription-PCR was performed for validation, and the results were largely consistent with those obtained by microarray analysis. The findings of this study might contribute to understanding of the molecular mechanisms of sex determination and differentiation in dioecious asparagus and provide a foundation for further studies of this plant.

Ion implantation, as a new biophysically mutagenic technique, has shown a great potential for horticultural plant breeding. Up to date, little is known about the mutation mechanism of ion implantation at the DNA level. To reveal the mutation effect of Fe+ ion implantation on Baiyangdian red lotus, the random amplified polymorphic DNA (RAPD) was used, and then the bands of mutants and the control in the radiation-sensitive sites were cloned to be sequenced for comparing their DNA sequences. The results indicated that the total base mutation rate of mutants was 0.87%, and there was different in the six mutants. The types of base changes included base transition, transversion, deletion, and insertion. Among the 159 base changes detected, the frequency of single base substitutions (61.01%) was higher than that of base deletions and insertions (38.99%), and the frequency of base transitions (44.65%) was 2.7 times of that of the base transversions (16.35%). The transitions between C and T accounted for largest proportion, A→G transitions and A→T transversions were also present at high frequency. Adenine, thymine, guanine or cytosine could be replaced by any of other three bases, except that there was no C → G substitution. However, thymine was more sensitive to the irradiation than other bases. In our study, we found many purine bases around the purine mutational sites, and many pyrimidine bases around the pyrimidine mutational sites. These will further help us to understand the mechanism of mutagenesis by ion implantation.