Transcriptome dataset for comparative analysis of differentially expressed genes between wild type and transgenic potato plants overexpressing Nuclear Factor Y subunit A7

Nuclear Factor Y (NF-Y) is divided into three different types of subunits, A, B, and C. NF-Ys play crucial roles in plants for controlling gene expression associated with various developmental processes and abiotic stresses, but it is mostly unknown the downstream genes regulated by NF-Ys in plant. One of the potato NF-Y genes, StNF-YA7, increased potato's drought tolerance when overexpressed under the control of constitutive CaMV 35S promoter. Therefore, it was of interest what genes are regulated by the increased expression level of StNF-YA7. To investigate the downstream genes of StNF-YA7, the transcriptome sequencing was carried out for four potato lines, including Solanum tuberosum L 'Superior' as wild type (WT), empty vector control (VC), and two StNF-YA7 overexpressor lines (designated to StNF-YA7 #19 & #26). The RNA sequencing data was produced by the Illumina NovaSeq 6000 sequencing system. The number of total raw reads obtained from the RNA sequencing was 36.7 million for WT, 36.2 for VC, 29.3 for StNF-YA7 #19, and 29.5 million for StNF-YA7 #26, respectively. The length of total raw reads for each sample was between 5.92 Gb (StNF-YA7 #19) and 7.42 Gb (WT), and after filtering raw quality reads, the total length was between 5.81 Gb (StNF-YA7 #19) and 7.29 Gb (WT). Each filtered clear read set of four transcriptomes was mapped on the potato reference genome, SolTub_3.0, and the percentage of mapped reads ranged from 89.8 % (VC) to 90.3 % (WT). GC contents range between 43.01 % (StNF-YA7 #19) and 42.44 % (StNF-YA7 #26). Q20 quality score ranges between 98.63 % (StNF-YA7 #26) and 98.74 % (VC).

Transcriptome dataset of two Pistacia species: Pistacia chinensis and Pistacia weinmannifolia

Pistacia chinensis and Pistacia weinmannifolia are small trees and are distributed in East Asia, in particular China. The data on P. chinensis presented in this article is associated with the research article, "DOI: 10.5010/JPB.2019.46.4.274" [1]. Both P. chinensis and P. weinmannifolia have long been used as ethnobotanical plants to treat various illnesses, including dysentery, inflammatory swelling, rheumatism, liver diseases, influenza, lung cancer, etc. Many studies have been carried out to delve into the pharmaceutical properties of these Pistacia species using plant extracts, but genomic studies are very rarely performed to date. To enrich the genetic information of these two species, RNA sequencing was conducted using a pair-end Illumina HiSeq2500 sequencing system, resulting in 2.6 G of raw data from P. chinensis (Accession no: SRR10136265) and 2.7 G bases from P. weinmannifolia (Accession no: SRR10136264). Transcriptome shotgun assembly using three different assembly tools generated a total of 18,524 non-redundant contigs (N50, 1104 bp) from P. chinensis and 18,956 from P. weinmannifolia (N50, 1137 bp). The data is accessible at NCBI BioProject: PRJNA566127. These data would be crucial for the identification of genes associated with the compounds exerting pharmaceutical properties and also for molecular marker development.

Morphological Variations between Korean and Southwestern Japanese Lilium leichtlinii Hook. f

This study aimed to examine detailed morphological variations within Lilium leichtlinii Hook. f. For investigation, two groups, Korean L. leichtlinii (KR group) and southwestern Japanese broad-leaved L. leichtlinii (JSW group), were compared. In total, 52 morphological characteristics (45 quantitative and 7 qualitative traits) were examined in 59 lily accessions (30 KR and 29 JSW). Forty quantitative traits showed significant heterogeneity (p < 0.05) between JSW and KR accessions, and all seven color-related qualitative traits also exhibited differences. Student’s t-tests and principal component analysis (PCA) revealed that major quantitative morphological differences between the two groups included plant height, internode length, upper leaf size, and number of new bulbs. Cluster analysis of 36 morphological traits showed that the KR and JSW accessions belonged to two distinct groups. All together, these results indicate that KR and JSW groups are distal within L. leichtlinii, suggesting that the two groups could be considered different varieties.

A putative tomato inositol polyphosphate 5-phosphatase, Le5PT1, is involved in plant growth and abiotic stress responses

Based on sequence similarity to Arabidopsis inositol polyphosphate 5-phosphatases (5PTases) involved in abiotic stress responses and development, four tomato cDNAs (Le5PT1-4) encoding putative 5PTase proteins were identified. The predicted protein sequences of the Le5PTs include conserved catalytic domains required for 5PTase enzyme activity. Le5PT1, 2, and 3 showed high amino acid sequence identity with At5PTase2, At5PTase1 and At5PTase3, and At5PTase5 and At5PTase6, respectively. The expression of Le5PT1 was downregulated soon after initiation of dehydration and salt stress as well as exposure to polyethylene glycol (PEG) and NaCl, but not by exogenous ABA treatment. On the other hand, the expression of Le5PT2 gradually increased with time in all treatments. Transgenic tobacco plants overexpressing Le5PT1 exhibited reduced growth in height, leaf area, and dry weight compared to wild type plants. Transgenic plants also had lower water use efficiency (WUE) than wild type and the downregulation of the drought-responsive gene, NtERD10B. Together these results suggest that Le5PT1 may have a negative role in response to water deficit through the repression of drought-inducible genes that in turn affects plant growth and development.

Leaf transcriptome data of two tropical medicinal plants: Sterculia lanceolata and Clausena excavata

The data presented in this article are associated to the research articles, “DOI: 10.1007/s11295-019-1348-3”, [1]; and “DOI: 10.1007/s13205-018-1162-x” [2]. Clausena excavata Burm. f. and Sterculia lanceolata Cav. are medicinal tree plants [3,4] native to Southeast Asia and China, and most members of both the genus Clausena and the genus Sterculia contain various valuable secondary metabolites with a great potential for drug development. Though many phytochemical studies have been conducted using plant extracts from various parts of these plants [4,5], there are very limited genetic resources available. RNA sequencing of C. excavata and S. lanceolata was conducted using pair-end Illumina HiSeq2500 sequencing system, from which the first de novo transcriptome data were produced for both genus Clausena and Sterculia. Transcriptome shotgun assembly using three different assembly tools [2] generated a total of 16,638 non-redundant contigs (N50, 900 bp) from C. excavata and 7,857 (N50, 423 bp) from S. lanceolata. The data are accessible at NCBI BioProject: PRJNA428402 for C. excavata [2] or PRJNA435648 for S. lanceolata[1].

Expression of potato RNA-binding proteins StUBA2a/b and StUBA2c induces hypersensitive-like cell death and early leaf senescence in Arabidopsis

The Arabidopsis thaliana genome encodes three RNA-binding proteins (RBPs), UBP1-associated protein 2a (UBA2a), UBA2b, and UBA2c, that contain two RNA-recognition motif (RRM) domains. They play important roles in wounding response and leaf senescence, and are homologs of Vicia faba abscisic-acid-activated protein kinase-interacting protein 1 (VfAKIP1). The potato (Solanum tuberosum) genome encodes at least seven AKIP1-like RBPs. Here, two potato RBPs have been characterized, StUBA2a/b and StUBA2c, that are homologous to VfAKIP1 and Arabidopsis UBA2s. Transient expression of StUBA2s induced a hypersensitive-like cell death phenotype in tobacco leaves, and an RRM-domain deletion assay of StUBA2s revealed that the first RRM domain is crucial for the phenotype. Unlike overexpression of Arabidopsis UBA2s, constitutive expression of StUBA2a/b in Arabidopsis did not cause growth arrest and lethality at the young seedling stage, but induced early leaf senescence. This phenotype was associated with increased expression of defence- and senescence-associated genes, including pathogen-related genes (PR) and a senescence-associated gene (SAG13), and it was aggravated upon flowering and ultimately resulted in a shortened life cycle. Leaf senescence of StUBA2a/b Arabidopsis plants was enhanced under darkness and was accompanied by H2O2 accumulation and altered expression of autophagy-associated genes, which likely cause cellular damage and are proximate causes of the early leaf senescence. Expression of salicylic acid signalling and biosynthetic genes was also upregulated in StUBA2a/b plants. Consistent with the localization of UBA2s-GFPs and VfAKIP1-GFP, soluble-modified GFP-StUBA2s localized in the nucleus within nuclear speckles. StUBA2s potentially can be considered for transgenic approaches to induce potato shoot senescence, which is desirable at harvest.

Origin and domestication of papaya Yh chromosome

Sex in papaya is controlled by a pair of nascent sex chromosomes. Females are XX, and two slightly different Y chromosomes distinguish males (XY) and hermaphrodites (XY(h)). The hermaphrodite-specific region of the Y(h) chromosome (HSY) and its X chromosome counterpart were sequenced and analyzed previously. We now report the sequence of the entire male-specific region of the Y (MSY). We used a BAC-by-BAC approach to sequence the MSY and resequence the Y regions of 24 wild males and the Y(h) regions of 12 cultivated hermaphrodites. The MSY and HSY regions have highly similar gene content and structure, and only 0.4% sequence divergence. The MSY sequences from wild males include three distinct haplotypes, associated with the populations' geographic locations, but gene flow is detected for other genomic regions. The Y(h) sequence is highly similar to one Y haplotype (MSY3) found only in wild dioecious populations from the north Pacific region of Costa Rica. The low MSY3-Y(h) divergence supports the hypothesis that hermaphrodite papaya is a product of human domestication. We estimate that Y(h) arose only ∼ 4000 yr ago, well after crop plant domestication in Mesoamerica >6200 yr ago but coinciding with the rise of the Maya civilization. The Y(h) chromosome has lower nucleotide diversity than the Y, or the genome regions that are not fully sex-linked, consistent with a domestication bottleneck. The identification of the ancestral MSY3 haplotype will expedite investigation of the mutation leading to the domestication of the hermaphrodite Y(h) chromosome. In turn, this mutation should identify the gene that was affected by the carpel-suppressing mutation that was involved in the evolution of males.

Chimeric promoter mediates guard cell-specific gene expression in tobacco under water deficit

The engineering of stomatal activity under water deficit through guard cell-specific gene regulation is an effective approach to improve drought tolerance of crops but it requires an appropriate promoter(s) inducible by water deficit in guard cells. We report that a chimeric promoter can induce guard cell-specific gene expression under water deficit. A chimeric promoter, p4xKST82-rd29B, was constructed using a tetramer of the 82 bp guard cell-specific regulatory region of potato KST1 promoter (4xKST82) and Arabidopsis dehydration-responsive rd29B promoter. Transgenic tobacco plants carrying p4xKST82-rd29B:mGFP-GUS exhibited GUS expression in response to water deficit. GUS enzyme activity of p4xKST82-rd29B:mGFP-GUS transgenic plants increased ~300 % by polyethylene glycol treatment compared to that of control plant but not by abscisic acid (ABA), indicating that the p4xKST82-rd29B chimeric promoter can be used to induce the guard cell-specific expression of genes of interest in response to water deficit in an ABA-independent manner.

Accumulation of interspersed and sex-specific repeats in the non-recombining region of papaya sex chromosomes

Background

The papaya Y chromosome has undergone a degenerative expansion from its ancestral autosome, as a consequence of recombination suppression in the sex determining region of the sex chromosomes. The non-recombining feature led to the accumulation of repetitive sequences in the male- or hermaphrodite-specific regions of the Y or the Y^h chromosome (MSY or HSY). Therefore, repeat composition and distribution in the sex determining region of papaya sex chromosomes would be informative to understand how these repetitive sequences might be involved in the early stages of sex chromosome evolution.

Results

Detailed composition of interspersed, sex-specific, and tandem repeats was analyzed from 8.1 megabases (Mb) HSY and 5.3 Mb corresponding X chromosomal regions. Approximately 77% of the HSY and 64% of the corresponding X region were occupied by repetitive sequences. Ty3-gypsy retrotransposons were the most abundant interspersed repeats in both regions. Comparative analysis of repetitive sequences between the sex determining region of papaya X chromosome and orthologous autosomal sequences of Vasconcellea monoica, a close relative of papaya lacking sex chromosomes, revealed distinctive differences in the accumulation of Ty3-Gypsy, suggesting that the evolution of the papaya sex determining region may accompany Ty3-Gypsy element accumulation. In total, 21 sex-specific repeats were identified from the sex determining region; 20 from the HSY and one from the X. Interestingly, most HSY-specific repeats were detected in two regions where the HSY expansion occurred, suggesting that the HSY expansion may result in the accumulation of sex-specific repeats or that HSY-specific repeats might play an important role in the HSY expansion. The analysis of simple sequence repeats (SSRs) revealed that longer SSRs were less abundant in the papaya sex determining region than the other chromosomal regions.

Conclusion

Major repetitive elements were Ty3-gypsy retrotransposons in both the HSY and the corresponding X. Accumulation of Ty3-Gypsy retrotransposons in the sex determining region of papaya X chromosome was significantly higher than that in the corresponding region of V. monoica, suggesting that Ty3-Gypsy could be crucial for the expansion and evolution of the sex determining region in papaya. Most sex-specific repeats were located in the two HSY expansion regions.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-335) contains supplementary material, which is available to authorized users.

A multistep screening method to identify genes using evolutionary transcriptome of plants

We introduced a multistep screening method to identify the genes in plants using microarrays and ribonucleic acid (RNA)-seq transcriptome data. Our method describes the process for identifying genes using the salt-tolerance response pathways of the potato (Solanum tuberosum) plant. Gene expression was analyzed using microarrays and RNA-seq experiments that examined three potato lines (high, intermediate, and low salt tolerance) under conditions of salt stress. We screened the orthologous genes and pathway genes involved in salinity-related biosynthetic pathways, and identified nine potato genes that were candidates for salinity-tolerance pathways. The nine genes were selected to characterize their phylogenetic reconstruction with homologous genes of Arabidopsis thaliana, and a Circos diagram was generated to understand the relationships among the selected genes. The involvement of the selected genes in salt-tolerance pathways was verified by reverse transcription polymerase chain reaction analysis. One candidate potato gene was selected for physiological validation by generating dehydration-responsive element-binding 1 (DREB1)-overexpressing transgenic potato plants. The DREB1 overexpression lines exhibited increased salt tolerance and plant growth when compared to that of the control. Although the nine genes identified by our multistep screening method require further characterization and validation, this study demonstrates the power of our screening strategy after the initial identification of genes using microarrays and RNA-seq experiments.

Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution

Sex determination in papaya is controlled by a recently evolved XY chromosome pair, with two slightly different Y chromosomes controlling the development of males (Y) and hermaphrodites (Y(h)). To study the events of early sex chromosome evolution, we sequenced the hermaphrodite-specific region of the Y(h) chromosome (HSY) and its X counterpart, yielding an 8.1-megabase (Mb) HSY pseudomolecule, and a 3.5-Mb sequence for the corresponding X region. The HSY is larger than the X region, mostly due to retrotransposon insertions. The papaya HSY differs from the X region by two large-scale inversions, the first of which likely caused the recombination suppression between the X and Y(h) chromosomes, followed by numerous additional chromosomal rearrangements. Altogether, including the X and/or HSY regions, 124 transcription units were annotated, including 50 functional pairs present in both the X and HSY. Ten HSY genes had functional homologs elsewhere in the papaya autosomal regions, suggesting movement of genes onto the HSY, whereas the X region had none. Sequence divergence between 70 transcripts shared by the X and HSY revealed two evolutionary strata in the X chromosome, corresponding to the two inversions on the HSY, the older of which evolved about 7.0 million years ago. Gene content differences between the HSY and X are greatest in the older stratum, whereas the gene content and order of the collinear regions are identical. Our findings support theoretical models of early sex chromosome evolution.

Construction of physical maps for the sex-specific regions of papaya sex chromosomes

Background

Papaya is a major fruit crop in tropical and subtropical regions worldwide. It is trioecious with three sex forms: male, female, and hermaphrodite. Sex determination is controlled by a pair of nascent sex chromosomes with two slightly different Y chromosomes, Y for male and Y^h for hermaphrodite. The sex chromosome genotypes are XY (male), XY^h (hermaphrodite), and XX (female). The papaya hermaphrodite-specific Y^h chromosome region (HSY) is pericentromeric and heterochromatic. Physical mapping of HSY and its X counterpart is essential for sequencing these regions and uncovering the early events of sex chromosome evolution and to identify the sex determination genes for crop improvement.

Results

A reiterate chromosome walking strategy was applied to construct the two physical maps with three bacterial artificial chromosome (BAC) libraries. The HSY physical map consists of 68 overlapped BACs on the minimum tiling path, and covers all four HSY-specific Knobs. One gap remained in the region of Knob 1, the only knob structure shared between HSY and X, due to the lack of HSY-specific sequences. This gap was filled on the physical map of the HSY corresponding region in the X chromosome. The X physical map consists of 44 BACs on the minimum tiling path with one gap remaining in the middle, due to the nature of highly repetitive sequences. This gap was filled on the HSY physical map. The borders of the non-recombining HSY were defined genetically by fine mapping using 1460 F₂ individuals. The genetically defined HSY spanned approximately 8.5 Mb, whereas its X counterpart extended about 5.4 Mb including a 900 Kb region containing the Knob 1 shared by the HSY and X. The 8.5 Mb HSY corresponds to 4.5 Mb of its X counterpart, showing 4 Mb (89%) DNA sequence expansion.

Conclusion

The 89% increase of DNA sequence in HSY indicates rapid expansion of the Y^h chromosome after genetic recombination was suppressed 2–3 million years ago. The genetically defined borders coincide with the common BACs on the minimum tiling paths of HSY and X. The minimum tiling paths of HSY and its X counterpart are being used for sequencing these X and Y^h-specific regions.

Metabolite profiling based on lipophilic compounds for quality assessment of perilla (Perilla frutescens) cultivars

Lipophilic compounds from Korean perilla ( Perilla frutescens ) seeds were characterized to determine the diversity among their phytochemicals and to analyze relationships between their contents. Twenty-four metabolites consisting of policosanol, phytosterol, tocopherol, and fatty acids were identified. The metabolite profiles were subjected to data mining processes, including principal component analysis (PCA), partial least-squares discriminate analysis (PLS-DA), and Pearson's correlation analysis. PLS-DA could distinguish between all cultivars except between Daesil and Daeyeup cultivars. Linolenic acid contents were positively correlated with β-sitosterol (r = 0.8367, P < 0.0001) and γ-tocopherol contents (r = 0. 7201, P < 0.001) among all perilla grains. The Daesil and Daeyeup cultivars appear to be good candidates for future breeding programs because they have simultaneously high linolenic acid, phytosterol, and tocopherol levels. These results demonstrate the use of metabolite profiling as a tool for assessing the quality of food.

The origin of the non-recombining region of sex chromosomes in Carica and Vasconcellea

Carica and Vasconcellea are two closely related sister genera in the family Caricaceae, and were once classified as two sections under Carica. Sex chromosomes have been found in papaya and originated approximately 2-3 million years ago. The objectives of this study were to determine whether sex chromosomes have evolved in Vasconcellea. Six X/Y gene pairs were cloned, sequenced and analyzed from three dioecious, one trioecious and one monoecious species of Vasconcellea. The isolation of distinctive X and Y alleles in dioecious and trioecious species of Vasconcellea demonstrated that sex chromosomes have evolved in this genus. Phylogenetic analyses indicated a monophyletic relationship between the X/Y alleles of Carica and those of Vasconcellea. Distinctive clusters of X/Y alleles were documented in V. parviflora and V. pulchra for all available gene sequences, and in V. goudatinana and V. cardinamarcensis for some X/Y alleles. The X and Y alleles within each species shared most single nucleotide polymorphism haplotypes that differed from other species. Limited evidence of gene conversion was documented among the X/Y alleles of some species, but was not sufficient to cause the evolutionary patterns reported herein. The Carica and Vasconcellea sex chromosomes may have originated from the same autosomes bearing the X allelic form that still exist in the monoecious species V. monoica, and have evolved independently after the speciation event that separated Carica from Vasconcellea. Within Vasconcellea, sex chromosomes have evolved at the species level, at least for some species.

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.

Prevalence of diabetes and impaired fasting glucose in Korea: Korean National Health and Nutrition Survey 2001

OBJECTIVE

The purpose of this study was to estimate the prevalence of diabetes and impaired fasting glucose (IFG) and their association with risk factors in the Korean population.

RESEARCH DESIGN AND METHODS

The Korean National Health and Nutrition Survey 2001 was a nationally representative survey with a stratified multistage sampling design. Data from a comprehensive questionnaire, a physical examination, and blood tests were obtained from 5,844 Korean adults (2,513 men and 3,331 women) aged >20 years.

RESULTS

The age-adjusted prevalence of diabetes in this Korean population was 7.6%, and the age-adjusted prevalences of previously diagnosed diabetes and newly diagnosed diabetes were 4.4 and 3.3%, respectively (fasting plasma glucose > or = 7.0 mmol/l). Overall, these results indicate that 8.1% or 1.4 million Korean men and 7.5% or 1.3 million Korean women have diabetes. The age-adjusted prevalence of IFG was 23.9%, using the new American Diabetes Association criteria (fasting plasma glucose 5.6-6.9 mmol/l). Diabetes prevalence increased with age and peaked in the oldest age-group; however, IFG prevalence did not show the same trend. Diabetes was found to be associated with age, BMI, blood pressure, triglyceride, HDL cholesterol, education levels, alcohol consumption, exercise, and a family history of diabetes.

CONCLUSIONS

This study shows that diabetes and IFG are common in Korea, and about one-half of diabetes cases remain undiagnosed. These results emphasize the need to develop an urgent public program to improve the detection, prevention, and treatment of diabetes.