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1.
Endocr Connect ; 13(2)2024 Feb 01.
Article in English | MEDLINE | ID: mdl-38078943

ABSTRACT

Objective: The aim of this study was to compare the differences in incident population, comorbidities, and glucose-lowering drug prescriptions between newly diagnosed patients with early-onset type 2 diabetes mellitus (T2DM) and those with late-onset T2DM to provide real-world evidence for clinical practice. Methods: This study was based on the Shanghai Hospital Link Database (SHLD). Anonymized electronic medical record (EHR) data from 2013 to 2021 were included in this study. Newly diagnosed patients with T2DM were defined as those without related diagnostic records or glucose-lowering medicine prescriptions in the past 3 years. Early-onset T2DM was defined as patients who were aged 18-40 years old at the first visit for T2DM to represent those who were born after the 1980s. And late-onset T2DM was defined as those aged 65-80 years old to represent those who were born in a relatively undeveloped period. Descriptive statistical analyses were performed to describe their incidence number, glucose-lowering drug prescriptions, and comorbidities at the first visit to the hospital between two T2DM groups. Results: There were a total of 35,457 newly diagnosed patients with early-onset T2DM and 149,108 newly diagnosed patients with late-onset T2DM included in this study. Patients with late-onset T2DM constituted the majority and their number increased by 2.5% on average by years, while the number of patients with early-onset T2DM remained stable each year. Compared with late-onset T2DM patients, more early-onset T2DM patients had dyslipidemia at the first visit to hospitals (9.5% vs 7.7%, P < 0.01) despite their significant age differences. Patients with early-onset T2DM were more likely to use metformin (74.8% vs 46.5, P < 0.01), dipeptidyl peptidase-4 inhibitors (DDP-4i) (16.7% vs 11.2%, P < 0.01), thiazolidinediones (TZD) (14.9% vs 8.4%, P < 0.01), sodium glucose cotransporter 2 inhibitors (SGLT2-i) (0.8% vs 0.3%, P < 0.01), and glucagon-like peptide 1 receptor agonists (GLP-1 RA) (3.7% vs 0.5%, P < 0.01) at their first visit to the hospital. Conclusions: Different characteristics were observed between patients with early-onset T2DM and those with late-onset T2DM. Compared with patients with late-onset T2DM, those with early-onset T2DM were more prone to dyslipidemia and had novel organ-protective drugs prescribed.

2.
iScience ; 26(10): 107979, 2023 Oct 20.
Article in English | MEDLINE | ID: mdl-37822506

ABSTRACT

Patients with type 2 diabetes mellitus (T2DM) are at a heightened risk of living with multiple comorbidities. However, the comprehension of the multimorbidity characteristics of T2DM is still scarce. This study aims to illuminate T2DM's prevalent comorbidities and their interrelationships using network analysis. Using electronic medical records (EMRs) from 496,408 Chinese patients with T2DM, we constructed male and female global multimorbidity networks and age- and sex-specific networks. Employing diverse network metrics, we assessed the structural properties of these networks. Furthermore, we identified hub, root, and burst diseases within these networks while scrutinizing their temporal trends. Our findings uncover interconnected T2DM comorbidities manifesting as emergence in clusters or age-specific outbreaks and core diseases in each sex that necessitate timely detection and intervention. This data-driven methodology offers a comprehensive comprehension of T2DM's multimorbidity, providing hypotheses for clinical considerations in the prevention and therapeutic strategies.

3.
Endocr Pract ; 29(10): 747-753, 2023 Oct.
Article in English | MEDLINE | ID: mdl-37422155

ABSTRACT

BACKGROUND: Cardiovascular disease (CVD) is the major cause of death among persons with diabetes. As the preventative use of statin has been proved to reduce CVD risks, understanding the current status and the trend in statin use is crucial to improve clinical treatment strategies. OBJECTIVE: Our study aimed to answer the question of what were the status and trend of statin use in Shanghai, China. METHODS: Our study estimated statin use and trends from 2015 to 2021 among 702 727 patients with type 2 diabetes mellitus (T2DM) based on electronic health records from the Shanghai Hospital Link Database. Patients were grouped according to the presence of CVDs, tested separately for statin primary and secondary prevention use, and stratified by age and sex. RESULTS: In the study population, 221 127 patients (31.5%) received statin therapy, and among patients with CVD, 157 622 patients (51.62%) received statin therapy for secondary prevention, but only 15% of patients received statins for primary prevention. The trend in the use of statins was still on the rise from 28.3% in 2015. Statin use increased with age (18-39 years, 14.0%; 40-59 years, 26.8%; 60-74 years, 33.35%; and 75 and over, 36.1%), and women (29.7%, n = 93 977) were less likely to receive statin therapy compared to men (32.9%, n = 127 150). CONCLUSION: Despite the rise in statin use in T2DM in recent decades, a large proportion of subjects with T2DM did not receive statin therapy.

4.
Plant Signal Behav ; 18(1): 2203571, 2023 12 31.
Article in English | MEDLINE | ID: mdl-37128906

ABSTRACT

As a kind of medicinal plant, Peucedanum praeruptorum Dunn has been over-harvested in the wild population, which leads to its artificial cultivation. The present study aims to analyze the effects of different plant growth-promoting rhizobacteria (PGPR) on the growth and physiological characteristics of P. Praeruptorum leaves. Compared with the CK, the content of malondialdehyde (MDA) was drastically reduced in the leaves of P. Praeruptorum in different treatment groups (P < 0.05), and with S6 showing the most significant reduction in MDA content (content was only about 1/3 that of the CK). The indicators of leaf area, length and width were found to be the highest in group S9, reaching a level that is 3.75, 3.08 and 1.48 times higher than those in group CK, respectively. Group S8 has the largest plant height, which is 1.22 times higher than that in group CK. S2 has the largest stem diameter, which is 1.69 times higher than that in group CK. Group S1 has the largest petiole length, which is 1.74 times higher than that in group CK. Group S6 has the largest chlorophyll content, which is 1.63 times higher than that in group CK. Group S2 has the highest content of soluble sugar and soluble protein, which are 2.02 times and 3.82 times higher than those in group CK. Group S9 exhibits the strongest CAT activity, which is 3.71 times higher than that in group CK. S5 exhibits the strongest SOD activity, which is 2.32 times higher than group CK. Group S1 exhibits the strongest POD activity, which is 5.94 times higher than that in group CK. In conclusion, the inoculation with PGPR is effective in improving the growth of P. Praeruptorum leaves and their physiological indicators, which provides guidance on the application of PGPR to achieve the high quality and yield of P. Praeruptorum.


Subject(s)
Plant Leaves , Plant Leaves/metabolism
5.
Phytochem Anal ; 34(3): 329-346, 2023 Apr.
Article in English | MEDLINE | ID: mdl-36740772

ABSTRACT

INTRODUCTION: Radix Angelicae sinensis (Danggui, DG) is known as one of the typical traditional Chinese medicines. DG material consists of a variety of volatile substances, polysaccharides, organic acids, ceramides, amino acids, vitamins, microelements, among others, and thus has been used for medicinal and edible purposes in a long history. The fragrance is of importance to assessing the DG material quality. OBJECTIVES: This study was to determine volatile flavour compositions of DG materials and to reveal the odour complexity. MATERIAL AND METHODS: Electronic nose (E-nose), integrated gas chromatography-mass spectrometry/olfactometry (GC-MS/O) and comprehensive two-dimensional gas chromatography-time-of-flight-mass spectrometry (GC × GC-TOF-MS), combined with solid-phase micro-extraction (SPME), were mainly used to address the flavour complexity of DG materials. RESULTS: Using the E-nose sensor responses, a total of 105 batches of DG samples cultivated in six provinces of China were categorised according to their odour differentiations, and a principal component analysis (PCA) model was established for evaluating the sample quality through a combination of Hotelling's T2 and Q-residual values in a statistical quantitative sense. By the GC-MS/O and GC × GC-TOF-MS analyses, 196 volatile flavour compounds were identified, 51 odour-active areas discerned and 39 odourants determined. It was terpenes and aromatics of the flavour compounds that mainly contributed to the odour attributes of DG herb. CONCLUSION: The SPME-GC × GC-TOF-MS method was the first time employed to analyse the volatile flavours of DG materials, and thus made a breakthrough in determining 196 flavour compounds, much more than those in any previous report. The work also made a significant step forward to link the flavour compositions and odour complexity of radix Angelicae sinensis by E-nose and GC-MS/O techniques. It not only provided a statistical PCA model that did not depend on any predetermined compositions or sensory properties for, but also a comprehensive insight into the quality evaluation of DG materials.


Subject(s)
Odorants , Volatile Organic Compounds , Gas Chromatography-Mass Spectrometry/methods , Odorants/analysis , Olfactometry/methods , Electronic Nose , Volatile Organic Compounds/analysis
6.
Plants (Basel) ; 12(3)2023 Jan 31.
Article in English | MEDLINE | ID: mdl-36771715

ABSTRACT

Paris polyphylla var. yunnanensis, a medicinal plant that originated in Yunnan (China), has been over-harvested in the wild population, resulting in its artificial cultivation. Given the negative environmental impacts of the excessive use of phosphorus (P) fertilization, the application of organophosphate-degrading bacteria (OPDB) is a sustainable approach for improving the P use efficiency in Paris polyphylla var. yunnanensis production. The present work aimed to analyze the effects of three organic phosphate-solubilizing bacteria of Bacillus on the yield and quality of P. polyphylla var. yunnanensis and the P concentrations in the soil. All the inoculation treatments distinctly increased the rhizome biomass, steroidal, and total saponin concentrations of the rhizomes and the Olsen-P and organic P in the soil. The highest growth rate of rhizomes biomass, steroidal saponins, available phosphorus, and total phosphorus content was seen in the S7 group, which was inoculated with all three OPDB strains, showing increases of 134.58%, 132.56%, 51.64%, and 17.19%, respectively. The highest total saponin content was found in the group inoculated with B. mycoides and B. wiedmannii, which increased by 33.68%. Moreover, the highest organic P content was seen in the group inoculated with B. wiedmannii and B. proteolyticus, which increased by 96.20%. In addition, the rhizome biomass was significantly positively correlated with the saponin concentration, together with the positive correlation between the Olsen-P and organic P and total P. It is concluded that inoculation with organophosphate-degrading bacteria improved the biomass and medicinal ingredients of the rhizome in P. polyphylla var. yunnanensis, coupled with increased soil P fertility, with a mixture of the three bacteria performing best.

7.
J Diabetes ; 15(1): 27-35, 2023 Jan.
Article in English | MEDLINE | ID: mdl-36526273

ABSTRACT

BACKGROUND: All-cause mortality risk prediction models for patients with type 2 diabetes mellitus (T2DM) in mainland China have not been established. This study aimed to fill this gap. METHODS: Based on the Shanghai Link Healthcare Database, patients diagnosed with T2DM and aged 40-99 years were identified between January 1, 2013 and December 31, 2016 and followed until December 31, 2021. All the patients were randomly allocated into training and validation sets at a 2:1 ratio. Cox proportional hazards models were used to develop the all-cause mortality risk prediction model. The model performance was evaluated by discrimination (Harrell C-index) and calibration (calibration plots). RESULTS: A total of 399 784 patients with T2DM were eventually enrolled, with 68 318 deaths over a median follow-up of 6.93 years. The final prediction model included age, sex, heart failure, cerebrovascular disease, moderate or severe kidney disease, moderate or severe liver disease, cancer, insulin use, glycosylated hemoglobin, and high-density lipoprotein cholesterol. The model showed good discrimination and calibration in the validation sets: the mean C-index value was 0.8113 (range 0.8110-0.8115) and the predicted risks closely matched the observed risks in the calibration plots. CONCLUSIONS: This study constructed the first 5-year all-cause mortality risk prediction model for patients with T2DM in south China, with good predictive performance.


Subject(s)
Diabetes Mellitus, Type 2 , Heart Failure , Humans , Diabetes Mellitus, Type 2/diagnosis , Risk Factors , China , Proportional Hazards Models
8.
G3 (Bethesda) ; 12(2)2022 02 04.
Article in English | MEDLINE | ID: mdl-35100332

ABSTRACT

Ananas comosus var. bracteatus f. tricolor (GL1) is a red pineapple accession whose mostly green leaves with chimeric white leaf margins turn red in spring and autumn and during flowering. It is an important ornamental plant and ideal plant research model for anthocyanin metabolism, chimeric leaf development, and photosynthesis. Here, we generated a highly contiguous chromosome-scale genome assembly for GL1 and compared it with other 3 published pineapple assemblies (var. comosus accessions MD2 and F153, and var. bracteatus accession CB5). The GL1 assembly has a total size of ∼461 Mb, with a contig N50 of ∼2.97 Mb and Benchmarking Universal Single-Copy Ortholog score of 97.3%. More than 99% of the contigs are anchored to 25 pseudochromosomes. Compared with the other 3 published pineapple assemblies, the GL1 assembly was confirmed to be more continuous. Our evolutionary analysis showed that the Bromeliaceae and Poaceae diverged from their nearest common ancestor ∼82.36 million years ago (MYA). Population structure analysis showed that while GL1 has not undergone admixture, bracteatus accession CB5 has resulted from admixture of 3 species of Ananas. Through classification of orthogroups, analysis of genes under positive selection, and analysis of presence/absence variants, we identified a series of genes related to anthocyanin metabolism and development of chimeric leaves. The structure and evolution of these genes were compared among the published pineapple assemblies with reveal candidate genes for these traits. The GL1 genome assembly and its comparisons with other 3 pineapple genome assemblies provide a valuable resource for the genetic improvement of pineapple and serve as a model for understanding the genomic basis of important traits in different pineapple varieties and other pan-cereal crops.


Subject(s)
Ananas , Genome, Plant , Pigmentation , Plant Leaves , Ananas/genetics , Chimera/genetics , Genomics/methods , Photosynthesis
9.
Front Genet ; 12: 716137, 2021.
Article in English | MEDLINE | ID: mdl-34745205

ABSTRACT

Reverse transcription quantitative real-time PCR (RT-qPCR) is a common way to study gene regulation at the transcriptional level due to its sensibility and specificity, but it needs appropriate reference genes to normalize data. Ananas comosus var. bracteatus, with white-green chimeric leaves, is an important pantropical ornamental plant. Up to date, no reference genes have been evaluated in Ananas comosus var. bracteatus. In this work, we used five common statistics tools (geNorm, NormFinder, BestKeeper, ΔCt method, RefFinder) to evaluate 10 candidate reference genes. The results showed that Unigene.16454 and Unigene.16459 were the optimal reference genes for different tissues, Unigene.16454 and zinc finger ran-binding domain-containing protein 2 (ZRANB2) for chimeric leaf at different developmental stages, isocitrate dehydrogenase [NADP] (IDH) and triacylglycerol lipase SDP1-like (SDP) for seedlings under different hormone treatments. The comprehensive results showed IDH, pentatricopeptide repeat-containing protein (PPRC), Unigene.16454, and caffeoyl-CoA O methyltransferase 5-like (CCOAOMT) are the top-ranked stable genes across all the samples. The stability of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was the least during all experiments. Furthermore, the reliability of recommended reference gene was validated by the detection of porphobilinogen deaminase (HEMC) expression levels in chimeric leaves. Overall, this study provides appropriate reference genes under three specific experimental conditions and will be useful for future research on spatial and temporal regulation of gene expression and multiple hormone regulation pathways in Ananas comosus var. bracteatus.

10.
BMC Genomics ; 22(1): 331, 2021 May 07.
Article in English | MEDLINE | ID: mdl-33962593

ABSTRACT

BACKGROUND: Ananas comosus var. bracteatus is a colorful plant used as a cut flower or landscape ornamental. The unique foliage color of this plant includes both green and red leaves and, as a trait of interest, deserves investigation. In order to explore the pigments behind the red section of the chimeric leaves, the green and red parts of chimeric leaves of Ananas comosus var. bracteatus were sampled and analyzed at phenotypic, cellular and molecular levels in this study. RESULTS: The CIELAB results indicated that the a* values and L* values samples had significant differences between two parts. Freehand sections showed that anthocyanin presented limited accumulation in the green leaf tissues but obviously accumulation in the epidermal cells of red tissues. Transcriptomic and metabolomic analyses were performed by RNA-seq and LC-ESI-MS/MS. Among the 508 identified metabolites, 10 kinds of anthocyanins were detected, with 6 significantly different between the two samples. The cyanidin-3,5-O-diglucoside content that accounts for nearly 95.6% in red samples was significantly higher than green samples. RNA-Seq analyses showed that 11 out of 40 anthocyanin-related genes were differentially expressed between the green and red samples. Transcriptome and metabolome correlations were determined by nine quadrant analyses, and 9 anthocyanin-related genes, including MYB5 and MYB82, were correlated with 7 anthocyanin-related metabolites in the third quadrant in which genes and metabolites showing consistent change. Particularly, the PCCs between these two MYB genes and cyanidin-3,5-O-diglucoside were above 0.95. CONCLUSION: Phenotypic colors are closely related to the tissue structures of different leaf parts of Ananas comosus var. bracteatus, and two MYB transcription factors might contribute to differences of anthocyanin accumulation in two parts of Ananas comosus var. bracteatus chimeric leaves. This study lay a foundation for further researches on functions of MYBs in Ananas comosus var. bracteatus and provides new insights to anthocyanin accumulation in different parts of chimeric leaves.


Subject(s)
Ananas , Ananas/genetics , Anthocyanins , Gene Expression Profiling , Gene Expression Regulation, Plant , Metabolome , Plant Leaves/genetics , Plant Leaves/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Tandem Mass Spectrometry , Transcriptome
11.
PeerJ ; 9: e11118, 2021.
Article in English | MEDLINE | ID: mdl-33850657

ABSTRACT

BACKGROUND: The chimeric leaves of Ananas comosus var. bracteatus are composed of normal green parts (Grs) and albino white parts (Whs). Although the underlying mechanism of albinism in A. comosus var. bracteatus leaves is not fully understood, it is likely associated with the chlorophyll (Chl) biosynthesis. In this biosynthetic process, porphobilinogen deaminase (PBGD) plays a crucial role by catalyzing the conversion of porphobilinogen (PBG) to uroporphyrinogen III (Urogen III). Therefore, its encoding gene AbhemC was investigated here in association with Chl biosynthesis and albinism in chimeric A. comosus var. bracteatus leaves. METHODS: The Chl content, main Chl biosynthesis precursor content, and main enzyme activity were determined and compared between the Whs and Grs of A. comosus var. bracteatus leaves. In addition, AbhemC was cloned and its transcriptional expression and prokaryotic protein expression were analyzed. Furthermore, RNAi-mediated silencing of AbhemC was produced and assessed in tobacco plants. RESULTS: The concentration of Chl a and Chl b in the Grs was significantly higher than that in the Whs, respectively. Additionally, the content of the Chl biosynthesis precursor Urogen III decreased significantly in the Whs compared with the Grs. Thus, the transition of PBG to Urogen III may be the first rate-limiting step leading to albinism in the chimeric leaves of A. comosus var. bracteatus. The gene AbhemC comprised 1,135 bp and was encoded into a protein with 371 amino acids; phylogenetically, AbhemC was most closely related to hemC of pineapple. Prokaryotic expression and in vitro enzyme activity analysis showed that the cloned mRNA sequence of AbhemC was successfully integrated and had PBGD activity. Compared with control plants, transgenic tobacco leaves with pFGC5941-AbhemC-RNAi vector were substantially less green with significantly reduced hemC expression and Chl content, as well as reduced PBGD enzyme activity and significantly decreased content of Chl biosynthesis precursors from Urogen III onwards. Our results suggest that the absence of hemC expression reduces the enzyme activity of PBGD, which blocks the transition of PBG to Urogen III, and in turn suppresses Chl synthesis leading to the pale-green leaf color. Therefore, we suggest that AbhemC plays an important role in Chl synthesis and may be an important factor in the albinism of A. comosus var. bracteatus leaves.

12.
BMC Genomics ; 21(1): 383, 2020 Jun 03.
Article in English | MEDLINE | ID: mdl-32493214

ABSTRACT

BACKGROUND: Lysine succinylation, an important protein posttranslational modification (PTM), is widespread and conservative. The regulatory functions of succinylation in leaf color has been reported. The chimeric leaves of Ananas comosus var. bracteatus are composed of normal green parts and albino white parts. However, the extent and function of lysine succinylation in chimeric leaves of Ananas comosus var. bracteatus has yet to be investigated. RESULTS: Compared to the green (Gr) parts, the global succinylation level was increased in the white (Wh) parts of chimeric leaves according to the Western blot and immunohistochemistry analysis. Furthermore, we quantitated the change in the succinylation profiles between the Wh and Gr parts of chimeric leaves using label-free LFQ intensity. In total, 855 succinylated sites in 335 proteins were identified, and 593 succinylated sites in 237 proteins were quantified. Compared to the Gr parts, 232 (61.1%) sites in 128 proteins were quantified as upregulated targets, and 148 (38.9%) sites in 70 proteins were quantified as downregulated targets in the Wh parts of chimeric leaves using a 1.5-fold threshold (P < 0.05). These proteins with altered succinylation level were mainly involved in crassulacean acid metabolism (CAM) photosynthesis, photorespiration, glycolysis, the citric acid cycle (CAC) and pyruvate metabolism. CONCLUSIONS: Our results suggested that the changed succinylation level in proteins might function in the main energy metabolism pathways-photosynthesis and respiration. Succinylation might provide a significant effect in the growth of chimeric leaves and the relationship between the Wh and Gr parts of chimeric leaves. This study not only provided a basis for further characterization on the function of succinylated proteins in chimeric leaves of Ananas comosus var. bracteatus but also provided a new insight into molecular breeding for leaf color chimera.


Subject(s)
Ananas/metabolism , Lysine/metabolism , Plant Proteins/metabolism , Succinic Acid/metabolism , Chimera/metabolism , Chromatography, Liquid , Color , Gene Expression Regulation, Plant , Glycolysis , Lysine/chemistry , Photosynthesis , Plant Leaves , Protein Processing, Post-Translational , Proteomics , Tandem Mass Spectrometry
13.
PLoS One ; 14(11): e0225602, 2019.
Article in English | MEDLINE | ID: mdl-31756232

ABSTRACT

Long noncoding RNAs (lncRNAs) have been reported to play key regulatory roles in plant growth, development, and biotic and abiotic stress physiology. Revealing the mechanism of lncRNA regulation in the albino portions of leaves is important for understanding the development of chimeric leaves in Ananas comosus var. bracteatus. In this study, a total of 3,543 candidate lncRNAs were identified, among which 1,451 were differentially expressed between completely green (CGr) and completely white (CWh) leaves. LncRNAs tend to have shorter transcripts, lower expression levels, and greater expression specificity than protein-coding genes. Predicted lncRNA targets were functionally annotated by the Gene Ontology (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. A lncRNA-mRNA interaction network was constructed, and 36 target mRNAs related to chlorophyll metabolism were predicted to interact with 86 lncRNAs. Among these, 25 significantly differentially expressed lncRNAs putatively interacted with 16 target mRNAs. Based on an expression pattern analysis of the lncRNAs and their target mRNAs, the lncRNAs targeting magnesium chelatase subunit H (ChlH), protochlorophyllide oxidoreductase (POR), and heme o synthase (COX10) were suggested as key regulators of chlorophyll metabolism. This study provides the first lncRNA database for A. comosus var. bracteatus and contributes greatly to understanding the mechanism of epigenetic regulation of leaf albinism.


Subject(s)
Ananas/genetics , RNA, Long Noncoding/metabolism , Chlorophyll/metabolism , Gene Expression Regulation, Plant , Gene Library , Gene Ontology , Lyases/genetics , Lyases/metabolism , Oxidoreductases Acting on CH-CH Group Donors/genetics , Oxidoreductases Acting on CH-CH Group Donors/metabolism , Photosynthesis/genetics , Plant Leaves/genetics , Plant Proteins/genetics , Plant Proteins/metabolism , RNA, Messenger/metabolism
14.
PeerJ ; 7: e7062, 2019.
Article in English | MEDLINE | ID: mdl-31275743

ABSTRACT

BACKGROUND: Ananas comosus var. bracteatus is an herbaceous perennial monocot cultivated as an ornamental plant for its chimeric leaves. Because of its genomic complexity, and because no genomic information is available in the public GenBank database, the complete structure of the mRNA transcript is unclear and there are limited molecular mechanism studies for Ananas comosus var. bracteatus. METHODS: Three size fractionated full-length cDNA libraries (1-2 kb, 2-3 kb, and 3-6 kb) were constructed and subsequently sequenced in five single-molecule real-time (SMRT) cells (2 cells, 2 cells, and 1 cell, respectively). RESULTS: In total, 19,838 transcripts were identified for alternative splicing (AS) analysis. Among them, 19,185 (96.7%) transcripts were functionally annotated. A total of 9,921 genes were identified by mapping the non-redundant isoforms to the reference genome. A total of 10,649 AS events were identified, the majority of which were intron retention events. The alternatively spliced genes had functions in the basic metabolism processes of the plant such as carbon metabolism, amino acid biosynthesis, and glycolysis. Fourteen genes related to chlorophyll biosynthesis were identified as having AS events. The distribution of the splicing sites and the percentage of conventional and non-canonical AS sites of the genes categorized in pathways related to the albino leaf phenotype (ko00860, ko00195, ko00196, and ko00710) varied greatly. The present results showed that there were 8,316 genes carrying at least one poly (A) site, which generated 21,873 poly (A) sites. These findings indicated that the quality of the gene structure and functional information of the obtained genome was greatly improved, which may facilitate further genetic study of Ananas comosus var. bracteatus.

15.
PeerJ ; 7: e7261, 2019.
Article in English | MEDLINE | ID: mdl-31333908

ABSTRACT

BACKGROUND: Ananas comosus var. bracteatus has high ornamental value due to its chimeric leaves. However, the chimeric trait is very unstable in red pineapple plants, and transcriptional variation between the two types of cells (white/green cells) and the molecular mechanism responsible for their albino phenotype remain poorly understood. METHODS: Comparative transcriptomic and proteomic analyses of the white parts (Whs) and green parts (Grs) of chimeric leaves were performed. RESULTS: In total, 1,685 differentially expressed genes (DEGs) (712 upregulated and 973 downregulated) and 1,813 differentially abundant proteins (DAPs) (1,018 with low abundance and 795 with high abundance) were identified. Based on Gene Ontology (Go) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, the DEGs were mostly involved in carbon fixation in photosynthetic organisms, porphyrin and chlorophyll metabolism and oxidative phosphorylation, while proteomic analysis revealed that DAPs were mostly related to ribosomes, photosynthesis, photosynthesis antennas, and porphyrin and chlorophyll metabolism. Combined analysis showed increased mRNA levels but low abundance of nine proteins level in Whs /Grs related to photosynthetic pigment and photosynthesis. Transcriptional changes, posttranscriptional regulation and translational alterations of key enzymes involved in chlorophyll biosynthesis and photosynthesis may play important roles in the albino parts of chimeric leaves.

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