Chromosome scale genome assembly and annotation of coconut cultivar Chowghat Green Dwarf DOI Creative Commons

M. K. Rajesh,

Roli Budhwar, Rohit Shukla

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Nov. 20, 2024

The high-quality genome of coconut (Cocos nucifera L.) is a crucial resource for enhancing agronomic traits and studying evolution within the Arecaceae family. We sequenced Chowghat Green Dwarf cultivar, which resistant to root (wilt) disease, utilizing Illumina, PacBio, ONT, Hi-C technologies produce chromosome-level ~ 2.68 Gb with scaffold N50 174 Mb; approximately 97% could be anchored 16 pseudo-molecules (2.62 Gb). In total, 34,483 protein-coding genes were annotated; BUSCO completeness score was 96.80%, while k-mer 87%. assembled includes 2.19 (81.64%) repetitive sequences, long terminal repeats (LTRs) constituting most abundant class at 53.76%. Additionally, our analysis confirms two whole-genome duplication (WGD) events in C. lineage. A genome-wide LTR insertion time revealed ancient divergence proliferation copia gypsy elements. addition, 1368 RGAs discovered CGD genome. also developed web server 'Kalpa Genome Resource' ( http://210.89.54.198:3000/ ), manage store comprehensive array genomic data, including genetic markers, structural functional annotations like metabolic pathways, transcriptomic profiles. has an embedded browser analyze visualize genome, its genomics elements, transcriptome data. in-built BLAST allows sequence homology searches against annotated & proteome sequences. dataset database will support comparative can expedite genome-driven breeding enhancement efforts tapping gains coconut.

Language: Английский

Integrated transcriptome and metabolome analyses reveal the differentially expressed metabolites and genes involved in lipid in olive fruits DOI Creative Commons

Jipeng Qu,

Xu Zhou,

Zhengsong Peng

et al.

PeerJ, Journal Year: 2025, Volume and Issue: 13, P. e18941 - e18941

Published: Feb. 17, 2025

Olive (Olea europaea L.) oil is well-known commercial product worldwide for its nutritional and therapeutic properties. The molecular mechanisms underlying lipid variations in different olive cultivars remain unclear. To investigate the mechanism involved synthesis metabolism, untargeted metabolome RNA-Seq analyses were performed based on two varieties of fruits, i.e., Kalinjot (JZ) with low content Coratina (KLD) high content. Totally, 38 compounds 375 differentially accumulated metabolites (DAMs) identified JZ KLD 24 showing higher contents than those JZ. Integrated transcriptome 48 expressed genes (DEGs) associated six DAMs from fruits. decanoic acid, sphinganine, leukotriene D4 fruits 2.33, 1.91, 1.53 times greater that respectively. In particular, BCCP, one ACC, seven KAR, EAR, FATA SPT observed involving to quality lipids These DEGs pathways fatty acid biosynthesis, arachidonic limonene degradation. This study provides a strong theoretical experimental foundation further revealing regulating metabolism cultivars.

Language: Английский

Citations

0
Transcriptome Analysis Reveals Key Genes Involved in Fatty Acid and Triacylglycerol Accumulation in Developing Sunflower Seeds DOI Open Access

Wanqiu Meng,

Linglu Zeng,

Xiuli Yang

et al.

Genes, Journal Year: 2025, Volume and Issue: 16(4), P. 393 - 393

Published: March 29, 2025

Background/Objectives: Sunflower (Helianthus annuus L.) is one of the four major global oilseed crops. Understanding molecular mechanisms regulating fatty acid synthesis and triacylglycerol (TAG) accumulation crucial for improving oil yield quality. In this study, sunflower cultivar ‘T302’, which was wild-cultivated in northwestern region China, analyzed content by targeted lipidomic analysis. RNA sequencing (RNA-seq) performed on 15 cDNA libraries from embryos at five developmental stages (10, 17, 24, 31, 38 days after flowering) to investigate gene expression patterns during accumulation. Differentially expressed genes (DEGs) related developing seeds were identified. WGCNA used gain deeper insights into underlying lipid metabolism. Results: The composition ‘T302’ consisted 86.61% unsaturated acids (UFA), mainly linoleic (48.47%) oleic (37.25%). Saturated (SFAs) accounted 13.39%, with palmitic (7.46%) stearic (5.04%) being most abundant. A total 81,676 unigenes generated RNA-seq data, 91 DEGs associated metabolism identified, including key enzymes such as FAD2-1, SAD, FATA, LACS, PDAT2, DGAT2. addition, we identified several novel candidate transcription factor genes, WRI1, LEC1, FUS3, ABI3, found regulate TAG seed maturation are worthy further investigation. This study provides valuable biosynthesis sunflower. factors provide potential targets breeding strategies increase modify compositions other

Language: Английский

Citations

0
Chemical Composition and Biological Activities of Torreya grandis Kernels: Characteristics of Polymethylene-Interrupted Fatty Acids and Polyphenolic Compounds and Their Potential Health Effects DOI Open Access

R. Liu,

Baogang Zhou,

Kundian Che

et al.

Forests, Journal Year: 2025, Volume and Issue: 16(5), P. 737 - 737

Published: April 25, 2025

Torreya grandis kernels, with their long cultivation history and significant economic value, have gained attention for characteristic chemical components. This review systematically evaluates recent research on the constituents biological activities of T. kernels. The key highlights include following. (1) Chemical composition: details unique fatty acid profile, particularly high content unsaturated acids rare polymethylene-interrupted polyunsaturated such as sciadonic acid. It also examines polyphenolic compounds (flavonoids, phenolic acids, biflavonoids like kayaflavone) volatile components dominated by D-limonene. Other constituents, proteins, amino vitamins, minerals, are covered. Advanced analytical techniques (Gas Chromatography–Mass Spectrometry, GC-MS; Liquid Chromatography–Tandem Mass LC-MS/MS) component identification discussed. (2) Biological activities: summarizes major kernel extracts These antioxidant effects (via polyphenol-mediated NF-E2-related factor 2 (Nrf2) pathway), anti-inflammatory properties PMI-PUFAs, inhibition 5-LOX, polyphenol regulation NF-κB), cardiovascular protection (potentially involving AMPKα/SREBP-1c pathway). Research gut microbiota enzyme is outlined. (3) gaps prospects: critically analyzes limitations in current research, including mechanism elucidation, interactions, bioavailability, safety assessment (especially lack human studies). Future directions should focus multiomics integration, structure–activity relationship analysis, standardization, rigorous clinical evaluation. provides a theoretical reference understanding scientific value kernels promoting sustainable development.

Language: Английский

Citations

0
Integration of CRISPR/Cas9 with multi-omics technologies to engineer secondary metabolite productions in medicinal plant: Challenges and Prospects DOI

Anupriya Borah,

Sumit Kumar Singh,

Rituja Chattopadhyay

et al.

Functional & Integrative Genomics, Journal Year: 2024, Volume and Issue: 24(6)

Published: Nov. 4, 2024

Language: Английский

Citations

3
Transcriptome and metabolome analysis reveals the mechanism of key nutrient formation in Hainan oil-camellia (Camellia hainanica) growth cycle DOI Creative Commons
Yuanhao Ding, Qingxia Wu, Zhiyang Li

et al.

Industrial Crops and Products, Journal Year: 2025, Volume and Issue: 230, P. 121122 - 121122

Published: May 5, 2025

Language: Английский

Citations

0
Chromosome scale genome assembly and annotation of coconut cultivar Chowghat Green Dwarf DOI Creative Commons

M. K. Rajesh,

Roli Budhwar, Rohit Shukla

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Nov. 20, 2024

The high-quality genome of coconut (Cocos nucifera L.) is a crucial resource for enhancing agronomic traits and studying evolution within the Arecaceae family. We sequenced Chowghat Green Dwarf cultivar, which resistant to root (wilt) disease, utilizing Illumina, PacBio, ONT, Hi-C technologies produce chromosome-level ~ 2.68 Gb with scaffold N50 174 Mb; approximately 97% could be anchored 16 pseudo-molecules (2.62 Gb). In total, 34,483 protein-coding genes were annotated; BUSCO completeness score was 96.80%, while k-mer 87%. assembled includes 2.19 (81.64%) repetitive sequences, long terminal repeats (LTRs) constituting most abundant class at 53.76%. Additionally, our analysis confirms two whole-genome duplication (WGD) events in C. lineage. A genome-wide LTR insertion time revealed ancient divergence proliferation copia gypsy elements. addition, 1368 RGAs discovered CGD genome. also developed web server 'Kalpa Genome Resource' ( http://210.89.54.198:3000/ ), manage store comprehensive array genomic data, including genetic markers, structural functional annotations like metabolic pathways, transcriptomic profiles. has an embedded browser analyze visualize genome, its genomics elements, transcriptome data. in-built BLAST allows sequence homology searches against annotated & proteome sequences. dataset database will support comparative can expedite genome-driven breeding enhancement efforts tapping gains coconut.

Language: Английский

Citations

0