Transcriptomic and metabolomic profiling of flavonoid biosynthesis provides novel insights into petals coloration in Asian cotton (Gossypium arboreum L.) DOI Creative Commons

Aishuang Xing,

Xiaoyang Wang, Mian Faisal Nazir

et al.

BMC Plant Biology, Journal Year: 2022, Volume and Issue: 22(1)

Published: Aug. 30, 2022

Abstract Background Asian cotton ( Gossypium arboreum L.), as a precious germplasm resource of with insect resistance and stress tolerance, possesses broad spectrum phenotypic variation related to pigmentation. Flower color affects pollination the ornamental value plants. Studying flower varieties improves rate hybridization thus enriches diversity resources. Meanwhile, it also impacts development horticultural industry. Unfortunately, there is clear lack studies concerning intricate mechanisms flower-color differentiation. Hereby, we report an integrative approach utilizing transcriptome metabolome in three cultivars. Results A total 215 differentially accumulated metabolites (DAMs) were identified, including 83 flavonoids (DAFs). Colorless kaempferol was more abundant white flowers, while gossypetin-fer showed specificity flowers. Quercetin gossypetin main contributors yellow petal formation. Pelargonidin 3-O-beta-D-glucoside cyanidin-3-O-(6''-Malonylglucoside) high accumulation levels purple petals. pigments promoted coloration. Moreover, 8178 expressed genes (DEGs) identified by RNA sequencing. The correlation results between anthocyanins DEGs explored, indicating that 10 key structural 29 transcription factors anthocyanin biosynthesis could be candidates for accumulation. Ultimately, constructed co-expression networks DAFs demonstrated interactions specific transcripts different Conclusion This study provides new insights into elucidating regulatory lays potential foundation generate highly attractive flowers pollinators.

Language: Английский

Genome reannotation of the sweetpotato (<i>Ipomoea batatas</i> (L.) Lam.) using extensive Nanopore and Illumina-based RNA-seq datasets DOI Creative Commons

Bei Liang,

Yang Zhou, Tianjia Liu

et al.

Tropical Plants, Journal Year: 2024, Volume and Issue: 3(1), P. 0 - 0

Published: Jan. 1, 2024

Sweetpotato (Ipomoea batatas (L.) Lam.) is a globally cultivated root crop of paramount significance. The hexaploid genome, known as 'Taizhong 6', has been sequenced and serves crucial reference genome for sweetpotato related species within the Convolvulaceae family. However, current annotation relies primarily on ab initio predictions and, to lesser extent, transcriptome datasets, which only predict coding sequences. Therefore, an improved highly desirable. Here, we present comprehensive reannotation leveraging 12 Nanopore full-length RNA libraries 190 Illumina RNA-seq libraries. annotation, named v1.0.a2, includes 42,751 gene models, with 97.4% complete BUSCOs. Within this set have modified or added 31,771 models identified 8,736 genes alternatively spliced isoforms. We also introduced new ID nomenclature (IbXXGXXXXX) improvement over previous (gene.gXXXXX). Additionally, annotated provided expression levels miRNAs their targets at different storage roots stages. Overall, our study contributes updated will significantly facilitate functional studies in promote genomic analyses across

Language: Английский

Citations

5
RNA-sequencing analysis revealed genes associated drought stress responses of different durations in hexaploid sweet potato DOI Creative Commons
Mohamed Hamed Arisha,

Muhammad Qadir Ahmad,

Wei Tang

et al.

Scientific Reports, Journal Year: 2020, Volume and Issue: 10(1)

Published: July 28, 2020

Purple-fleshed sweet potato (PFSP) is an important food crop, as it a rich source of nutrients and anthocyanin pigments. Drought has become major threat to sustainable sweetpotato production, resulting in huge yield losses. Therefore, the present study was conducted identify drought stress-responsive genes using next-generation (NGS) third-generation sequencing (TGS) techniques. Five cDNA libraries were constructed from seedling leaf segments treated with 30% solution polyethylene glycol (PEG-6000) for 0, 1, 6, 12, 48 h second-generation sequencing. Leaf samples taken upper third seedlings after stress used construction sequencing; however, untreated plants collected controls. A total 184,259,679 clean reads obtained second then assembled into 17,508 unigenes average length 1,783 base pairs. Out unigenes, 642 (3.6%) failed hit any homologs databases, which might be considered novel genes. 2, 920, 1578, 2,418 up-regulated 3,834, 2,131, 3,337 down-regulated 1 h, 6 12 library identified, respectively versus control. In addition, stress, 540 486 414 significantly differentially expressed detected. It found that several gene families including Basic Helix-loop-helix (bHLH), basic leucine zipper (bZIP), Cystein2/Histidine2 (C2H2), C3H, Ethylene-responsive transcription factor (ERF), Homo domain-leucine (HD-ZIP), MYB, NAC (NAM, ATAF1/2, CUC2), Thiol specific antioxidant WRKY showed responses stress. total, 17,472 simple sequence repeats 510,617 single nucleotide polymorphisms identified based on transcriptome PFSP. About 96.55% sequences are not available online genomics resources. will enrich annotated enhance understanding mechanisms tolerance through genetic manipulation. Moreover, represents resource genomic studies potato.

Language: Английский

Citations

37
Integrative transcriptome and proteome analyses provide new insights into different stages of Akebia trifoliata fruit cracking during ripening DOI Creative Commons

Juan Niu,

Yaliang Shi,

Kunyong Huang

et al.

Biotechnology for Biofuels, Journal Year: 2020, Volume and Issue: 13(1)

Published: Aug. 20, 2020

Akebia trifoliata (Thunb.) Koidz may have applications as a new potential source of biofuels owing to its high seed count, oil content, and in-field yields. However, the pericarp A. cracks longitudinally during fruit ripening, which increases incidence pests diseases can lead decay deterioration, resulting in significant losses yield. Few studies evaluated mechanisms underlying cracking.In this study, by observing cell wall structure pericarp, we found that became thinner looser showed substantial breakdown cracking compared with non-cracking fruit. Moreover, integrative analyses transcriptome proteome profiles at different stages ripening demonstrated changes expression various genes proteins after cracking. Furthermore, mRNA levels 20 differentially expressed were analyzed, parallel reaction monitoring analysis involved metabolism was conducted. Among molecular targets, pectate lyases pectinesterase, are pentose glucuronate interconversion, β-galactosidase 2, is galactose metabolism, significantly upregulated fruits than fruits. This suggested they might play crucial roles cracking.Our findings provided insights into influencing trait established basis for further research on breeding cracking-resistant varieties increase yields biorefineries.

Language: Английский

Citations

37
Portal of Juglandaceae: A comprehensive platform for Juglandaceae study DOI Creative Commons
Wenlei Guo, Junhao Chen, Jian Li

et al.

Horticulture Research, Journal Year: 2020, Volume and Issue: 7(1)

Published: March 15, 2020

Juglandaceae species are plants of great economic value and have been cultivated, domesticated, utilized by human society for a long time. Their edible, nutrient-rich nuts tough, durable wood attracted the attention botanists breeders. With advent genomics era, genome sequencing family has greatly accelerated, large amount data generated. In this paper, we introduce Portal (PJU), tool to bring all these together. The PJU contains genomes, gene-coding sequences, protein various types annotation information, expression data, miRNA which configured with BLAST, JBrowse, our self-developed synteny analysis tool. user-friendly straightforward interface that performs variety query tasks few simple operations. future, hope will serve as hub study family.

Language: Английский

Citations

33
Disruption of the bHLH transcription factor Abnormal Tapetum 1 causes male sterility in watermelon DOI Creative Commons
Ruimin Zhang, Jingjing Chang,

Jiayue Li

et al.

Horticulture Research, Journal Year: 2021, Volume and Issue: 8

Published: Jan. 1, 2021

Although male sterility has been identified as a useful trait for hybrid vigor utilization and seed production, its underlying molecular mechanisms in Cucurbitaceae species are still largely unclear. Here, spontaneous male-sterile watermelon mutant, Se18, was reported to have abnormal tapetum development, which resulted completely aborted pollen grains. Map-based cloning demonstrated that the causal gene Citrullus lanatus Abnormal Tapetum 1 (ClATM1) encodes basic helix-loop-helix (bHLH) transcription factor with 10-bp deletion produces truncated protein without bHLH interaction functional (BIF) domain Se18 plants. qRT-PCR RNA situ hybridization showed ClATM1 is specifically expressed layer microsporocytes during stages 6-8a of anther development. The genetic function regulating development verified by CRISPR/Cas9-mediated mutagenesis. Moreover, significantly downregulated displaying clear dose effect at transcriptional level. Subsequent dual-luciferase reporter, β-glucuronidase (GUS) activity, yeast one-hybrid assays indicated could activate own expression through promoter binding. Collectively, first cloned from watermelon, self-regulatory activity provides new insights into mechanism

Language: Английский

Citations

30
Comparative and phylogenetic analyses of the chloroplast genomes of mangrove plants DOI Creative Commons

Jigui Yuan,

Wei Gu,

Haijie Yang

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 31, 2025

Mangrove ecosystems play a crucial role in coastal environment by stabilizing shorelines, reducing erosion, and providing habitat for diverse wildlife. However, there are fewer studies on the genetic management of mangrove plants. In this study, chloroplast genome Hibiscus tiliaceus L. was obtained through whole resequencing. The complete species 161,764 bp length comprised 84 protein-coding genes, eight rRNA (ribosomal RNA) 37 tRNA (transfer genes. We conducted comparative analysis genomes 26 found conservation structure among these plants, including number were noticeable differences SSRs (simple sequence repeats), repeat sequences, borders IR (inverted repeat) regions, indicating differentiation Besides, we special distribution certain genes species. Moreover, phylogenetic based data clearly revealed that neither true plants nor semi-mangrove monophyletic. These results will be useful to help understand relationships which could assist management, conservation, restoration ecosystems.

Language: Английский

Citations

0
Insights into the Role of Gasotransmitters Mediating Salt Stress Responses in Plants DOI
Suhas Balasaheb Karle, Akankhya Guru,

Padmanabh Dwivedi

et al.

Journal of Plant Growth Regulation, Journal Year: 2021, Volume and Issue: 40(6), P. 2259 - 2275

Published: Jan. 13, 2021

Language: Английский

Citations

26
Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution DOI Creative Commons
Jiawei Zhou, Shuo Zhang, Jie Wang

et al.

Scientific Reports, Journal Year: 2021, Volume and Issue: 11(1)

Published: May 4, 2021

The chloroplast is one of two organelles containing a separate genome that codes for essential and distinct cellular functions such as photosynthesis. Given the importance chloroplasts in plant metabolism, genomic architecture gene content have been strongly conserved through long periods time are useful molecular tools evolutionary inferences. At present, complete genomes from over 4000 species deposited into publicly accessible databases. Despite large number genomes, comprehensive analyses regarding not conducted many lineages with sampling. In this study, we employed genus Populus to assess how more comprehensively sampled can be used understanding evolution broadly studied lineage angiosperms. We comparative across order elucidate variation key features size, number, content, repeat type SSR (Simple Sequence Repeat) abundance, boundary positioning between four main units genome. found some annotations were variable owing part errors assembly or data checking provided corrected annotations. also phylogenetic including dating divergence times throughout genus. Lastly, utilized re-sequencing describe variations pan-chloroplast at population level P. euphratica. paper provide blueprint types available well methods building upon existing datasets improve inference.

Language: Английский

Citations

25
Drought tolerance improvement in Solanum lycopersicum: an insight into “OMICS” approaches and genome editing DOI
Sima Taheri, Saikat Gantait, Parisa Azizi

et al.

3 Biotech, Journal Year: 2022, Volume and Issue: 12(3)

Published: Feb. 8, 2022

Language: Английский

Citations

17
Plant immune inducer ZNC promotes rutin accumulation and enhances resistance to Botrytis cinerea in tomato DOI Creative Commons
Haipeng Zhao,

Xiangyu Ding,

Xiaomeng Chu

et al.

Stress Biology, Journal Year: 2023, Volume and Issue: 3(1)

Published: Aug. 22, 2023

Gray mold is a destructive disease caused by Botrytis cinerea, pervasive plant pathogen, which poses threat to both tomato growth and postharvest storage. The utilization of induced resistance presents potential strategy for combating pathogenic attacks. ZNC (zhinengcong), an extract derived from the endophytic fungus Paecilomyces variotii, has been discovered play vital role in preventing diverse forms bacterial infections. Nevertheless, precise mechanism behind its ability enhance fungi remains unclear. In this study, we found that exogenous spraying could significantly improve plants B. cinerea. results metabolomic analysis high-performance liquid chromatography (HPLC) demonstrated responded treatment accumulating high levels rutin. Additional transcriptome uncovered rutin enhances possible initiating generation reactive oxygen species (ROS) phosphorylation mitogen-activated protein kinases (MPKs) related genes expression during initial phase invasion addition, also might activate immunity eliciting ethylene (ET) jasmonic acid (JA)-mediated pathways. Therefore, immune inducer bright application prospects value control gray mold.

Language: Английский

Citations

10