1
|
Xie N, Guo Q, Li H, Yuan G, Gui Q, Xiao Y, Liao M, Yang L. Integrated transcriptomic and WGCNA analyses reveal candidate genes regulating mainly flavonoid biosynthesis in Litsea coreana var. sinensis. BMC PLANT BIOLOGY 2024; 24:231. [PMID: 38561656 PMCID: PMC10985888 DOI: 10.1186/s12870-024-04949-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
Litsea coreana Levl. var. sinensis (Allen) Yang et P. H. Huang is a popular ethnic herb and beverage plant known for its high flavonoid content, which has been linked to a variety of pharmacological benefits and crucial health-promoting impacts in humans. The progress in understanding the molecular mechanisms of flavonoid accumulation in this plant has been hindered due to the deficiency of genomic and transcriptomic resources. We utilized a combination of Illumina and Oxford Nanopore Technology (ONT) sequencing to generate a de novo hybrid transcriptome assembly. In total, 126,977 unigenes were characterized, out of which 107,977 were successfully annotated in seven public databases. Within the annotated unigenes, 3,781 were categorized into 58 transcription factor families. Furthermore, we investigated the presence of four valuable flavonoids-quercetin-3-O-β-D-galactoside, quercetin-3-O-β-D-glucoside, kaempferol-3-O-β-D-galactoside, and kaempferol-3-O-β-D-glucoside in 98 samples, using high-performance liquid chromatography. A weighted gene co-expression network analysis identified two co-expression modules, MEpink and MEturquoise, that showed strong positive correlation with flavonoid content. Within these modules, four transcription factor genes (R2R3-MYB, NAC, WD40, and ARF) and four key enzyme-encoding genes (CHI, F3H, PAL, and C4H) emerged as potential hub genes. Among them, the R2R3-MYB (LcsMYB123) as a homologous gene to AtMYB123/TT2, was speculated to play a significant role in flavonol biosynthesis based on phylogenetic analysis. Our findings provided a theoretical foundation for further research into the molecular mechanisms of flavonoid biosynthesis. Additionally, The hybrid transcriptome sequences will serve as a valuable molecular resource for the transcriptional annotation of L. coreana var. sinensis, which will contribute to the improvement of high-flavonoid materials.
Collapse
Affiliation(s)
- Na Xie
- Institute for Forest Resources and Environment of Guizhou, College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Qiqaing Guo
- Institute for Forest Resources and Environment of Guizhou, College of Forestry, Guizhou University, Guiyang, 550025, China.
| | - Huie Li
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Gangyi Yuan
- Institute for Forest Resources and Environment of Guizhou, College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Qin Gui
- Institute for Forest Resources and Environment of Guizhou, College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Yang Xiao
- Institute for Forest Resources and Environment of Guizhou, College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Mengyun Liao
- Institute for Forest Resources and Environment of Guizhou, College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Lan Yang
- Institute for Forest Resources and Environment of Guizhou, College of Forestry, Guizhou University, Guiyang, 550025, China
| |
Collapse
|
2
|
Walter M, Puniamoorthy N. Discovering novel reproductive genes in a non-model fly using de novo GridION transcriptomics. Front Genet 2022; 13:1003771. [PMID: 36568389 PMCID: PMC9768217 DOI: 10.3389/fgene.2022.1003771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/16/2022] [Indexed: 12/12/2022] Open
Abstract
Gene discovery has important implications for investigating phenotypic trait evolution, adaptation, and speciation. Male reproductive tissues, such as accessory glands (AGs), are hotspots for recruitment of novel genes that diverge rapidly even among closely related species/populations. These genes synthesize seminal fluid proteins that often affect post-copulatory sexual selection-they can mediate male-male sperm competition, ejaculate-female interactions that modify female remating and even influence reproductive incompatibilities among diverging species/populations. Although de novo transcriptomics has facilitated gene discovery in non-model organisms, reproductive gene discovery is still challenging without a reference database as they are often novel and bear no homology to known proteins. Here, we use reference-free GridION long-read transcriptomics, from Oxford Nanopore Technologies (ONT), to discover novel AG genes and characterize their expression in the widespread dung fly, Sepsis punctum. Despite stark population differences in male reproductive traits (e.g.: Body size, testes size, and sperm length) as well as female re-mating, the male AG genes and their secretions of S. punctum are still unknown. We implement a de novo ONT transcriptome pipeline incorporating quality-filtering and rigorous error-correction procedures, and we evaluate gene sequence and gene expression results against high-quality Illumina short-read data. We discover highly-expressed reproductive genes in AG transcriptomes of S. punctum consisting of 40 high-quality and high-confidence ONT genes that cross-verify against Illumina genes, among which 26 are novel and specific to S. punctum. Novel genes account for an average of 81% of total gene expression and may be functionally relevant in seminal fluid protein production. For instance, 80% of genes encoding secretory proteins account for 74% total gene expression. In addition, median sequence similarities of ONT nucleotide and protein sequences match within-Illumina sequence similarities. Read-count based expression quantification in ONT is congruent with Illumina's Transcript per Million (TPM), both in overall pattern and within functional categories. Rapid genomic innovation followed by recruitment of de novo genes for high expression in S. punctum AG tissue, a pattern observed in other insects, could be a likely mechanism of evolution of these genes. The study also demonstrates the feasibility of adapting ONT transcriptomics for gene discovery in non-model systems.
Collapse
|
3
|
D’Auria JC, Cohen SP, Leung J, Glockzin K, Glockzin KM, Gervay-Hague J, Zhang D, Meinhardt LW. United States tea: A synopsis of ongoing tea research and solutions to United States tea production issues. FRONTIERS IN PLANT SCIENCE 2022; 13:934651. [PMID: 36212324 PMCID: PMC9538180 DOI: 10.3389/fpls.2022.934651] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/25/2022] [Indexed: 06/01/2023]
Abstract
Tea is a steeped beverage made from the leaves of Camellia sinensis. Globally, this healthy, caffeine-containing drink is one of the most widely consumed beverages. At least 50 countries produce tea and most of the production information and tea research is derived from international sources. Here, we discuss information related to tea production, genetics, and chemistry as well as production issues that affect or are likely to affect emerging tea production and research in the United States. With this review, we relay current knowledge on tea production, threats to tea production, and solutions to production problems to inform this emerging market in the United States.
Collapse
Affiliation(s)
- John C. D’Auria
- Metabolic Diversity Group, Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Stephen P. Cohen
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
| | - Jason Leung
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
| | - Kayla Glockzin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Kyle Mark Glockzin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Jacquelyn Gervay-Hague
- Department of Chemistry, University of California, University of California, Davis, Davis, CA, United States
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
| | - Lyndel W. Meinhardt
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
| |
Collapse
|
4
|
Diwan D, Rashid MM, Vaishnav A. Current understanding of plant-microbe interaction through the lenses of multi-omics approaches and their benefits in sustainable agriculture. Microbiol Res 2022; 265:127180. [PMID: 36126490 DOI: 10.1016/j.micres.2022.127180] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/28/2022]
Abstract
The success of sustainable agricultural practices has now become heavily dependent on the interactions between crop plants and their associated microbiome. Continuous advancement in high throughput sequencing platforms, omics-based approaches, and gene editing technologies has remarkably accelerated this area of research. It has enabled us to characterize the interactions of plants with associated microbial communities more comprehensively and accurately. Furthermore, the genomic and post-genomic era has significantly refined our perspective toward the complex mechanisms involved in those interactions, opening new avenues for efficiently deploying the knowledge in developing sustainable agricultural practices. This review focuses on our fundamental understanding of plant-microbe interactions and the contribution of existing multi-omics approaches, including those under active development and their tremendous success in unraveling different aspects of the complex network between plant hosts and microbes. In addition, we have also discussed the importance of sustainable and eco-friendly agriculture and the associated outstanding challenges ahead.
Collapse
Affiliation(s)
- Deepti Diwan
- Washington University School of Medicine, Saint Louis, MO 63110, USA.
| | - Md Mahtab Rashid
- Department of Plant Pathology, Bihar Agricultural University, Sabour, Bhagalpur, Bihar 813210, India; Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Anukool Vaishnav
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh 281121, India; Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich CH-8008, Switzerland; Plant-Soil Interaction Group, Agroscope (Reckenholz), Reckenholzstrasse 191, Zürich 8046, Switzerland
| |
Collapse
|
5
|
Liu NN, Ren ZY, Ren QD, Chang ZG, Li JL, Li XA, Sun ZY, He JM, Niu QS, Xing XM. Full length transcriptomes analysis of cold-resistance of Apis cerana in Changbai Mountain during overwintering period. Gene 2022; 830:146503. [PMID: 35487395 DOI: 10.1016/j.gene.2022.146503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/21/2022] [Accepted: 04/14/2022] [Indexed: 11/15/2022]
Abstract
Apis cerana in Changbai Mountain is an ecological type of Apis cerana, which is an excellent breeding material with cold-resistant developed by long-term natural selection under the ecological conditions. However, the physiological and molecular mechanisms of Changbai Mountain population under cold stress are still unclear. In this study, the Nanopore sequencing was carried out for the transcriptome of Apis cerana in Changbai Mountain in the coldest period of overwintering, which will provide a reference to the cold-resistant mechanism. We determined 5,941 complete ORF sequences, 1,193 lncRNAs, 619 TFs, 10,866 SSRs and functional annotations of 11,599 new transcripts. Our results showed that the myosin family and the C2H2 zinc finger protein transcription factor family possibly have significant impacts on the response mechanism of cold stress during overwintering. In addition, the cold environment alters genes expression profiles in honeybees via different AS and APA mechanisms. These altered genes in Hippo, Foxo, and MARK pathways help them counter the stress of cold in overwinter period. Our results might provide clues about the response of eastern honeybees to extreme cold, and reflect the possible genetic basis of physiological changes.
Collapse
Affiliation(s)
- Nan-Nan Liu
- Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun, Jilin 130112, PR China; Apiculture Science Institute of Jilin Province, Jilin, Jilin 132108, PR China.
| | - Zhong-Yuan Ren
- Jilin Institute of Chemical Technology, Jilin, Jilin 132022, PR China
| | - Qing-Dan Ren
- Jilin Provincial Animal Husbandry General Station, Changchun, Jilin 130699, PR China
| | - Zhi-Guang Chang
- Apiculture Science Institute of Jilin Province, Jilin, Jilin 132108, PR China
| | - Jie-Luan Li
- Apiculture Science Institute of Jilin Province, Jilin, Jilin 132108, PR China
| | - Xing-An Li
- Apiculture Science Institute of Jilin Province, Jilin, Jilin 132108, PR China
| | - Zhi-Yu Sun
- Apiculture Science Institute of Jilin Province, Jilin, Jilin 132108, PR China
| | - Jin-Ming He
- Apiculture Science Institute of Jilin Province, Jilin, Jilin 132108, PR China
| | - Qing-Sheng Niu
- Apiculture Science Institute of Jilin Province, Jilin, Jilin 132108, PR China.
| | - Xiu-Mei Xing
- Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun, Jilin 130112, PR China.
| |
Collapse
|
6
|
Liang Y, Gong Z, Wang J, Zheng J, Ma Y, Min L, Chen Q, Li Z, Qu Y, Chen Q, Li X. Nanopore-Based Comparative Transcriptome Analysis Reveals the Potential Mechanism of High-Temperature Tolerance in Cotton (Gossypium hirsutum L.). PLANTS 2021; 10:plants10112517. [PMID: 34834881 PMCID: PMC8618236 DOI: 10.3390/plants10112517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022]
Abstract
Extreme high temperatures are threatening cotton production around the world due to the intensification of global warming. To cope with high-temperature stress, heat-tolerant cotton cultivars have been bred, but the heat-tolerant mechanism remains unclear. This study selected heat-tolerant (‘Xinluzao36′) and heat-sensitive (‘Che61-72′) cultivars of cotton treated with high-temperature stress as plant materials and performed comparative nanopore sequencing transcriptome analysis to reveal the potential heat-tolerant mechanism of cotton. Results showed that 120,605 nonredundant sequences were generated from the raw reads, and 78,601 genes were annotated. Differentially expressed gene (DEG) analysis showed that a total of 19,600 DEGs were screened; the DEGs involved in the ribosome, heat shock proteins, auxin and ethylene signaling transduction, and photosynthesis pathways may be attributed to the heat tolerance of the heat-tolerant cotton cultivar. This study also predicted a total of 5118 long non-coding RNAs (lncRNAs)and 24,462 corresponding target genes. Analysis of the target genes revealed that the expression of some ribosomal, heat shock, auxin and ethylene signaling transduction-related and photosynthetic proteins may be regulated by lncRNAs and further participate in the heat tolerance of cotton. This study deepens our understandings of the heat tolerance of cotton.
Collapse
Affiliation(s)
- Yajun Liang
- Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830001, China; (Y.L.); (Q.C.); (Y.Q.)
- Xinjiang Academy of Agricultural Science, Urumqi 830001, China; (Z.G.); (J.W.); (J.Z.)
| | - Zhaolong Gong
- Xinjiang Academy of Agricultural Science, Urumqi 830001, China; (Z.G.); (J.W.); (J.Z.)
| | - Junduo Wang
- Xinjiang Academy of Agricultural Science, Urumqi 830001, China; (Z.G.); (J.W.); (J.Z.)
| | - Juyun Zheng
- Xinjiang Academy of Agricultural Science, Urumqi 830001, China; (Z.G.); (J.W.); (J.Z.)
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (Y.M.); (L.M.)
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (Y.M.); (L.M.)
| | - Qin Chen
- Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830001, China; (Y.L.); (Q.C.); (Y.Q.)
| | - Zhiqiang Li
- Adsen Biotechnology Co., Ltd., Urumqi 830022, China;
| | - Yanying Qu
- Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830001, China; (Y.L.); (Q.C.); (Y.Q.)
| | - Quanjia Chen
- Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830001, China; (Y.L.); (Q.C.); (Y.Q.)
- Correspondence: (Q.C.); (X.L.)
| | - Xueyuan Li
- Xinjiang Academy of Agricultural Science, Urumqi 830001, China; (Z.G.); (J.W.); (J.Z.)
- Correspondence: (Q.C.); (X.L.)
| |
Collapse
|