1
|
Lan S, Zhai T, Zhang X, Xu L, Gao J, Lai C, Chen Y, Lai Z, Lin Y. Genome-wide identification and expression analysis of the GAD family reveal their involved in embryogenesis and hormones responses in Dimocarpus longan Lour. Gene 2024; 927:148698. [PMID: 38908456 DOI: 10.1016/j.gene.2024.148698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/06/2024] [Accepted: 06/13/2024] [Indexed: 06/24/2024]
Abstract
Glutamate decarboxylase (GAD) is involved in GABA metabolism and plays an essential regulatory role in plant growth, abiotic stresses, and hormone response. This study investigated the expression mechanism of the GAD family during longan early somatic embryogenesis (SE) and identified 6 GAD genes based on the longan genome. Homology analysis indicated that DlGAD genes had a closer relationship with dicotyledonous plants. The analysis of cis-acting elements in the promoter region suggests that the GAD genes were associated with various stress responses and hormones. RNA sequencing (RNA-Seq) and the qRT-PCR data indicated that most DlGAD genes were highly expressed in the incomplete compact pro-embryogenic cultures (ICpEC) and upregulated in longan embryogenic callus (EC) after treatments with 2,4-D, high temperature (35 °C), IAA, and ABA. Moreover, the RNA-Seq analysis also revealed that DlGADs exhibit different expression patterns in various tissues and organs. The subcellular localization results showed that DlGAD5 was localized in the cytoplasm, suggesting that it played a role in the cytoplasm. Transient overexpression of DlGAD5 enhanced the expression levels of DlGADs and increased the activity of glutamate decarboxylase in longan embryogenic callus (EC), while the content of glutamic acid decreased. Thus, the DlGAD gene can play an important role in the early somatic embryogenesis of longan by responding to hormones such as IAA and ABA. DlGAD5 can affect the growth and development of longan by stimulating the expression of the DlGAD gene family, thereby increasing the GAD activity in the early SE of longan, participating in hormone synthesis and signaling pathways.
Collapse
Affiliation(s)
- Shuoxian Lan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Tingkai Zhai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xueying Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Luzhen Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Jie Gao
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Chunwang Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yan Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
| |
Collapse
|
2
|
Xu X, Zhang C, Lai C, Zhang Z, Wu J, Su Q, Gan Y, Zhang Z, Chen Y, Guo R, Lin Y, Lai Z. Genome-Wide Identification and Expression Analysis of Bx Involved in Benzoxazinoids Biosynthesis Revealed the Roles of DIMBOA during Early Somatic Embryogenesis in Dimocarpus longan Lour. PLANTS (BASEL, SWITZERLAND) 2024; 13:1373. [PMID: 38794443 PMCID: PMC11125010 DOI: 10.3390/plants13101373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/04/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024]
Abstract
Benzoxazinoids (BXs) are tryptophan-derived indole metabolites and play a role in various physiological processes, such as auxin metabolism. Auxin is essential in the process of somatic embryogenesis (SE) in plants. In this study, we used bioinformatics, transcriptome data, exogenous treatment experiments, and qPCR analysis to study the evolutionary pattern of Bx genes in green plants, the regulatory mechanism of DlBx genes during early SE, and the effect of 2,4-dihydroxy-7-methoxy-1,4-benzoxazine-3-one (DIMBOA) on the early SE in Dimocarpus longan Lour. The results showed that 27 putative DlBxs were identified in the longan genome; the Bx genes evolved independently in monocots and dicots, and the main way of gene duplication for the DlBx was tandem duplication (TD) and the DlBx were strongly constrained by purification selection during evolution. The transcriptome data indicated varying expression levels of DlBx during longan early SE, and most DlBxs responded to light, temperature, drought stress, and 2,4-dichlorophenoxyacetic acid (2,4-D) treatment; qRT-PCR results showed DlBx1, DlBx6g and DlBx6h were responsive to auxin, and treatment with 0.1mg/L DIMBOA for 9 days significantly upregulated the expression levels of DlBx1, DlBx3g, DlBx6c, DlBx6f, DlB6h, DlBx7d, DlBx8, and DlBx9b. The correlation analysis showed a significantly negative correlation between the expression level of DlBx1 and the endogenous IAA contents; DIMBOA significantly promoted the early SE and significantly changed the endogenous IAA content, and the IAA content increased significantly at the 9th day and decreased significantly at the 13th day. Therefore, the results suggested that DIMBOA indirectly promote the early SE by changing the endogenous IAA content via affecting the expression level of DlBx1 and hydrogen peroxide (H2O2) content in longan.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.X.); (C.Z.); (C.L.); (Z.Z.); (J.W.); (Q.S.); (Y.G.); (Z.Z.); (Y.C.); (R.G.); (Y.L.)
| |
Collapse
|
3
|
Zheng K, Lu J, He X, Lan S, Zhai T, Cao S, Lin Y. Genome-Wide Identification and Expression Analysis of GATA Family Genes in Dimocarpus longan Lour. Int J Mol Sci 2024; 25:731. [PMID: 38255805 PMCID: PMC10815313 DOI: 10.3390/ijms25020731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
GATA transcription factors, which are DNA-binding proteins with type IV zinc finger binding domains, have a role in transcriptional regulation in biological organisms. They have an indispensable role in the growth and development of plants, as well as in improvements in their ability to face various environmental stresses. To date, GATAs have been identified in many gene families, but the GATA gene in longan (Dimocarpus longan Lour) has not been studied in previous explorations. Various aspects of genes in the longan GATA family, including their identification and classification, the distribution of their positions on chromosomes, their exon/intron structures, a synteny analysis, their expression at different temperatures, concentration of PEG, early developmental stages of somatic embryos and their expression levels in different tissues, and concentrations of exogenous hormones, were investigated in this study. This study showed that the 22 DlGATAs could be divided into four subfamilies. There were 10 pairs of homologous GATA genes in the synteny analysis of DlGATA and AtGATA. Four segmental replication motifs and one pair of tandem duplication events were present among the DlGATA family members. The cis-acting elements located in promoter regions were also found to be enriched with light-responsive elements, which contained related hormone-responsive elements. In somatic embryos, DlGATA4 is upregulated for expression at the globular embryo (GE) stage. We also found that DlGATA expression was strongly up-regulated in roots and stems. The study demonstrated the expression of DlGATA under hormone (ABA and IAA) treatments in embryogenic callus of longan. Under ABA treatment, DlGATA4 was up-regulated and the other DlGATA genes did not respond significantly. Moreover, as demonstrated with qRT-PCR, the expression of DlGATA genes showed strong up-regulated expression levels under 100 μmol·L-1 concentration IAA treatment. This experiment further studied these and simulated their possible connections with a drought response mechanism, while correlating them with their expression under PEG treatment. Overall, this experiment explored the GATA genes and dug into their evolution, structure, function, and expression profile, thus providing more information for a more in-depth study of the characteristics of the GATA family of genes.
Collapse
Affiliation(s)
- Kehui Zheng
- College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Jiayue Lu
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Xinyu He
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Shuoxian Lan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Tingkai Zhai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Shijiang Cao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| |
Collapse
|
4
|
Zhao H, Li X, Xiao X, Wang T, Liu L, Li C, Wu H, Shan Z, Wu Q. Evaluating Tartary Buckwheat Genotypes with High Callus Induction Rates and the Transcriptomic Profiling during Callus Formation. PLANTS (BASEL, SWITZERLAND) 2023; 12:3663. [PMID: 37960020 PMCID: PMC10647830 DOI: 10.3390/plants12213663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023]
Abstract
Due to their complex genotypes, low in vitro regeneration rates, and difficulty in obtaining transgenic plants, studies concerning basic biological research and molecular breeding in Tartary buckwheat (TB) are greatly limited. In this study, the hypocotyls of 60 genotypes of TB (TBC1~60) were used as explants. Of these, TBC14 was selected due to a high callus induction rate of 97.78% under dark and a proliferation coefficient (PC) of 28.2 when cultured on MS medium supplemented with 2.0 mg/L of 2,4-D and 1.5 mg/L of 6-BA. Subsequently, the samples of the calli obtained from TBC14 were collected at 0, 10, 20, and 30 d, and their transcriptomes were sequenced where identified. GO enrichment led to the detection of the most significant active gene set, which was the DNA binding transcription factor activity. The DEGs related to the pathways concerning metabolism, the biosynthesis of secondary metabolites, and hormone signal transduction were the most enriched in the KEGG database. The sets of MYB, AP2/ERF, and bHLH TFs exhibited the highest number of DEGs. Using this enrichment analysis, 421 genes encoding TFs, 47 auxin- and cytokinin-related genes, and 6 signal transduction-associated genes were screened that may play significant roles in callus formation (CF) in TB. Furthermore, FtPinG0008123200.01 (bZIP), a key gene promoting CF, was screened in terms of the weighted gene co-expression network associated with the various stages of CF. Our study not only provides valuable information about the molecular mechanism of CF but also reveals new genes involved in this process.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Qi Wu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya’an 625014, China; (H.Z.); (X.L.); (X.X.); (T.W.); (L.L.); (C.L.); (H.W.); (Z.S.)
| |
Collapse
|
5
|
Huang S, Qiao Y, Lv X, Li J, Han D, Guo D. Transcriptome sequencing and DEG analysis in different developmental stages of floral buds induced by potassium chlorate in Dimocarpus longan. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2022; 39:259-272. [PMID: 36349234 PMCID: PMC9592951 DOI: 10.5511/plantbiotechnology.22.0526a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/26/2022] [Indexed: 06/16/2023]
Abstract
Potassium chlorate can promote off-season flowering in longan, but the molecular mechanisms are poorly understood. In this study, four-year-old 'Shixia' longan trees were injected in the trunk with potassium chlorate, and terminal buds were sampled and analyzed using transcriptomics and bioinformatics tools. To generate a reference longan transcriptome, we obtained 207,734 paired-end reads covering a total of 58,514,149 bp, which we assembled into 114,445 unigenes. Using this resource, we identified 3,265 differentially expressed genes (DEGs) that were regulated in longan terminal buds in response to potassium chlorate treatment for 2, 6 or 30 days, including 179 transcription factor genes. By reference to the Arabidopsis literature, we then defined 38 longan genes involved in flowering, from which we constructed the longan flowering pathway. According to RNA-seq data, at least 24 of these genes, which participate in multiple signaling pathways, are involved in potassium chlorate-stimulated floral induction, and the differential regulation in terminal buds of ten floral pathway genes (GI, CO, GID1, GA4, GA5, FLC, AP1, LFY, FT and SOC1) was confirmed by qRT-PCR. These data will contribute to an improved understanding of the functions of key genes involved in longan floral induction by potassium chlorate.
Collapse
Affiliation(s)
- Shilian Huang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs; Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, Guangdong, China
| | - Yanchun Qiao
- Guangzhou Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Xinmin Lv
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs; Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, Guangdong, China
| | - Jianguang Li
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs; Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, Guangdong, China
| | - Dongmei Han
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs; Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, Guangdong, China
| | - Dongliang Guo
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs; Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, Guangdong, China
| |
Collapse
|
6
|
Enríquez-González C, Garcidueñas-Piña C, Castellanos-Hernández OA, Enríquez-Aranda S, Loera-Muro A, Ocampo G, Pérez-Molphe Balch E, Morales-Domínguez JF. De Novo Transcriptome of Mammillaria bombycina (Cactaceae) under In Vitro Conditions and Identification of Glyoxalase Genes. PLANTS 2022; 11:plants11030399. [PMID: 35161380 PMCID: PMC8838482 DOI: 10.3390/plants11030399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 11/16/2022]
Abstract
Mammillaria bombycina is a cactus distributed in the central region of Mexico. Cactaceae have the particularity of surviving drought and high temperatures, which is why in vitro propagation studies have been carried out successfully to preserve this species and use it as a study model in cacti. In this contribution, a de novo transcriptome of M. bombycina was produced under in vitro conditions for the identification and expression of genes related to abiotic stress. Samples were sequenced using an Illumina platform, averaging 24 million clean readings. From assembly and annotation, 84,975 transcripts were generated, 55% of which were unigenes. Among these, the presence of 13 isoforms of genes belonging to glyoxalase I, II and III were identified. An analysis of the qRT-PCR expression of these genes was performed under in vitro and ex vitro conditions and dehydration at 6 and 24 h. The highest expression was observed under greenhouse conditions and dehydration at 24 h, according to the control. The de novo assembly of the M. bombycina transcriptome remains a study model for future work in cacti.
Collapse
Affiliation(s)
- Carolina Enríquez-González
- Centro de Ciencias Básicas, Departamento de Química, Universidad Autónoma de Aguascalientes, Av. Universidad 940, Aguascalientes 20100, Mexico
| | - Cristina Garcidueñas-Piña
- Centro de Ciencias Básicas, Departamento de Química, Universidad Autónoma de Aguascalientes, Av. Universidad 940, Aguascalientes 20100, Mexico
| | - Osvaldo Adrián Castellanos-Hernández
- Centro de Investigación en Biología Molecular Vegetal, Centro Universitario de la Ciénega, Universidad de Guadalajara, Av. Universidad, 1115, Linda Vista, Ocotlán 47810, Mexico
| | - Sergio Enríquez-Aranda
- Centro de Ciencias Básicas, Departamento de Sistemas de la Información, Universidad Autónoma de Aguascalientes, Av. Universidad 940, Aguascalientes 20100, Mexico
| | - Abraham Loera-Muro
- CONACyT Centro de Investigaciones Biológicas del Noroeste S.C., Av. Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz 23096, Mexico
| | - Gilberto Ocampo
- Centro de Ciencias Básicas, Departamento de Biología, Universidad Autónoma de Aguascalientes, Av. Universidad 940, Aguascalientes 20100, Mexico
| | - Eugenio Pérez-Molphe Balch
- Centro de Ciencias Básicas, Departamento de Química, Universidad Autónoma de Aguascalientes, Av. Universidad 940, Aguascalientes 20100, Mexico
| | - José Francisco Morales-Domínguez
- Centro de Ciencias Básicas, Departamento de Química, Universidad Autónoma de Aguascalientes, Av. Universidad 940, Aguascalientes 20100, Mexico
| |
Collapse
|
7
|
Yang E, Zheng M, Zou X, Huang X, Yang H, Chen X, Zhang J. Global Transcriptomic Analysis Reveals Differentially Expressed Genes Involved in Embryogenic Callus Induction in Drumstick ( Moringa oleifera Lam.). Int J Mol Sci 2021; 22:ijms222212130. [PMID: 34830008 PMCID: PMC8619801 DOI: 10.3390/ijms222212130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/01/2021] [Accepted: 11/06/2021] [Indexed: 12/25/2022] Open
Abstract
The plant embryogenic callus (EC) is an irregular embryogenic cell mass with strong regenerative ability that can be used for propagation and genetic transformation. However, difficulties with EC induction have hindered the breeding of drumstick, a tree with diverse potential commercial uses. In this study, three drumstick EC cDNA libraries were sequenced using an Illumina NovaSeq 6000 system. A total of 7191 differentially expressed genes (DEGs) for embryogenic callus development were identified, of which 2325 were mapped to the KEGG database, with the categories of plant hormone signal transduction and Plant-pathogen interaction being well-represented. The results obtained suggest that auxin and cytokinin metabolism and several embryogenesis-labeled genes are involved in embryogenic callus induction. Additionally, 589 transcription factors from 20 different families were differentially expressed during EC formation. The differential expression of 16 unigenes related to auxin signaling pathways was validated experimentally by quantitative real time PCR (qRT-PCR) using samples representing three sequential developmental stages of drumstick EC, supporting their apparent involvement in drumstick EC formation. Our study provides valuable information about the molecular mechanism of EC formation and has revealed new genes involved in this process.
Collapse
Affiliation(s)
- Endian Yang
- Department of Forestry, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (E.Y.); (M.Z.); (X.Z.); (X.H.); (H.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou 510642, China
| | - Mingyang Zheng
- Department of Forestry, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (E.Y.); (M.Z.); (X.Z.); (X.H.); (H.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou 510642, China
| | - Xuan Zou
- Department of Forestry, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (E.Y.); (M.Z.); (X.Z.); (X.H.); (H.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou 510642, China
| | - Xiaoling Huang
- Department of Forestry, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (E.Y.); (M.Z.); (X.Z.); (X.H.); (H.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Heyue Yang
- Department of Forestry, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (E.Y.); (M.Z.); (X.Z.); (X.H.); (H.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Xiaoyang Chen
- Department of Forestry, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (E.Y.); (M.Z.); (X.Z.); (X.H.); (H.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (X.C.); (J.Z.)
| | - Junjie Zhang
- Department of Forestry, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (E.Y.); (M.Z.); (X.Z.); (X.H.); (H.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou 510642, China
- Correspondence: (X.C.); (J.Z.)
| |
Collapse
|
8
|
Xu X, Chen X, Shen X, Chen R, Zhu C, Zhang Z, Chen Y, Lin W, Xu X, Lin Y, Lai Z. Genome-wide identification and characterization of DEAD-box helicase family associated with early somatic embryogenesis in Dimocarpus longan Lour. JOURNAL OF PLANT PHYSIOLOGY 2021; 258-259:153364. [PMID: 33465637 DOI: 10.1016/j.jplph.2021.153364] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 01/01/2021] [Accepted: 01/03/2021] [Indexed: 06/12/2023]
Abstract
DEAD-box (DDX) proteins belong to the largest subfamily of RNA helicase SF2, which contributes to all biological processes of RNA metabolism in the plant kingdom. Till now, no significant data are available regarding studies on DDX in Somatic Embryogenesis (SE) of woody plants. It is important to investigate the biological function of the DlDDX family in longan SE. Thus, a comprehensive analysis of 58 longan DEAD-box (DlDDX) genes characterization was performed by genome-wide identification and transcript abundance validation analysis. Homologous evolution has revealed that some DlDDXs in longan had high sequence similarity with Mus musculus, Citrus and Saccharomyces cerevisiae, indicating that DlDDXs were highly conservative in the animal, plant, and microorganism. Remarkably, gene duplication, purifying selection, and alternative splicing events, and new auxiliary domains have likely contributed to the functional evolution of DlDDX, indicating that DlDDX appeared neofunctionalization in longan. Besides, DlDDX3, 15, 28, 36 might interact with protein complex (MAC3A, MAC3B, CDC5, CBP20) of miRNA biosynthesis. Notably, DlDDX28 contained a novel auxiliary domain (CAF-1 p150), which might contribute to DNA demethylation in longan early SE. 4 DlDDX genes significantly expressed not only in early SE and zygotic embryogenesis (ZE) but also up-regulated at high levels in 'Honghezi' and 'Quanlongbaihe' with abortive seeds, which are of great significance. Moreover, some DlDDXs presented abiotic stress-response dynamic expression patterns by ABA, SA, JA, and NaCl treatments during early SE. Hence, DEAD-box is essential to SE development and seed abortive in longan.
Collapse
Affiliation(s)
- Xiaoping Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaohui Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xu Shen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Rongzhu Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Zhu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenzhong Lin
- Quanzhou Agricultural Science Research Institute, Quanzhou, 362212, China
| | - Xuhan Xu
- Institut de la Recherche Interdisciplinaire de Toulouse, IRIT-ARI, 31300, Toulouse, France
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
9
|
Zheng W, Xie T, Yu X, Chen N, Zhang Z. Characterization of bZIP transcription factors from Dimocarpus longan Lour. and analysis of their tissue-specific expression patterns and response to heat stress. J Genet 2020. [DOI: 10.1007/s12041-020-01229-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
10
|
Zhou GC, Li W, Zhang YM, Liu Y, Zhang M, Meng GQ, Li M, Wang YL. Distinct Evolutionary Patterns of NBS-Encoding Genes in Three Soapberry Family (Sapindaceae) Species. Front Genet 2020; 11:737. [PMID: 32754204 PMCID: PMC7365912 DOI: 10.3389/fgene.2020.00737] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/19/2020] [Indexed: 12/22/2022] Open
Abstract
Nucleotide-binding site (NBS)-type disease resistance genes (R genes) play key roles in plant immune responses and have co-evolved with pathogens over the course of plant lifecycles. Comparative genomic studies tracing the dynamic evolution of NBS-encoding genes have been conducted using many important plant lineages. However, studies on Sapindaceae species have not been performed. In this study, a discrepant number of NBS-encoding genes were identified in the genomes of Xanthoceras sorbifolium (180), Dinnocarpus longan (568), and Acer yangbiense (252). These genes were unevenly distributed and usually clustered as tandem arrays on chromosomes, with few existed as singletons. The phylogenetic analysis revealed that NBS-encoding genes formed three monophyletic clades, RPW8-NBS-LRR (RNL), TIR-NBS-LRR (TNL), and CC-NBS-LRR (CNL), which were distinguished by amino acid motifs. The NBS-encoding genes of the X. sorbifolium, D. longan, and A. yangbiense genomes were derived from 181 ancestral genes (three RNL, 23 TNL, and 155 CNL), which exhibited dynamic and distinct evolutionary patterns due to independent gene duplication/loss events. Specifically, X. sorbifolium exhibited a “first expansion and then contraction” evolutionary pattern, while A. yangbiense and D. longan exhibited a “first expansion followed by contraction and further expansion” evolutionary pattern. However, further expansion in D. longan was stronger than in A. yangbiense after divergence, suggesting that D. longan gained more genes in response to various pathogens. Additionally, the ancient and recent expansion of CNL genes generated the dominance of this subclass in terms of gene numbers, while the low copy number status of RNL genes was attributed to their conserved functions.
Collapse
Affiliation(s)
- Guang-Can Zhou
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Wen Li
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Yan-Mei Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yang Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Ming Zhang
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Guo-Qing Meng
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Min Li
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Yi-Lei Wang
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| |
Collapse
|
11
|
Xu X, Chen X, Chen Y, Zhang Q, Su L, Chen X, Chen Y, Zhang Z, Lin Y, Lai Z. Genome-wide identification of miRNAs and their targets during early somatic embryogenesis in Dimocarpus longan Lour. Sci Rep 2020; 10:4626. [PMID: 32170163 PMCID: PMC7069941 DOI: 10.1038/s41598-020-60946-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/07/2020] [Indexed: 11/09/2022] Open
Abstract
miRNAs are endogenous regulatory factors that play pivotal roles in post-transcriptional regulation. However, their specific roles in early somatic embryogenesis (SE) remain unclear. Study of the SE system is fundamental for clarifying the molecular mechanisms in Dimocarpus longan. We identified 289 known miRNAs from 106 different miRNA families and 1087 novel miRNAs during early longan SE, including embryogenic callus (EC), incomplete pro-embryogenic culture (ICpEC), globular embryo (GE), and non-embryogenic callus (NEC). The abundances of known miRNAs were concentrated in GE. The differentially expression (DE) miRNAs showed five expression patterns during early SE. Largely miRNAs were expressed highly and specially in EC, ICpEC, and GE, respectively. Some miRNAs and putative target genes were enriched in lignin metabolism. Most potential targets were related to the pathways of plant hormone signal transduction, alternative splicing, tyrosine metabolism and sulfur metabolism in early longan SE. The regulatory relationships between dlo-miR166a-3p and DlHD-zip8, dlo-miR397a and DlLAC7, dlo-miR408-3p and DlLAC12 were confirmed by RNA ligase-mediated rapid amplification of cDNA ends. The expression patterns of eight DE miRNAs detected by qRT-PCR were consistent with RNA-seq. Finally, the miRNA regulatory network in early SE was constructed, which provided new insight into molecular mechanism of early SE in longan.
Collapse
Affiliation(s)
- Xiaoping Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaohui Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yan Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qinglin Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liyao Su
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xu Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
12
|
Zhang QL, Su LY, Zhang ST, Xu XP, Chen XH, Li X, Jiang MQ, Huang SQ, Chen YK, Zhang ZH, Lai ZX, Lin YL. Analyses of microRNA166 gene structure, expression, and function during the early stage of somatic embryogenesis in Dimocarpus longan Lour. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 147:205-214. [PMID: 31869733 DOI: 10.1016/j.plaphy.2019.12.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/11/2019] [Accepted: 12/11/2019] [Indexed: 06/10/2023]
Abstract
MicroRNA166 (miR166) contributes to post-transcriptional regulation by binding the mRNAs of HD-ZIP III genes, which affects plant growth and development. The structural characteristics, expression, and functions of miR166 genes during the early somatic embryogenesis stage in Dimocarpus longan remain unknown. We isolated the transcripts of pri-miR166 S78 with two transcription initiation sites (TSSs) and pri-miR166 S338 with one TSS. These sequences contain potential smORFs and encode different miRNA peptides (miPEPs). Additionally, their promoters contain cis-acting elements responsive to diverse stimuli. The pre-miR166 S78 and pre-miR166 S338 expression levels were up-regulated in response to 2,4-D, abscisic acid, and ethylene. Although the expression patterns induced by hormones were similar, there were differences in the extent of the response, with pre-miR166 S338 more responsive than pre-miR166 S78. Thus, miRNA transcription and maturation are not simply linearly correlated. Moreover, pre-miR166 S78 and pre-miR166 S338 expression levels were down-regulated, whereas ATHB15 (target gene) expression was up-regulated, from the longan embryonic callus to the globular embryo stages. These results are indicative of a negative regulatory relationship between miR166 and ATHB15 during the early somatic embryogenesis stage in longan. At the same stages, miR166a.2-agomir, miR166a.2-antagomir, and miPEP166 S338 increased or decreased the expression of miR166a.2 and ATHB15, but with no consistent patterns or linear synchronization, from which we've found some reasons for it.
Collapse
Affiliation(s)
- Q L Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - L Y Su
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - S T Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - X P Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - X H Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - X Li
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - M Q Jiang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - S Q Huang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Y K Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Z H Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Z X Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Y L Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
| |
Collapse
|
13
|
Chen Y, Xu X, Liu Z, Zhang Z, XuHan X, Lin Y, Lai Z. Global scale transcriptome analysis reveals differentially expressed genes involve in early somatic embryogenesis in Dimocarpus longan Lour. BMC Genomics 2020; 21:4. [PMID: 31898486 PMCID: PMC6941269 DOI: 10.1186/s12864-019-6393-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/12/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Somatic embryogenesis (SE) is a process of somatic cells that dedifferentiate to totipotent embryonic stem cells and generate embryos in vitro. Longan SE has been established and wildly used as model system for studying embryogenesis in woody plants, SE-related genes had been characterized. In spite of that, a comprehensive overview of SE at a molecular level is still absent. To understand the molecular mechanisms during longan SE, we examined the transcriptome changes by using Illumina HiSeq from the four distinct developmental stages, including non-embryogenic callus (NEC), embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC), globular embryos (GE). RESULTS RNA-seq of the four samples generated a total of 243.78 million high quality reads, approximately 81.5% of the data were mapped to longan genome. The cDNA libraries of NEC, EC, ICpEC and GE, generated 22,743, 19,745, 21,144, 21,102 expressed transcripts, 1935, 1710, 1816, 1732 novel transcripts, 2645, 366, 505, 588 unique genes, respectively. Comparative transcriptome analysis showed that a total of 10,642, 4180, 5846 and 1785 genes were differentially expressed in the pairwise comparisons of NEC_vs_EC, EC_vs_ICpEC, EC_vs_GE, ICpEC_vs_GE, respectively. Among them, plant hormones signalling related genes were significantly enriched, especially the auxin and cytokinin signalling components. The transcripts of flavonoid biosynthesis related genes were mainly expressed in NEC, while fatty acid biosynthesis related genes mainly accumulated in early SE. In addition, the extracelluar protein encoding genes LTP, CHI, GLP, AGP, EP1 were related to longan SE. Combined with the FPKM value of longan nine tissues transcription, 27 SE specific or preferential genes (LEC1, LEC1-like, PDF1.3, GH3.6, AGL80, PIN1, BBM, WOX9, WOX2, ABI3, et al.) and 28 NEC preferential genes (LEA5, CNOT3, DC2.15, PR1-1, NsLTP2, DIR1, PIP1, PIP2.1, TIP2-1, POD-P7 and POD5 et al.) were characterized as molecular markers for longan early SE. qRT-PCR validation of SE-related genes showed a high correlation between RNA-seq and qRT-PCR data. CONCLUSION This study provides new insights into the role of the transcriptome during early SE in longan. Differentially expressed genes reveal that plant hormones signalling, flavonoid and fatty acid biosynthesis, and extracelluar protein related genes were involved in longan early SE. It could serve as a valuable platform resource for further functional studies addressing embryogenesis in woody plants.
Collapse
Affiliation(s)
- Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiaoping Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhuanxia Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xu XuHan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Institut de la Recherche Interdisciplinaire de Toulouse, IRIT-ARI, 31300 Toulouse, France
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhongxion Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| |
Collapse
|
14
|
Li SN, Cheng P, Bai YQ, Shi Y, Yu JY, Li RC, Zhou RN, Zhang ZG, Wu XX, Chen QS. Analysis of Soybean Somatic Embryogenesis Using Chromosome Segment Substitution Lines and Transcriptome Sequencing. Genes (Basel) 2019; 10:E943. [PMID: 31752416 PMCID: PMC6896167 DOI: 10.3390/genes10110943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 11/05/2019] [Accepted: 11/18/2019] [Indexed: 12/15/2022] Open
Abstract
Soybean is an important cash crop that is widely used as a source of vegetable protein and edible oil. The regeneration ability of soybean directly affects the application of biotechnology. In this study, we used the exogenous hormone 2,4-D to treat immature embryos. Different levels of somatic incidence were selected from the chromosome segment substitution lines (CSSLs) constructed by SN14 and ZYD00006. Transcriptome sequencing of extreme materials was performed, and 2666 differentially expressed genes were obtained. At the same time, a difference table was generated by combining the data on CSSL rearrangement. In the extreme materials, a total of 93 differentially expressed genes were predicted and were then analyzed by cluster analysis and Gene Ontology (GO) annotation. After screening and annotating the target genes, three differentially expressed genes with hormone pathways were identified. The expression patterns of the target genes were verified by real-time quantitative PCR (qRT-PCR). Haplotype polymorphism detection and linkage disequilibrium analysis were performed on the candidate gene Glyma.09g248200. This study provided more information on the regulation network of soybean somatic embryogenesis and regeneration processes, and further identified important genes in the soybean regeneration process and provided a theoretical basis for accelerating the application of biotechnology to soybean for improving its breeding efficiency.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Zhan-Guo Zhang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China; (S.-N.L.); (P.C.); (Y.-Q.B.); (Y.S.); (J.-Y.Y.); (R.-C.L.); (R.-N.Z.)
| | - Xiao-Xia Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China; (S.-N.L.); (P.C.); (Y.-Q.B.); (Y.S.); (J.-Y.Y.); (R.-C.L.); (R.-N.Z.)
| | - Qing-Shan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China; (S.-N.L.); (P.C.); (Y.-Q.B.); (Y.S.); (J.-Y.Y.); (R.-C.L.); (R.-N.Z.)
| |
Collapse
|
15
|
Chery JG, Acevedo-Rodríguez P, Rothfels CJ, Specht CD. Phylogeny of Paullinia L. (Paullinieae: Sapindaceae), a diverse genus of lianas with dynamic fruit evolution. Mol Phylogenet Evol 2019; 140:106577. [PMID: 31415869 DOI: 10.1016/j.ympev.2019.106577] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/03/2019] [Accepted: 08/07/2019] [Indexed: 11/28/2022]
Abstract
Paullinia L. is a genus of c. 220 mostly Neotropical forest-dwelling lianas that display a wide diversity of fruit morphologies. Paullinia resembles other members of the Paullinieae tribe in being a climber with stipulate compound leaves and paired inflorescence tendrils. However, it is distinct in having capsular fruits with woody, coriaceous, or crustaceous pericarps. While consistent in this basic plan, the pericarps of Paullinia fruits are otherwise highly variable-in some species they are winged, whereas in others they are without wings or covered with spines. With the exception of the water-dispersed indehiscent spiny fruits of some members of Paullinia sect. Castanella, all species are dehiscent, opening their capsules while they are still attached to the branch, to reveal arillate animal-dispersed seeds. Here we present a molecular phylogeny of Paullinia derived from 11 molecular markers, including nine newly-developed single-copy nuclear markers amplified by microfluidics PCR. This is the first broadly sampled molecular phylogeny for the genus. Paullinia is supported as monophyletic and is sister to Cardiospermum L., which together are sister to Serjania Mill + Urvillea Kunth. We apply this novel phylogenetic hypothesis to test previous infrageneric classifications and to infer that unwinged fruits represent the ancestral condition, from which there were repeated evolutionary transitions and reversals. However, because the seeds of both winged and unwinged fruits are dispersed by animals, we conclude that the repeated transitions in fruit morphology may relate to visual display strategies to attract animal dispersers, and do not represent transitions to wind dispersal.
Collapse
Affiliation(s)
- Joyce G Chery
- Department of Biology, Pennsylvania State University, State College, PA 16803, USA.
| | - Pedro Acevedo-Rodríguez
- Smithsonian National Museum of Natural History, 10th and Constitution Avenue, NW, Washington, DC 20560, USA
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Chelsea D Specht
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, NY 14853 USA
| |
Collapse
|
16
|
RNA Sequencing of Peripheral Blood Revealed that the Neurotropic TRK Receptor Signaling Pathway Shows Apparent Correlation in Recovery Following Spinal Cord Injury at Small Cohort. J Mol Neurosci 2019; 68:221-233. [PMID: 30993646 DOI: 10.1007/s12031-019-01273-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/29/2019] [Indexed: 12/14/2022]
Abstract
Spinal cord injury (SCI) can be lethal; however, the precise mechanisms underlying healing are unclear, limiting the development of effective therapies. In this study, the molecular mechanisms involved in SCI were investigated. Clinical peripheral blood samples from normal individuals and patients with incomplete SCI (ISCI) and complete SCI (CSCI) were analyzed by RNA-Seq. The expression levels of EPHA4, CDK16, BAD, MAP2 Normal 2, EGR, and RHOB differed significantly between the SCI group and normal individuals, and these results were verified by q-PCR. A gene ontology (GO) enrichment analysis showed that differentially expressed genes were mostly enriched for the neurotrophin TRK receptor signaling pathway. We verified the expression of neurotrophic factors and found that they were all expressed most highly in the SCI group. The results of this study demonstrate that neurotrophic factors are highly expressed after SCI and the neurotrophin TRK receptor signaling pathway may be involved in the initiation of nerve system regeneration.
Collapse
|
17
|
Guo Y, Zhu C, Zhao S, Zhang S, Wang W, Fu H, Li X, Zhou C, Chen L, Lin Y, Lai Z. De novo transcriptome and phytochemical analyses reveal differentially expressed genes and characteristic secondary metabolites in the original oolong tea (Camellia sinensis) cultivar 'Tieguanyin' compared with cultivar 'Benshan'. BMC Genomics 2019; 20:265. [PMID: 30943892 PMCID: PMC6446291 DOI: 10.1186/s12864-019-5643-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/25/2019] [Indexed: 01/16/2023] Open
Abstract
Background The two original plants of the oolong tea cultivar (‘Tieguanyin’) are “Wei shuo” ‘Tieguanyin’—TGY (Wei) and “Wang shuo” ‘Tieguanyin’—TGY (Wang). Another cultivar, ‘Benshan’ (BS), is similar to TGY in its aroma, taste, and genetic make-up, but it lacks the “Yin Rhyme” flavor. We aimed to identify differences in biochemical characteristics and gene expression among these tea plants. Results The results of spectrophotometric, high performance liquid chromatography (HPLC), and gas chromatography-mass spectrometry (GC-MS) analyses revealed that TGY (Wei) and TGY (Wang) had deeper purple-colored leaves and higher contents of anthocyanin, catechins, caffeine, and limonene compared with BS. Analyses of transcriptome data revealed 12,420 differentially expressed genes (DEGs) among the cultivars. According to a Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the flavonoid, caffeine, and limonene metabolic pathways were highly enriched. The transcript levels of the genes involved in these three metabolic pathways were not significantly different between TGY (Wei) and TGY (Wang), except for two unigenes encoding IMPDH and SAMS, which are involved in caffeine metabolism. The comparison of TGY vs. BS revealed eight up-regulated genes (PAL, C4H, CHS, F3’H, F3H, DFR, ANS, and ANR) and two down-regulated genes (FLS and CCR) in flavonoid metabolism, four up-regulated genes (AMPD, IMPDH, SAMS, and 5′-Nase) and one down-regulated XDH gene in caffeine metabolism; and two down-regulated genes (ALDH and HIBADH) in limonene degradation. In addition, the expression levels of the transcription factor (TF) PAP1 were significantly higher in TGY than in BS. Therefore, high accumulation of flavonoids, caffeine, and limonene metabolites and the expression patterns of their related genes in TGY might be beneficial for the formation of the “Yin Rhyme” flavor. Conclusions Transcriptomic, HPLC, and GC-MS analyses of TGY (Wei), TGY (Wang), and BS indicated that the expression levels of genes related to secondary metabolism and high contents of catechins, anthocyanin, caffeine, and limonene may contribute to the formation of the “Yin Rhyme” flavor in TGY. These findings provide new insights into the relationship between the accumulation of secondary metabolites and sensory quality, and the molecular mechanisms underlying the formation of the unique flavor “Yin Rhyme” in TGY. Electronic supplementary material The online version of this article (10.1186/s12864-019-5643-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yuqiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Zhu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shanshan Zhao
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shuting Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenjian Wang
- Anxi Tea Research Institute, Anxi, 362400, China
| | - Haifeng Fu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaozhen Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chengzhe Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lan Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
18
|
Zhang H, Chen J, Zhang F, Song Y. Transcriptome analysis of callus from melon. Gene 2019; 684:131-138. [PMID: 30321656 DOI: 10.1016/j.gene.2018.10.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 09/21/2018] [Accepted: 10/11/2018] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To identify the key genes promoting the differentiation of melon non-embryogenic callus into embryogenic callus. METHODS The transcriptome sequencing analysis was used to analyze the mRNA sequence in embryogenic callus (Z) and non-embryogenic callus (F); transcript mapping, gene expression analysis, cluster analysis, classification analysis and enrichment analysis were then used to detect the differentially expressed genes and enriched pathways. RESULTS The correlation coefficient between sample Z and sample F was 0.929 after transcript mapping. The overall gene expression levels in sample Z were higher as compared with sample F. Furthermore, cluster analysis showed that the expression of genes involved in photosynthesis was increased in sample Z when comparing to F. Besides, the classification of differential Gene Ontology (GO) showed that many metabolic processes were affected with the metabolism enhanced in embryogenic callus. Interestingly, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis further demonstrated the high metabolic activity and active secondary metabolite formation in the embryogenic callus. CONCLUSION The genes associated with photosynthesis, metabolic pathways and biosynthesis of secondary metabolites may promote the differentiation of callus into embryogenic callus.
Collapse
Affiliation(s)
- Huijun Zhang
- Anhui Key Laboratory of Plant Resources and Biology, School of Life Science, Huaibei Normal University, No. 100 Dongshan Road, Huaibei 235000, Anhui Province, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture/Northeast Agricultural University, Haerbing 150030, Heilongjiang Province, China
| | - Jinfeng Chen
- College of Horticulture, Nanjing Agricultural University, NO.1 weigang, Nanjing 210095, Jiangsu, China.
| | - Fei Zhang
- Anhui Key Laboratory of Plant Resources and Biology, School of Life Science, Huaibei Normal University, No. 100 Dongshan Road, Huaibei 235000, Anhui Province, China
| | - Yunxian Song
- Anhui Key Laboratory of Plant Resources and Biology, School of Life Science, Huaibei Normal University, No. 100 Dongshan Road, Huaibei 235000, Anhui Province, China
| |
Collapse
|
19
|
Phylogenomics recovers monophyly and early Tertiary diversification of Dipteronia (Sapindaceae). Mol Phylogenet Evol 2019; 130:9-17. [DOI: 10.1016/j.ympev.2018.09.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/16/2018] [Accepted: 09/19/2018] [Indexed: 11/23/2022]
|
20
|
Chen Y, Li X, Su L, Chen X, Zhang S, Xu X, Zhang Z, Chen Y, XuHan X, Lin Y, Lai Z. Genome-wide identification and characterization of long non-coding RNAs involved in the early somatic embryogenesis in Dimocarpus longan Lour. BMC Genomics 2018; 19:805. [PMID: 30400813 PMCID: PMC6219066 DOI: 10.1186/s12864-018-5158-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 10/11/2018] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are involved in variable cleavage, transcriptional interference, regulation of DNA methylation and protein modification. However, the regulation of lncRNAs in plant somatic embryos remains unclear. The longan (Dimocarpus longan) somatic embryogenesis (SE) system is a good system for research on longan embryo development. RESULTS In this study, 7643 lncRNAs obtained during early SE in D. longan were identified by high-throughput sequencing, among which 6005 lncRNAs were expressed. Of the expressed lncRNAs, 4790 were found in all samples and 160 were specifically expressed in embryogenic callus (EC), 154 in incomplete embryogenic compact structures (ICpECs), and 376 in globular embryos (GEs). We annotated the 6005 expressed lncRNAs, and 1404 lncRNAs belonged to 506 noncoding RNA (ncRNA) families and 4682 lncRNAs were predicted to target protein-coding genes. The target genes included 5051 cis-regulated target genes (5712 pairs) and 1605 trans-regulated target genes (3618 pairs). KEGG analysis revealed that most of the differentially expressed target genes (mRNAs) of the lncRNAs were enriched in the "plant-pathogen interaction" and "plant hormone signaling" pathways during early longan SE. Real-time quantitative PCR confirmed that 20 selected lncRNAs showed significant differences in expression and that five lncRNAs were related to auxin response factors. Compared with the FPKM expression trends, 16 lncRNA expression trends were the same in qPCR. In lncRNA-miRNA-mRNA relationship prediction, 40 lncRNAs were predicted to function as eTMs for 15 miRNAs and 7 lncRNAs were identified as potential miRNA precursors. In addition, we verified the lncRNA-miRNA-mRNA regulatory relationships by transient expression of miRNAs (miR172a, miR159a.1 and miR398a). CONCLUSION Analyses of lncRNAs during early longan SE showed that differentially expressed lncRNAs were involved in expression regulation at each SE stage, and may form a regulatory network with miRNAs and mRNAs. These findings provide new insights into lncRNAs and lay a foundation for future functional analysis of lncRNAs during early longan SE.
Collapse
Affiliation(s)
- Yan Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Xue Li
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Liyao Su
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Xu Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Shuting Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Xiaoping Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Xu XuHan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Institut de la Recherche Interdisciplinaire de Toulouse, IRIT-ARI, 31300 Toulouse, France
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| |
Collapse
|
21
|
Chai M, Wang S, He J, Chen W, Fan Z, Li J, Wang Y. De novo Assembly and Transcriptome Characterization of Opisthopappus (Asteraceae) for Population Differentiation and Adaption. Front Genet 2018; 9:371. [PMID: 30283491 PMCID: PMC6156141 DOI: 10.3389/fgene.2018.00371] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/22/2018] [Indexed: 11/16/2022] Open
Abstract
Opisthopappus Shih (Asteraceae), an endangered genus endemic to the Taihang Mountains of China, is a high-value ornamental and medicinal plant consisting of two species, Opisthopappus longilobus shih and Opisthopappus taihangensis (Ling) Shih. However, the evolutionary relationships and the taxonomic characteristics between the two species remain unknown. In this study, high-throughput transcriptome sequencing was used to analyze the differential metabolic activity and gene expression and screened special molecular markers for exploring the genetic variation and species differentiation in Opisthopappus Shih. The results showed that 33,974 unigenes with an average size of 801 bp were obtained with optimization of de novo assembly. The comprehensive functional annotation based on Gene Ontology (GO), Cluster of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG) revealed that these unigenes were mainly related to many physiological, metabolic, and molecular processes. Furthermore, the comparative transcriptome analysis indicated that 3,410 differentially expressed genes were mainly involved in lipid, carbohydrate and amino acid metabolism, xenobiotics biodegradation and metabolism as well as environment adaptation via KEGG. Such as the CYP710A, GST, HSP90A and so on, could be the potential candidate genes for further investigating the molecular mechanism of physiological variations between O. taihangensis and O. longilobus. In addition, the potential 71,804 high quality single nucleotide polymorphisms (SNPs) and 1,444 simple sequence repeats (SSRs) were estimated. Based on the predicted SNP, we have developed eight SNP markers for population genetic analysis in Opisthopappus Shih. A significantly high level of genetic differentiation between the populations of O. longilobus and O. taihangensis were found, and they were clearly grouped into two distinct genetic clusters. These results conformed to the record of Flora Reipublicae Popularis Sinicae (FRPS) and unsupported the taxonomic status in the Flora of China. The transcriptome analysis of Opisthopappus Shih can contribute to in-depth exploring of internal mechanisms in species variation and differentiation based on molecular evidence. With the rich and valuable data resources, the more novel structural, functional, and comparative genomic studies will provide comprehensive insights into the evolutionary relationships between O. taihangensis and O. longilobus.
Collapse
Affiliation(s)
- Min Chai
- College of Life Science, Shanxi Normal University, Linfen, China
| | - Shengnan Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juan He
- College of Life Science, Shanxi Normal University, Linfen, China
| | - Wei Chen
- College of Life Science, Shanxi Normal University, Linfen, China
| | - Zelu Fan
- College of Life Science, Shanxi Normal University, Linfen, China
| | - Jia Li
- College of Life Science, Shanxi Normal University, Linfen, China
| | - Yiling Wang
- College of Life Science, Shanxi Normal University, Linfen, China
| |
Collapse
|
22
|
Seed-Specific Gene MOTHER of FT and TFL1(MFT) Involved in Embryogenesis, Hormones and Stress Responses in Dimocarpus longan Lour. Int J Mol Sci 2018; 19:ijms19082403. [PMID: 30110985 PMCID: PMC6122071 DOI: 10.3390/ijms19082403] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/09/2018] [Accepted: 08/10/2018] [Indexed: 11/30/2022] Open
Abstract
Mother of FT and TFL1 (MFT) belongs to phosphatidylethanolamine-binding protein (PEBP) family, which plays an important role in flowering time regulation, seed development, and germination. To gain insight into the molecular function of DlMFT in Dimocarpus longan Lour., we isolated DlMFT and its promoter sequence from longan embryogenic callus (EC). Bioinformatic analysis indicated that the promoter contained multiphytohormones and light responsive regulatory elements. Subcellular localization showed that the given the DlMFT signal localized in the nucleus, expression profiling implied that DlMFT showed significant upregulation during somatic embryogenesis (SE) and zygotic embryogenesis (ZE), and particular highly expressed in late or maturation stages. The accumulation of DlMFT was mainly detected in mature fruit and seed, while it was undetected in abortive seeds, and notably decreased during seed germination. DlMFT responded differentially to exogenous hormones in longan EC. Auxins, salicylic acid (SA) and methyl jasmonate (MeJa) suppressed its expression, however, abscisic acid (ABA), brassinosteroids (BR) showed the opposite function. Meanwhile, DlMFT differentially responded to various abiotic stresses. Our study revealed that DlMFT might be a key regulator of longan somatic and zygotic embryo development, and in seed germination, it is involved in complex plant hormones and abiotic stress signaling pathways.
Collapse
|
23
|
Lin Y, Min J, Lai R, Wu Z, Chen Y, Yu L, Cheng C, Jin Y, Tian Q, Liu Q, Liu W, Zhang C, Lin L, Zhang D, Thu M, Zhang Z, Liu S, Zhong C, Fang X, Wang J, Yang H, Varshney RK, Yin Y, Lai Z. Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics. Gigascience 2018; 6:1-14. [PMID: 28368449 PMCID: PMC5467034 DOI: 10.1093/gigascience/gix023] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 03/23/2017] [Indexed: 11/13/2022] Open
Abstract
Longan (Dimocarpus longan Lour.), an important subtropical fruit in the family Sapindaceae, is grown in more than 10 countries. Longan is an edible drupe fruit and a source of traditional medicine with polyphenol-rich traits. Tree size, alternate bearing, and witches' broom disease still pose serious problems. To gain insights into the genomic basis of longan traits, a draft genome sequence was assembled. The draft genome (about 471.88 Mb) of a Chinese longan cultivar, "Honghezi," was estimated to contain 31 007 genes and 261.88 Mb of repetitive sequences. No recent whole-genome-wide duplication event was detected in the genome. Whole-genome resequencing and analysis of 13 cultivated D. longan accessions revealed the extent of genetic diversity. Comparative transcriptome studies combined with genome-wide analysis revealed polyphenol-rich and pathogen resistance characteristics. Genes involved in secondary metabolism, especially those from significantly expanded (DHS, SDH, F3΄H, ANR, and UFGT) and contracted (PAL, CHS, and F3΄5΄H) gene families with tissue-specific expression, may be important contributors to the high accumulation levels of polyphenolic compounds observed in longan fruit. The high number of genes encoding nucleotide-binding site leucine-rich repeat (NBS-LRR) and leucine-rich repeat receptor-like kinase proteins, as well as the recent expansion and contraction of the NBS-LRR family, suggested a genomic basis for resistance to insects, fungus, and bacteria in this fruit tree. These data provide insights into the evolution and diversity of the longan genome. The comparative genomic and transcriptome analyses provided information about longan-specific traits, particularly genes involved in its polyphenol-rich and pathogen resistance characteristics.
Collapse
Affiliation(s)
- Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | | | - Ruilian Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | | | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Lili Yu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Chunzhen Cheng
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | | | - Qilin Tian
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | | | - Weihua Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | | | - Lixia Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Dongmin Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Minkyaw Thu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Shengcai Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Chunshui Zhong
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | | | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.,School of Plant Biology, The University of Western Australia, Crawley, Perth, Australia
| | - Ye Yin
- BGI-Shenzhen, Shenzhen 518083, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| |
Collapse
|
24
|
Góngora-Castillo E, Nic-Can GI, Galaz-Ávalos RM, Loyola-Vargas VM. Elaboration of Transcriptome During the Induction of Somatic Embryogenesis. Methods Mol Biol 2018; 1815:411-427. [PMID: 29981139 DOI: 10.1007/978-1-4939-8594-4_29] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Somatic embryogenesis (SE) is one of the most studied developmental processes due to its applications, such as plant micropropagation, transformation, and germplasm conservation. The use of massive techniques of sequencing, as well as the use of subtractive hybridization and macroarrays, has led to the identification of hundreds of genes involved in the SE process. These have been important developments to study the molecular aspects of the progress of SE. With the advent of the new massive techniques for sequencing RNA, it has been possible to see a more complete picture of whole processes. In this chapter we present a technique to handle the elaboration of the transcriptome from the extraction of RNA until the assembly of the complete transcriptome.
Collapse
Affiliation(s)
- Elsa Góngora-Castillo
- CONACYT Research Fellow-Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, Mexico.
| | - Geovanny I Nic-Can
- CONACYT Research Fellow-Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Rosa M Galaz-Ávalos
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, Mexico
| | - Víctor M Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, Mexico
| |
Collapse
|
25
|
Li H, Hu T, Amombo E, Fu J. Genome-wide identification of heat stress-responsive small RNAs in tall fescue (Festuca arundinacea) by high-throughput sequencing. JOURNAL OF PLANT PHYSIOLOGY 2017; 213:157-165. [PMID: 28388488 DOI: 10.1016/j.jplph.2017.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/07/2017] [Accepted: 03/09/2017] [Indexed: 05/21/2023]
Abstract
MicroRNAs (miRNAs) play vital roles in the adaptive response of plants to various abiotic and biotic stresses. Tall fescue (Festuca arundinacea Schreb.) is a major cool-season forage and turf grass species which is severely influenced by heat stress. To unravel possible heat stress-responsive miRNAs, high-throughput sequencing was employed for heat-tolerant PI578718 and heat-sensitive PI234881 genotypes growing in presence and absence of heat stress (40°C for 36h). By searching against the miRBase database, among 1421 reference monocotyledon miRNAs, more than 850 were identified in all samples. Among these miRNAs, 1.46% and 2.29% were differentially expressed in PI234881 and PI578718 under heat stress, respectively, and most of them were down-regulated. In addition, a total of 170 novel miRNAs belonging to 145 miRNA families were identified. Furthermore, putative targets of differentially expressed miRNAs were predicted. The regulation of selected miRNAs by heat stress was revalidated through quantitative reverse transcription PCR (qRT-PCR) analysis. Most of these miRNAs shared similar expression patterns; however, some showed distinct expression patterns under heat stress, with their putative targets displaying different transcription levels. This is the first genome-wide miRNA identification in tall fescue. miRNAs specific to PI578718, or those that exhibited differential expression profiles between the two genotypes under high temperature, were probably associated with the variation in thermotolerance of tall fescue. The differentially expressed miRNAs between these two tall fescue genotypes and their putative targeted genes will provide essential information for further study on miRNAs mediating heat response and facilitate to improve turf grass breeding.
Collapse
Affiliation(s)
- Huiying Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Lumo Street, Wuhan City, Hubei 430074, PR China
| | - Tao Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Lumo Street, Wuhan City, Hubei 430074, PR China
| | - Erick Amombo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Lumo Street, Wuhan City, Hubei 430074, PR China
| | - Jinmin Fu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Lumo Street, Wuhan City, Hubei 430074, PR China.
| |
Collapse
|
26
|
Jamaluddin ND, Mohd Noor N, Goh HH. Genome-wide transcriptome profiling of Carica papaya L. embryogenic callus. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:357-368. [PMID: 28461724 PMCID: PMC5391361 DOI: 10.1007/s12298-017-0429-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/24/2017] [Accepted: 03/06/2017] [Indexed: 05/22/2023]
Abstract
Genome-wide transcriptome profiling is a powerful tool to study global gene expression patterns in plant development. We report the first transcriptome profile analysis of papaya embryogenic callus to improve our understanding on genes associated with somatic embryogenesis. By using 3' mRNA-sequencing, we generated 6,190,687 processed reads and 47.0% were aligned to papaya genome reference, in which 21,170 (75.4%) of 27,082 annotated genes were found to be expressed but only 41% was expressed at functionally high levels. The top 10% of genes with high transcript abundance were significantly enriched in biological processes related to cell proliferation, stress response, and metabolism. Genes functioning in somatic embryogenesis such as SERK and LEA, hormone-related genes, stress-related genes, and genes involved in secondary metabolite biosynthesis pathways were highly expressed. Transcription factors such as NAC, WRKY, MYB, WUSCHEL, Agamous-like MADS-box protein and bHLH important in somatic embryos of other plants species were found to be expressed in papaya embryogenic callus. Abundant expression of enolase and ADH is consistent with proteome study of papaya somatic embryo. Our study highlights that some genes related to secondary metabolite biosynthesis, especially phenylpropanoid biosynthesis, were highly expressed in papaya embryogenic callus, which might have implication for cell factory applications. The discovery of all genes expressed in papaya embryogenic callus provides an important information into early biological processes during the induction of embryogenesis and useful for future research in other plant species.
Collapse
Affiliation(s)
- Nur Diyana Jamaluddin
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM, 43600 Bangi, Selangor Darul Ehsan Malaysia
| | - Normah Mohd Noor
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM, 43600 Bangi, Selangor Darul Ehsan Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM, 43600 Bangi, Selangor Darul Ehsan Malaysia
| |
Collapse
|
27
|
Du ZQ, Jin YH. Comparative transcriptome and potential antiviral signaling pathways analysis of the gills in the red swamp crayfish, Procambarus clarkii infected with White Spot Syndrome Virus (WSSV). Genet Mol Biol 2017; 40:168-180. [PMID: 28222204 PMCID: PMC5409774 DOI: 10.1590/1678-4685-gmb-2016-0133] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/05/2016] [Indexed: 11/21/2022] Open
Abstract
Red swamp crayfish is an important model organism for research of the invertebrate
innate immunity mechanism. Its excellent disease resistance against bacteria, fungi,
and viruses is well-known. However, the antiviral mechanisms of crayfish remain
unclear. In this study, we obtained high-quality sequence reads from normal and white
spot syndrome virus (WSSV)-challenged crayfish gills. For group normal (GN),
39,390,280 high-quality clean reads were randomly assembled to produce 172,591
contigs; whereas, 34,011,488 high-quality clean reads were randomly assembled to
produce 182,176 contigs for group WSSV-challenged (GW). After GO annotations
analysis, a total of 35,539 (90.01%), 14,931 (37.82%), 28,221 (71.48%), 25,290
(64.05%), 15,595 (39.50%), and 13,848 (35.07%) unigenes had significant matches with
sequences in the Nr, Nt, Swiss-Prot, KEGG, COG and GO databases, respectively.
Through the comparative analysis between GN and GW, 12,868 genes were identified as
differentially up-regulated DEGs, and 9,194 genes were identified as differentially
down-regulated DEGs. Ultimately, these DEGs were mapped into different signaling
pathways, including three important signaling pathways related to innate immunity
responses. These results could provide new insights into crayfish antiviral immunity
mechanism.
Collapse
Affiliation(s)
- Zhi-Qiang Du
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, Inner Mongolia Autonomous Region, China
| | - Yan-Hui Jin
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, Inner Mongolia Autonomous Region, China
| |
Collapse
|
28
|
Qiu L, Jiang B, Fang J, Shen Y, Fang Z, Rm SK, Yi K, Shen C, Yan D, Zheng B. Analysis of transcriptome in hickory (Carya cathayensis), and uncover the dynamics in the hormonal signaling pathway during graft process. BMC Genomics 2016; 17:935. [PMID: 27855649 PMCID: PMC5114764 DOI: 10.1186/s12864-016-3182-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 10/21/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hickory (Carya cathayensis), a woody plant with high nutritional and economic value, is widely planted in China. Due to its long juvenile phase, grafting is a useful technique for large-scale cultivation of hickory. To reveal the molecular mechanism during the graft process, we sequenced the transcriptomes of graft union in hickory. RESULTS In our study, six RNA-seq libraries yielded a total of 83,676,860 clean short reads comprising 4.19 Gb of sequence data. A large number of differentially expressed genes (DEGs) at three time points during the graft process were identified. In detail, 777 DEGs in the 7 d vs 0 d (day after grafting) comparison were classified into 11 enriched Gene Ontology (GO) categories, and 262 DEGs in the 14 d vs 0 d comparison were classified into 15 enriched GO categories. Furthermore, an overview of the PPI network was constructed by these DEGs. In addition, 20 genes related to the auxin-and cytokinin-signaling pathways were identified, and some were validated by qRT-PCR analysis. CONCLUSIONS Our comprehensive analysis provides basic information on the candidate genes and hormone signaling pathways involved in the graft process in hickory and other woody plants.
Collapse
Affiliation(s)
- Lingling Qiu
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China
| | - Bo Jiang
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China
| | - Jia Fang
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China.,Center for Cultivation of Subtropical Forest Resources (CCSFR), Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China
| | - Yike Shen
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China.,Center for Cultivation of Subtropical Forest Resources (CCSFR), Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China
| | - Zhongxiang Fang
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China.,Center for Cultivation of Subtropical Forest Resources (CCSFR), Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China
| | - Saravana Kumar Rm
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China.,Center for Cultivation of Subtropical Forest Resources (CCSFR), Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China
| | - Keke Yi
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chenjia Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Daoliang Yan
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China. .,Center for Cultivation of Subtropical Forest Resources (CCSFR), Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China.
| | - Bingsong Zheng
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China. .,Center for Cultivation of Subtropical Forest Resources (CCSFR), Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China.
| |
Collapse
|
29
|
Yi G, Zhao T, Yin Z, Tang P, Qiu Y, Yao X. Mining and characterizing EST-SSR markers from ESTs of Torreya grandis. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.02.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
30
|
Fang Z, Lai C, Zhang Y, Lai Z. Molecular cloning, structural and expression profiling of DlRan genes during somatic embryogenesis in Dimocarpus longan Lour. SPRINGERPLUS 2016; 5:181. [PMID: 27026877 PMCID: PMC4766155 DOI: 10.1186/s40064-016-1887-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 02/16/2016] [Indexed: 11/18/2022]
Abstract
To clone and examine expression profiles of DlRan genes during somatic embryogenesis in Dimocarpus longan Lour. Thirty cDNA sequences and two genomic sequences encoding DlRan proteins were isolated from longan embryogenic cultures. Structural analysis of DlRan genes revealed that the longan Ran gene family is more expanded than that of Arabidopsis. Expression analysis of DlRan genes during somatic embryogenesis uncovered a high abundance of DlRan genes in early embryogenic cultures and heart- and torpedo-shaped embryos. The expression of DlRan genes in embryogenic calli was affected by exogenous 2,4-dichlorophenoxyacetic acid treatment. DlRan is involved in 2,4-D induced somatic embryogenesis and development of somatic embryos in longan.
Collapse
Affiliation(s)
- Zhizhen Fang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002 Fujian China
| | - Chengchun Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002 Fujian China
| | - Yaling Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002 Fujian China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002 Fujian China
| |
Collapse
|
31
|
Shi X, Zhang C, Liu Q, Zhang Z, Zheng B, Bao M. De novo comparative transcriptome analysis provides new insights into sucrose induced somatic embryogenesis in camphor tree (Cinnamomum camphora L.). BMC Genomics 2016; 17:26. [PMID: 26727885 PMCID: PMC4700650 DOI: 10.1186/s12864-015-2357-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 09/11/2015] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Somatic embryogenesis is a notable illustration of cell totipotency, by which somatic cells undergo dedifferentiation and then differentiate into somatic embryos. Our previous work demonstrated that pretreatment of immature zygotic embryos with 0.5 M sucrose solution for 72 h efficiently induced somatic embryo initiation in camphor tree. To better understand the molecular basis of somatic embryogenesis induced by osmotic stress, de novo transcriptome sequencing of three tissues of camphor tree (immature zygotic embryos, sucrose-pretreated immature zygotic embryos, and somatic embryos induced from sucrose-pretreated zygotic embryos) were conducted using Illumina Hiseq 2000 platform. RESULTS A total of 30.70 G high quality clean reads were obtained from cDNA libraries of the three samples. The overall de novo assembly of cDNA sequence data generated 205592 transcripts, with an average length of 998 bp. 114229 unigenes (55.56 % of all transcripts) with an average length of 680 bp were annotated with gene descriptions, gene ontology terms or metabolic pathways based on Blastx search against Nr, Nt, Swissprot, GO, COG/KOG, and KEGG databases. CEGMA software identified 237 out of 248 ultra-conserved core proteins as 'complete' in the transcriptome assembly, showing a completeness of 95.6 %. A total of 897 genes previously annotated to be potentially involved in somatic embryogenesis were identified. Comparative transcriptome analysis showed that a total of 3335 genes were differentially expressed in the three samples. The differentially expressed genes were divided into six groups based on K-means clustering. Expression level analysis of 52 somatic embryogenesis-related genes indicated a high correlation between RNA-seq and qRT-PCR data. Gene enrichment analysis showed significantly differential expression of genes responding to stress and stimulus. CONCLUSIONS The present work reported a de novo transcriptome assembly and global analysis focused on gene expression changes during initiation and formation of somatic embryos in camphor tree. Differential expression of somatic embryogenesis-related genes indicates that sucrose induced somatic embryogenesis may share or partly share the mechanisms of somatic embryogenesis induced by plant hormones. This study provides comprehensive transcript information and gene expression data for camphor tree. It could also serve as an important platform resource for further functional studies in plant embryogenesis.
Collapse
Affiliation(s)
- Xueping Shi
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Cuijie Zhang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Qinhong Liu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Zhe Zhang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Bo Zheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| |
Collapse
|
32
|
Induction and quantitative proteomic analysis of cell dedifferentiation during callus formation of lotus (Nelumbo nucifera Gaertn.spp. baijianlian). J Proteomics 2016; 131:61-70. [DOI: 10.1016/j.jprot.2015.10.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/29/2015] [Accepted: 10/08/2015] [Indexed: 11/23/2022]
|
33
|
Liu CH, Fan C. De novo Transcriptome Assembly of Floral Buds of Pineapple and Identification of Differentially Expressed Genes in Response to Ethephon Induction. FRONTIERS IN PLANT SCIENCE 2016; 7:203. [PMID: 26955375 PMCID: PMC4767906 DOI: 10.3389/fpls.2016.00203] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 02/05/2016] [Indexed: 05/11/2023]
Abstract
A remarkable characteristic of pineapple is its ability to undergo floral induction in response to external ethylene stimulation. However, little information is available regarding the molecular mechanism underlying this process. In this study, the differentially expressed genes (DEGs) in plants exposed to 1.80 mL·L(-1) (T1) or 2.40 mL·L(-1) ethephon (T2) compared with Ct plants (control, cleaning water) were identified using RNA-seq and gene expression profiling. Illumina sequencing generated 65,825,224 high-quality reads that were assembled into 129,594 unigenes with an average sequence length of 1173 bp. Of these unigenes, 24,775 were assigned to specific KEGG pathways, of which metabolic pathways and biosynthesis of secondary metabolites were the most highly represented. Gene Ontology (GO) analysis of the annotated unigenes revealed that the majority were involved in metabolic and cellular processes, cell and cell part, catalytic activity and binding. Gene expression profiling analysis revealed 3788, 3062, and 758 DEGs in the comparisons of T1 with Ct, T2 with Ct, and T2 with T1, respectively. GO analysis indicated that these DEGs were predominantly annotated to metabolic and cellular processes, cell and cell part, catalytic activity, and binding. KEGG pathway analysis revealed the enrichment of several important pathways among the DEGs, including metabolic pathways, biosynthesis of secondary metabolites and plant hormone signal transduction. Thirteen DEGs were identified as candidate genes associated with the process of floral induction by ethephon, including three ERF-like genes, one ETR-like gene, one LTI-like gene, one FT-like gene, one VRN1-like gene, three FRI-like genes, one AP1-like gene, one CAL-like gene, and one AG-like gene. qPCR analysis indicated that the changes in the expression of these 13 candidate genes were consistent with the alterations in the corresponding RPKM values, confirming the accuracy and credibility of the RNA-seq and gene expression profiling results. Ethephon-mediated induction likely mimics the process of vernalization in the floral transition in pineapple by increasing LTI, FT, and VRN1 expression and promoting the up-regulation of floral meristem identity genes involved in flower development. The candidate genes screened can be used in investigations of the molecular mechanisms of the flowering pathway and of various other biological mechanisms in pineapple.
Collapse
Affiliation(s)
- Chuan-He Liu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural SciencesGuangzhou, China
- Key Laboratory of South Subtropical Fruit Biology, Genetic Resource Utilization Ministry of AgricultureGuangzhou, China
- *Correspondence: Chuan-He Liu
| | - Chao Fan
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural SciencesGuangzhou, China
- Key Laboratory of South Subtropical Fruit Biology, Genetic Resource Utilization Ministry of AgricultureGuangzhou, China
| |
Collapse
|
34
|
Castro JC, Maddox JD, Cobos M, Requena D, Zimic M, Bombarely A, Imán SA, Cerdeira LA, Medina AE. De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis. BMC Genomics 2015; 16:997. [PMID: 26602763 PMCID: PMC4658800 DOI: 10.1186/s12864-015-2225-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 11/17/2015] [Indexed: 01/13/2023] Open
Abstract
Background Myrciaria dubia is an Amazonian fruit shrub that produces numerous bioactive phytochemicals, but is best known by its high L-ascorbic acid (AsA) content in fruits. Pronounced variation in AsA content has been observed both within and among individuals, but the genetic factors responsible for this variation are largely unknown. The goals of this research, therefore, were to assemble, characterize, and annotate the fruit transcriptome of M. dubia in order to reconstruct metabolic pathways and determine if multiple pathways contribute to AsA biosynthesis. Results In total 24,551,882 high-quality sequence reads were de novo assembled into 70,048 unigenes (mean length = 1150 bp, N50 = 1775 bp). Assembled sequences were annotated using BLASTX against public databases such as TAIR, GR-protein, FB, MGI, RGD, ZFIN, SGN, WB, TIGR_CMR, and JCVI-CMR with 75.2 % of unigenes having annotations. Of the three core GO annotation categories, biological processes comprised 53.6 % of the total assigned annotations, whereas cellular components and molecular functions comprised 23.3 and 23.1 %, respectively. Based on the KEGG pathway assignment of the functionally annotated transcripts, five metabolic pathways for AsA biosynthesis were identified: animal-like pathway, myo-inositol pathway, L-gulose pathway, D-mannose/L-galactose pathway, and uronic acid pathway. All transcripts coding enzymes involved in the ascorbate-glutathione cycle were also identified. Finally, we used the assembly to identified 6314 genic microsatellites and 23,481 high quality SNPs. Conclusions This study describes the first next-generation sequencing effort and transcriptome annotation of a non-model Amazonian plant that is relevant for AsA production and other bioactive phytochemicals. Genes encoding key enzymes were successfully identified and metabolic pathways involved in biosynthesis of AsA, anthocyanins, and other metabolic pathways have been reconstructed. The identification of these genes and pathways is in agreement with the empirically observed capability of M. dubia to synthesize and accumulate AsA and other important molecules, and adds to our current knowledge of the molecular biology and biochemistry of their production in plants. By providing insights into the mechanisms underpinning these metabolic processes, these results can be used to direct efforts to genetically manipulate this organism in order to enhance the production of these bioactive phytochemicals. The accumulation of AsA precursor and discovery of genes associated with their biosynthesis and metabolism in M. dubia is intriguing and worthy of further investigation. The sequences and pathways produced here present the genetic framework required for further studies. Quantitative transcriptomics in concert with studies of the genome, proteome, and metabolome under conditions that stimulate production and accumulation of AsA and their precursors are needed to provide a more comprehensive view of how these pathways for AsA metabolism are regulated and linked in this species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2225-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Juan C Castro
- Unidad Especializada de Biotecnología, Centro de Investigaciones de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonía Peruana (UNAP), Pasaje Los Paujiles S/N, San Juan Bautista, Iquitos, Perú. .,Círculo de Investigación en Plantas con Efecto en Salud (FONDECYT N° 010-2014), Lima, Perú.
| | - J Dylan Maddox
- Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum of Natural History, Chicago, IL, USA.
| | - Marianela Cobos
- Laboratorio de Biotecnología y Bioenergética, Universidad Científica del Perú (UCP), Av. Abelardo Quiñones km 2.5, San Juan Bautista, Iquitos, Perú.
| | - David Requena
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo (LID), Facultad de Ciencias, Universidad Peruana Cayetano Heredia (UPCH), Av. Honorio Delgado 430, San Martín de Porres, Lima, Perú. .,FARVET S.A.C. Carretera Panamericana Sur N° 766 Km 198.5, Chincha Alta, Ica, Perú.
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo (LID), Facultad de Ciencias, Universidad Peruana Cayetano Heredia (UPCH), Av. Honorio Delgado 430, San Martín de Porres, Lima, Perú. .,FARVET S.A.C. Carretera Panamericana Sur N° 766 Km 198.5, Chincha Alta, Ica, Perú.
| | | | - Sixto A Imán
- Área de Conservación de Recursos Fitogenéticos, Instituto Nacional de Innovación Agraria (INIA), Calle San Roque 209, Iquitos, Perú.
| | - Luis A Cerdeira
- Unidad Especializada de Biotecnología, Centro de Investigaciones de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonía Peruana (UNAP), Pasaje Los Paujiles S/N, San Juan Bautista, Iquitos, Perú.
| | - Andersson E Medina
- Unidad Especializada de Biotecnología, Centro de Investigaciones de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonía Peruana (UNAP), Pasaje Los Paujiles S/N, San Juan Bautista, Iquitos, Perú.
| |
Collapse
|
35
|
Sun H, Liu Y, Gai Y, Geng J, Chen L, Liu H, Kang L, Tian Y, Li Y. De novo sequencing and analysis of the cranberry fruit transcriptome to identify putative genes involved in flavonoid biosynthesis, transport and regulation. BMC Genomics 2015; 16:652. [PMID: 26330221 PMCID: PMC4556307 DOI: 10.1186/s12864-015-1842-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 08/14/2015] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Cranberries (Vaccinium macrocarpon Ait.), renowned for their excellent health benefits, are an important berry crop. Here, we performed transcriptome sequencing of one cranberry cultivar, from fruits at two different developmental stages, on the Illumina HiSeq 2000 platform. Our main goals were to identify putative genes for major metabolic pathways of bioactive compounds and compare the expression patterns between white fruit (W) and red fruit (R) in cranberry. RESULTS In this study, two cDNA libraries of W and R were constructed. Approximately 119 million raw sequencing reads were generated and assembled de novo, yielding 57,331 high quality unigenes with an average length of 739 bp. Using BLASTx, 38,460 unigenes were identified as putative homologs of annotated sequences in public protein databases, including NCBI NR, NT, Swiss-Prot, KEGG, COG and GO. Of these, 21,898 unigenes mapped to 128 KEGG pathways, with the metabolic pathways, secondary metabolites, glycerophospholipid metabolism, ether lipid metabolism, starch and sucrose metabolism, purine metabolism, and pyrimidine metabolism being well represented. Among them, many candidate genes were involved in flavonoid biosynthesis, transport and regulation. Furthermore, digital gene expression (DEG) analysis identified 3,257 unigenes that were differentially expressed between the two fruit developmental stages. In addition, 14,473 simple sequence repeats (SSRs) were detected. CONCLUSIONS Our results present comprehensive gene expression information about the cranberry fruit transcriptome that could facilitate our understanding of the molecular mechanisms of fruit development in cranberries. Although it will be necessary to validate the functions carried out by these genes, these results could be used to improve the quality of breeding programs for the cranberry and related species.
Collapse
Affiliation(s)
- Haiyue Sun
- College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China.
| | - Yushan Liu
- College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China.
| | - Yuzhuo Gai
- College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China.
| | - Jinman Geng
- College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China.
| | - Li Chen
- College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China.
| | - Hongdi Liu
- College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China.
| | - Limin Kang
- College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China.
| | - Youwen Tian
- College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China.
| | - Yadong Li
- College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China.
| |
Collapse
|
36
|
Gao JP, Wang D, Cao LY, Sun HF. Transcriptome sequencing of Codonopsis pilosula and identification of candidate genes involved in polysaccharide biosynthesis. PLoS One 2015; 10:e0117342. [PMID: 25719364 PMCID: PMC4342239 DOI: 10.1371/journal.pone.0117342] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 12/22/2014] [Indexed: 01/01/2023] Open
Abstract
Background Codonopsis pilosula (Franch.) Nannf. is one of the most widely used medicinal plants. Although chemical and pharmacological studies have shown that codonopsis polysaccharides (CPPs) are bioactive compounds and that their composition is variable, their biosynthetic pathways remain largely unknown. Next-generation sequencing is an efficient and high-throughput technique that allows the identification of candidate genes involved in secondary metabolism. Principal Findings To identify the components involved in CPP biosynthesis, a transcriptome library, prepared using root and other tissues, was assembled with the help of Illumina sequencing. A total of 9.2 Gb of clean nucleotides was obtained comprising 91,175,044 clean reads, 102,125 contigs, and 45,511 unigenes. After aligning the sequences to the public protein databases, 76.1% of the unigenes were annotated. Among these annotated unigenes, 26,189 were assigned to Gene Ontology categories, 11,415 to Clusters of Orthologous Groups, and 18,848 to Kyoto Encyclopedia of Genes and Genomes pathways. Analysis of abundance of transcripts in the library showed that genes, including those encoding metallothionein, aquaporin, and cysteine protease that are related to stress responses, were in the top list. Among genes involved in the biosynthesis of CPP, those responsible for the synthesis of UDP-L-arabinose and UDP-xylose were highly expressed. Significance To our knowledge, this is the first study to provide a public transcriptome dataset prepared from C. pilosula and an outline of the biosynthetic pathway of polysaccharides in a medicinal plant. Identified candidate genes involved in CPP biosynthesis provide understanding of the biosynthesis and regulation of CPP at the molecular level.
Collapse
Affiliation(s)
- Jian Ping Gao
- College of Pharmacy, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Dong Wang
- College of Pharmacy, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ling Ya Cao
- College of Pharmacy, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Hai Feng Sun
- College of Chemistry & Chemical Engineering, Shanxi University, Taiyuan, Shanxi, China
| |
Collapse
|
37
|
Yan X, Zhang X, Lu M, He Y, An H. De novo sequencing analysis of the Rosa roxburghii fruit transcriptome reveals putative ascorbate biosynthetic genes and EST-SSR markers. Gene 2015; 561:54-62. [PMID: 25701597 DOI: 10.1016/j.gene.2015.02.054] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/15/2015] [Accepted: 02/03/2015] [Indexed: 10/24/2022]
Abstract
Rosa roxburghii Tratt. is a well-known ornamental rose species native to China. In addition, the fruits of this species are valued for their nutritional and medicinal characteristics, especially their high ascorbic acid (AsA) levels. Nevertheless, AsA biosynthesis in R. roxburghii fruit has not been explored in detail because of a lack of genomic resources for this species. High-throughput transcriptomic sequencing generating large volumes of transcript sequence data can aid in gene discovery and molecular marker development. In this study, we generated more than 53 million clean reads using Illumina paired-end sequencing technology. De novo assembly yielded 106,590 unigenes, with an average length of 343 bp. On the basis of sequence similarity to known proteins, 9301 and 2393 unigenes were classified into Gene Ontology and Clusters of Orthologous Group categories, respectively. There were 7480 unigenes assigned to 124 pathways in the Kyoto Encyclopedia of Gene and Genome pathway database. BLASTx searches identified 498 unique putative transcripts encoding various transcription factors, some known to regulate fruit development. qRT-PCR validated the expressions of most of the genes encoding the main enzymes involved in ascorbate biosynthesis. In addition, 9131 potential simple sequence repeat (SSR) loci were identified among the unigenes. One hundred and two primer pairs were synthesized and 71 pairs produced an amplification product during initial screening. Among the amplified products, 30 were polymorphic in the 16 R. roxburghii germplasms tested. Our study was the first to produce a large volume of transcriptome data from R. roxburghii. The resulting sequence collection is a valuable resource for gene discovery and marker-assisted selective breeding in this rose species.
Collapse
Affiliation(s)
- Xiuqin Yan
- Guizhou Engineering Research Center for Fruit Crops, Agricultural College, Guizhou University, Guiyang 550025, PR China
| | - Xue Zhang
- Guizhou Engineering Research Center for Fruit Crops, Agricultural College, Guizhou University, Guiyang 550025, PR China
| | - Min Lu
- Guizhou Engineering Research Center for Fruit Crops, Agricultural College, Guizhou University, Guiyang 550025, PR China
| | - Yong He
- Guizhou Tongjitang Pharmaceutical Co. Ltd, Guiyang 550025, PR China
| | - Huaming An
- Guizhou Engineering Research Center for Fruit Crops, Agricultural College, Guizhou University, Guiyang 550025, PR China.
| |
Collapse
|
38
|
Lin Y, Lin L, Lai R, Liu W, Chen Y, Zhang Z, XuHan X, Lai Z. MicroRNA390-Directed TAS3 Cleavage Leads to the Production of tasiRNA-ARF3/4 During Somatic Embryogenesis in Dimocarpus longan Lour. FRONTIERS IN PLANT SCIENCE 2015; 6:1119. [PMID: 26734029 PMCID: PMC4680215 DOI: 10.3389/fpls.2015.01119] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 11/26/2015] [Indexed: 05/18/2023]
Abstract
Trans-acting short-interfering RNAs (tasiRNAs) originate from TAS3 families through microRNA (miRNA) 390-guided cleavage of primary transcripts and target auxin response factors (ARF3/-4), which are involved in the normal development of lateral roots and flowers in plants. However, their roles in embryo development are still unclear. Here, the pathway miR390-TAS3-ARF3/-4 was identified systematically for the first time during somatic embryo development in Dimocarpus longan. We identified the miR390 primary transcript and promoter. The promoter contained cis-acting elements responsive to stimuli such as light, salicylic acid, anaerobic induction, fungal elicitor, circadian control, and heat stress. The longan TAS3 transcript, containing two miR390-binding sites, was isolated; the miR390- guided cleavage site located near the 3' end of the TAS3 transcript was verified. Eight TAS3-tasiRNAs with the 21-nucleotides phase were found among longan small RNA data, further confirming that miR390-directed TAS3 cleavage leads to the production of tasiRNA in longan. Among them, TAS3_5'D5+ and 5'D6+ tasiRNAs were highly abundant, and verified to target ARF3 and -4, implying that miR390-guided TAS3 cleavage with 21-nucleotides phase leading to the production of tasiRNA-ARF is conserved in plants. Pri-miR390 was highly expressed in friable-embryogenic callus (EC), and less expressed in incomplete compact pro-embryogenic cultures, while miR390 showed its lowest expression in EC and highest expression in torpedo-shaped embryos (TEs). DlTAS3 and DlARF4 both exhibited their lowest expressions in EC, and reached their peaks in the globular embryos stage, which were mainly inversely proportional to the expression of miR390, especially at the globular embryos to cotyledonary embryos (CEs) stages. While DlARF3 showed little variation from the EC to TEs stages, and exhibited its lowest expression in the CEs stage. There was a general lack of correlation between the expressions of DlARF3 and miR390. In addition, pri-miR390, DlTAS3, DlARF3 and -4 were up-regulated by 2,4-D in a concentration-dependent manner. They were also preferentially expressed in roots, pulp, and seeds of 'Sijimi' longan, implying their extended roles in the development of longan roots and fruit. This study provided insights into a possible role of miR390-tasiRNAs-ARF in plant somatic embryo development.
Collapse
|
39
|
Niu J, An J, Wang L, Fang C, Ha D, Fu C, Qiu L, Yu H, Zhao H, Hou X, Xiang Z, Zhou S, Zhang Z, Feng X, Lin S. Transcriptomic analysis revealed the mechanism of oil dynamic accumulation during developing Siberian apricot (Prunus sibirica L.) seed kernels for the development of woody biodiesel. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:29. [PMID: 25834637 PMCID: PMC4381669 DOI: 10.1186/s13068-015-0213-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 01/27/2015] [Indexed: 05/11/2023]
Abstract
BACKGROUND Siberian apricot (Prunus sibirica L.) has emerged as a novel potential source of biodiesel in China, but the molecular regulatory mechanism of oil accumulation in Siberian apricot seed kernels (SASK) is still unknown at present. To better develop SASK oil as woody biodiesel, it is essential to profile transcriptome and to identify the full repertoire of potential unigenes involved in the formation and accumulation of oil SASK during the different developing stages. RESULTS We firstly detected the temporal patterns for oil content and fatty acid (FA) compositions of SASK in 7 different developing stages. The best time for obtaining the high quality and quantity of SASK oil was characterized at 60 days after flowering (DAF), and the representative periods (10, 30, 50, 60, and 70 DAF) were selected for transcriptomic analysis. By Illumina/Solexa sequencings, approximately 65 million short reads (average length = 96 bp) were obtained, and then assembled into 124,070 unigenes by Trinity strategy (mean size = 829.62 bp). A total of 3,000, 2,781, 2,620, and 2,675 differentially expressed unigenes were identified at 30, 50, 60, and 70 DAF (10 DAF as the control) by DESeq method, respectively. The relationship between the unigene transcriptional profiles and the oil dynamic patterns in developing SASK was comparatively analyzed, and the specific unigenes encoding some known enzymes and transcription factors involved in acetyl-coenzyme A (acetyl-CoA) formation and oil accumulation were determined. Additionally, 5 key metabolic genes implicated in SASK oil accumulation were experimentally validated by quantitative real-time PCR (qRT-PCR). Our findings could help to construction of oil accumulated pathway and to elucidate the molecular regulatory mechanism of increased oil production in developing SASK. CONCLUSIONS This is the first study of oil temporal patterns, transcriptome sequencings, and differential profiles in developing SASK. All our results will serve as the important foundation to further deeply explore the regulatory mechanism of SASK high-quality oil accumulation, and may also provide some reference for researching the woody biodiesel plants.
Collapse
Affiliation(s)
- Jun Niu
- />College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Jiyong An
- />College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Libing Wang
- />Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 10091 China
| | - Chengliang Fang
- />Jigongshan National Nature Reserve, Xingyang, 464133 China
| | - Denglong Ha
- />Jigongshan National Nature Reserve, Xingyang, 464133 China
| | - Chengyu Fu
- />Liaocheng Food and Drug Administration, Liaocheng, 252000 Shandong China
| | - Lin Qiu
- />Jigongshan National Nature Reserve, Xingyang, 464133 China
| | - Haiyan Yu
- />Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 10091 China
| | - Haiyan Zhao
- />Jigongshan National Nature Reserve, Xingyang, 464133 China
| | - Xinyu Hou
- />College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Zheng Xiang
- />College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Sufan Zhou
- />College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Zhixiang Zhang
- />College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Xinyi Feng
- />College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Shanzhi Lin
- />College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| |
Collapse
|
40
|
Wang B, Tan HW, Fang W, Meinhardt LW, Mischke S, Matsumoto T, Zhang D. Developing single nucleotide polymorphism (SNP) markers from transcriptome sequences for identification of longan (Dimocarpus longan) germplasm. HORTICULTURE RESEARCH 2015; 2:14065. [PMID: 26504559 PMCID: PMC4595986 DOI: 10.1038/hortres.2014.65] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 05/03/2023]
Abstract
Longan (Dimocarpus longan Lour.) is an important tropical fruit tree crop. Accurate varietal identification is essential for germplasm management and breeding. Using longan transcriptome sequences from public databases, we developed single nucleotide polymorphism (SNP) markers; validated 60 SNPs in 50 longan germplasm accessions, including cultivated varieties and wild germplasm; and designated 25 SNP markers that unambiguously identified all tested longan varieties with high statistical rigor (P<0.0001). Multiple trees from the same clone were verified and off-type trees were identified. Diversity analysis revealed genetic relationships among analyzed accessions. Cultivated varieties differed significantly from wild populations (F st=0.300; P<0.001), demonstrating untapped genetic diversity for germplasm conservation and utilization. Within cultivated varieties, apparent differences between varieties from China and those from Thailand and Hawaii indicated geographic patterns of genetic differentiation. These SNP markers provide a powerful tool to manage longan genetic resources and breeding, with accurate and efficient genotype identification.
Collapse
Affiliation(s)
- Boyi Wang
- Yunnan Forestry Technological College, Kunming 650224, Yunnan, China
- Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
| | - Hua-Wei Tan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Wanping Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Lyndel W Meinhardt
- Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
| | - Sue Mischke
- Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
| | - Tracie Matsumoto
- Tropical Plant Genetic Resources and Disease Research, USDA-ARS, Hilo, HI 96720, USA
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
| |
Collapse
|
41
|
Ma Q, Zhou W, Zhang P. Transition from somatic embryo to friable embryogenic callus in cassava: dynamic changes in cellular structure, physiological status, and gene expression profiles. FRONTIERS IN PLANT SCIENCE 2015; 6:824. [PMID: 26500668 PMCID: PMC4594424 DOI: 10.3389/fpls.2015.00824] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/22/2015] [Indexed: 05/20/2023]
Abstract
Friable embryogenic callus (FEC) is considered as the most suitable material for efficient genetic transformation of cassava. Heavy genotype dependence of FEC induction and amenability to somaclonal variation limits the production and maintenance of reliable FEC. Identifying key elements involved in biological processes from somatic embryos (SEs) to FEC at different stages provides critical insights for FEC improvement. Cytological observation showed a dramatic change of subcellular structures among SEs, fresh FEC (FFEC), and old FEC (OFEC). Decrease of sucrose and increase of fructose and glucose were detected in OFEC. A total of 6871 differentially expressed genes (DEGs) were identified from SEs, FFEC, and OFEC by RNA-seq. Analysis of the DEGs showed that FEC induction was accompanied by the process of dedifferentiation, whereas the epigenetics modification occurred during the continuous subculturing process. The cell structure was reconstructed, mainly including the GO terms of "cell periphery" and "external encapsulating structure"; in parallel, the internal mechanisms changed correspondingly, including the biological process of glycolysis and metabolisms of alanine, aspartate, and glutamate. The significant reduction of genomic DNA methylation in OFEC indicated altered gene expression via chromatin modification. These results indicate that the induction and long-term subculture of FEC is a complicated biological process involving changes of genome modification, gene expression, and subcellular reconstruction. The findings will be useful for improving FEC induction and maintenance from farmer-preferred cassava cultivars recalcitrant to genetic transformation, hence improving cassava through genetic engineering.
Collapse
Affiliation(s)
| | | | - Peng Zhang
- *Correspondence: Peng Zhang, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032 Shanghai, China
| |
Collapse
|
42
|
Lin Y, Lai Z, Tian Q, Lin L, Lai R, Yang M, Zhang D, Chen Y, Zhang Z. Endogenous target mimics down-regulate miR160 mediation of ARF10, -16, and -17 cleavage during somatic embryogenesis in Dimocarpus longan Lour. FRONTIERS IN PLANT SCIENCE 2015; 6:956. [PMID: 26594219 PMCID: PMC4633511 DOI: 10.3389/fpls.2015.00956] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 10/20/2015] [Indexed: 05/20/2023]
Abstract
MicroRNA160 plays a critical role in plant development by negatively regulating the auxin response factors ARF10, -16, and -17. However, the ways in which miR160 expression is regulated at the transcriptional level, and how miR160 interacts with its targets during plant embryo development, remain unknown. Here, we studied the regulatory relationships among endogenous target mimics (eTMs), and miR160 and its targets, and their involvement in hormone signaling and somatic embryogenesis (SE) in Dimocarpus longan. We identified miR160 family members and isolated the miR160 precursor, primary transcript, and promoter. The promoter contained cis-acting elements responsive to stimuli such as light, abscisic acid, salicylic acid (SA) and heat stress. The pri-miR160 was down-regulated in response to SA but up-regulated by gibberellic acid, ethylene, and methyl jasmonate treatment, suggesting that pri-miR160 was associated with hormone transduction. Dlo-miR160a, -a(∗) and -d(∗) reached expression peaks in torpedo-shaped embryos, globular embryos and cotyledonary embryos, respectively, but were barely detectable in friable-embryogenic callus. This suggests that they have expression-related and functional diversity, especially during the middle and later developmental stages of SE. Four potential eTMs for miR160 were identified. Two of them, glucan endo-1,3-beta- glucosidase-like protein 2-like and calpain-type cysteine protease DEK1, were confirmed to control the corresponding dlo-miR160a(∗) expression level. This suggests that they may function to abolish the binding between dlo-miR160a(∗) and its targets. These two eTMs also participated in 2,4-D and ABA signal transduction. DlARF10, -16, and -17 targeting by dlo-miR160a was confirmed; their expression levels were higher in friable-embryogenic callus and incomplete compact pro-embryogenic cultures and responded to 2,4-D, suggesting they may play a major role in the early stages of longan SE dependent on 2,4-D. The eTMs, miR160, and ARF10, -16, and -17 exhibited tissue specificity in 'Sijimi' longan vegetative and reproductive organs, but were not significant negatively correlated. These results provide insights into the possible role of the eTM-miR160-ARF10-16-17 pathway in longan somatic embryo development.
Collapse
|
43
|
Lin Y, Lai Z, Tian Q, Lin L, Lai R, Yang M, Zhang D, Chen Y, Zhang Z. Endogenous target mimics down-regulate miR160 mediation of ARF10, -16, and -17 cleavage during somatic embryogenesis in Dimocarpus longan Lour. FRONTIERS IN PLANT SCIENCE 2015. [PMID: 26594219 DOI: 10.1007/s11032-015-0420-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
MicroRNA160 plays a critical role in plant development by negatively regulating the auxin response factors ARF10, -16, and -17. However, the ways in which miR160 expression is regulated at the transcriptional level, and how miR160 interacts with its targets during plant embryo development, remain unknown. Here, we studied the regulatory relationships among endogenous target mimics (eTMs), and miR160 and its targets, and their involvement in hormone signaling and somatic embryogenesis (SE) in Dimocarpus longan. We identified miR160 family members and isolated the miR160 precursor, primary transcript, and promoter. The promoter contained cis-acting elements responsive to stimuli such as light, abscisic acid, salicylic acid (SA) and heat stress. The pri-miR160 was down-regulated in response to SA but up-regulated by gibberellic acid, ethylene, and methyl jasmonate treatment, suggesting that pri-miR160 was associated with hormone transduction. Dlo-miR160a, -a(∗) and -d(∗) reached expression peaks in torpedo-shaped embryos, globular embryos and cotyledonary embryos, respectively, but were barely detectable in friable-embryogenic callus. This suggests that they have expression-related and functional diversity, especially during the middle and later developmental stages of SE. Four potential eTMs for miR160 were identified. Two of them, glucan endo-1,3-beta- glucosidase-like protein 2-like and calpain-type cysteine protease DEK1, were confirmed to control the corresponding dlo-miR160a(∗) expression level. This suggests that they may function to abolish the binding between dlo-miR160a(∗) and its targets. These two eTMs also participated in 2,4-D and ABA signal transduction. DlARF10, -16, and -17 targeting by dlo-miR160a was confirmed; their expression levels were higher in friable-embryogenic callus and incomplete compact pro-embryogenic cultures and responded to 2,4-D, suggesting they may play a major role in the early stages of longan SE dependent on 2,4-D. The eTMs, miR160, and ARF10, -16, and -17 exhibited tissue specificity in 'Sijimi' longan vegetative and reproductive organs, but were not significant negatively correlated. These results provide insights into the possible role of the eTM-miR160-ARF10-16-17 pathway in longan somatic embryo development.
Collapse
Affiliation(s)
- Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Qilin Tian
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Lixia Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Ruilian Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Manman Yang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Dongmin Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| |
Collapse
|
44
|
Hu T, Sun X, Zhang X, Nevo E, Fu J. An RNA sequencing transcriptome analysis of the high-temperature stressed tall fescue reveals novel insights into plant thermotolerance. BMC Genomics 2014; 15:1147. [PMID: 25527327 PMCID: PMC4378353 DOI: 10.1186/1471-2164-15-1147] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 12/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tall fescue (Festuca arundinacea Schreb.) is major cool-season forage and turf grass species worldwide, but high-temperature is a major environmental stress that dramatically threaten forage production and turf management of tall fescue. However, very little is known about the whole-genome molecular mechanisms contributing to thermotolerance. The objectives of this study were to analyzed genome-wide gene expression profiles in the leaves of two tall fescue genotypes, heat tolerant 'PI578718' and heat sensitive 'PI234881' using high-throughput RNA sequencing. RESULTS A total of 262 million high-quality paired-end reads were generated and assembled into 31,803 unigenes with an average length of 1,840 bp. Of these, 12,974 unigenes showed different expression patterns in response to heat stress and were categorized into 49 Gene Ontology functional subcategories. In addition, the variance of enrichment degree in each functional subcategory between PI578718 and PI234881 increased with increasing treatment time. Cell division and cell cycle genes showed a massive increase in transcript abundance in heat-stressed plants and more activated genes were detected in PI 578718 by Kyoto Encyclopedia of Genes and Genomes pathways analysis. Low molecular weight heat shock protein (LMW-HSP, HSP20) showed activated in two stressed genotypes and high molecular weight HSP (HMW-HSP, HSP90) just in PI578718. Assimilation such as photosynthesis, carbon fixation, CH4, N, S metabolism decreased along with increased dissimilation such as oxidative phosphorylation. CONCLUSIONS The assembled transcriptome of tall fescue could serve as a global description of expressed genes and provide more molecular resources for future functional characterization analysis of genomics in cool-season turfgrass in response to high-temperature. Increased cell division, LMW/HMW-HSP, dissimilation and antioxidant transcript amounts in tall fescue were correlated with successful resistance to high temperature stress.
Collapse
Affiliation(s)
| | | | | | - Eviatar Nevo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan 430074, Hubei, P,R, China.
| | | |
Collapse
|
45
|
Verma M, Ghangal R, Sharma R, Sinha AK, Jain M. Transcriptome analysis of Catharanthus roseus for gene discovery and expression profiling. PLoS One 2014; 9:e103583. [PMID: 25072156 PMCID: PMC4114786 DOI: 10.1371/journal.pone.0103583] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 06/28/2014] [Indexed: 12/02/2022] Open
Abstract
The medicinal plant, Catharanthus roseus, accumulates wide range of terpenoid indole alkaloids, which are well documented therapeutic agents. In this study, deep transcriptome sequencing of C. roseus was carried out to identify the pathways and enzymes (genes) involved in biosynthesis of these compounds. About 343 million reads were generated from different tissues (leaf, flower and root) of C. roseus using Illumina platform. Optimization of de novo assembly involving a two-step process resulted in a total of 59,220 unique transcripts with an average length of 1284 bp. Comprehensive functional annotation and gene ontology (GO) analysis revealed the representation of many genes involved in different biological processes and molecular functions. In total, 65% of C. roseus transcripts showed homology with sequences available in various public repositories, while remaining 35% unigenes may be considered as C. roseus specific. In silico analysis revealed presence of 11,620 genic simple sequence repeats (excluding mono-nucleotide repeats) and 1820 transcription factor encoding genes in C. roseus transcriptome. Expression analysis showed roots and leaves to be actively participating in bisindole alkaloid production with clear indication that enzymes involved in pathway of vindoline and vinblastine biosynthesis are restricted to aerial tissues. Such large-scale transcriptome study provides a rich source for understanding plant-specialized metabolism, and is expected to promote research towards production of plant-derived pharmaceuticals.
Collapse
Affiliation(s)
- Mohit Verma
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Rajesh Ghangal
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Raghvendra Sharma
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Alok K. Sinha
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Mukesh Jain
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
- * E-mail:
| |
Collapse
|
46
|
Liu S, Kuang H, Lai Z. Transcriptome analysis by Illumina high-throughout paired-end sequencing reveals the complexity of differential gene expression during in vitro plantlet growth and flowering in Amaranthus tricolor L. PLoS One 2014; 9:e100919. [PMID: 24963660 PMCID: PMC4071066 DOI: 10.1371/journal.pone.0100919] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 06/02/2014] [Indexed: 11/18/2022] Open
Abstract
Amaranthus tricolor L. is a C4 plant, which is consumed as a major leafy vegetable in some tropical countries. Under conditions of high temperature and short daylight, Am. tricolor readily bolts and blooms, degrading leaf quality. A preliminary in vitro flowering study demonstrated that the flowering control pathway in Am. tricolor may differ from that of Arabidopsis. Nevertheless, no transcriptome analysis of the flowering process in Amaranthus has been conducted. To study Am. tricolor floral regulatory mechanisms, we conducted a large-scale transcriptome analysis--based on Illumina HiSeq sequencing of cDNA libraries generated from Am. tricolor at young seedling (YSS), adult seedling (ASS), flower bud (FBS), and flowering (FS) stages. A total of 99,312 unigenes were obtained. Using BLASTX, 43,088 unigenes (43.39%) were found to have significant similarity with accessions in Nr, Nt, and Swiss-Prot databases. Of these unigenes, 11,291 were mapped to 266 KEGG pathways. Further analysis of the four digital transcriptomes revealed that 735, 17,184, 274, and 206 unigenes were specifically expressed during YSS, ASS, FBS, and FS, respectively, with 59,517 unigenes expressed throughout the four stages. These unigenes were involved in many metabolic pathways related to in vitro flowering. Among these pathways, 259 unigenes were associated with ubiquitin-mediated proteolysis, indicating its importance for in vitro flowering in Am. tricolor. Other pathways, such as circadian rhythm and cell cycle, also had important roles. Finally, 26 unigenes were validated by qRT-PCR in samples from Am. tricolor at YSS, ASS, FBS, and FS; their differential expressions at the various stages indicate their possible roles in Am. tricolor growth and development, but the results were somewhat similar to Arabidopsis. Because unigenes involved in many metabolic pathways or of unknown function were revealed to regulate in vitro plantlet growth and flowering in Am. tricolor, the process appears to be highly complex in this species.
Collapse
Affiliation(s)
- Shengcai Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Huaqin Kuang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- * E-mail:
| |
Collapse
|