1
|
Yang L, Liu J, Guo W, Zheng Z, Xu Y, Xia H, Xiao T. Insights into the multi-chromosomal mitochondrial genome structure of the xero-halophytic plant Haloxylon Ammodendron (C.A.Mey.) Bunge ex Fenzl. BMC Genomics 2024; 25:123. [PMID: 38287293 PMCID: PMC10823707 DOI: 10.1186/s12864-024-10026-6] [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: 08/29/2023] [Accepted: 01/18/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Haloxylon ammodendron holds significance as an ecological plant, showcasing remarkable adaptability to desert conditions, halophytic environments, and sand fixation. With its potential for carbon sequestration, it emerges as a promising candidate for environmental sustainability. Furthermore, it serves as a valuable C4 plant model, offering insights into the genetic foundations of extreme drought tolerance. Despite the availability of plastid and nuclear genomes, the absence of a mitochondrial genome (mitogenome or mtDNA) hinders a comprehensive understanding of its its mtDNA structure, organization, and phylogenetic implications. RESULTS In the present study, the mitochondrial genome of H. ammodendron was assembled and annotated, resulting in a multi-chromosomal configuration with two circular chromosomes. The mtDNA measured 210,149 bp in length and contained 31 protein-coding genes, 18 tRNA and three rRNA. Our analysis identified a total of 66 simple sequence repeats along with 27 tandem repeats, 312 forward repeats, and 303 palindromic repeats were found. Notably, 17 sequence fragments displayed homology between the mtDNA and chloroplast genome (cpDNA), spanning 5233 bp, accounting for 2.49% of the total mitogenome size. Additionally, we predicted 337 RNA editing sites, all of the C-to-U conversion type. Phylogenetic inference confidently placed H. ammodendron in the Amaranthacea family and its close relative, Suaeda glacum. CONCLUSIONS H. ammodendron mtDNA showed a multi-chromosomal structure with two fully circularized molecules. This newly characterized mtDNA represents a valuable resource for gaining insights into the basis of mtDNA structure variation within Caryophyllales and the evolution of land plants, contributing to their identification, and classification.
Collapse
Affiliation(s)
- Lulu Yang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518055, China
| | - Jia Liu
- Biomedical Research Center, Tongji University Suzhou Institute, Suzhou, Jiangsu, 215101, China
| | - Wenjun Guo
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, China
| | - Zehan Zheng
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518055, China
| | - Yafei Xu
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518055, China
| | - Houjun Xia
- Center for Cancer Immunology, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Guangdong, 518055, China.
| | - Tian Xiao
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518055, China.
| |
Collapse
|
2
|
Yang F, Lv G. Metabolomic Analysis of the Response of Haloxylon ammodendron and Haloxylon persicum to Drought. Int J Mol Sci 2023; 24:ijms24109099. [PMID: 37240446 DOI: 10.3390/ijms24109099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/14/2023] [Accepted: 05/21/2023] [Indexed: 05/28/2023] Open
Abstract
Haloxylon ammodendron and Haloxylon persicum, as typical desert plants in arid areas, show strong drought tolerance and environmental adaptability and are therefore ideal model plants for studying the molecular mechanisms of drought tolerance. A metabolomic analysis of H. ammodendron and H. persicum in their natural environment is lacking, and their metabolic response to drought therefore remains unclear. To elucidate the response of H. ammodendron and H. persicum to drought at the metabolic level, a non-targeted metabolomics analysis was carried out herein. Under a dry environment, H. ammodendron exhibited 296 and 252 differentially expressed metabolites (DEMs) in the positive and negative ion modes, respectively, whereas 452 and 354 DEMs were identified in the positive and negative ion modes in H. persicum, respectively. The results indicated that H. ammodendron responds to drought by increasing the content of organic nitrogen compounds and lignans, neolignans, and related compounds, and reducing the content of alkaloids and derivatives. By contrast, H. persicum adapts to the dry environment by increasing the content of organic acids and their derivatives and reducing the content of lignans, neolignans, and related compounds. In addition, H. ammodendron and H. persicum improved their osmoregulation ability, reactive oxygen species detoxification ability, and cell membrane stability by regulating the key metabolic pathways and anabolism of associated metabolites. This is the first metabolomics report on the response of H. ammodendron and H. persicum to drought in their natural environment, providing a foundation for the further study of their regulatory mechanisms under drought stress.
Collapse
Affiliation(s)
- Fang Yang
- School of Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi 830017, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Jinghe 833300, China
| | - Guanghui Lv
- School of Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi 830017, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Jinghe 833300, China
| |
Collapse
|
3
|
Fan Y, Zhao Q, Duan H, Bi S, Hao X, Xu R, Bai R, Yu R, Lu W, Bao T, Wuriyanghan H. Large-scale mRNA transfer between Haloxylon ammodendron (Chenopodiaceae) and herbaceous root holoparasite Cistanche deserticola (Orobanchaceae). iScience 2022; 26:105880. [PMID: 36686392 PMCID: PMC9852350 DOI: 10.1016/j.isci.2022.105880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/27/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
Exchanges of mRNA were shown between host and stem parasites but not root parasites. Cistanche deserticola (Orobanchaceae) is a holoparasitic herb which parasitizes on the roots of woody plant Haloxylon ammodendron (Chenopodiaceae). We used transcriptome sequencing and bioinformatic analyses to identify nearly ten thousand mobile mRNAs. Transcript abundance appears to be a driving force for transfer event and mRNA exchanges occur through haustorial junction. Mobility of selected mRNAs was confirmed in situ and in sunflower-Orobanche cumana heterologous parasitic system. Four C. deserticola →H. ammodendron mobile mRNAs appear to facilitate haustorium development. Of interest, two mobile mRNAs of putative resistance genes CdNLR1 and CdNLR2 cause root-specific hypersensitive response and retard parasite development, which might contribute to parasitic equilibrium. The present study provides evidence for the large-scale mRNA transfer event between a woody host and a root parasite, and demonstrates the functional relevance of six C. deserticola genes in host-parasite interactions.
Collapse
Affiliation(s)
- Yanyan Fan
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Qiqi Zhao
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Huimin Duan
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Shuxin Bi
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Xiaomin Hao
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Rui Xu
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Runyao Bai
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Ruonan Yu
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Wenting Lu
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Tiejun Bao
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China,Corresponding author
| | - Hada Wuriyanghan
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China,Corresponding author
| |
Collapse
|
4
|
Dynamic Transcriptome Analysis Reveals Transcription Factors Involved in the Synthesis of Ethyl Acetate in Aroma-Producing Yeast. Genes (Basel) 2022; 13:genes13122341. [PMID: 36553608 PMCID: PMC9777979 DOI: 10.3390/genes13122341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Ethyl acetate is an important flavor element that is a vital component of baijiu. To date, the transcription factors that can help identify the molecular mechanisms involved in the synthesis of ethyl acetate have not been studied. In the present study, we sequenced and assembled the Wickerhamomyces anomalus strain YF1503 transcriptomes to identify transcription factors. We identified 307 transcription factors in YF1503 using high-throughput RNA sequencing. Some transcription factors, such as C2H2, bHLH, MYB, and bZIP, were up-regulated, and these might play a role in ethyl acetate synthesis. According to the trend of ethyl acetate content, heat map results and STEM, twelve genes were selected for verification of expression levels using quantitative real-time PCR. This dynamic transcriptome analysis presents fundamental information on the transcription factors and pathways that are involved in the synthesis of ethyl acetate in aroma-producing yeast. Of significant interest is the discovery of the roles of various transcription factor genes in the synthesis of ethyl acetate.
Collapse
|
5
|
Yang F, Lv G. Combined analysis of transcriptome and metabolome reveals the molecular mechanism and candidate genes of Haloxylon drought tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:1020367. [PMID: 36330247 PMCID: PMC9622360 DOI: 10.3389/fpls.2022.1020367] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Haloxylon ammodendron and Haloxylon persicum, as typical desert plants, show strong drought tolerance and environmental adaptability. They are ideal model plants for studying the molecular mechanisms of drought tolerance. Transcriptomic and metabolomic analyses were performed to reveal the response mechanisms of H. ammodendron and H. persicum to a drought environment at the levels of transcription and physiological metabolism. The results showed that the morphological structures of H. ammodendron and H. persicum showed adaptability to drought stress. Under drought conditions, the peroxidase activity, abscisic acid content, auxin content, and gibberellin content of H. ammodendron increased, while the contents of proline and malondialdehyde decreased. The amino acid content of H. persicum was increased, while the contents of proline, malondialdehyde, auxin, and gibberellin were decreased. Under drought conditions, 12,233 and 17,953 differentially expressed genes (DEGs) were identified in H. ammodendron and H. persicum , respectively, including members of multiple transcription factor families such as FAR1, AP2/ERF, C2H2, bHLH, MYB, C2C2, and WRKY that were significantly up-regulated under drought stress. In the positive ion mode, 296 and 452 differential metabolites (DEMs) were identified in H. ammodendron and H. persicum, respectively; in the negative ion mode, 252 and 354 DEMs were identified, primarily in carbohydrate and lipid metabolism. A combined transcriptome and metabolome analysis showed that drought stress promoted the glycolysis/gluconeogenesis pathways of H. ammodendron and H. persicum and increased the expression of amino acid synthesis pathways, consistent with the physiological results. In addition, transcriptome and metabolome were jointly used to analyze the expression changes of the genes/metabolites of H. ammodendron and H. persicum that were associated with drought tolerance but were regulated differently in the two plants. This study identified drought-tolerance genes and metabolites in H. ammodendron and H. persicum and has provided new ideas for studying the drought stress response of Haloxylon.
Collapse
Affiliation(s)
- Fang Yang
- School of Ecology and Environment, Xinjiang University, Urumqi, China
- Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Jinghe, China
| | - Guanghui Lv
- School of Ecology and Environment, Xinjiang University, Urumqi, China
- Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Jinghe, China
| |
Collapse
|
6
|
Yang F, Lv G. Characterization of the gene expression profile response to drought stress in Haloxylon using PacBio single-molecule real-time and Illumina sequencing. FRONTIERS IN PLANT SCIENCE 2022; 13:981029. [PMID: 36051288 PMCID: PMC9424927 DOI: 10.3389/fpls.2022.981029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Haloxylon ammodendron and Haloxylon persicum are important drought-tolerant plants in northwest China. The whole-genome sequencing of H. ammodendron and H. persicum grown in their natural environment is incomplete, and their transcriptional regulatory network in response to drought environment remains unclear. To reveal the transcriptional responses of H. ammodendron and H. persicum to an arid environment, we performed single-molecule real-time (SMRT) and Illumina RNA sequencing. In total, 20,246,576 and 908,053 subreads and 435,938 and 210,334 circular consensus sequencing (CCS) reads were identified by SMRT sequencing of H. ammodendron and H. persicum, and 15,238 and 10,135 unigenes, respectively, were successfully obtained. In addition, 9,794 and 7,330 simple sequence repeats (SSRs) and 838 and 71 long non-coding RNAs were identified. In an arid environment, the growth of H. ammodendron was restricted; plant height decreased significantly; basal and branch diameters became thinner and hydrogen peroxide (H2O2) content and peroxidase (POD) activity were increased. Under dry and wet conditions, 11,803 and 15,217 differentially expressed genes (DEGs) were identified in H. ammodendron and H. persicum, respectively. There were 319 and 415 DEGs in the signal transduction pathways related to drought stress signal perception and transmission, including the Ca2+ signal pathway, the ABA signal pathway, and the MAPK signal cascade. In addition, 217 transcription factors (TFs) and 398 TFs of H. ammodendron and H. persicum were differentially expressed, including FAR1, MYB, and AP2/ERF. Bioinformatic analysis showed that under drought stress, the expression patterns of genes related to active oxygen [reactive oxygen species (ROS)] scavenging, functional proteins, lignin biosynthesis, and glucose metabolism pathways were altered. Thisis the first full-length transcriptome report concerning the responses of H. ammodendron and H. persicum to drought stress. The results provide a foundation for further study of the adaptation to drought stress. The full-length transcriptome can be used in genetic engineering research.
Collapse
Affiliation(s)
- Fang Yang
- School of Ecology and Environment, Xinjiang University, Ürümqi, China
- Key Laboratory of Oasis Ecology, Ministry of Education, Ürümqi, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Ürümqi, China
| | - Guanghui Lv
- School of Ecology and Environment, Xinjiang University, Ürümqi, China
- Key Laboratory of Oasis Ecology, Ministry of Education, Ürümqi, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Ürümqi, China
| |
Collapse
|
7
|
Li Y, Li S, Liang Z, Cai Q, Zhou T, Zhao C, Wu X. RNA-seq Analysis of Rhizoctonia solani AG-4HGI Strain BJ-1H Infected by a New Viral Strain of Rhizoctonia solani Partitivirus 2 Reveals a Potential Mechanism for Hypovirulence. PHYTOPATHOLOGY 2022; 112:1373-1385. [PMID: 34965159 DOI: 10.1094/phyto-08-21-0349-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Rhizoctonia solani partitivirus 2 (RsPV2), in the genus Alphapartitivirus, confers hypovirulence on R. solani AG-1-IA, the causal agent of rice sheath blight. In this study, a new strain of RsPV2 obtained from R. solani AG-4HGI strain BJ-1H, the causal agent of black scurf on potato, wasidentified and designated as Rhizoctonia solani partitivirus 2 strain BJ-1H (RsPV2-BJ). An RNA sequencing analysis of strain BJ-1H and the virus RsPV2-BJ-free strain BJ-1H-VF derived from strain BJ-1H was conducted to investigate the potential molecular mechanism of hypovirulence induced by RsPV2-BJ. In total, 14,319 unigenes were obtained, and 1,341 unigenes were identified as differentially expressed genes (DEGs), with 570 DEGs being down-regulated and 771 being up-regulated. Notably, several up-regulated DEGs were annotated to cell wall degrading enzymes, including β-1,3-glucanases. Strain BJ-1H exhibited increased expression of β-1,3-glucanase after RsPV2-BJ infection, suggesting that cell wall autolysis activity in R. solani AG-4HGI strain BJ-1H might be promoted by RsPV2-BJ, inducing hypovirulence in its host fungus R. solani AG-4HGI. To the best of our knowledge, this is the first report on the potential mechanism of hypovirulence induced by a mycovirus in R. solani.
Collapse
Affiliation(s)
- Yuting Li
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Siwei Li
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Zhijian Liang
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Qingnian Cai
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Tao Zhou
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Can Zhao
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
- College of Horticulture, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| |
Collapse
|
8
|
Metabolic Pathways Involved in the Drought Stress Response of Nitraria tangutorum as Revealed by Transcriptome Analysis. FORESTS 2022. [DOI: 10.3390/f13040509] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Drought resistance in plants is controlled by multiple genes. To identify the genes that mediate drought stress responses and to assess the associated metabolic pathways in the desert shrub Nitraria tangutorum, we conducted a transcriptome analysis of plants under control (maximum field capacity) and drought (20% of the maximum field capacity) conditions. We analyzed differentially expressed genes (DEGs) of N. tangutorum and their enrichment in the KEGG metabolic pathways database, and explored the molecular biological mechanisms underlying the answer to its drought tolerance. Between the control and drought groups, 119 classified metabolic pathways annotated 3047 DEGs in the KEGG database. For drought tolerance, nitrate reductase (NR) gene expression was downregulated, indicating that NR activity was decreased to improve drought tolerance. In ammonium assimilation, drought stress inhibited glutamine formation. Protochlorophyllide reductase (1.3.1.33) expression was upregulated to promote chlorophyll a synthesis, whereas divinyl reductase (1.3.1.75) expression was downregulated to inhibit chlorophyll-ester a synthesis. The expression of the chlorophyll synthase (2.5.1.62) gene was downregulated, which affected the synthesis of chlorophyll a and b. Overall, drought stress appeared to improve the ability to convert chlorophyll b into chlorophyll a. Our data serve as a theoretical foundation for further elucidating the growth regulatory mechanism of desert xerophytes, thereby facilitating the development and cultivation of new, drought-resistant genotypes for the purpose of improving desert ecosystems.
Collapse
|
9
|
Wang M, Zhang L, Tong S, Jiang D, Fu Z. Chromosome-level genome assembly of a xerophytic plant, Haloxylon ammodendron. DNA Res 2022; 29:dsac006. [PMID: 35266513 PMCID: PMC8946665 DOI: 10.1093/dnares/dsac006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/09/2022] [Indexed: 01/30/2023] Open
Abstract
Haloxylon ammodendron is a xerophytic perennial shrub or small tree that has a high ecological value in anti-desertification due to its high tolerance to drought and salt stress. Here, we report a high-quality, chromosome-level genome assembly of H. ammodendron by integrating PacBio's high-fidelity sequencing and Hi-C technology. The assembled genome size was 685.4 Mb, of which 99.6% was assigned to nine pseudochromosomes with a contig N50 value of 23.6 Mb. Evolutionary analysis showed that both the recent substantial amplification of long terminal repeat retrotransposons and tandem gene duplication may have contributed to its genome size expansion and arid adaptation. An ample amount of low-GC genes was closely related to functions that may contribute to the desert adaptation of H. ammodendron. Gene family clustering together with gene expression analysis identified differentially expressed genes that may play important roles in the direct response of H. ammodendron to water-deficit stress. We also identified several genes possibly related to the degraded scaly leaves and well-developed root system of H. ammodendron. The reference-level genome assembly presented here will provide a valuable genomic resource for studying the genome evolution of xerophytic plants, as well as for further genetic breeding studies of H. ammodendron.
Collapse
Affiliation(s)
- Mingcheng Wang
- Institute for Advanced Study, Chengdu University, Chengdu 610106, China
| | - Lei Zhang
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, College of Biological Science & Engineering, North Minzu University, Yinchuan 750001, China
| | - Shaofei Tong
- MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu 610105, China
| | - Dechun Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Zhixi Fu
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
| |
Collapse
|
10
|
He A, Niu S, Yang D, Ren W, Zhao L, Sun Y, Meng L, Zhao Q, Paré PW, Zhang J. Two PGPR strains from the rhizosphere of Haloxylon ammodendron promoted growth and enhanced drought tolerance of ryegrass. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 161:74-85. [PMID: 33578287 DOI: 10.1016/j.plaphy.2021.02.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Haloxylon ammodendron, a typical xerophyte, tolerates various abiotic stresses and is widely distributed in desert areas. Two PGPR strains, Bacillus sp. WM13-24 and Pseudomonas sp. M30-35, were previously isolated from the rhizosphere of H. ammodendron in Tengger Desert, Gansu province, northwest China. The aim of this study was to investigate the role of M30-35 and WM13-24 in drought stress alleviation of ryegrass (Lolium perenne L.). Under normal condition, both M30-35 and WM13-24 increased shoot fresh and dry weight, chlorophyll content, total nitrogen and phosphorus contents and altered phytohormone distribution compared to control. Moreover, after 7 days of drought stress, WM13-24 and M30-35 enhanced photosynthetic capacity, relative water content, the activities of catalase (CAT) and peroxidase (POD) and proline content, resulted in decreased malondialdehyde (MDA) content, relative membrane permeability (RMP) and H2O2 accumulation; interestingly, the two strains decreased ABA content in leaves. This study demonstrated that the two PGPR strains promoted ryegrass growth and root development via regulating plant hormone distribution and enhanced drought tolerance of ryegrass through improving the activities of antioxidant enzymes, regulating ABA signaling and maintaining plant growth. Our results indicated that PGPR strains from rhizosphere of the desert plant species could be considered as promising bioinoculants for grass plants.
Collapse
Affiliation(s)
- Aolei He
- State Key Laboratory of Grassland Agro-ecosystems, Center of Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, PR China
| | - Shuqi Niu
- State Key Laboratory of Grassland Agro-ecosystems, Center of Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, PR China
| | - Di Yang
- State Key Laboratory of Grassland Agro-ecosystems, Center of Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, PR China
| | - Wei Ren
- State Key Laboratory of Grassland Agro-ecosystems, Center of Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, PR China
| | - Lingyu Zhao
- State Key Laboratory of Grassland Agro-ecosystems, Center of Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, PR China
| | - Yunya Sun
- State Key Laboratory of Grassland Agro-ecosystems, Center of Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, PR China
| | - Laisheng Meng
- Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, PR China
| | - Qi Zhao
- State Key Laboratory of Grassland Agro-ecosystems, Center of Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, PR China
| | - Paul W Paré
- State Key Laboratory of Grassland Agro-ecosystems, Center of Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, PR China; Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
| | - Jinlin Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Center of Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, PR China.
| |
Collapse
|
11
|
De novo transcriptome sequencing and analysis of salt-, alkali-, and drought-responsive genes in Sophora alopecuroides. BMC Genomics 2020; 21:423. [PMID: 32576152 PMCID: PMC7310485 DOI: 10.1186/s12864-020-06823-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 06/12/2020] [Indexed: 02/06/2023] Open
Abstract
Background Salinity, alkalinity, and drought stress are the main abiotic stress factors affecting plant growth and development. Sophora alopecuroides L., a perennial leguminous herb in the genus Sophora, is a highly salt-tolerant sand-fixing pioneer species distributed mostly in Western Asia and northwestern China. Few studies have assessed responses to abiotic stress in S. alopecuroides. The transcriptome of the genes that confer stress-tolerance in this species has not previously been sequenced. Our objective was to sequence and analyze this transcriptome. Results Twelve cDNA libraries were constructed in triplicate from mRNA obtained from Sophora alopecuroides for the control and salt, alkali, and drought treatments. Using de novo assembly, 902,812 assembled unigenes were generated, with an average length of 294 bp. Based on similarity searches, 545,615 (60.43%) had at least one significant match in the Nr, Nt, Pfam, KOG/COG, Swiss-Prot, and GO databases. In addition, 1673 differentially expressed genes (DEGs) were obtained from the salt treatment, 8142 from the alkali treatment, and 17,479 from the drought treatment. A total of 11,936 transcription factor genes from 82 transcription factor families were functionally annotated under salt, alkali, and drought stress, these include MYB, bZIP, NAC and WRKY family members. DEGs were involved in the hormone signal transduction pathway, biosynthesis of secondary metabolites and antioxidant enzymes; this suggests that these pathways or processes may be involved in tolerance towards salt, alkali, and drought stress in S. alopecuroides. Conclusion Our study first reported transcriptome reference sequence data in Sophora alopecuroides, a non-model plant without a reference genome. We determined digital expression profile and discovered a broad survey of unigenes associated with salt, alkali, and drought stress which provide genomic resources available for Sophora alopecuroides.
Collapse
|
12
|
Thayale Purayil F, Rajashekar B, S. Kurup S, Cheruth AJ, Subramaniam S, Hassan Tawfik N, M.A. Amiri K. Transcriptome Profiling of Haloxylon persicum (Bunge ex Boiss and Buhse) an Endangered Plant Species under PEG-Induced Drought Stress. Genes (Basel) 2020; 11:genes11060640. [PMID: 32531994 PMCID: PMC7349776 DOI: 10.3390/genes11060640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 01/06/2023] Open
Abstract
Haloxylon persicum is an endangered western Asiatic desert plant species, which survives under extreme environmental conditions. In this study, we focused on transcriptome analysis of H. persicum to understand the molecular mechanisms associated with drought tolerance. Two different periods of polyethylene glycol (PEG)-induced drought stress (48 h and 72 h) were imposed on H. persicum under in vitro conditions, which resulted in 18 million reads, subsequently assembled by de novo method with more than 8000 transcripts in each treatment. The N50 values were 1437, 1467, and 1524 for the control sample, 48 h samples, and 72 h samples, respectively. The gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis resulted in enrichment of mitogen-activated protein kinase (MAPK) and plant hormone signal transduction pathways under PEG-induced drought conditions. The differential gene expression analysis (DGEs) revealed significant changes in the expression pattern between the control and the treated samples. The KEGG analysis resulted in mapping transcripts with 138 different pathways reported in plants. The differential expression of drought-responsive transcription factors depicts the possible signaling cascades involved in drought tolerance. The present study provides greater insight into the fundamental transcriptome reprogramming of desert plants under drought.
Collapse
Affiliation(s)
- Fayas Thayale Purayil
- Department of Integrative Agriculture, College of Food and Agriculture, United Arab Emirates University, P.O. Box. Al-Ain 15551, UAE; (F.T.P.); (A.J.C.); (N.H.T.)
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box. Al Ain 15551, UAE
| | - Balaji Rajashekar
- Institute of Computer Science, University of Tartu, 50409 Tartu, Estonia;
- Celixa, Bangalore, Karnataka 560020, India
| | - Shyam S. Kurup
- Department of Integrative Agriculture, College of Food and Agriculture, United Arab Emirates University, P.O. Box. Al-Ain 15551, UAE; (F.T.P.); (A.J.C.); (N.H.T.)
- Correspondence: (S.S.K.); (K.M.A.)
| | - Abdul Jaleel Cheruth
- Department of Integrative Agriculture, College of Food and Agriculture, United Arab Emirates University, P.O. Box. Al-Ain 15551, UAE; (F.T.P.); (A.J.C.); (N.H.T.)
| | - Sreeramanan Subramaniam
- School of Biological Sciences, Universiti Sains Malaysia (USM), Minden Heights, Georgetown, Penang 11800, Malaysia;
| | - Nadia Hassan Tawfik
- Department of Integrative Agriculture, College of Food and Agriculture, United Arab Emirates University, P.O. Box. Al-Ain 15551, UAE; (F.T.P.); (A.J.C.); (N.H.T.)
| | - Khaled M.A. Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box. Al Ain 15551, UAE
- Department of Biology, College of Science, United Arab Emirates University, P.O. Box. Al Ain 15551, UAE
- Correspondence: (S.S.K.); (K.M.A.)
| |
Collapse
|
13
|
Gong L, Zhang H, Liu X, Gan X, Nie F, Yang W, Zhang L, Chen Y, Song Y, Zhang H. Ectopic expression of HaNAC1, an ATAF transcription factor from Haloxylon ammodendron, improves growth and drought tolerance in transgenic Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 151:535-544. [PMID: 32305820 DOI: 10.1016/j.plaphy.2020.04.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 04/05/2020] [Accepted: 04/06/2020] [Indexed: 06/11/2023]
Abstract
NAC transcription factors play a pivotal role in plant growth, development and response to abiotic stress. However, their biological functions in desert trees are largely unknown. In this work, the NAC transcription factor HaNAC1 from Haloxylon ammodendron, a typical wooden plant normally grown in desert, was isolated, and its possible role in plant growth and resistance to drought stress was investigated. HaNAC1 encodes an ATAF subfamily transcription factor containing one NAC domain with five conserved regions. Quantitative real time PCR analyses revealed that HaNAC1 was ubiquitously expressed in various tissues and organs such as roots, stems, leaves and seeds, with a predominant expression in stems. Further studies demonstrated that expression of HaNAC1 was significantly induced by osmotic stress in Haloxylon ammodendron seedlings, and subcellular localization analysis indicated that GFP-HaNAC1 fusion protein was localized to the nucleus in Arabidopsis leaf protoplast. Ectopic expression of HaNAC1 led to promoted growth and drought tolerance in transgenic Arabidopsis, accompanied with up-regulated expression of stress-inducible marker genes, and increased accumulation of proline, IAA and ABA under both normal and drought stress conditions. In addition, co-immunoprecipitation and Bi-molecular fluorescence complementation assays illustrated that HaNAC1 directly interacted with AtNAC32. All these results suggest that HaNAC1 is involved in both the growth and drought resistance of Haloxylon ammodendron, and could be used as a promising candidate gene for the breeding of crops with augmented tolerance to drought stress.
Collapse
Affiliation(s)
- Lei Gong
- Ningxia Key Laboratory for Agrobiotechnology, Agricultural Bio-Technology Center, Ningxia Academy of Agriculture and Forestry Science, 590 Huanghe East Road, Yinchuan, Ningxia Hui Nationality Autonomous Region, 750002, China
| | - Haiwen Zhang
- School of Life Sciences, Ningxia University, 489 Helanshan West Road, Yinchuan, Ningxia Hui Nationality Autonomous Region, 750021, China
| | - Xuan Liu
- Ningxia Key Laboratory for Agrobiotechnology, Agricultural Bio-Technology Center, Ningxia Academy of Agriculture and Forestry Science, 590 Huanghe East Road, Yinchuan, Ningxia Hui Nationality Autonomous Region, 750002, China
| | - Xiaoyan Gan
- Ningxia Key Laboratory for Agrobiotechnology, Agricultural Bio-Technology Center, Ningxia Academy of Agriculture and Forestry Science, 590 Huanghe East Road, Yinchuan, Ningxia Hui Nationality Autonomous Region, 750002, China
| | - Fengjie Nie
- Ningxia Key Laboratory for Agrobiotechnology, Agricultural Bio-Technology Center, Ningxia Academy of Agriculture and Forestry Science, 590 Huanghe East Road, Yinchuan, Ningxia Hui Nationality Autonomous Region, 750002, China
| | - Wenjing Yang
- Ningxia Key Laboratory for Agrobiotechnology, Agricultural Bio-Technology Center, Ningxia Academy of Agriculture and Forestry Science, 590 Huanghe East Road, Yinchuan, Ningxia Hui Nationality Autonomous Region, 750002, China
| | - Li Zhang
- Ningxia Key Laboratory for Agrobiotechnology, Agricultural Bio-Technology Center, Ningxia Academy of Agriculture and Forestry Science, 590 Huanghe East Road, Yinchuan, Ningxia Hui Nationality Autonomous Region, 750002, China
| | - Yuchao Chen
- Ningxia Key Laboratory for Agrobiotechnology, Agricultural Bio-Technology Center, Ningxia Academy of Agriculture and Forestry Science, 590 Huanghe East Road, Yinchuan, Ningxia Hui Nationality Autonomous Region, 750002, China
| | - Yuxia Song
- Ningxia Key Laboratory for Agrobiotechnology, Agricultural Bio-Technology Center, Ningxia Academy of Agriculture and Forestry Science, 590 Huanghe East Road, Yinchuan, Ningxia Hui Nationality Autonomous Region, 750002, China.
| | - Hongxia Zhang
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai, 264025, China; Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China.
| |
Collapse
|
14
|
Zhang Y, Gao X, Li J, Gong X, Yang P, Gao J, Wang P, Feng B. Comparative analysis of proso millet (Panicum miliaceum L.) leaf transcriptomes for insight into drought tolerance mechanisms. BMC PLANT BIOLOGY 2019; 19:397. [PMID: 31510928 PMCID: PMC6737659 DOI: 10.1186/s12870-019-2001-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 08/30/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Drought stress is a major abiotic stress that causes huge losses in agricultural production. Proso millet (Panicum miliaceum L.) can efficiently adapt to drought stress and provides important information and gene resources to improve drought tolerance. However, its complex drought-responsive mechanisms remain unclear. RESULTS Among 37 core Chinese proso millet cultivars, Jinshu 6 (JS6) was selected as the drought-sensitive test material, whereas Neimi 5 (NM5) was selected as the drought-tolerant test material under PEG-induced water stress. After sequencing, 1695 differentially expressed genes (DEGs) were observed in JS6 and NM5 without PEG-induced water stress (JS6CK and NM5CK). A total of 833 and 2166 DEGs were found in the two cultivars under simulated drought by using 20% PEG-6000 for 6 (JS6T6 and NM5T6) and 24 h (JS6T24 and NM5T24), respectively. The DEGs in JS6T6 and JS6T24 treatments were approximately 0.298- and 0.754-fold higher than those in NM5T6 and NM5T24, respectively. Compared with the respective controls, more DEGs were found in T6 treatments than in T24 treatments. A delay in the transcriptional responses of the ROS scavenging system to simulated drought treatment and relatively easy recovery of the expression of photosynthesis-associated genes were observed in NM5. Compared with JS6, different regulation strategies were observed in the jasmonic acid (JA) signal transduction pathway of NM5. CONCLUSION Under PEG-induced water stress, NM5 maintained highly stable gene expression levels. Compared with drought-sensitive cultivars, the different regulation strategies in the JA signal transduction pathway in drought-tolerant cultivars may be one of the driving forces underlying drought stress tolerance.
Collapse
Affiliation(s)
- Yuyu Zhang
- College of Agronomy, Northwest A&F University / State Key Laboratory of Crop Stress Biology in Arid Areas, Yangling, 712100 Shaanxi China
| | - Xiaoli Gao
- College of Agronomy, Northwest A&F University / State Key Laboratory of Crop Stress Biology in Arid Areas, Yangling, 712100 Shaanxi China
| | - Jing Li
- College of Agronomy, Northwest A&F University / State Key Laboratory of Crop Stress Biology in Arid Areas, Yangling, 712100 Shaanxi China
| | - Xiangwei Gong
- College of Agronomy, Northwest A&F University / State Key Laboratory of Crop Stress Biology in Arid Areas, Yangling, 712100 Shaanxi China
| | - Pu Yang
- College of Agronomy, Northwest A&F University / State Key Laboratory of Crop Stress Biology in Arid Areas, Yangling, 712100 Shaanxi China
| | - Jinfeng Gao
- College of Agronomy, Northwest A&F University / State Key Laboratory of Crop Stress Biology in Arid Areas, Yangling, 712100 Shaanxi China
| | - Pengke Wang
- College of Agronomy, Northwest A&F University / State Key Laboratory of Crop Stress Biology in Arid Areas, Yangling, 712100 Shaanxi China
| | - Baili Feng
- College of Agronomy, Northwest A&F University / State Key Laboratory of Crop Stress Biology in Arid Areas, Yangling, 712100 Shaanxi China
| |
Collapse
|
15
|
Sui J, Qu C, Yang J, Zhang W, Ji Y. Transcriptome changes in the phenylpropanoid pathway in senescing leaves of Toona sinensis. ACTA PHYSIOLOGIAE PLANTARUM 2019; 41:126. [PMID: 32214546 PMCID: PMC7088779 DOI: 10.1007/s11738-019-2915-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 05/27/2019] [Accepted: 06/03/2019] [Indexed: 05/04/2023]
Abstract
Toona sinensis is a deciduous tree native to eastern and southeastern Asia that has important culinary and cultural values. To expand current knowledge of the transcriptome and functional genomics in this species, a de novo transcriptome sequence analysis of young and mature leaf tissues of T. sinensis was performed using the Illumina platform. Over 8.1 Gb of data were generated, assembled into 64,541 unigenes, and annotated with known biological functions. Proteins involved in primary metabolite biosynthesis were identified based on similarities to known proteins, including some related to biosynthesis of carbohydrates, amino acids, lipids, and energy. Analysis of unigenes differentially expressed between young and mature leaves (transcriptomic libraries 'YL' and 'ML', respectively) showed that the KEGG pathways of phenylpropanoid, naringenin, lignin, cutin, suberin, and wax biosynthesis were significantly enriched in mature leaves. These results not only expand knowledge of transcriptome characteristics for this valuable species, but also provide a useful transcriptomic dataset to accelerate the researches on its metabolic mechanisms and functional genomics. This study can also further the understanding of unique aromatic metabolism and Chinese medicinal properties of T. sinensis.
Collapse
Affiliation(s)
- Juanjuan Sui
- Engineering Technology Research Center of Anti-aging Chinese Herbal Medicine, Fuyang Normal University, Fuyang, 236037 Anhui China
| | - Changqing Qu
- Engineering Technology Research Center of Anti-aging Chinese Herbal Medicine, Fuyang Normal University, Fuyang, 236037 Anhui China
| | - Jingxia Yang
- Engineering Technology Research Center of Anti-aging Chinese Herbal Medicine, Fuyang Normal University, Fuyang, 236037 Anhui China
| | - Wenna Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193 China
| | - Yuntao Ji
- Engineering Technology Research Center of Anti-aging Chinese Herbal Medicine, Fuyang Normal University, Fuyang, 236037 Anhui China
| |
Collapse
|
16
|
Fan L, Wang G, Hu W, Pantha P, Tran KN, Zhang H, An L, Dassanayake M, Qiu QS. Transcriptomic view of survival during early seedling growth of the extremophyte Haloxylon ammodendron. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 132:475-489. [PMID: 30292980 DOI: 10.1016/j.plaphy.2018.09.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/08/2018] [Accepted: 09/18/2018] [Indexed: 05/27/2023]
Abstract
Seedling establishment in an extreme environment requires an integrated genomic and physiological response to survive multiple abiotic stresses. The extremophyte, Haloxylon ammodendron is a pioneer species capable of colonizing temperate desert sand dunes. We investigated the induced and basal transcriptomes in H. ammodendron under water-deficit stress during early seedling establishment. We find that not only drought-responsive genes, but multiple genes in pathways associated with salt, osmotic, cold, UV, and high-light stresses were induced, suggesting an altered regulatory stress response system. Additionally, H. ammodendron exhibited enhanced biotic stress tolerance by down-regulation of genes that were generally up-regulated during pathogen entry in susceptible plants. By comparing the H. ammodendron basal transcriptome to six closely related transcriptomes in Amaranthaceae, we detected enriched basal level transcripts in H. ammodendron that shows preadaptation to abiotic stress and pathogens. We found transcripts that were generally maintained at low levels and some induced only under abiotic stress in the stress-sensitive model, Arabidopsis thaliana to be highly expressed under basal conditions in the Amaranthaceae transcriptomes including H. ammodendron. H. ammodendron shows coordinated expression of genes that regulate stress tolerance and seedling development resource allocation to support survival against multiple stresses in a sand dune dominated temperate desert environment.
Collapse
Affiliation(s)
- Ligang Fan
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, 222 South Tianshui Road, Lanzhou, Gansu, 730000, China
| | - Guannan Wang
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
| | - Wei Hu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, 222 South Tianshui Road, Lanzhou, Gansu, 730000, China
| | - Pramod Pantha
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
| | - Kieu-Nga Tran
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
| | - Hua Zhang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, 222 South Tianshui Road, Lanzhou, Gansu, 730000, China
| | - Lizhe An
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, 222 South Tianshui Road, Lanzhou, Gansu, 730000, China
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA.
| | - Quan-Sheng Qiu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, 222 South Tianshui Road, Lanzhou, Gansu, 730000, China.
| |
Collapse
|
17
|
Liu L, Hui N, Liang LX, Zhang XX, Li LB, Sun QW. Sphingobacterium haloxyli sp. nov., an endophytic bacterium isolated from Haloxylon ammodendron stems in Kumtag desert. Int J Syst Evol Microbiol 2018; 68:3279-3284. [PMID: 30156529 DOI: 10.1099/ijsem.0.002982] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, aerobic, non-spore-forming, rod-shaped, bacterial strain, designated 5JN-11T, was isolated from Haloxylonammodendron stems in Kumtag desert, Xinjiang province, China. Strain 5JN-11T grew at salinities of 0-6 % (w/v; optimum 0-2 %), a pH of 7.0-9.0 (pH 7.0-8.0) and temperatures of 20-42 °C (28-30 °C). Based on 16S rRNA gene sequences, the strain was designated a member of the genus Sphingobacterium and the phylogenetic analysis showed that strain 5JN-11T shared the highest similarity to Sphingobacterium gobiense H7T, followed by Sphingobacterium chuzhouense DH-5T and Sphingobacterium arenae H-12T. The unfinished draft genome of strain 5JN-11T was 4.69 Mb. The G+C content of strain 5JN-11T was 42.8 mol%. The average nucleotide identity to S. gobiense H7T was 90.5 %. The respiratory quinone was MK-7, and the major polar lipids were phosphatidylethanolamine and phosphoglycolipid. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH. On the basis of phenotypic, genotypic and phylogenetic evidence, strain 5JN-11T represents a novel species in the genus Sphingobacterium, for which the name Sphingobacteriumhaloxyli sp. nov. is proposed. The type strain is 5JN-11T (=ACCC 60072T=KCTC 62457T).
Collapse
Affiliation(s)
- Lei Liu
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Nan Hui
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Li-Xiong Liang
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Xiao-Xia Zhang
- 2Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Lu-Bin Li
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Qi-Wu Sun
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| |
Collapse
|
18
|
Wang B, Du H, Yao Z, Ren C, Ma L, Wang J, Zhang H, Ma H. Validation of reference genes for accurate normalization of gene expression with quantitative real-time PCR in Haloxylon ammodendron under different abiotic stresses. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:455-463. [PMID: 29692553 PMCID: PMC5911265 DOI: 10.1007/s12298-018-0520-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 10/20/2017] [Accepted: 02/08/2018] [Indexed: 05/27/2023]
Abstract
Haloxylon ammodendron plays an important role in maintaining the structure and function of the entire ecosystem where it grows. No suitable reference genes have been reported in H. ammodendron plants to date. In this study, a total of 8 reference genes (18S, ACT1, ACT7, UBC18, TUA5, GAPDH, EF-1α and UBQ10) were selected from the available trancriptome database, and the expression stability of these 8 candidate genes was validated under different abiotic stress with three different statistical algorithms (geNorm, NormFinder and BestKeeper). The results produced from different models were in agreement with each other essentially: 18S and TUA5 were the most stable genes under drought stress, 18S, the most stable gene under heat stress and mechanical damage, ACT7 and UBC18, stable under salt stress while TUA5 and GAPDH expressed constantly under mechanical damage, and ACT1 expressed steadily under cold conditions. Expression profiles of several stress response genes, including FT-5, FT-9, DREB2A and DREB2C, were further confirmed with various candidate reference genes. None of the candidate genes showed a constant expression among all tested samples. Hence, it's essential to use more than one reference gene in order to guarantee the accuracy of quantitative real-time PCR. The results of this study will contribute to the accuracy and reliability in transcripts quantification, which is of significance to transcription-based studies and applications in this important shrub H. ammodendron.
Collapse
Affiliation(s)
- Bo Wang
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Huihui Du
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Zhengpei Yao
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Cai Ren
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Li Ma
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Jiao Wang
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Hua Zhang
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Hao Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| |
Collapse
|
19
|
Tan X, Sun J, Ning H, Qin Z, Miao Y, Sun T, Zhang X. De novo transcriptome sequencing and comprehensive analysis of the heat stress response genes in the basidiomycetes fungus Ganoderma lucidum. Gene 2018; 661:139-151. [PMID: 29605602 DOI: 10.1016/j.gene.2018.03.093] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/14/2018] [Accepted: 03/28/2018] [Indexed: 12/22/2022]
Abstract
Ganoderma lucidum is a valuable basidiomycete with numerous pharmacological compounds, which is widely consumed throughout China. We previously found that the polysaccharide content of Ganoderma lucidum fruiting bodies could be significantly improved by 45.63% with treatment of 42 °C heat stress (HS) for 2 h. To further investigate genes involved in HS response and explore the mechanisms of HS regulating the carbohydrate metabolism in Ganoderma lucidum, high-throughput RNA-Seq was conducted to analyse the difference between control and heat-treated mycelia at transcriptome level. We sequenced six cDNA libraries with three from control group (mycelia cultivated at 28 °C) and three from heat-treated group (mycelia subjected to 42 °C for 2 h). A total of 99,899 transcripts were generated using Trinity method and 59,136 unigenes were annotated by seven public databases. Among them, 2790 genes were identified to be differential expressed genes (DEGs) under HS condition, which included 1991 up-regulated and 799 down-regulated. 176 DEGs were then manually classified into five main responsive-related categories according to their putative functions and possible metabolic pathways. These groups include stress resistance-related factors; protein assembly, transportation and degradation; signal transduction; carbohydrate metabolism and energy provision-related process; other related functions, suggesting that a series of metabolic pathways in Ganoderma lucidum are activated by HS and the response mechanism involves a complex molecular network which needs further study. Remarkably, 48 DEGs were found to regulate carbohydrate metabolism, both in carbohydrate hydrolysis for energy provision and polysaccharide synthesis. In summary, this comprehensive transcriptome analysis will provide enlarged resource for further investigation into the molecular mechanisms of basidiomycete under HS condition.
Collapse
Affiliation(s)
- Xiaoyan Tan
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Junshe Sun
- Chinese Academy of Agricultural Engineering, Beijing 100125, China
| | - Huijuan Ning
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Zifang Qin
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yuxin Miao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Tian Sun
- Tianfangjian (China) Pharma Company Ltd, Guangzhou 510623, China.
| | - Xiuqing Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| |
Collapse
|
20
|
Hou DY, Shi LC, Yang MM, Li J, Zhou S, Zhang HX, Xu HW. De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform. PLoS One 2018; 13:e0192610. [PMID: 29451882 PMCID: PMC5815590 DOI: 10.1371/journal.pone.0192610] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 01/27/2018] [Indexed: 01/06/2023] Open
Abstract
Cornus officinalis is one of the most widely used medicinal plants in China and other East Asian countries to cure diseases such as liver, kidney, cardiovascular diseases and frequent urination for thousands of years. It is a Level 3 protected species, and is one of the 42 national key protected wild species of animals and plants in China. However, the genetics and molecular biology of C. officinalis are poorly understood, which has hindered research on the molecular mechanism of its metabolism and utilization. Hence, enriching its genomic data and information is very important. In recent years, the fast-growing technology of next generation sequencing has provided an effective path to gain genomic information from nonmodel species. This study is the first to explore the leaf and fruit tissue transcriptome of C. officinalis using the Illumina HiSeq 4000 platform. A total of 57,954,134 and 60,971,652 clean reads from leaf and fruit were acquired, respectively (GenBank number SRP115440). The pooled reads from all two libraries were assembled into 56,392 unigenes with an average length 856 bp. Among these, 41,146 unigenes matched with sequences in the NCBI nonredundant protein database. The Gene Ontology database assigned 24,336 unigenes with biological process (83.26%), cellular components (53.58%), and molecular function (83.93%). In addition, 10,808 unigenes were assigned a KOG functional classification by the KOG database. Searching against the KEGG pathway database indicated that 18,435 unigenes were mapped to 371 KEGG pathways. Moreover, the edgeR database identified 4,585 significant differentially expressed genes (DEGs), of which 1,392 were up-regulated and 3,193 were down-regulated in fruit tissue compared with leaf tissue. Finally, we explored 581 transcription factors with 50 transcription factor gene families. Most DEGs and transcription factors were related to terpene biosynthesis and secondary metabolic regulation. This study not only represented the first de novo transcriptomic analysis of C. officinalis but also provided fundamental information on its genes and biosynthetic pathway. These findings will help us explore the molecular metabolism mechanism of terpene biosynthesis in C. officinalis.
Collapse
Affiliation(s)
- Dian-Yun Hou
- Agricultural College, Henan University of Science and Technology, Luoyang, Henan Province, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-di Herbs, Luoyang, Henan Province, China
- * E-mail:
| | - Lin-Chun Shi
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Meng-Meng Yang
- Agricultural College, Henan University of Science and Technology, Luoyang, Henan Province, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-di Herbs, Luoyang, Henan Province, China
| | - Jiong Li
- Chinese Medicinal Materials Production Technology Service Center, Department of Agriculture of Henan Province, Zhengzhou, Henan Province, China
| | - Shuang Zhou
- Agricultural College, Henan University of Science and Technology, Luoyang, Henan Province, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-di Herbs, Luoyang, Henan Province, China
| | - Hong-Xiao Zhang
- Agricultural College, Henan University of Science and Technology, Luoyang, Henan Province, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-di Herbs, Luoyang, Henan Province, China
| | - Hua-Wei Xu
- Agricultural College, Henan University of Science and Technology, Luoyang, Henan Province, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-di Herbs, Luoyang, Henan Province, China
| |
Collapse
|
21
|
Yadav R, Lone SA, Gaikwad K, Singh NK, Padaria JC. Transcriptome sequence analysis and mining of SSRs in Jhar Ber (Ziziphus nummularia (Burm.f.) Wight & Arn) under drought stress. Sci Rep 2018; 8:2406. [PMID: 29402924 PMCID: PMC5799245 DOI: 10.1038/s41598-018-20548-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 01/02/2018] [Indexed: 11/09/2022] Open
Abstract
Ziziphus nummularia (Burm.f.) Wight & Arn., a perennial shrub that thrives in the arid regions, is naturally tolerant to drought. However, there are limited studies on the genomics of drought tolerance in Ziziphus sp. In this study, RNA-sequencing of one month old seedlings treated with PEG 6000 was performed using Roche GS-FLX454 Titanium pyrosequencing. A total of 367,176 raw sequence reads were generated, and upon adapter trimming and quality filtration 351,872 reads were assembled de novo into 32,739 unigenes. Further characterization of the unigenes indicated that 73.25% had significant hits in the protein database. Kyoto encyclopedia of genes and genomes database (KEGG) identified 113 metabolic pathways from the obtained unigenes. A large number of drought-responsive genes were obtained and among them differential gene expression of 16 highly induced genes was validated by qRT-PCR analysis. To develop genic-markers, 3,425 simple sequence repeats (SSRs) were identified in 2,813 unigene sequences. The data generated shall serve as an important reservoir for the identification and characterization of drought stress responsive genes for development of drought tolerant crops.
Collapse
Affiliation(s)
- Radha Yadav
- Biotechnology and Climate Change Group, National Research Centre on Plant Biotechnology (ICAR-NRCPB), New Delhi, 110012, India
| | - Showkat Ahmad Lone
- Biotechnology and Climate Change Group, National Research Centre on Plant Biotechnology (ICAR-NRCPB), New Delhi, 110012, India
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, 202002, India
| | - Kishor Gaikwad
- Biotechnology and Climate Change Group, National Research Centre on Plant Biotechnology (ICAR-NRCPB), New Delhi, 110012, India
| | - Nagendra Kumar Singh
- Biotechnology and Climate Change Group, National Research Centre on Plant Biotechnology (ICAR-NRCPB), New Delhi, 110012, India
| | - Jasdeep Chatrath Padaria
- Biotechnology and Climate Change Group, National Research Centre on Plant Biotechnology (ICAR-NRCPB), New Delhi, 110012, India.
| |
Collapse
|
22
|
Han C, Li Q, Li X, Zhang Z, Huang J. De novo assembly, characterization and annotation for the transcriptome of Sphaeroma terebrans and microsatellite marker discovery. Genes Genomics 2017; 40:167-176. [PMID: 29892920 DOI: 10.1007/s13258-017-0618-4] [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] [Received: 07/26/2017] [Accepted: 10/05/2017] [Indexed: 12/12/2022]
Abstract
Sphaeroma terebrans, an economically and ecologically important marine wood-boring isopod, is mainly distributed in tropical and subtropical mangroves. Nevertheless, available genomic and transcriptomic information for this isopod is extremely deficient. Here, we first performed the assembly of S. terebrans transcriptome by Illumina sequencing. A total of 51,092 high-quality unigenes with an average length of 641 bp were obtained and 19,915 unigenes were successfully annotated in four public databases. Only 9932 out of 19915 unigenes were commonly annotated by all four databases. In addition, 9609 unigenes were categorized into 54 function categories of Gene Ontology (GO), and 14,512 unigenes were successfully grouped into 25 functional categories of the EuKaryotic Orthologous Groups (KOG) database. Moreover, 11,507 unigenes were assigned to 228 pathways of the Kyoto Encyclopedia of Genes and Genomes (KEGG). Out of 51,092 unigenes, a total of 4257 different microsatellites with motifs range from di- to hexa-nucleotide were identified from 3324 unigene sequences. Among 64 primer pairs selected for validation, 35 were successful in PCR amplification and 13 exhibited obvious repeat polymorphisms in the wild population of S. terebrans in Dongzhaigang (Hainan Island). The transcriptome dataset and the identified microsatellite markers (SSRs) will provide abundant information for researches on the discovery of new genes, metabolic mechanism and genetic diversity of S. terebrans.
Collapse
Affiliation(s)
- Chong Han
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Qiang Li
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Xiufeng Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Zhipeng Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jianrong Huang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, China.
| |
Collapse
|
23
|
Batista ANL, Santos-Pinto JRAD, Batista JM, Souza-Moreira TM, Santoni MM, Zanelli CF, Kato MJ, López SN, Palma MS, Furlan M. The Combined Use of Proteomics and Transcriptomics Reveals a Complex Secondary Metabolite Network in Peperomia obtusifolia. JOURNAL OF NATURAL PRODUCTS 2017; 80:1275-1286. [PMID: 28422496 DOI: 10.1021/acs.jnatprod.6b00827] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Peperomia obtusifolia, an ornamental plant from the Piperaceae family, accumulates a series of secondary metabolites with interesting biological properties. From a biosynthesis standpoint, this species produces several benzopyrans derived from orsellinic acid, which is a polyketide typically found in fungi. Additionally, the chiral benzopyrans were reported as racemic and/or as diastereomeric mixtures, which raises questions about the level of enzymatic control in the cyclization step for the formation of the 3,4-dihydro-2H-pyran moiety. Therefore, this article describes the use of shotgun proteomic and transcriptome studies as well as phytochemical profiling for the characterization of the main biosynthesis pathways active in P. obtusifolia. This combined approach resulted in the identification of a series of proteins involved in its secondary metabolism, including tocopherol cyclase and prenyltransferases. The activity of these enzymes was supported by the phytochemical profiling performed in different organs of P. obtusifolia. However, the polyketide synthases possibly involved in the production of orsellinic acid could not be identified, suggesting that orsellinic acid may be produced by endophytes intimately associated with the plant.
Collapse
Affiliation(s)
- Andrea N L Batista
- Instituto de Química, Universidade Estadual Paulista (Unesp) , Araraquara, SP 14800-060, Brazil
| | | | - João M Batista
- Departamento de Química, Universidade Federal de São Carlos-UFSCar , São Carlos, SP 13565-905, Brazil
| | - Tatiana M Souza-Moreira
- Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista (Unesp) , Araraquara, SP 14801-902, Brazil
| | - Mariana M Santoni
- Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista (Unesp) , Araraquara, SP 14801-902, Brazil
| | - Cleslei F Zanelli
- Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista (Unesp) , Araraquara, SP 14801-902, Brazil
| | - Massuo J Kato
- Instituto de Química, Universidade de São Paulo-USP , São Paulo, SP 05508-000, Brazil
| | - Silvia N López
- CONICET, Farmacognosia, Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario , Rosario, Santa Fe S2002LRK, Argentina
| | - Mario S Palma
- Instituto de Biociências, Universidade Estadual Paulista (Unesp) , Rio Claro, SP 13506-900, Brazil
| | - Maysa Furlan
- Instituto de Química, Universidade Estadual Paulista (Unesp) , Araraquara, SP 14800-060, Brazil
| |
Collapse
|
24
|
Wang P, Wang F, Yang J. De novo assembly and analysis of the Pugionium cornutum (L.) Gaertn. transcriptome and identification of genes involved in the drought response. Gene 2017; 626:290-297. [PMID: 28552570 DOI: 10.1016/j.gene.2017.05.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 04/28/2017] [Accepted: 05/24/2017] [Indexed: 01/12/2023]
Abstract
Pugionium cornutum (L.) Gaertn. is a xerophytic plant species widely distributed in sandy and desert habitats in northwest China. However, the molecular mechanism of drought tolerance in P. cornutum has received little attention. At present, there is limited available transcriptome information for P. cormutum in public databases. Illumina sequencing was used to identify drought-responsive genes and to further characterize the molecular basis of drought tolerance in P. cornutum. In total, 51,385 unigenes with an average length of 825.32bp were obtained by de novo transcriptome assembly. Among these unigenes, 35,276 were annotated with gene descriptions, conserved domains, gene ontology terms, and metabolic pathways. In addition, the results showed that differentially expressed genes (DEGs) were mainly involved in photosynthesis, nitrogen metabolism, and plant hormone signal transduction pathways, notably ascorbate and aldarate metabolism, which could be an alternative pathway to enhance antioxidant capacity in P. cornutum in response to drought stress. These results provide an important clue about the effects of accumulation of ROS on ascorbic acid biosynthesis in P. cornutum. In addition, we found that transcription of most genes involved in ascorbic acid metabolism was altered under drought stress. Additionally, 93 drought-inducible transcription factor genes were identified in the DEGs under drought conditions; these included DREB, AP2/EREBP, B-2a, ERF2, MYB and Zinc finger family. The results of this study provide further insight into the molecular mechanisms of stress tolerance in P. cornutum, and also identify some attractive candidate genes and valuable information for improving drought stress tolerance in other species through genetic engineering.
Collapse
Affiliation(s)
- Ping Wang
- College of Agronomy, Inner Mongolia Agricultural University, Inner Mongolia Autonomous Region Key Laboratory of Wild Peculiar Vegetable Germplasm Resource and Germplasm Enhancement, Huhhot 010019, China.
| | - Fengfeng Wang
- College of Agronomy, Inner Mongolia Agricultural University, Inner Mongolia Autonomous Region Key Laboratory of Wild Peculiar Vegetable Germplasm Resource and Germplasm Enhancement, Huhhot 010019, China
| | - Jing Yang
- College of Agronomy, Inner Mongolia Agricultural University, Inner Mongolia Autonomous Region Key Laboratory of Wild Peculiar Vegetable Germplasm Resource and Germplasm Enhancement, Huhhot 010019, China
| |
Collapse
|
25
|
Dong W, Xu C, Li D, Jin X, Li R, Lu Q, Suo Z. Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae). PeerJ 2016; 4:e2699. [PMID: 27867769 PMCID: PMC5111891 DOI: 10.7717/peerj.2699] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/18/2016] [Indexed: 12/11/2022] Open
Abstract
The Haloxylon genus belongs to the Amaranthaceae (formerly Chenopodiaceae) family. The small trees or shrubs in this genus are referred to as the King of psammophytic plants, and perform important functions in environmental protection, including wind control and sand fixation in deserts. To better understand these beneficial plants, we sequenced the chloroplast (cp) genomes of Haloxylon ammodendron (HA) and Haloxylon persicum (HP) and conducted comparative genomic analyses on these and two other representative Amaranthaceae species. Similar to other higher plants, we found that the Haloxylon cp genome is a quadripartite, double-stranded, circular DNA molecule of 151,570 bp in HA and 151,586 bp in HP. It contains a pair of inverted repeats (24,171 bp in HA and 24,177 bp in HP) that separate the genome into a large single copy region of 84,214 bp in HA and 84,217 bp in HP, and a small single copy region of 19,014 bp in HA and 19,015 bp in HP. Each Haloxylon cp genome contains 112 genes, including 78 coding, 30 tRNA, and four ribosomal RNA genes. We detected 59 different simple sequence repeat loci, including 44 mono-nucleotide, three di-nucleotide, one tri-nucleotide, and 11 tetra-nucleotide repeats. Comparative analysis revealed only 67 mutations between the two species, including 44 substitutions, 23 insertions/deletions, and two micro-inversions. The two inversions, with lengths of 14 and 3 bp, occur in the petA-psbJ intergenic region and rpl16 intron, respectively, and are predicted to form hairpin structures with repeat sequences of 27 and 19 bp, respectively, at the two ends. The ratio of transitions to transversions was 0.76. These results are valuable for future studies on Haloxylon genetic diversity and will enhance our understanding of the phylogenetic evolution of Amaranthaceae.
Collapse
Affiliation(s)
- Wenpan Dong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Delu Li
- Gansu Desert Control Research Institute , Gansu , China
| | - Xiaobai Jin
- Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences , Beijing , China
| | - Ruili Li
- Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences , Beijing , China
| | - Qi Lu
- Institute of Desertification Studies, Chinese Academy of Forestry , Beijing , China
| | - Zhili Suo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences , Beijing , China
| |
Collapse
|
26
|
De Novo Assembly and Characterization of Bud, Leaf and Flowers Transcriptome from Juglans Regia L. for the Identification and Characterization of New EST-SSRs. FORESTS 2016. [DOI: 10.3390/f7100247] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
27
|
De novo assembly and characterization of leaf transcriptome for the development of EST-SSR markers of the non-model species Indigofera szechuensis. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
28
|
Wang Y, Li X, Zhou W, Li T, Tian C. De novo assembly and transcriptome characterization of spruce dwarf mistletoe Arceuthobium sichuanense uncovers gene expression profiling associated with plant development. BMC Genomics 2016; 17:771. [PMID: 27716052 PMCID: PMC5045590 DOI: 10.1186/s12864-016-3127-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 09/26/2016] [Indexed: 12/02/2022] Open
Abstract
Background The parasitic flowering plant dwarf mistletoe (Arceuthobium spp., Viscaceae) is one of the most destructive forest pests, posing a major threat to numerous conifer species worldwide. Arceuthobium sichuanense (spruce dwarf mistletoe, SDM) infects Qinghai spruce (Picea crassifolia) and causes severe damage to spruce forests in Northwest China. SDM is a Chinese native parasitic plant and acquires carbohydrates and mineral nutrition from its hosts. However, underlying molecular basis of the physiological development is largely unknown. Investigations of these physiological traits have been hampered by the lack of genomic resources for this species. Results In this study, to investigate the transcriptomic processes underlying physiological traits and development in SDM, we used RNA from four major tissues (i.e., shoots, flowers, fruits, and seeds) for de novo assembly and to annotate the transcriptome of this species. We uncovered the annotated transcriptome and performed whole genome expression profiling to uncover transcriptional dynamics during physiological development, and we identified key gene categories involved in the process of sexual development. The assembled SDM transcriptome reported in this work contains 331,347 assembled transcripts; 226,687 unigenes were functionally annotated by Gene Ontology analysis. RNA-Seq analysis using this reference transcriptome identified 22,641 differentially expressed genes from shoots, flowers, fruits, and seeds. These genes are enriched in processes including organic substance metabolism, cellular metabolism, biosynthesis, and cellular component. In addition, genes related to transport, transcription, hormone biosynthesis and signaling, carbohydrate metabolism, and photosynthesis were differentially expressed between tissues. Conclusion This work reveals tissue-specific gene expression patterns and pathways of SDM and implied to a difference between photosynthetic and non-photosynthetic tissues in plants. The data can potentially be used for future investigations on endophytic parasitism and SDM-spruce interaction, and it dramatically increases the available genomic resources for Arceuthobium and dwarf mistletoe communities. This preliminary study of the Arceuthobium transcriptome provides excellent opportunities for characterizing plant parasitic genes with unknown functions. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3127-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yonglin Wang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China.
| | - Xuewu Li
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China.,Academy of Forest Inventory and Planning, State Forestry Administration, Beijing, China
| | - Weifen Zhou
- Forest Pest Control and Quarantine Station of Qinghai Province, Xining, China
| | - Tao Li
- Xianmi Forest Park of Qinghai Province, Menyuan, Qinghai, China
| | - Chengming Tian
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China.
| |
Collapse
|
29
|
De Novo Assembly and Comparative Transcriptome Analysis Provide Insight into Lysine Biosynthesis in Toona sinensis Roem. Int J Genomics 2016; 2016:6735209. [PMID: 27376077 PMCID: PMC4914729 DOI: 10.1155/2016/6735209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/07/2016] [Accepted: 05/05/2016] [Indexed: 11/17/2022] Open
Abstract
Toona sinensis Roem is a popular leafy vegetable in Chinese cuisine and is also used as a traditional Chinese medicine. In this study, leaf samples were collected from the same plant on two development stages and then used for high-throughput Illumina RNA-sequencing (RNA-Seq). 125,884 transcripts and 54,628 unigenes were obtained through de novo assembly. A total of 25,570 could be annotated with known biological functions, which indicated that the T. sinensis leaves and shoots were undergoing multiple developmental processes especially for active metabolic processes. Analysis of differentially expressed unigenes between the two libraries showed that the lysine biosynthesis was an enriched KEGG pathway, and candidate genes involved in the lysine biosynthesis pathway in T. sinensis leaves and shoots were identified. Our results provide a primary analysis of the gene expression files of T. sinensis leaf and shoot on different development stages and afford a valuable resource for genetic and genomic research on plant lysine biosynthesis.
Collapse
|
30
|
Wang H, Lei Y, Wan L, Yan L, Lv J, Dai X, Ren X, Guo W, Jiang H, Liao B. Comparative transcript profiling of resistant and susceptible peanut post-harvest seeds in response to aflatoxin production by Aspergillus flavus. BMC PLANT BIOLOGY 2016; 16:54. [PMID: 26922489 PMCID: PMC4769821 DOI: 10.1186/s12870-016-0738-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 02/17/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND Aflatoxin contamination caused by Aspergillus flavus in peanut (Arachis hypogaea) including in pre- and post-harvest stages seriously affects industry development and human health. Even though resistance to aflatoxin production in post-harvest peanut has been identified, its molecular mechanism has been poorly understood. To understand the mechanism of peanut response to aflatoxin production by A. flavus, RNA-seq was used for global transcriptome profiling of post-harvest seed of resistant (Zhonghua 6) and susceptible (Zhonghua 12) peanut genotypes under the fungus infection and aflatoxin production stress. RESULT A total of 128.72 Gb of high-quality bases were generated and assembled into 128, 725 unigenes (average length 765 bp). About 62, 352 unigenes (48.43%) were annotated in the NCBI non-redundant protein sequences, NCBI non-redundant nucleotide sequences, Swiss-Prot, KEGG Ortholog, Protein family, Gene Ontology, or eukaryotic Ortholog Groups database and more than 93% of the unigenes were expressed in the samples. Among obtained 30, 143 differentially expressed unigenes (DEGs), 842 potential defense-related genes, including nucleotide binding site-leucine-rich repeat proteins, polygalacturonase inhibitor proteins, leucine-rich repeat receptor-like kinases, mitogen-activated protein kinase, transcription factors, ADP-ribosylation factors, pathogenesis-related proteins and crucial factors of other defense-related pathways, might contribute to peanut response to aflatoxin production. Notably, DEGs involved in phenylpropanoid-derived compounds biosynthetic pathway were induced to higher levels in the resistant genotype than in the susceptible one. Flavonoid, stilbenoid and phenylpropanoid biosynthesis pathways were enriched only in the resistant genotype. CONCLUSIONS This study provided the first comprehensive analysis of transcriptome of post-harvest peanut seeds in response to aflatoxin production, and would contribute to better understanding of molecular interaction between peanut and A. flavus. The data generated in this study would be a valuable resource for genetic and genomic studies on crops resistance to aflatoxin contamination.
Collapse
Affiliation(s)
- Houmiao Wang
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
- Chinese Academy of Agricultural Sciences-International Crop Research Institute for the Semi-Arid Tropics Joint Laboratory for Groundnut Aflatoxin Management, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Yong Lei
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
- Chinese Academy of Agricultural Sciences-International Crop Research Institute for the Semi-Arid Tropics Joint Laboratory for Groundnut Aflatoxin Management, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Liyun Wan
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
- Chinese Academy of Agricultural Sciences-International Crop Research Institute for the Semi-Arid Tropics Joint Laboratory for Groundnut Aflatoxin Management, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Liying Yan
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
- Chinese Academy of Agricultural Sciences-International Crop Research Institute for the Semi-Arid Tropics Joint Laboratory for Groundnut Aflatoxin Management, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Jianwei Lv
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
- Chinese Academy of Agricultural Sciences-International Crop Research Institute for the Semi-Arid Tropics Joint Laboratory for Groundnut Aflatoxin Management, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Xiaofeng Dai
- Institute of Agro-Products Processing Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Xiaoping Ren
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
- Chinese Academy of Agricultural Sciences-International Crop Research Institute for the Semi-Arid Tropics Joint Laboratory for Groundnut Aflatoxin Management, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Wei Guo
- Institute of Agro-Products Processing Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Huifang Jiang
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
- Chinese Academy of Agricultural Sciences-International Crop Research Institute for the Semi-Arid Tropics Joint Laboratory for Groundnut Aflatoxin Management, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Boshou Liao
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
- Chinese Academy of Agricultural Sciences-International Crop Research Institute for the Semi-Arid Tropics Joint Laboratory for Groundnut Aflatoxin Management, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| |
Collapse
|
31
|
Deng T, Pang C, Lu X, Zhu P, Duan A, Tan Z, Huang J, Li H, Chen M, Liang X. De Novo Transcriptome Assembly of the Chinese Swamp Buffalo by RNA Sequencing and SSR Marker Discovery. PLoS One 2016; 11:e0147132. [PMID: 26766209 PMCID: PMC4713091 DOI: 10.1371/journal.pone.0147132] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/29/2015] [Indexed: 01/11/2023] Open
Abstract
The Chinese swamp buffalo (Bubalis bubalis) is vital to the lives of small farmers and has tremendous economic importance. However, a lack of genomic information has hampered research on augmenting marker assisted breeding programs in this species. Thus, a high-throughput transcriptomic sequencing of B. bubalis was conducted to generate transcriptomic sequence dataset for gene discovery and molecular marker development. Illumina paired-end sequencing generated a total of 54,109,173 raw reads. After trimming, de novo assembly was performed, which yielded 86,017 unigenes, with an average length of 972.41 bp, an N50 of 1,505 bp, and an average GC content of 49.92%. A total of 62,337 unigenes were successfully annotated. Among the annotated unigenes, 27,025 (43.35%) and 23,232 (37.27%) unigenes showed significant similarity to known proteins in NCBI non-redundant protein and Swiss-Prot databases (E-value < 1.0E-5), respectively. Of these annotated unigenes, 14,439 and 15,813 unigenes were assigned to the Gene Ontology (GO) categories and EuKaryotic Ortholog Group (KOG) cluster, respectively. In addition, a total of 14,167 unigenes were assigned to 331 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Furthermore, 17,401 simple sequence repeats (SSRs) were identified as potential molecular markers. One hundred and fifteen primer pairs were randomly selected for amplification to detect polymorphisms. The results revealed that 110 primer pairs (95.65%) yielded PCR amplicons and 69 primer pairs (60.00%) presented polymorphisms in 35 individual buffaloes. A phylogenetic analysis showed that the five swamp buffalo populations were clustered together, whereas two river buffalo breeds clustered separately. In the present study, the Illumina RNA-seq technology was utilized to perform transcriptome analysis and SSR marker discovery in the swamp buffalo without using a reference genome. Our findings will enrich the current SSR markers resources and help spearhead molecular genetic research studies on the swamp buffalo.
Collapse
Affiliation(s)
- Tingxian Deng
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Chunying Pang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Xingrong Lu
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Peng Zhu
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Anqin Duan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Zhengzhun Tan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Jian Huang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Hui Li
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Mingtan Chen
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Xianwei Liang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
- * E-mail:
| |
Collapse
|
32
|
De novo assembly and characterization of the leaf, bud, and fruit transcriptome from the vulnerable tree Juglans mandshurica for the development of 20 new microsatellite markers using Illumina sequencing. Mol Genet Genomics 2015; 291:849-62. [DOI: 10.1007/s00438-015-1147-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/13/2015] [Indexed: 01/08/2023]
|
33
|
Liu Y, Zhang P, Song M, Hou J, Qing M, Wang W, Liu C. Transcriptome Analysis and Development of SSR Molecular Markers in Glycyrrhiza uralensis Fisch. PLoS One 2015; 10:e0143017. [PMID: 26571372 PMCID: PMC4646622 DOI: 10.1371/journal.pone.0143017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 10/29/2015] [Indexed: 12/31/2022] Open
Abstract
Licorice is an important traditional Chinese medicine with clinical and industrial applications. Genetic resources of licorice are insufficient for analysis of molecular biology and genetic functions; as such, transcriptome sequencing must be conducted for functional characterization and development of molecular markers. In this study, transcriptome sequencing on the Illumina HiSeq 2500 sequencing platform generated a total of 5.41 Gb clean data. De novo assembly yielded a total of 46,641 unigenes. Comparison analysis using BLAST showed that the annotations of 29,614 unigenes were conserved. Further study revealed 773 genes related to biosynthesis of secondary metabolites of licorice, 40 genes involved in biosynthesis of the terpenoid backbone, and 16 genes associated with biosynthesis of glycyrrhizic acid. Analysis of unigenes larger than 1 Kb with a length of 11,702 nt presented 7,032 simple sequence repeats (SSR). Sixty-four of 69 randomly designed and synthesized SSR pairs were successfully amplified, 33 pairs of primers were polymorphism in in Glycyrrhiza uralensis Fisch., Glycyrrhiza inflata Bat., Glycyrrhiza glabra L. and Glycyrrhiza pallidiflora Maxim. This study not only presents the molecular biology data of licorice but also provides a basis for genetic diversity research and molecular marker-assisted breeding of licorice.
Collapse
Affiliation(s)
- Yaling Liu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 100102, PR China
- College of Life Science, Shanxi Agricultural University, Taigu, 030801, Shanxi Province, PR China
| | - Pengfei Zhang
- College of Life Science, Shanxi Agricultural University, Taigu, 030801, Shanxi Province, PR China
| | - Meiling Song
- College of Life Science, Shanxi Agricultural University, Taigu, 030801, Shanxi Province, PR China
| | - Junling Hou
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 100102, PR China
| | - Mei Qing
- School of Inner Mongolia Medical University, Hohhot, 010059, PR China
- * E-mail: (MQ); (WW); (CL)
| | - Wenquan Wang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 100102, PR China
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, PR China
- * E-mail: (MQ); (WW); (CL)
| | - Chunsheng Liu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 100102, PR China
- * E-mail: (MQ); (WW); (CL)
| |
Collapse
|
34
|
Ma X, Wang P, Zhou S, Sun Y, Liu N, Li X, Hou Y. De novo transcriptome sequencing and comprehensive analysis of the drought-responsive genes in the desert plant Cynanchum komarovii. BMC Genomics 2015; 16:753. [PMID: 26444539 PMCID: PMC4594960 DOI: 10.1186/s12864-015-1873-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 08/21/2015] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Cynanchum komarovii Al Iljinski is a xerophytic plant species widely distributing in the severely adverse environment of the deserts in northwest China. At present, the detailed transcriptomic and genomic data for C. komarovii are still insufficient in public databases. RESULTS To investigate changes of drought-responsive genes and explore the mechanisms of drought tolerance in C. komarovii, approximately 27.5 GB sequencing data were obtained using Illumina sequencing technology. After de novo assembly 148,715 unigenes were generated with an average length of 604 bp. Among these unigenes, 85,106 were annotated with gene descriptions, conserved domains, gene ontology terms, and metabolic pathways. The results showed that a great number of unigenes were significantly affected by drought stress. We identified 3134 unigenes as reliable differentially expressed genes (DEGs). During drought stress, the regulatory genes were involved in signaling transduction pathways and in controlling the expression of functional genes. Moreover, C. komarovii activated many functional genes that directly protected against stress and improved tolerance to adapt drought condition. Importantly, the DEGs were involved in biosynthesis, export, and regulation of plant cuticle, suggesting that plant cuticle may play a vital role in response to drought stress and the accumulation of cuticle may allow C. komarovii to improve the tolerance to drought stress. CONCLUSION This is the first large-scale reference sequence data of C. komarovii, which enlarge the genomic resources of this species. Our comprehensive transcriptome analysis will provide a valuable resource for further investigation into the molecular adaptation of desert plants under drought condition and facilitate the exploration of drought-tolerant candidate genes.
Collapse
Affiliation(s)
- Xiaowen Ma
- College of Science, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, China.
| | - Ping Wang
- College of Science, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, China.
| | - Sihong Zhou
- College of Science, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, China.
| | - Yun Sun
- College of Science, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, China.
| | - Nana Liu
- College of Science, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, China.
| | - Xiaoning Li
- College of Science, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, China.
| | - Yuxia Hou
- College of Science, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, China.
| |
Collapse
|
35
|
Hu L, Hao C, Fan R, Wu B, Tan L, Wu H. De Novo Assembly and Characterization of Fruit Transcriptome in Black Pepper (Piper nigrum). PLoS One 2015; 10:e0129822. [PMID: 26121657 PMCID: PMC4488137 DOI: 10.1371/journal.pone.0129822] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/12/2015] [Indexed: 11/18/2022] Open
Abstract
Black pepper is one of the most popular and oldest spices in the world and valued for its pungent constituent alkaloids. Pinerine is the main bioactive compound in pepper alkaloids, which perform unique physiological functions. However, the mechanisms of piperine synthesis are poorly understood. This study is the first to describe the fruit transcriptome of black pepper by sequencing on Illumina HiSeq 2000 platform. A total of 56,281,710 raw reads were obtained and assembled. From these raw reads, 44,061 unigenes with an average length of 1,345 nt were generated. During functional annotation, 40,537 unigenes were annotated in Gene Ontology categories, Kyoto Encyclopedia of Genes and Genomes pathways, Swiss-Prot database, and Nucleotide Collection (NR/NT) database. In addition, 8,196 simple sequence repeats (SSRs) were detected. In a detailed analysis of the transcriptome, housekeeping genes for quantitative polymerase chain reaction internal control, polymorphic SSRs, and lysine/ornithine metabolism-related genes were identified. These results validated the availability of our database. Our study could provide useful data for further research on piperine synthesis in black pepper.
Collapse
Affiliation(s)
- Lisong Hu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Science (CATAS), Wanning, Hainan 571533, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, Hainan 571533, China
| | - Chaoyun Hao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Science (CATAS), Wanning, Hainan 571533, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, Hainan 571533, China
| | - Rui Fan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Science (CATAS), Wanning, Hainan 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, Hainan 571533, China
| | - Baoduo Wu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Science (CATAS), Wanning, Hainan 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, Hainan 571533, China
| | - Lehe Tan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Science (CATAS), Wanning, Hainan 571533, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, Hainan 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, Hainan 571533, China
| | - Huasong Wu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Science (CATAS), Wanning, Hainan 571533, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, Hainan 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, Hainan 571533, China
- * E-mail:
| |
Collapse
|