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Pham MP, Vu DD, Bei C, Bui TTX, Vu DG, Shah SNM. Characterisation of the Cinnamomumparthenoxylon (Jack) Meisn (Lauraceae) transcriptome using Illumina paired-end sequencing and EST-SSR markers development for population genetics. Biodivers Data J 2024; 12:e123405. [PMID: 38919771 PMCID: PMC11196892 DOI: 10.3897/bdj.12.e123405] [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: 03/19/2024] [Accepted: 05/30/2024] [Indexed: 06/27/2024] Open
Abstract
Cinnamomumparthenoxylon is an endemic and endangered species with significant economic and ecological value in Vietnam. A better understanding of the genetic architecture of the species will be useful when planning management and conservation. We aimed to characterize the transcriptome of C.parthenoxylon, develop novel molecular markers, and assess the genetic variability of the species. First, transcriptome sequencing of five trees (C.parthenoxylon) based on root, leaf, and stem tissues was performed for functional annotation analysis and development of novel molecular markers. The transcriptomes of C.parthenoxylon were analyzed via an Illumina HiSeqTM 4000 sequencing system. A total of 27,363,199 bases were generated for C.parthenoxylon. De novo assembly indicated that a total of 160,435 unigenes were generated (average length = 548.954 bp). The 51,691 unigenes were compared against different databases, i.e. COG, GO, KEGG, KOG, Pfam, Swiss-Prot, and NR for functional annotation. Furthermore, a total of 12,849 EST-SSRs were identified. Of the 134 primer pairs, 54 were randomly selected for testing, with 15 successfully amplified across nine populations of C.parthenoxylon. We uncovered medium levels of genetic diversity (PIC = 0.52, Na = 3.29, Ne = 2.18, P = 94.07%, Ho = 0.56 and He = 0.47) within the studied populations. The molecular variance was 10% among populations and low genetic differentiation (Fst = 0.06) indicated low gene flow (Nm = 2.16). A reduction in the population size of C.parthenoxylon was detected using BOTTLENECK (VP population). The structure analysis suggested two optimal genetic clusters related to gene flow among the populations. Analysis of molecular variance (AMOVA) revealed higher genetic variation within populations (90%) than among populations (10%). The UPGMA approach and DAPC divided the nine populations into three main clusters. Our findings revealed a significant fraction of the transcriptome sequences and these newlydeveloped novel EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity and molecular marker-assisted selection in C.parthenoxylon. This study provides comprehensive genetic resources for the breeding and conservation of different varieties of C.parthenoxylon.
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Affiliation(s)
- Mai-Phuong Pham
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology, Hanoi, VietnamGraduate University of Science and Technology (GUST), Vietnam Academy of Science and TechnologyHanoiVietnam
- Join Vietnam–Russia Tropical Science and Technology Research Center, Hanoi, VietnamJoin Vietnam–Russia Tropical Science and Technology Research CenterHanoiVietnam
| | - Dinh Duy Vu
- Join Vietnam–Russia Tropical Science and Technology Research Center, Hanoi, VietnamJoin Vietnam–Russia Tropical Science and Technology Research CenterHanoiVietnam
| | - Cui Bei
- Jiangsu Vocational Institute of Architectural Technology, School of Architectural Decoration, Xuzhou 221100, Jiangsu, ChinaJiangsu Vocational Institute of Architectural Technology, School of Architectural Decoration, Xuzhou 221100JiangsuChina
| | - Thi Tuyet Xuan Bui
- Institute of Ecology and Biological Resource, Vietnam Academy of Science and Technology, Hanoi, VietnamInstitute of Ecology and Biological Resource, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Dinh Giap Vu
- Institute of Technology, Hanoi University of Industry (HaUI), Hanoi, VietnamInstitute of Technology, Hanoi University of Industry (HaUI)HanoiVietnam
| | - Syed Noor Muhammad Shah
- Department of Horticulture, Faculty of Agriculture, Gomal University, Dera Ismail Khan, PakistanDepartment of Horticulture, Faculty of Agriculture, Gomal UniversityDera Ismail KhanPakistan
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Wang Z, Ni L, Liu L, Yuan H, Gu C. IlAP2, an AP2/ERF Superfamily Gene, Mediates Cadmium Tolerance by Interacting with IlMT2a in Iris lactea var. chinensis. PLANTS (BASEL, SWITZERLAND) 2023; 12:823. [PMID: 36840170 PMCID: PMC9959467 DOI: 10.3390/plants12040823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/10/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Cadmium (Cd) stress has a major impact on ecosystems, so it is important to find suitable Cd-tolerant plants while elucidating the responsible molecular mechanism for phytoremediation to manage Cd soil contamination. Iris lactea var. chinensis is an ornamental perennial groundcover plant with strong tolerance to Cd. Previous studies found that IlAP2, an AP2/ERF superfamily gene, may be an interacting partner of the metallothionein gene IlMT2a, which plays a key role in Cd tolerance. To study the role of IlAP2 in regulating Cd tolerance in I. lactea, we analyzed its regulation function and mechanism based on a yeast two-hybrid assay, a bimolecular fluorescence complementation test, quantitative real-time PCR, transgenics and transcriptome sequencing. The results showed that IlAP2 interacts with IlMT2a and may cooperate with other transcription factors to regulate genes involved in signal transduction and plant hormones, leading to reduced Cd toxicity by hindering Cd transport. These findings provide insights into the mechanism of IlAP2-mediated stress responses to Cd and important gene resources for improving plant stress tolerance in phytoremediation.
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Affiliation(s)
- Zhiquan Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Longjie Ni
- College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Liangqin Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Haiyan Yuan
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Chunsun Gu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
- College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China
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Zhang Y, Zhang R, Song Z, Fu W, Yun L, Gao J, Hu G, Wang Z, Wu H, Zhang G, Wu J. Iris lactea var. chinensis plant drought tolerance depends on the response of proline metabolism, transcription factors, transporters and the ROS-scavenging system. BMC PLANT BIOLOGY 2023; 23:17. [PMID: 36617566 PMCID: PMC9827652 DOI: 10.1186/s12870-022-04019-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Iris lactea var. chinensis, a perennial herbaceous species, is widely distributed and has good drought tolerance traits. However, there is little information in public databases concerning this herb, so it is difficult to understand the mechanism underlying its drought tolerance. RESULTS In this study, we used Illumina sequencing technology to conduct an RNA sequencing (RNA-seq) analysis of I. lactea var. chinensis plants under water-stressed conditions and rehydration to explore the potential mechanisms involved in plant drought tolerance. The resulting de novo assembled transcriptome revealed 126,979 unigenes, of which 44,247 were successfully annotated. Among these, 1187 differentially expressed genes (DEGs) were identified from a comparison of the water-stressed treatment and the control (CK) treatment (T/CK); there were 481 upregulated genes and 706 downregulated genes. Additionally, 275 DEGs were identified in the comparison of the rehydration treatment and the water-stressed treatment (R/T). Based on Quantitative Real-time Polymerase Chain Reaction (qRT-PCR) analysis, the expression levels of eight randomly selected unigenes were consistent with the transcriptomic data under water-stressed and rehydration treatment, as well as in the CK. According to Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, proline metabolism-related DEGs, including those involved in the 'proline catabolic process', the 'proline metabolic process', and 'arginine and proline metabolism', may play important roles in plant drought tolerance. Additionally, these DEGs encoded 43 transcription factors (TFs), 46 transporters, and 22 reactive oxygen species (ROS)-scavenging system-related proteins. Biochemical analysis and histochemical detection showed that proline and ROS were accumulated under water-stressed conditions, which is consistent with the result of the transcriptomic analysis. CONCLUSIONS In summary, our transcriptomic data revealed that the drought tolerance of I. lactea var. chinensis depends on proline metabolism, the action of TFs and transporters, and a strong ROS-scavenging system. The related genes found in this study could help us understand the mechanisms underlying the drought tolerance of I. lactea var. chinensis.
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Affiliation(s)
- Yue Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Ruihai Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Zhen Song
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Weidong Fu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Lingling Yun
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jinhui Gao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Guang Hu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Zhonghui Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hanwen Wu
- Wagga Wagga Agricultural Institute, NSW Department of Primary Industries, Wagga Wagga, New South Wales 2650 Australia
| | - Guoliang Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jiahe Wu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
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Tie FF, Fu YY, Hu N, Chen Z, Wang HL. Isolation of oligostilbenes from Iris lactea Pall. var. chinensis (Fisch.) Koidz and their anti-inflammatory activities. RSC Adv 2022; 12:32912-32922. [PMID: 36425180 PMCID: PMC9667474 DOI: 10.1039/d2ra05176a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/10/2022] [Indexed: 10/28/2023] Open
Abstract
Iris lactea Pall. var. chinensis (Fisch.) Koidz (Iris lactea) is an herbaceous perennial widely distributed in China, India, and South Korea. Iris lactea has been extensively used in traditional Chinese medicine. The present study isolated a new oligostilbene (compound 1), together with three known oligostilbenes (compounds 2, 3 and 4) from the seeds of Iris lactea. The structures of these compounds were elucidated by HRESIMS, NMR, and chemical analyses. The network-based pharmacologic analysis platform was used to predict the target proteins related to inflammation of isolated compounds. Furthermore, the isolated compounds were tested for their anti-inflammatory effects in LPS-stimulated RAW 264.7 cells. In this network, 138 candidate targets of compounds related to its therapeutic effect on inflammation were identified. In addition, compounds 1, 2, 3 and 4 significantly decreased NO content and the IL-6 levels as well as the expression of COX-2 in LPS-stimulated RAW 264.7 cells.
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Affiliation(s)
- Fang-Fang Tie
- CAS Key Laboratory of Tibetan Medicine Research, Qinghai Provincial Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology Xining 810008 P. R. China +869716143857 +8613997384106
| | - Yang-Yang Fu
- CAS Key Laboratory of Tibetan Medicine Research, Qinghai Provincial Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology Xining 810008 P. R. China +869716143857 +8613997384106
| | - Na Hu
- CAS Key Laboratory of Tibetan Medicine Research, Qinghai Provincial Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology Xining 810008 P. R. China +869716143857 +8613997384106
| | - Zhi Chen
- Key Laboratory of Medicinal Animal and Plant Resources of Qinghai-Tibetan Plateau in Qinghai Province Xining 810008 P. R. China
| | - Hong-Lun Wang
- CAS Key Laboratory of Tibetan Medicine Research, Qinghai Provincial Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology Xining 810008 P. R. China +869716143857 +8613997384106
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Li D, Shao L, Xu T, Wang X, Zhang R, Zhang K, Xia Y, Zhang J. Hybrid RNA Sequencing Strategy for the Dynamic Transcriptomes of Winter Dormancy in an Evergreen Herbaceous Perennial, Iris japonica. Front Genet 2022; 13:841957. [PMID: 35368689 PMCID: PMC8965894 DOI: 10.3389/fgene.2022.841957] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/11/2022] [Indexed: 11/30/2022] Open
Abstract
Japanese iris (Iris japonica) is a popular perennial ornamental that originated in China; it has a long display period and remains green outdoors throughout the year. winter dormancy characteristics contribute greatly to the evergreenness of herbaceous perennials. Thus, it is crucial to explore the mechanism of winter dormancy in this evergreen herbaceous perennial. Here, we used the hybrid RNA-seq strategy including single-molecule real-time (SMRT) and next-generation sequencing (NGS) technologies to generate large-scale Full-length transcripts to examine the shoot apical meristems of Japanese iris. A total of 10.57 Gb clean data for SMRT and over 142 Gb clean data for NGS were generated. Using hybrid error correction, 58,654 full-length transcripts were acquired and comprehensively analysed, and their expression levels were validated by real-time qPCR. This is the first full-length RNA-seq study in the Iris genus; our results provide a valuable resource and improve understanding of RNA processing in this genus, for which little genomic information is available as yet. In addition, our data will facilitate in-depth analyses of winter dormancy mechanisms in herbaceous perennials, especially evergreen monocotyledons.
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Affiliation(s)
| | | | | | | | | | | | - Yiping Xia
- *Correspondence: Jiaping Zhang, ; Yiping Xia,
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Wang Z, Ni L, Liu D, Fu Z, Hua J, Lu Z, Liu L, Yin Y, Li H, Gu C. Genome-Wide Identification and Characterization of NAC Family in Hibiscus hamabo Sieb. et Zucc. under Various Abiotic Stresses. Int J Mol Sci 2022; 23:ijms23063055. [PMID: 35328474 PMCID: PMC8949087 DOI: 10.3390/ijms23063055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/02/2022] [Accepted: 03/09/2022] [Indexed: 12/31/2022] Open
Abstract
NAC transcription factor is one of the largest plant gene families, participating in the regulation of plant biological and abiotic stresses. In this study, 182 NAC proteins (HhNACs) were identified based on genomic datasets of Hibiscus hamabo Sieb. et Zucc (H. hamabo). These proteins were divided into 19 subfamilies based on their phylogenetic relationship, motif pattern, and gene structure analysis. Expression analysis with RNA-seq revealed that most HhNACs were expressed in response to drought and salt stress. Research of quantitative real-time PCR analysis of nine selected HhNACs supported the transcriptome data’s dependability and suggested that HhNAC54 was significantly upregulated under multiple abiotic stresses. Overexpression of HhNAC54 in Arabidopsis thaliana (A. thaliana) significantly increased its tolerance to salt. This study provides a basis for a comprehensive analysis of NAC transcription factor and insight into the abiotic stress response mechanism in H. hamabo.
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Affiliation(s)
- Zhiquan Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (Z.W.); (J.H.); (Z.L.); (L.L.); (Y.Y.)
| | - Longjie Ni
- College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China; (L.N.); (D.L.); (Z.F.); (H.L.)
| | - Dina Liu
- College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China; (L.N.); (D.L.); (Z.F.); (H.L.)
| | - Zekai Fu
- College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China; (L.N.); (D.L.); (Z.F.); (H.L.)
| | - Jianfeng Hua
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (Z.W.); (J.H.); (Z.L.); (L.L.); (Y.Y.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Zhiguo Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (Z.W.); (J.H.); (Z.L.); (L.L.); (Y.Y.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Liangqin Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (Z.W.); (J.H.); (Z.L.); (L.L.); (Y.Y.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Yunlong Yin
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (Z.W.); (J.H.); (Z.L.); (L.L.); (Y.Y.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Huogen Li
- College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China; (L.N.); (D.L.); (Z.F.); (H.L.)
| | - Chunsun Gu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (Z.W.); (J.H.); (Z.L.); (L.L.); (Y.Y.)
- College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China; (L.N.); (D.L.); (Z.F.); (H.L.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
- Correspondence: ; Tel.: +86-25-84347051
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Punia H, Tokas J, Malik A, Sangwan S, Rani A, Yashveer S, Alansi S, Hashim MJ, El-Sheikh MA. Genome-Wide Transcriptome Profiling, Characterization, and Functional Identification of NAC Transcription Factors in Sorghum under Salt Stress. Antioxidants (Basel) 2021; 10:antiox10101605. [PMID: 34679740 PMCID: PMC8533442 DOI: 10.3390/antiox10101605] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/03/2021] [Accepted: 10/04/2021] [Indexed: 01/11/2023] Open
Abstract
Salinity stress has become a significant concern to global food security. Revealing the mechanisms that enable plants to survive under salinity has immense significance. Sorghum has increasingly attracted researchers interested in understanding the survival and adaptation strategies to high salinity. However, systematic analysis of the DEGs (differentially expressed genes) and their relative expression has not been reported in sorghum under salt stress. The de novo transcriptomic analysis of sorghum under different salinity levels from 60 to 120 mM NaCl was generated using Illumina HiSeq. Approximately 323.49 million high-quality reads, with an average contig length of 1145 bp, were assembled de novo. On average, 62% of unigenes were functionally annotated to known proteins. These DEGs were mainly involved in several important metabolic processes, such as carbohydrate and lipid metabolism, cell wall biogenesis, photosynthesis, and hormone signaling. SSG 59-3 alleviated the adverse effects of salinity by suppressing oxidative stress (H2O2) and stimulating enzymatic and non-enzymatic antioxidant activities (SOD, APX, CAT, APX, POX, GR, GSH, ASC, proline, and GB), as well as protecting cell membrane integrity (MDA and electrolyte leakage). Significant up-regulation of transcripts encoding the NAC, MYB, and WRYK families, NHX transporters, the aquaporin protein family, photosynthetic genes, antioxidants, and compatible osmolyte proteins were observed. The tolerant line (SSG 59-3) engaged highly efficient machinery in response to elevated salinity, especially during the transport and influx of K+ ions, signal transduction, and osmotic homeostasis. Our data provide insights into the evolution of the NAC TFs gene family and further support the hypothesis that these genes are essential for plant responses to salinity. The findings may provide a molecular foundation for further exploring the potential functions of NAC TFs in developing salt-resistant sorghum lines.
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Affiliation(s)
- Himani Punia
- Department of Biochemistry, College of Basic Sciences & Humanities, CCS Haryana Agricultural University, Hisar 125 004, Haryana, India;
- Correspondence: (H.P.); (J.T.)
| | - Jayanti Tokas
- Department of Biochemistry, College of Basic Sciences & Humanities, CCS Haryana Agricultural University, Hisar 125 004, Haryana, India;
- Correspondence: (H.P.); (J.T.)
| | - Anurag Malik
- Department of Seed Science & Technology, College of Agriculture, CCS Haryana Agricultural University, Hisar 125 004, Haryana, India;
| | - Sonali Sangwan
- Department of Molecular Biology, Biotechnology & Bioinformatics, College of Basic Sciences & Humanities, CCS Haryana Agricultural University, Hisar 125 004, Haryana, India; (S.S.); (S.Y.)
| | - Anju Rani
- Department of Biochemistry, College of Basic Sciences & Humanities, CCS Haryana Agricultural University, Hisar 125 004, Haryana, India;
| | - Shikha Yashveer
- Department of Molecular Biology, Biotechnology & Bioinformatics, College of Basic Sciences & Humanities, CCS Haryana Agricultural University, Hisar 125 004, Haryana, India; (S.S.); (S.Y.)
| | - Saleh Alansi
- Department of Biology, IBB University, Ibb, Yemen;
| | - Maha J. Hashim
- School of Life Sciences, Medical School (E Floor), Queens Medical Centre, Nottingham NG7 2UH, UK;
| | - Mohamed A. El-Sheikh
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
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Genome-Wide Identification and Expression Analysis of BBX Transcription Factors in Iris germanica L. Int J Mol Sci 2021; 22:ijms22168793. [PMID: 34445524 PMCID: PMC8396303 DOI: 10.3390/ijms22168793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 11/17/2022] Open
Abstract
The family of B-box (BBX) transcription factors contains one or two B-BOX domains and sometimes also features a highly conserved CCT domain, which plays important roles in plant growth, development and stress response. Nevertheless, no systematic study of the BBX gene family in Iris germanica L. has been undertaken. In this study, a set of six BBX TF family genes from I. germanica was identified based on transcriptomic sequences, and clustered into three clades according to phylogenetic analysis. A transient expression analysis revealed that all six BBX proteins were localized in the nucleus. A yeast one-hybrid assay demonstrated that IgBBX3 has transactivational activity, while IgBBX1, IgBBX2, IgBBX4, and IgBBX5 have no transcriptional activation ability. The transcript abundance of IgBBXs in different tissues was divided into two major groups. The expression of IgBBX1, IgBBX2, IgBBX3 and IgBBX5 was higher in leaves, whereas IgBBX4 and IgBBX6 was higher in roots. The stress response patterns of six IgBBX were detected under phytohormone treatments and abiotic stresses. The results of this study lay the basis for further research on the functions of BBX gene family members in plant hormone and stress responses, which will promote their application in I. germanica breeding.
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De novo transcriptome characterization of Iris atropurpurea (the Royal Iris) and phylogenetic analysis of MADS-box and R2R3-MYB gene families. Sci Rep 2021; 11:16246. [PMID: 34376711 PMCID: PMC8355218 DOI: 10.1038/s41598-021-95085-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
The Royal Irises (section Oncocyclus) are a Middle-Eastern group of irises, characterized by extremely large flowers with a huge range of flower colors and a unique pollination system. The Royal Irises are considered to be in the course of speciation and serve as a model for evolutionary processes of speciation and pollination ecology. However, no transcriptomic and genomic data are available for these plants. Transcriptome sequencing is a valuable resource for determining the genetic basis of ecological-meaningful traits, especially in non-model organisms. Here we describe the de novo transcriptome assembly of Iris atropurpurea, an endangered species endemic to Israel's coastal plain. We sequenced and analyzed the transcriptomes of roots, leaves, and three stages of developing flower buds. To identify genes involved in developmental processes we generated phylogenetic gene trees for two major gene families, the MADS-box and MYB transcription factors, which play an important role in plant development. In addition, we identified 1503 short sequence repeats that can be developed for molecular markers for population genetics in irises. This first reported transcriptome for the Royal Irises, and the data generated, provide a valuable resource for this non-model plant that will facilitate gene discovery, functional genomic studies, and development of molecular markers in irises, to complete the intensive eco-evolutionary studies of this group.
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Cai X, Zhang B, Wang S, Cheng Y, Wang H. Characterization and phylogenetic analysis of the chloroplast genome of Iris lactea var. chinensis. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1490-1491. [PMID: 33997284 PMCID: PMC8081313 DOI: 10.1080/23802359.2020.1847611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Iris lactea var. chinensis is a well-regarded ornamental plant in the genus Iris (family Iridaceae). In this report, we present the complete chloroplast (cp) genome sequence of I. lactea var. chinensis for the first time. The complete cp genome of I. lactea var. chinensis was assembled using high-throughput sequencing, and phylogenetic analysis was undertaken based on a dataset of coding regions. The cp genome of I. lactea var. chinensis measures 152,409 bp in length, with regions having two inverted copies (IR 26,026 bp), and separated by the large single copy (LSC 82,256 bp) and small single copy (SSC 18,101 bp) regions. The cp genome encodes 133 unique genes, including 87 different protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Based on a dataset of 69 chloroplast coding regions, the maximum-likelihood (ML) phylogenetic tree analysis indicated that Iris lactea var. chinensis clusters closely with Iris sanguinea. Thus, the complete chloroplast genome presented in this report may provide valuable genetic information not only for the future exploitation and utilization of this plant resource but also for further research investigating its relationship with other Iris species.
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Affiliation(s)
- Xiaoran Cai
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Bin Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Shuai Wang
- College of Life Science, Henan Agricultural University, Zhengzhou, China
| | - Yueqin Cheng
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Hongwei Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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Ni L, Wang Z, Guo J, Pei X, Liu L, Li H, Yuan H, Gu C. Full-Length Transcriptome Sequencing and Comparative Transcriptome Analysis to Evaluate Drought and Salt Stress in Iris lactea var. chinensis. Genes (Basel) 2021; 12:434. [PMID: 33803672 PMCID: PMC8002972 DOI: 10.3390/genes12030434] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
Iris lactea var. chinensis (I. lactea var. chinensis) is a perennial herb halophyte with salt and drought tolerance. In this study, full-length transcripts of I. lactea var. chinensis were sequenced using the PacBio RSII sequencing platform. Moreover, the transcriptome was investigated under NaCl or polyethylene glycol (PEG) stress. Approximately 30.89 G subreads were generated and 31,195 unigenes were obtained by clustering the same isoforms by the PacBio RSII platform. A total of 15,466 differentially expressed genes (DEGs) were obtained under the two stresses using the Illumina platform. Among them, 9266 and 8390 DEGs were obtained under high concentrations of NaCl and PEG, respectively. In total, 3897 DEGs with the same expression pattern under the two stresses were obtained. The transcriptome expression profiles of I. lactea var. chinensis under NaCl or PEG stress obtained in this study may provide a resource for the same and different response mechanisms against different types of abiotic stress. Furthermore, the stress-related genes found in this study can provide data for future molecular breeding.
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Affiliation(s)
- Longjie Ni
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.N.); (Z.W.); (J.G.); (X.P.); (L.L.); (H.Y.)
- College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China;
| | - Zhiquan Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.N.); (Z.W.); (J.G.); (X.P.); (L.L.); (H.Y.)
| | - Jinbo Guo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.N.); (Z.W.); (J.G.); (X.P.); (L.L.); (H.Y.)
| | - Xiaoxiao Pei
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.N.); (Z.W.); (J.G.); (X.P.); (L.L.); (H.Y.)
| | - Liangqin Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.N.); (Z.W.); (J.G.); (X.P.); (L.L.); (H.Y.)
| | - Huogen Li
- College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China;
| | - Haiyan Yuan
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.N.); (Z.W.); (J.G.); (X.P.); (L.L.); (H.Y.)
| | - Chunsun Gu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.N.); (Z.W.); (J.G.); (X.P.); (L.L.); (H.Y.)
- College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China;
- Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
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de novo transcriptomic profiling of differentially expressed genes in grass halophyte Urochondra setulosa under high salinity. Sci Rep 2021; 11:5548. [PMID: 33692429 PMCID: PMC7970929 DOI: 10.1038/s41598-021-85220-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 02/22/2021] [Indexed: 01/31/2023] Open
Abstract
Soil salinity is one of the major limiting factors for crop productivity across the world. Halophytes have recently been a source of attraction for exploring the survival and tolerance mechanisms at extreme saline conditions. Urochondra setulosa is one of the obligate grass halophyte that can survive in up to 1000 mM NaCl. The de novo transcriptome of Urochondra leaves at different salt concentrations of 300-500 mM NaCl was generated on Illumina HiSeq. Approximately 352.78 million high quality reads with an average contig length of 1259 bp were assembled de novo. A total of 120,231 unigenes were identified. On an average, 65% unigenes were functionally annotated to known proteins. Approximately 35% unigenes were specific to Urochondra. Differential expression revealed significant enrichment (P < 0.05) of transcription factors, transporters and metabolites suggesting the transcriptional regulation of ion homeostasis and signalling at high salt concentrations in this grass. Also, about 143 unigenes were biologically related to salt stress responsive genes. Randomly selected genes of important pathways were validated for functional characterization. This study provides useful information to understand the gene regulation at extremely saline levels. The study offers the first comprehensive evaluation of Urochondra setulosa leaf transcriptome. Examining non-model organisms that can survive in harsh environment can provide novel insights into the stress coping mechanisms which can be useful to develop improved agricultural crops.
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Fan Z, Gao Y, Ren Y, Guan C, Liu R, Zhang Q. To bloom once or more times: the reblooming mechanisms of Iris germanica revealed by transcriptome profiling. BMC Genomics 2020; 21:553. [PMID: 32787785 PMCID: PMC7430825 DOI: 10.1186/s12864-020-06951-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 07/27/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The reblooming bearded iris (Iris germanica) can bloom twice a year, in spring and autumn. The extended ornamental period makes it more popular and brings additional commercial values. However, little is known about the reblooming mechanisms, making the breeding programs time-consuming and labor-wasting. Therefore, a comparative transcriptome profiling was conducted on once-bloomers and rebloomers from the same F1 generation on six development stages, and the candidate genes associated with reblooming were identified. RESULTS A total of 100,391 unigenes were generated, the mean length being 785 bp. In the three comparisons (the floral initiation stage of spring flowering in once-bloomers (OB-T1) vs the floral initiation stage of spring flowering in rebloomers (RB-T1); RB-T1 vs the floral initiation stage of autumn flowering in rebloomers (RB-T5); OB-T1 vs RB-T5), a total of 690, 3515 and 2941 differentially expressed genes (DEGs) were annotated against the public databases, respectively. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis focused on the photoperiod response, the temperature insensitivity and the growth speed, to remove the redundant DEGs and figure out the candidate key genes. As a result, the following four genes, PHYTOCHROME A (PHYA), GIGANTEA (GI), SHORT VEGETATIVE PERIOD (SVP) and AUXIN RESPONSE FACTOR (ARF), were considered to be involved in the second floral initiation of the rebloomers. CONCLUSION This research provides valuable information for the discovery of the reblooming-related genes. The insights into the molecular mechanisms of reblooming may accelerate the breeding of bearded iris and other perennials.
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Affiliation(s)
- Zhuping Fan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, China
| | - Yike Gao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, China.
| | - Yi Ren
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, China
| | - Chunjing Guan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, China
| | - Rong Liu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, China
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Li L, Zhao Y, Han G, Guo J, Meng Z, Chen M. Progress in the Study and Use of Seawater Vegetables. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:5998-6006. [PMID: 32374599 DOI: 10.1021/acs.jafc.0c00346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
As global soil salinization increases, halophytes that can grow in saline soils are the primary choice for improving soil quality. Some halophytes can even be irrigated with seawater and used as vegetables. These so-called seawater vegetables include those that can be planted on saline and alkali soils and some edible halophytes and ordinary vegetables that are salt-tolerant. The cultivation of seawater vegetables on saline soil has become a matter of increasing interest. In this review, we focus on the salt-tolerance mechanisms and potential applications of some seawater vegetables. We also summarize their value to health, medicine, industry, and the economy as a whole. Further improvement and development to support the use of seawater vegetables will require in-depth research at the cellular and molecular levels.
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Affiliation(s)
- Lingyu Li
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, Shandong 250014, P.R. China
| | - Yang Zhao
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, Shandong 250014, P.R. China
| | - Guoliang Han
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, Shandong 250014, P.R. China
| | - Jianrong Guo
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, Shandong 250014, P.R. China
| | - Zhe Meng
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, Shandong 250014, P.R. China
| | - Min Chen
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, Shandong 250014, P.R. China
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Chen Z, Zhao X, Hu Z, Leng P. Nitric oxide modulating ion balance in Hylotelephium erythrostictum roots subjected to NaCl stress based on the analysis of transcriptome, fluorescence, and ion fluxes. Sci Rep 2019; 9:18317. [PMID: 31797954 PMCID: PMC6892800 DOI: 10.1038/s41598-019-54611-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/14/2019] [Indexed: 11/08/2022] Open
Abstract
Soil salinization is one of the main stress factors that affect both growth and development of plants. Hylotelephium erythrostictum exhibits strong resistance to salt, but the underlying genetic mechanisms remain unclear. In this study, hydroponically cultured seedlings of H. erythrostictum were exposed to 200 mM NaCl. RNA-Seq was used to determine root transcriptomes at 0, 5, and 10 days, and potential candidate genes with differential expression were analyzed. Transcriptome sequencing generated 89.413 Gb of raw data, which were assembled into 111,341 unigenes, 82,081 of which were annotated. Differentially expressed genes associated to Na+ and K+ transport, Ca2+ channel, calcium binding protein, and nitric oxide (NO) biosynthesis had high expression levels in response to salt stress. An increased fluorescence intensity of NO indicated that it played an important role in the regulation of the cytosolic K+/Na+ balance in response to salt stress. Exogenous NO donor and NO biosynthesis inhibitors significantly increased and decreased the Na+ efflux, respectively, thus causing the opposite effect for K+ efflux. Moreover, under salt stress, exogenous NO donors and NO biosynthesis inhibitors enhanced and reduced Ca2+ influx, respectively. Combined with Ca2+ reagent regulation of Na+ and K+ fluxes, this study identifies how NaCl-induced NO may function as a signaling messenger that modulates the K+/Na+ balance in the cytoplasm via the Ca2+ signaling pathway. This enhances the salt resistance in H. erythrostictum roots.
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Affiliation(s)
- Zhixin Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Xueqi Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Zenghui Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China.
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China.
- Beijing Collaborative Innovation Center for Eco-environmental Improvement with Forestry and Fruit Trees, Beijing, 102206, China.
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, China.
| | - Pingsheng Leng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China.
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China.
- Beijing Collaborative Innovation Center for Eco-environmental Improvement with Forestry and Fruit Trees, Beijing, 102206, China.
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16
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The Endophytic Fungus Chaetomium cupreum Regulates Expression of Genes Involved in the Tolerance to Metals and Plant Growth Promotion in Eucalyptus globulus Roots. Microorganisms 2019; 7:microorganisms7110490. [PMID: 31717780 PMCID: PMC6920756 DOI: 10.3390/microorganisms7110490] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/20/2019] [Accepted: 10/24/2019] [Indexed: 11/16/2022] Open
Abstract
The endophytic strain Chaetomium cupreum isolated from metal-contaminated soil was inoculated in Eucalyptus globulus roots to identify genes involved in metal stress response and plant growth promotion. We analyzed the transcriptome of E. globulus roots inoculated with C. cupreum. De novo sequencing, assembly, and analysis were performed to identify molecular mechanisms involved in metal stress tolerance and plant growth promotion. A total of 393,371,743 paired-end reads were assembled into 135,155 putative transcripts. It was found that 663 genes significantly changed their expression in the presence of treatment, of which 369 were up-regulated and 294 were down-regulated. We found differentially expressed genes (DEGs) encoding metal transporters, transcription factors, stress and defense response proteins, as well as DEGs involved in auxin biosynthesis and metabolism. Our results showed that the inoculation of C. cupreum enhanced tolerance to metals and growth promotion on E. globulus. This study provides new information to understand molecular mechanisms involved in plant–microbe interactions under metals stress.
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Zhang X, Han C, Gao H, Cao Y. Comparative transcriptome analysis of the garden asparagus (Asparagus officinalis L.) reveals the molecular mechanism for growth with arbuscular mycorrhizal fungi under salinity stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 141:20-29. [PMID: 31125808 DOI: 10.1016/j.plaphy.2019.05.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/08/2019] [Accepted: 05/12/2019] [Indexed: 06/09/2023]
Abstract
Soil salinity is one of the most abiotic stress factors that severely affects the growth and development of many plants, which can ultimately threaten crop yield. Arbuscular mycorrhiza fungi (AMF) has been proven to be effective in mitigating salinity stress by symbiosis in many crops. Asparagus officinalis are perennial plants grown in saline-alkaline soil, however, limited information on their molecular mechanisms has restricted efficient application of AMF to garden asparagus under salinity stress. In this study, we conducted a transcriptome analysis on the leaves of garden asparagus to identify gene expression under salinity stress. Seedlings were grown in 4 treatments, including non-inoculated AMF using distilled water (NI), inoculated AMF using distilled water (AMF), non-inoculated with salinity stress (NI + S), and inoculated with salinity stress (AMF + S). A total of 6019 novel genes were obtained based on the reference-guided assembly of the garden asparagus transcriptome. Results revealed that 455 differentially expressed genes (DEGs) were identified when comparing NI + S to AMF + S. However, among the up-regulated DEGs, 41 DEGs were down-regulated, while 242 DEGs had no differences in their expression levels when comparing NI to NI + S. These DEGs' expression patterns may be key induced by AMF under salinity stress. Additionally, the GO and KEGG enrichment analyses of 455 DEGs revealed that these genes mainly participate in the improvement of the internal environment in plant cells, nitrogen metabolic-related processes, and possible photoprotection mechanisms. These findings provide insight into enhanced salinity stress adaptation by AMF inoculation, as well as salt-tolerant candidate genes for further functional analyses.
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Affiliation(s)
- Xuhong Zhang
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, China
| | - Changzhi Han
- College of Biodiversity Conservation and Utilization, Southwest Forestry University, Kunming, 650224, China; The Key Laboratory of Forest Disaster Warning and Control of Yunnan Province (Southwest Forestry University), China
| | - Huimin Gao
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, China
| | - Yanpo Cao
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, China.
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An Integrated Transcriptome and Proteome Analysis Reveals Putative Regulators of Adventitious Root Formation in Taxodium 'Zhongshanshan'. Int J Mol Sci 2019; 20:ijms20051225. [PMID: 30862088 PMCID: PMC6429173 DOI: 10.3390/ijms20051225] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/02/2019] [Accepted: 03/07/2019] [Indexed: 02/07/2023] Open
Abstract
Adventitious root (AR) formation from cuttings is the primary manner for the commercial vegetative propagation of trees. Cuttings is also the main method for the vegetative reproduction of Taxodium ‘Zhongshanshan’, while knowledge of the molecular mechanisms regulating the processes is limited. Here, we used mRNA sequencing and an isobaric tag for relative and absolute quantitation-based quantitative proteomic (iTRAQ) analysis to measure changes in gene and protein expression levels during AR formation in Taxodium ‘Zhongshanshan’. Three comparison groups were established to represent the three developmental stages in the AR formation process. At the transcript level, 4743 genes showed an expression difference in the comparison groups as detected by RNA sequencing. At the protein level, 4005 proteins differed in their relative abundance levels, as indicated by the quantitative proteomic analysis. A comparison of the transcriptome and proteome data revealed regulatory aspects of metabolism during AR formation and development. In summary, hormonal signal transduction is different at different developmental stages during AR formation. Other factors related to carbohydrate and energy metabolism and protein degradation and some transcription factor activity levels, were also correlated with AR formation. Studying the identified genes and proteins will provide further insights into the molecular mechanisms controlling AR formation.
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Li L, Li M, Qi X, Tang X, Zhou Y. De novo transcriptome sequencing and analysis of genes related to salt stress response in Glehnia littoralis. PeerJ 2018; 6:e5681. [PMID: 30294511 PMCID: PMC6170154 DOI: 10.7717/peerj.5681] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/30/2018] [Indexed: 12/02/2022] Open
Abstract
Soil salinity is one of the major environmental stresses affecting plant growth, development, and reproduction. Salt stress also affects the accumulation of some secondary metabolites in plants. Glehnia littoralis is an endangered medicinal halophyte that grows in coastal habitats. Peeled and dried Glehnia littoralis roots, named Radix Glehniae, have been used traditionally as a Chinese herbal medicine. Although Glehnia littoralis has great ecological and commercial value, salt-related mechanisms in Glehnia littoralis remain largely unknown. In this study, we analysed the transcriptome of Glehnia littoralis in response to salt stress by RNA-sequencing to identify potential salt tolerance gene networks. After de novo assembly, we obtained 105,875 unigenes, of which 75,559 were annotated in public databases. We identified 10,335 differentially expressed genes (DEGs; false discovery rate <0.05 and |log2 fold-change| ≥ 1) between NaCl treatment (GL2) and control (GL1), with 5,018 upregulated and 5,317 downregulated DEGs. To further this investigation, we performed Gene Ontology (GO) analysis and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis. DEGs involved in secondary metabolite biosynthetic pathways, plant signal transduction pathways, and transcription factors in response to salt stress were analysed. In addition, we tested the gene expression of 15 unigenes by quantitative real-time PCR (qRT-PCR) to confirm the RNA-sequencing results. Our findings represent a large-scale assessment of the Glehnia littoralis gene resource, and provide useful information for exploring its molecular mechanisms of salt tolerance. Moreover, genes enriched in metabolic pathways could be used to investigate potential biosynthetic pathways of active compounds by Glehnia littoralis.
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Affiliation(s)
- Li Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Mimi Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Xiwu Qi
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Xingli Tang
- Nanjing Agricultural University, Nanjing, China
| | - Yifeng Zhou
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China.,Nanjing Agricultural University, Nanjing, China.,Dongtai Institute of Tidal Flat, Nanjing Branch of Chinese Academy of Sciences, Dongtai, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
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20
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Gu C, Liu L, Song A, Liu Z, Zhang Y, Huang S. Iris lactea var. chinensis (Fisch.) cysteine-rich gene llCDT1 enhances cadmium tolerance in yeast cells and Arabidopsis thaliana. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 157:67-72. [PMID: 29605645 DOI: 10.1016/j.ecoenv.2018.03.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/15/2018] [Accepted: 03/23/2018] [Indexed: 06/08/2023]
Abstract
UNLABELLED IlCDT1, a cysteine-rich protein, was isolated from Iris lactea var. chinensis (Fisch.) (I. lactea var. chinensis). Its transcription was up-regulated by the exogenous application of Cd. The truncated IlCDT1 (25-54) containing 14 Cys residues confers Cd tolerance to yeast as the intact IlCDT1, indicating that Cys residues are required for Cd tolerance presumably by chelating Cd. When the gene was constitutively expressed in A. thaliana, root length of transgenic lines was longer than that of wild-type under 100 μM or 200 μM Cd stress. However, Cd absorption in wild-type was more than in two trangenic lines under 100 μM Cd exposure. IlCDT1 may directly bind Cd, through chelating Cd and avoiding the Cd uptake into the cells. Together, IlCDT1 may be a promising gene for the Cd tolerance improvement. SUMMARY Cysteine-rich gene llCDT1 enhances cadmium tolerance in yeast cells and Arabidopsis thaliana.
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Affiliation(s)
- Chunsun Gu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Liangqin Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210014, China
| | - Aiping Song
- College of Horticulture, Nanjing Agricultural University, Nanjing 210014, China
| | - Zhaolei Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210014, China
| | - Yongxia Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Suzhen Huang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
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