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Song M, Zhang Y, Jia Q, Huang S, An R, Chen N, Zhu Y, Mu J, Hu S. Systematic analysis of MADS-box gene family in the U's triangle species and targeted mutagenesis of BnaAG homologs to explore its role in floral organ identity in Brassica napus. FRONTIERS IN PLANT SCIENCE 2023; 13:1115513. [PMID: 36714735 PMCID: PMC9878456 DOI: 10.3389/fpls.2022.1115513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
MADS-box transcription factors play an important role in regulating floral organ development and participate in environmental responses. To date, the MADS-box gene family has been widely identified in Brassica rapa (B. rapa), Brassica oleracea (B. oleracea), and Brassica napus (B. napus); however, there are no analogous reports in Brassica nigra (B. nigra), Brassica juncea (B. juncea), and Brassica carinata (B. carinata). In this study, a whole-genome survey of the MADS-box gene family was performed for the first time in the triangle of U species, and a total of 1430 MADS-box genes were identified. Based on the phylogenetic relationship and classification of MADS-box genes in Arabidopsis thaliana (A. thaliana), 1430 MADS-box genes were categorized as M-type subfamily (627 genes), further divided into Mα, Mβ, Mγ, and Mδ subclades, and MIKC-type subfamily (803 genes), further classified into 35 subclades. Gene structure and conserved protein motifs of MIKC-type MADS-box exhibit diversity and specificity among different subclades. Comparative analysis of gene duplication events and syngenic gene pairs among different species indicated that polyploidy is beneficial for MIKC-type gene expansion. Analysis of transcriptome data within diverse tissues and stresses in B. napus showed tissue-specific expression of MIKC-type genes and a broad response to various abiotic stresses, particularly dehydration stress. In addition, four representative floral organ mutants (wtl, feml, aglf-2, and aglf-1) in the T0 generation were generated by editing four AGAMOUS (BnaAG) homoeologs in B. napus that enriched the floral organ variant phenotype. In brief, this study provides useful information for investigating the function of MADS-box genes and contributes to revealing the regulatory mechanisms of floral organ development in the genetic improvement of new varieties.
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Affiliation(s)
- Min Song
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Yanfeng Zhang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Qingli Jia
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Shuhua Huang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Ran An
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Nana Chen
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Yantao Zhu
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Jianxin Mu
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Shengwu Hu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
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Transcriptome Analysis and Metabolic Profiling of Green and Red Mizuna ( Brassica rapa L. var. japonica). Foods 2020; 9:foods9081079. [PMID: 32784373 PMCID: PMC7466343 DOI: 10.3390/foods9081079] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 11/17/2022] Open
Abstract
Mizuna (Brassica rapa L. var. japonica), a member of the family Brassicaceae, is rich in various health-beneficial phytochemicals, such as glucosinolates, phenolics, and anthocyanins. However, few studies have been conducted on genes associated with metabolic traits in mizuna. Thus, this study provides a better insight into the metabolic differences between green and red mizuna via the integration of transcriptome and metabolome analyses. A mizuna RNAseq analysis dataset showed 257 differentially expressed unigenes (DEGs) with a false discovery rate (FDR) of <0.05. These DEGs included the biosynthesis genes of secondary metabolites, such as anthocyanins, glucosinolates, and phenolics. Particularly, the expression of aliphatic glucosinolate biosynthetic genes was higher in the green cultivar. In contrast, the expression of most genes related to indolic glucosinolates, phenylpropanoids, and flavonoids was higher in the red cultivar. Furthermore, the metabolic analysis showed that 14 glucosinolates, 12 anthocyanins, five phenolics, and two organic acids were detected in both cultivars. The anthocyanin levels were higher in red than in green mizuna, while the glucosinolate levels were higher in green than in red mizuna. Consistent with the results of phytochemical analyses, the transcriptome data revealed that the expression levels of the phenylpropanoid and flavonoid biosynthesis genes were significantly higher in red mizuna, while those of the glucosinolate biosynthetic genes were significantly upregulated in green mizuna. A total of 43 metabolites, such as amino acids, carbohydrates, tricarboxylic acid (TCA) cycle intermediates, organic acids, and amines, was identified and quantified in both cultivars using gas chromatography coupled with time-of-flight mass spectrometry (GC-TOFMS). Among the identified metabolites, sucrose was positively correlated with anthocyanins, as previously reported.
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Kim S, Nie H, Jun B, Kim J, Lee J, Kim S, Kim E, Kim S. Functional genomics by integrated analysis of transcriptome of sweet potato (Ipomoea batatas (L.) Lam.) during root formation. Genes Genomics 2020; 42:581-596. [PMID: 32240514 DOI: 10.1007/s13258-020-00927-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 03/26/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Sweet potato is easily propagated by cuttings. But the molecular biological mechanism of adventitious root formation are not yet clear. OBJECTIVE To understand the molecular mechanisms of adventitious root formation from stem cuttings in sweet potato. METHODS RNA-seq analysis was performed using un-rooted stem (0 day) and rooted stem (3 days). Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, comparison with Arabidopsis transcription factors (TFs) of DEGs were conducted to investigate the characteristics of genes and TFs involved in root formation. In addition, qRT-PCR analysis using roots at 0, 3, 6, 9, and 12 days after planting was performed to confirm RNA-seq reliability and related genes expression. RESULTS 42,459 representative transcripts and 2092 DEGs were obtained through the RNA-seq analysis. The DEGs indicated the GO terms related to the single-organism metabolic process and cell periphery, and involved in the biosynthesis of secondary metabolites, and phenylpropanoid biosynthesis in KEGG pathways. The comparison with Arabidopsis thaliana TF database showed that 3 TFs (WRKY, NAC, bHLH) involved in root formation of sweet potato. qRT-PCR analysis, which was conducted to confirm the reliability of RNA-seq analysis, indicated that some metabolisms including oxidative stress and wounding, transport, hormone may be involved in adventitious root formation. CONCLUSIONS The detected genes related to secondary metabolism, some hormone (auxin, gibberellin), transports, etc. and 3 TFs (WRKY, NAC, bHLH) may have functions in adventitious roots formation. This results provide valuable resources for future research on the adventitious root formation of sweet potato.
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Affiliation(s)
- Sujung Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea
| | - Hualin Nie
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea
| | - Byungki Jun
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea.,NH Seed Research Development Center, Nonghyup Agribusiness Group Incorporation, Anseong, 17558, Korea
| | - Jiseong Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea
| | - Jeongeun Lee
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea
| | - Seungill Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea
| | - Ekyune Kim
- College of Pharmacy, Catholic University of Daegu, Gyeongsan, Gyeongbuk, 38430, Korea
| | - Sunhyung Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea.
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Santos SA, Vidigal PMP, Thrimawithana A, Betancourth BML, Guimarães LMS, Templeton MD, Alfenas AC. Comparative genomic and transcriptomic analyses reveal different pathogenicity-related genes among three eucalyptus fungal pathogens. Fungal Genet Biol 2020; 137:103332. [PMID: 31926322 DOI: 10.1016/j.fgb.2019.103332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/30/2019] [Accepted: 12/27/2019] [Indexed: 01/26/2023]
Abstract
Ceratocystis fimbriata is an important plant pathogen known to cause Ceratocystis Wilt (CW), a prevalent fungal disease known to affect Eucalyptus spp. plantations in Brazil. To better understand the molecular mechanisms related to pathogenicity in eucalyptus, we generated a high-quality assembly and annotation of the Ce. fimbriata LPF1912 isolate (LPF1912) genome, as well as the first transcriptome of LPF1912 from 16 eucalyptus clones at three infection incubation periods (12, 18, and 24 h). The LPF1912 genome assembly contains 805 scaffolds, totaling 31.8 Mb, with 43% of the genome estimated to be coding sequence comprised of 7,390 protein-coding genes of which 626 (8.5%) were classified as secreted proteins, 120 ribosomal RNAs, and 532 transfer RNAs. Comparative genomic analysis among three eucalyptus fungal pathogens (Ce. fimbriata, Ce. eucalypticola, and Calonectria pseudoreteaudii), showed high similarity in the proteome (21.81%) and secretome (52.01%) of LPF1912 and Ce. eucalypticola. GO annotation of pathogenicity-related genes of LPF1912 and Ce. eucalypticola, revealed enrichment in cell wall degrading enzymes (CWDEs), and lipid/cutin metabolism for Ca. pseudoreteaudii. Additionally, a transcriptome analysis between resistant and susceptible eucalyptus clones to CW infection indicated that a majority (11) of LPF1912 differentially expressed genes had GO terms associated with enzymatic functions, such as the polygalacturonase gene family, confirming the crucial role of CWDEs for Ce. fimbriata pathogenicity. Finally, our genomic and transcriptomic analysis approach provides a better understanding of the mechanisms involved in Ce. fimbriata pathogenesis, as well as a framework for further studies.
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Affiliation(s)
- Samuel A Santos
- Laboratory of Forest Pathology, Department of Plant Pathology, Universidade Federal de Viçosa, Minas Gerais State, Brazil; The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Pedro M P Vidigal
- Núcleo de Análise de Biomoléculas (NuBioMol), Centro de Ciências Biológicas, Universidade Federal de Viçosa, Minas Gerais State, Brazil
| | - Amali Thrimawithana
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Blanca M L Betancourth
- Laboratory of Forest Pathology, Department of Plant Pathology, Universidade Federal de Viçosa, Minas Gerais State, Brazil
| | - Lúcio M S Guimarães
- Laboratory of Forest Pathology, Department of Plant Pathology, Universidade Federal de Viçosa, Minas Gerais State, Brazil
| | - Matthew D Templeton
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Acelino C Alfenas
- Laboratory of Forest Pathology, Department of Plant Pathology, Universidade Federal de Viçosa, Minas Gerais State, Brazil.
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Tang X, Hao YJ, Lu JX, Lu G, Zhang T. Transcriptomic analysis reveals the mechanism of thermosensitive genic male sterility (TGMS) of Brassica napus under the high temperature inducement. BMC Genomics 2019; 20:644. [PMID: 31409283 PMCID: PMC6691554 DOI: 10.1186/s12864-019-6008-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 07/30/2019] [Indexed: 11/24/2022] Open
Abstract
Background The thermo-sensitive genic male sterility (TGMS) of Brassica napus facilitates reproductive researches and hybrid seed production. Considering the complexity and little information about the molecular mechanism involved in B. napus TGMS, comparative transcriptomic analyses were peroformed for the sterile (160S-MS) and fertile (160S-MF) flowers to identify potential crucial genes and pathways associated with TGMS. Results In total, RNA-seq analysis showed that 2202 genes (561 up-regulated and 1641 down-regulated) were significantly differentially expressed in the fertile flowers of 160S-MF at 25 °C when compared the sterile flower of 160S-MS at 15 °C. Detailed analysis revealed that expression changes in genes encoding heat shock proteins, antioxidant, skeleton protein, GTPase and calmodulin might be involved in TGMS of B. napus. Moreover, gene expression of some key members in plant hormone signaling pathways, such as auxin, gibberellins, jasmonic acid, abscisic acid, brassinosteroid signalings, were significantly surppressed in the flowers of 160S, suggesting that these genes might be involved in the regulation in B. napus TGMS. Here, we also found that transcription factor MADS, NFY, HSF, MYB/C and WRKY might play a crucial role in male fertility under the high temperature condition. Conclusion High temperature can significant affect gene expression in the flowers. The findings in the current study improve our understanding of B. napus TGMS at the molecular level and also provide an effective foundation for male fertility researches in other important economic crops. Electronic supplementary material The online version of this article (10.1186/s12864-019-6008-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xin Tang
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China
| | - You-Jin Hao
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China
| | - Jun-Xing Lu
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China
| | - Geng Lu
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China
| | - Tao Zhang
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China.
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Xu Y, Zeng A, Song L, Li J, Yan J. Comparative transcriptomics analysis uncovers alternative splicing events and molecular markers in cabbage (Brassica oleracea L.). PLANTA 2019; 249:1599-1615. [PMID: 30771045 DOI: 10.1007/s00425-019-03108-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/07/2019] [Indexed: 05/20/2023]
Abstract
Alternative splicing (AS) events were identified and verified in cabbage by comparative transcriptome analysis. The corresponding markers were developed and the germplasm resources were identified. Alternative splicing (AS) is a central regulatory mechanism that greatly contributes to plant gene expression and transcriptome diversity. A large body of evidence has shown that AS complexity is relevant for plant development, evolution, complexity, and adaptation. Both insertion/deletion (InDel) and single nucleotide polymorphism (SNP) are typically co-dominant inheritance markers and have abundant polymorphisms. These have been widely used for marker-assisted selection, genetic mapping, and germplasm identification in plants. However, little is known about the molecular mechanisms underlying AS events and the development of markers including SNP and InDel from the cabbage transcriptome. In this study, three cabbage transcriptome datasets were collected and aligned to the cabbage reference genome to analyze AS events and marker development. 31,524 AS events were identified from three cabbage genotypes, accounting for 20.8% of the total cabbage genes. Alternative 3' splice site donor (A3SS) was the most frequent type of the four main AS events in cabbage. 70,475 InDels and 706,269 SNPs were identified with average frequencies of 1 InDel/6.9 kb and 1 SNP/0.7 kb, respectively. 71,942 potential SSRs were identified in 53,129 assembled unigenes with a density of 1 SSR/6.8 kb. The ratio of SNPs with synonymous/non-synonymous mutations was 1:0.65. 142 InDels and 36 SNPs were randomly selected and validated via Sanger sequencing and polymorphism was found among 66.2% of the InDels and 78.6% of the SNPs. Furthermore, 35 informative InDel markers were successfully used for genetic diversity analysis on 36 cabbage accessions. These results facilitate understanding of the molecular regulation mechanism underlying AS events in cabbage. They also provide molecular marker resource data for genetic mapping construction and germplasm identification, and facilitate the genetic improvement of cabbage via breeding.
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Affiliation(s)
- Yuanyuan Xu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Aisong Zeng
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China.
| | - Lixiao Song
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Jiaqing Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Jiyong Yan
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China.
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Ali M, Hussain RM, Rehman NU, She G, Li P, Wan X, Guo L, Zhao J. De novo transcriptome sequencing and metabolite profiling analyses reveal the complex metabolic genes involved in the terpenoid biosynthesis in Blue Anise Sage (Salvia guaranitica L.). DNA Res 2018; 25:597-617. [PMID: 30188980 PMCID: PMC6289780 DOI: 10.1093/dnares/dsy028] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 07/25/2018] [Indexed: 02/04/2023] Open
Abstract
Many terpenoid compounds have been extracted from different tissues of Salvia guaranitica. However, the molecular genetic basis of terpene biosynthesis pathways is virtually unknown. In this study, approximately 4 Gb of raw data were generated from the transcriptome of S. guaranitica leaves using Illumina HiSeq 2000 sequencing. After filtering and removing the adapter sequences from the raw data, the number of reads reached 32 million, comprising 186 million of high-quality nucleotide bases. A total of 61,400 unigenes were assembled de novo and annotated for establishing a valid database for studying terpenoid biosynthesis. We identified 267 unigenes that are putatively involved in terpenoid metabolism (including, 198 mevalonate and methyl-erythritol phosphate (MEP) pathways, terpenoid backbone biosynthesis genes and 69 terpene synthases genes). Moreover, three terpene synthase genes were studied for their functions in terpenoid biosynthesis by using transgenic Arabidopsis; most transgenic Arabidopsis plants expressing these terpene synthetic genes produced increased amounts of terpenoids compared with wild-type control. The combined data analyses from the transcriptome and metabolome provide new insights into our understanding of the complex metabolic genes in terpenoid-rich blue anise sage, and our study paves the way for the future metabolic engineering of the biosynthesis of useful terpene compounds in S. guaranitica.
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Affiliation(s)
- Mohammed Ali
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Egyptian Deserts Gene Bank, North Sinai Research Station, Department of Plant Genetic Resources, Desert Research Center, Egypt
| | - Reem M Hussain
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Naveed Ur Rehman
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Guangbiao She
- State Key Laboratories of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Penghui Li
- State Key Laboratories of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Xiaochun Wan
- State Key Laboratories of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jian Zhao
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratories of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
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Jin SW, Rahim MA, Afrin KS, Park JI, Kang JG, Nou IS. Transcriptome profiling of two contrasting ornamental cabbage (Brassica oleracea var. acephala) lines provides insights into purple and white inner leaf pigmentation. BMC Genomics 2018; 19:797. [PMID: 30400854 PMCID: PMC6219265 DOI: 10.1186/s12864-018-5199-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/23/2018] [Indexed: 12/04/2022] Open
Abstract
Background Ornamental cabbage (Brassica oleracea var. acephala) is an attractive landscape plant that remains colorful at low temperatures during winter. Its key feature is its inner leaf coloration, which can include red, pink, lavender, blue, violet and white. Some ornamental cabbages exhibit variation in leaf color pattern linked to leaf developmental stage. However, little is known about the molecular mechanism underlying changes in leaf pigmentation pattern between developmental stages. Results The transcriptomes of six ornamental cabbage leaf samples were obtained using Illumina sequencing technology. A total of 339.75 million high-quality clean reads were assembled into 46,744 transcripts and 46,744 unigenes. Furthermore, 12,771 genes differentially expressed across the different lines and stages were identified by pairwise comparison. We identified 74 and 13 unigenes as differentially expressed genes related to the anthocyanin biosynthetic pathway and chlorophyll metabolism, respectively. Among them, three unigenes (BoC4H2, BoUGT9, and BoGST21) and six unigenes (BoHEMA1, BoCRD1, BoPORC1, BoPORC2, BoCAO, and BoCLH1) were found as candidates for the genes encoding enzymes in the anthocyanin biosynthetic pathway and chlorophyll metabolism, respectively. In addition, two unigenes (BoRAX3 and BoTRB1) as MYB candidates, two unigenes (BoMUTE1, and BHLH168-like) as bHLH candidates were identified for purple pigmentation in ornamental cabbage. Conclusion Our results indicate that the purple inner leaves of purple ornamental cabbage result from a high level of anthocyanin biosynthesis, a high level of chlorophyll degradation and an extremely low level of chlorophyll biosynthesis, whereas the bicolor (purple/green) outer leaves are due to a moderate level of anthocyanin biosynthesis, a high level of chlorophyll degradation and a very low level of chlorophyll biosynthesis. In white ornamental cabbage, the white inner leaves are due to an extremely low level or absence of anthocyanin biosynthesis, a high level of chlorophyll degradation and a very low level of chlorophyll biosynthesis, whereas the bicolor (white/green) leaves are due to a high level of chlorophyll degradation and a low level of chlorophyll biosynthesis and absence of anthocyanin biosynthesis. These results provide insight into the molecular mechanisms underlying inner and bicolor leaf pigmentation in ornamental cabbage and offer a platform for assessing related ornamental species. Electronic supplementary material The online version of this article (10.1186/s12864-018-5199-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Si-Won Jin
- Department of Horticulture, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Md Abdur Rahim
- Department of Horticulture, Sunchon National University, Suncheon, 57922, Republic of Korea.,Department of Genetics and Plant Breeding, Sher-e-Bangla Agricultural University, Dhaka-1207, Bangladesh
| | - Khandker Shazia Afrin
- Department of Horticulture, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Jong-Goo Kang
- Department of Horticulture, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Suncheon, 57922, Republic of Korea.
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Lawrence SD, Novak NG. Comparative analysis of the genetic variability within the Q-type C2H2 zinc-finger transcription factors in the economically important cabbage, canola and Chinese cabbage genomes. Hereditas 2018; 155:29. [PMID: 30258345 PMCID: PMC6150991 DOI: 10.1186/s41065-018-0065-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/22/2018] [Indexed: 12/29/2022] Open
Abstract
Background Brassica oleracea, B. rapa and B. napus encompass many economically important vegetable and oil crops; such as cabbage, broccoli, canola and Chinese cabbage. The genome sequencing of these species allows for gene discovery with an eye towards discerning the natural variability available for future breeding. The Q-type C2H2 zinc-finger protein (ZFP) transcription factors contain zinc finger motifs with a conserved QALGGH as part of the motif and they may play a critical role in the plants response to stress. While they may contain from one to five ZF domains (ZFD) this work focuses on the ZFPs that contain two zinc-fingers, which bind to the promoter of genes, and negatively regulate transcription via the EAR motif. B. oleracea and rapa are diploid and evolved into distinct species about 3.7 million years ago. B. napus is polyploid and formed by fusion of the diploids about 7500 years ago. Results This work identifies a total of 146 Q-type C2H2-ZFPs with 37 in B. oleracea, 35 in B. rapa and 74 in B. napus. The level of sequence similarity and arrangement of these genes on their chromosomes have mostly remained intact in B. napus, when compared to the chromosomes inherited from either B. rapa or oleracea. In contrast, the difference between the protein sequences of the orthologs of B. rapa and oleracea is greater and their organization on the chromosomes is much more divergent. In general, the 146 proteins are highly conserved especially within the known motifs. Differences within subgroups of ZFPs were identified. Considering that B. napus has twice the number of these proteins in its genome, RNA-Seq data was mined and the expression of 68 of the 74 genes was confirmed. Conclusion Alignment of these proteins gives a snapshot of the variability that may be available naturally in Brassica species. The aim is to study how different ZFPs bind different genes or how dissimilar EAR motifs alter the negative regulation of the genes bound to the ZFP. Results from such studies could be used to enhance tolerance in future Brassica breeding programs. Electronic supplementary material The online version of this article (10.1186/s41065-018-0065-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Susan D Lawrence
- Invasive Insect Biocontrol and Behavior Lab, USDA-ARS, 10300 Baltimore Ave., BARC-West Bldg 007, Rm 301, Beltsville, MD 20705 USA
| | - Nicole G Novak
- Invasive Insect Biocontrol and Behavior Lab, USDA-ARS, 10300 Baltimore Ave., BARC-West Bldg 007, Rm 301, Beltsville, MD 20705 USA
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Cheng CH, Shen BN, Shang QW, Liu LYD, Peng KC, Chen YH, Chen FF, Hu SF, Wang YT, Wang HC, Wu HY, Lo CT, Lin SS. Gene-to-Gene Network Analysis of the Mediation of Plant Innate Immunity by the Eliciting Plant Response-Like 1 (Epl1) Elicitor of Trichoderma formosa. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:683-691. [PMID: 29436965 DOI: 10.1094/mpmi-01-18-0002-ta] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
A new clade, Trichoderma formosa, secretes eliciting plant response-like 1 (Epl1), a small peptide elicitor that stimulates plant immunity. Nicotiana benthamiana pretreated with Epl1 for 3 days developed immunity against Tomato mosaic virus (ToMV) infection. The transcriptome profiles of T. formosa and N. benthamiana were obtained by deep sequencing; the transcript of Epl1 is 736 nt in length and encodes a 12-kDa peptide. Identifying critical genes in Epl1-mediated immunity was challenging due to high similarity between the transcriptome expression profiles of Epl1-treated and ToMV-infected N. benthamiana samples. Therefore, an efficient bioinformatics data mining approach was used for high-throughput transcriptomic assays in this study. We integrated gene-to-gene network analysis into the ContigViews transcriptome database, and genes related to jasmonic acid and ethylene signaling, salicylic acid signaling, leucine-rich repeats, transcription factors, and histone variants were hubs in the gene-to-gene networks. In this study, the Epl1 of T. formosa triggers plant immunity against various pathogen infections. Moreover, we demonstrated that high-throughput data mining and gene-to-gene network analysis can be used to identify critical candidate genes for further studies on the mechanisms of plant immunity.
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Affiliation(s)
- Chi-Hua Cheng
- 1 Department of Biotechnology, National Formosa University, Yulin, Taiwan
| | - Bing-Nan Shen
- 2 Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Qian-Wen Shang
- 2 Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | | | - Kou-Cheng Peng
- 4 Institute of Biotechnology, National Dong-Hwa University, Hualien, Taiwan
| | - Yan-Huey Chen
- 2 Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Fang-Fang Chen
- 2 Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Sin-Fen Hu
- 2 Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Yu-Tai Wang
- 5 National Center for High-Performance Computing, National Applied Research Laboratories, Hsinchu, Taiwan
| | - Hao-Ching Wang
- 6 Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Hsin-Yi Wu
- 7 Instrumentation Center, National Taiwan University
| | - Chaur-Tsuen Lo
- 1 Department of Biotechnology, National Formosa University, Yulin, Taiwan
| | - Shih-Shun Lin
- 2 Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
- 5 National Center for High-Performance Computing, National Applied Research Laboratories, Hsinchu, Taiwan
- 8 Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan; and
- 9 Center of Biotechnology, National Taiwan University
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11
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Rehman HM, Nawaz MA, Shah ZH, Ludwig-Müller J, Chung G, Ahmad MQ, Yang SH, Lee SI. Comparative genomic and transcriptomic analyses of Family-1 UDP glycosyltransferase in three Brassica species and Arabidopsis indicates stress-responsive regulation. Sci Rep 2018; 8:1875. [PMID: 29382843 PMCID: PMC5789830 DOI: 10.1038/s41598-018-19535-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 01/03/2018] [Indexed: 12/25/2022] Open
Abstract
In plants, UGTs (UDP-glycosyltransferases) glycosylate various phytohormones and metabolites in response to biotic and abiotic stresses. Little is known about stress-responsive glycosyltransferases in plants. Therefore, it is important to understand the genomic and transcriptomic portfolio of plants with regard to biotic and abiotic stresses. Here, we identified 140, 154, and 251 putative UGTs in Brassica rapa, Brassica oleracea, and Brassica napus, respectively, and clustered them into 14 major phylogenetic groups (A–N). Fourteen major KEGG pathways and 24 biological processes were associated with the UGTs, highlighting them as unique modulators against environmental stimuli. Putative UGTs from B. rapa and B. oleracea showed a negative selection pressure and biased gene fractionation pattern during their evolution. Polyploidization increased the intron proportion and number of UGT-containing introns among Brassica. The putative UGTs were preferentially expressed in developing tissues and at the senescence stage. Differential expression of up- and down-regulated UGTs in response to phytohormone treatments, pathogen responsiveness and abiotic stresses, inferred from microarray and RNA-Seq data in Arabidopsis and Brassica broaden the glycosylation impact at the molecular level. This study identifies unique candidate UGTs for the manipulation of biotic and abiotic stress pathways in Brassica and Arabidopsis.
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Affiliation(s)
- Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Korea
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Korea
| | - Zahid Hussain Shah
- Department of Arid Land Agriculture, King Abdul-Aziz University, Jeddah, Saudi Arabia
| | - Jutta Ludwig-Müller
- Institut für Botanik, Technische Universität Dresden, 01062, Dresden, Germany
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Korea
| | - Muhammad Qadir Ahmad
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, 6000, Pakistan
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Korea.
| | - Soo In Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju, 54874, Republic of Korea.
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12
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Liu XQ, Yu CY, Dong JG, Xu AX, Hu SW. De novo transcriptome reconstruction of a thermo-sensitive male sterility mutant in rapeseed ( Brassica napus; Brassicaceae). APPLICATIONS IN PLANT SCIENCES 2017; 5:apps.1700077. [PMID: 29299393 PMCID: PMC5749817 DOI: 10.3732/apps.1700077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 10/17/2017] [Indexed: 05/23/2023]
Abstract
PREMISE OF THE STUDY SP2S is a spontaneous thermo-sensitive genic male sterility (TGMS) mutation that facilitates two-line hybrid breeding in Brassica napus (Brassicaceae). De novo assembly of the floral bud transcriptome of SP2S can provide a foundation for deciphering the transcriptional regulation of SP2S in response to temperature change. METHODS mRNAs of the young floral buds of SP2S and its near-isogenic line SP2F grown under cool (16°C)/warm (22°C) conditions were sequenced on an Illumina Solexa platform, producing 239.7 million short reads with a total length of 19.95 Gbp. RESULTS The reads were assembled de novo using the Trinity program, resulting in 135,702 transcripts with an average length of 784 bp, an N50 value of 1221 bp, and a total length of 107 Mbp. We identified 24,157 cDNA-derived simple sequence repeats in the assembly. We found 137 and 195 single-nucleotide polymorphisms and 49 and 51 differentially regulated KEGG orthology groups when comparing sample SP2S at 22°C vs. SP2S at 16°C and sample SP2S at 22°C vs. SP2F at 22°C, respectively. DISCUSSION The numerous differentially expressed genes and the derived single-nucleotide polymorphisms show abnormal transcriptional regulation in the TGMS system. These results outline an intricate transcriptional regulation that occurred in the rapeseed TGMS SP2S when the temperature changed.
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Affiliation(s)
- Xi-Qiong Liu
- College of Agronomy, Northwest A&F University, 3 Taicheng Road, Yangling 712100, People’s Republic of China
| | - Cheng-Yu Yu
- College of Agronomy, Northwest A&F University, 3 Taicheng Road, Yangling 712100, People’s Republic of China
| | - Jun-Gang Dong
- College of Agronomy, Northwest A&F University, 3 Taicheng Road, Yangling 712100, People’s Republic of China
| | - Ai-Xia Xu
- College of Agronomy, Northwest A&F University, 3 Taicheng Road, Yangling 712100, People’s Republic of China
| | - Sheng-Wu Hu
- College of Agronomy, Northwest A&F University, 3 Taicheng Road, Yangling 712100, People’s Republic of China
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Ali M, Li P, She G, Chen D, Wan X, Zhao J. Transcriptome and metabolite analyses reveal the complex metabolic genes involved in volatile terpenoid biosynthesis in garden sage (Salvia officinalis). Sci Rep 2017; 7:16074. [PMID: 29167468 PMCID: PMC5700130 DOI: 10.1038/s41598-017-15478-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 10/27/2017] [Indexed: 11/29/2022] Open
Abstract
A large number of terpenoid compounds have been extracted from different tissues of S. officinalis. However, the molecular genetic basis of terpene biosynthesis pathways is virtually unknown. In this study, approximately 6.6 Gb of raw data were generated from the transcriptome of S. officinalis leaves using Illumina HiSeq 2000 sequencing. After filtering and removing the adapter sequences from the raw data, the number of reads reached 21 million, comprising 98 million of high-quality nucleotide bases. 48,671 unigenes were assembled de novo and annotated for establishing a valid database for studying terpenoid biosynthesis. We identified 135 unigenes that are putatively involved in terpenoid metabolism, including 70 mevalonate and methyl-erythritol phosphate pathways, terpenoid backbone biosynthesis genes, and 65 terpene synthase genes. Moreover, five terpene synthase genes were studied for their functions in terpenoid biosynthesis by using transgenic tobacco; most transgenic tobacco plants expressing these terpene synthetic genes produced increased amounts of terpenoids compared with wild-type control. The combined data analyses from the transcriptome and metabolome provide new insights into our understanding of the complex metabolic genes in terpenoid-rich sage, and our study paves the way for the future metabolic engineering of the biosynthesis of useful terpene compounds in S. officinalis.
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Affiliation(s)
- Mohammed Ali
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Penghui Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangbiao She
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Daofu Chen
- Wuhan Doublehelix Biology Science and Technology Co. Ltd, Wuhan, 430070, China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jian Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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Liu XQ, Liu ZQ, Yu CY, Dong JG, Hu SW, Xu AX. TGMS in Rapeseed ( Brassica napus) Resulted in Aberrant Transcriptional Regulation, Asynchronous Microsporocyte Meiosis, Defective Tapetum, and Fused Sexine. FRONTIERS IN PLANT SCIENCE 2017; 8:1268. [PMID: 28775729 PMCID: PMC5517502 DOI: 10.3389/fpls.2017.01268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 07/05/2017] [Indexed: 06/07/2023]
Abstract
The thermo-sensitive genic male sterility (TGMS) line SP2S is a spontaneous rapeseed mutation with several traits that are favorable for the production of two-line hybrids. To uncover the key cellular events and genetic regulation associated with TGMS expression, a combined study using cytological observation, transcriptome profiling, and gene expression analysis was conducted for SP2S and its near-isogenic line SP2F grown under warm conditions. Asynchronous microsporocyte meiosis and abnormal tapetal plastids and elaioplasts were demonstrated in the anther of SP2S. The tetrad microspore did not undergo mitosis before the cytoplasm degenerated. Delayed degradation of the tetrad wall, which led to tetrad microspore aggregation, resulted in postponement of sexine (outer layer of pollen exine) formation and sexine fusion in the tetrad. The nexine (foot layer of exine) was also absent. The delay of tetrad wall degradation and abnormality of the exine structure suggested that the defective tapetum lost important functions. Based on transcriptomic comparisons between young flower buds of SP2S and SP2F plants, a total of 465 differentially expressed transcripts (DETs) were identified, including 303 up-regulated DETs and 162 down-regulated DETs in SP2S. Several genes encoding small RNA degrading nuclease 2, small RNA 2'-O-methyltransferase, thioredoxin reductase 2, regulatory subunit A alpha isoform of serine/threonine-protein phosphatase 2A, glycine rich protein 1A, transcription factor bHLH25, leucine-rich repeat receptor kinase At3g14840 like, and fasciclin-like arabinogalactan proteins FLA19 and FLA20 were greatly depressed in SP2S. Interestingly, a POLLENLESS3-LIKE 2 gene encoding the Arabidopsis MS5 homologous protein, which is necessary for microsporocyte meiosis, was down-regulated in SP2S. Other genes that were up-regulated in SP2S encoded glucanase A6, ethylene-responsive transcription factor 1A-like, pollen-specific SF3, stress-associated endoplasmic reticulum protein 2, WRKY transcription factors and pentatricopeptide repeat (PPR) protein At1g07590. The tapetum-development-related genes, including BnEMS1, BnDYT1, and BnAMS, were slightly up-regulated in 3-mm-long flower buds or their anthers, and their downstream genes, BnMS1 and BnMYB80, which affect callose dissolution and exine formation, were greatly up-regulated in SP2S. This aberrant genetic regulation corresponded well with the cytological abnormalities. The results suggested that expression of TGMS associates with complex transcriptional regulation.
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Affiliation(s)
| | | | - Cheng-Yu Yu
- Department of Plant Science and Technology, College of Agronomy, Northwest A&F UniversityYangling, China
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Singh V, Goel R, Pande V, Asif MH, Mohanty CS. De novo sequencing and comparative analysis of leaf transcriptomes of diverse condensed tannin-containing lines of underutilized Psophocarpus tetragonolobus (L.) DC. Sci Rep 2017; 7:44733. [PMID: 28322296 PMCID: PMC5359716 DOI: 10.1038/srep44733] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/13/2017] [Indexed: 11/09/2022] Open
Abstract
Condensed tannin (CT) or proanthocyanidin (PA) is a unique group of phenolic metabolite with high molecular weight with specific structure. It is reported that, the presence of high-CT in the legumes adversely affect the nutrients in the plant and impairs the digestibility upon consumption by animals. Winged bean (Psophocarpus tetragonolobus (L.) DC.) is one of the promising underutilized legume with high protein and oil-content. One of the reasons for its underutilization is due to the presence of CT. Transcriptome sequencing of leaves of two diverse CT-containing lines of P. tetragonolobus was carried out on Illumina Nextseq 500 sequencer to identify the underlying genes and contigs responsible for CT-biosynthesis. RNA-Seq data generated 102586 and 88433 contigs for high (HCTW) and low CT (LCTW) lines of P. tetragonolobus, respectively. Based on the similarity searches against gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) database revealed 5210 contigs involved in 229 different pathways. A total of 1235 contigs were detected to differentially express between HCTW and LCTW lines. This study along with its findings will be helpful in providing information for functional and comparative genomic analysis of condensed tannin biosynthesis in this plant in specific and legumes in general.
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Affiliation(s)
- Vinayak Singh
- Plant Molecular Biology and Genetic Engineering Division, CSIR-National Botanical Research Institute, Lucknow-226 001 Uttar Pradesh, India.,Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, 263001 India
| | - Ridhi Goel
- Plant Molecular Biology and Genetic Engineering Division, CSIR-National Botanical Research Institute, Lucknow-226 001 Uttar Pradesh, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, 263001 India
| | - Mehar Hasan Asif
- Plant Molecular Biology and Genetic Engineering Division, CSIR-National Botanical Research Institute, Lucknow-226 001 Uttar Pradesh, India
| | - Chandra Sekhar Mohanty
- Plant Molecular Biology and Genetic Engineering Division, CSIR-National Botanical Research Institute, Lucknow-226 001 Uttar Pradesh, India
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16
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Vigna BBZ, de Oliveira FA, de Toledo-Silva G, da Silva CC, do Valle CB, de Souza AP. Leaf transcriptome of two highly divergent genotypes of Urochloa humidicola (Poaceae), a tropical polyploid forage grass adapted to acidic soils and temporary flooding areas. BMC Genomics 2016; 17:910. [PMID: 27835957 PMCID: PMC5106776 DOI: 10.1186/s12864-016-3270-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 11/05/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Urochloa humidicola (Koronivia grass) is a polyploid (6x to 9x) species that is used as forage in the tropics. Facultative apospory apomixis is present in most of the genotypes of this species, although one individual has been described as sexual. Molecular studies have been restricted to molecular marker approaches for genetic diversity estimations and linkage map construction. The objectives of the present study were to describe and compare the leaf transcriptome of two important genotypes that are highly divergent in terms of their phenotypes and reproduction modes: the sexual BH031 and the aposporous apomictic cultivar BRS Tupi. RESULTS We sequenced the leaf transcriptome of Koronivia grass using an Illumina GAIIx system, which produced 13.09 Gb of data that consisted of 163,575,526 paired-end reads between the two libraries. We de novo-assembled 76,196 transcripts with an average length of 1,152 bp and filtered 35,093 non-redundant unigenes. A similarity search against the non-redundant National Center of Biotechnology Information (NCBI) protein database returned 65 % hits. We annotated 24,133 unigenes in the Phytozome database and 14,082 unigenes in the UniProtKB/Swiss-Prot database, assigned 108,334 gene ontology terms to 17,255 unigenes and identified 5,324 unigenes in 327 known metabolic pathways. Comparisons with other grasses via a reciprocal BLAST search revealed a larger number of orthologous genes for the Panicum species. The unigenes were involved in C4 photosynthesis, lignocellulose biosynthesis and flooding stress responses. A search for functional molecular markers revealed 4,489 microsatellites and 560,298 single nucleotide polymorphisms (SNPs). A quantitative real-time PCR analysis validated the RNA-seq expression analysis and allowed for the identification of transcriptomic differences between the two evaluated genotypes. Moreover, 192 unannotated sequences were classified as containing complete open reading frames, suggesting that the new, potentially exclusive genes should be further investigated. CONCLUSION The present study represents the first whole-transcriptome sequencing of U. humidicola leaves, providing an important public information source of transcripts and functional molecular markers. The qPCR analysis indicated that the expression of certain transcripts confirmed the differential expression observed in silico, which demonstrated that RNA-seq is useful for identifying differentially expressed and unique genes. These results corroborate the findings from previous studies and suggest a hybrid origin for BH031.
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Affiliation(s)
| | - Fernanda Ancelmo de Oliveira
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Guilherme de Toledo-Silva
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
- Present Address: Department of Biochemistry, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, SC Brazil
| | - Carla Cristina da Silva
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | | | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
- Department of Plant Biology, Biology Institute, UNICAMP, Campinas, SP Brazil
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17
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Lee J, Kim J, Choi JP, Lee M, Kim MK, Lee YH, Hur Y, Nou IS, Park SU, Min SR, Kim H. Intracellular Ca(2+) and K(+) concentration in Brassica oleracea leaf induces differential expression of transporter and stress-related genes. BMC Genomics 2016; 17:211. [PMID: 26955874 PMCID: PMC4784358 DOI: 10.1186/s12864-016-2512-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 02/23/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND One of the most important members of the genus Brassica, cabbage, requires a relatively high level of calcium for normal growth (Plant Cell Environ 7: 397-405, 1984; Plant Physiol 60: 854-856, 1977). Localized Ca(2+) deficiency in cabbage leaves causes tip-burn, bringing about serious economic losses (Euphytica 9:203-208, 1960; Ann Bot 43:363-372, 1979; Sci Hortic 14:131-138, 1981). Although it has been known that the occurrence of tip-burn is related to Ca(2+) deficiency, there is limited information on the underlying mechanisms of tip-burn or the relationship between Ca(2+) and tip-burn incidence. To obtain more information on the genetic control of tip-burn symptoms, we focused on the identification of genes differentially expressed in response to increasing intracellular Ca(2+) and K(+) concentrations in B. oleracea lines derived from tip-burn susceptible, tip-burn resistant cabbages (B. oleracea var. capitata), and kale (B. oleracea var. acephala). RESULTS We compared the levels of major macronutrient cations, including Ca(2+) and K(+), in three leaf segments, the leaf apex (LA), middle of leaf (LM), and leaf base (LB), of tip-burn susceptible, tip-burn resistant cabbages, and kale. Ca(2+) and K(+) concentrations were highest in kale, followed by tip-burn resistant and then tip-burn susceptible cabbages. These cations generally accumulated to a greater extent in the LB than in the LA. Transcriptome analysis identified 58,096 loci as putative non-redundant genes in the three leaf segments of the three B. oleracea lines and showed significant changes in expression of 27,876 loci based on Ca(2+) and K(+) levels. Among these, 1844 loci were identified as tip-burn related phenotype-specific genes. Tip-burn resistant cabbage and kale-specific genes were largely related to stress and transport activity based on GO annotation. Tip-burn resistant cabbage and kale plants showed phenotypes clearly indicative of heat-shock, freezing, and drought stress tolerance compared to tip-burn susceptible cabbages, demonstrating a correlation between intracellular Ca(2+) and K(+) concentrations and tolerance of abiotic stress with differential gene expression. We selected 165 genes that were up- or down-regulated in response to increasing Ca(2+) and K(+) concentrations in the three leaf segments of the three plant lines. Gene ontology enrichment analysis indicated that these genes participated in regulatory metabolic processes or stress responses. CONCLUSIONS Our results indicate that the genes involved in regulatory metabolic processes or stress responses were differentially expressed in response to increasing Ca(2+) and K(+) concentrations in the B. oleracea leaf. Our transcriptome data and the genes identified may serve as a starting point for understanding the mechanisms underlying essential macronutrient deficiencies in plants, as well as the features of tip-burn in cabbage and other Brassica species.
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Affiliation(s)
- Jeongyeo Lee
- Korea Research Institute of Bioscience and Biotechnology, 125 Gwahangno, Yuseong-gu, Daejeon, 305-806, Republic of Korea.
| | - Jungeun Kim
- Korea Research Institute of Bioscience and Biotechnology, 125 Gwahangno, Yuseong-gu, Daejeon, 305-806, Republic of Korea.
| | - Jae-Pil Choi
- Korea Research Institute of Bioscience and Biotechnology, 125 Gwahangno, Yuseong-gu, Daejeon, 305-806, Republic of Korea.
| | - MiYe Lee
- Korea Research Institute of Bioscience and Biotechnology, 125 Gwahangno, Yuseong-gu, Daejeon, 305-806, Republic of Korea.
| | - Min Keun Kim
- Environment-friendly Agriculture Research Division, Gyeongsangnam-do Agricultural Research and Extension Service, Jinju, 660-360, Republic of Korea.
| | - Young Han Lee
- Environment-friendly Agriculture Research Division, Gyeongsangnam-do Agricultural Research and Extension Service, Jinju, 660-360, Republic of Korea.
| | - Yoonkang Hur
- Department of Biological Sciences, College of Biological Sciences, Chungnam National University, Daejeon, 305-764, Republic of Korea.
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Jeonnam, 540-742, Republic of Korea.
| | - Sang Un Park
- Department of Crop Science, College of Agriculture & Life Sciences, Chungnam National University, Daejeon, 305-764, Republic of Korea.
| | - Sung Ran Min
- Korea Research Institute of Bioscience and Biotechnology, 125 Gwahangno, Yuseong-gu, Daejeon, 305-806, Republic of Korea.
| | - HyeRan Kim
- Korea Research Institute of Bioscience and Biotechnology, 125 Gwahangno, Yuseong-gu, Daejeon, 305-806, Republic of Korea. .,Systems and Bioengineering, University of Science and Technology, 217 Gajung-ro, Daejeon, Republic of Korea.
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Zhang L, Long Y, Fu C, Xiang J, Gan J, Wu G, Jia H, Yu L, Li M. Different Gene Expression Patterns between Leaves and Flowers in Lonicera japonica Revealed by Transcriptome Analysis. FRONTIERS IN PLANT SCIENCE 2016; 7:637. [PMID: 27242839 PMCID: PMC4861853 DOI: 10.3389/fpls.2016.00637] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/25/2016] [Indexed: 05/20/2023]
Abstract
The perennial and evergreen twining vine, Lonicera japonica is an important herbal medicine with great economic value. However, gene expression information for flowers and leaves of L. japonica remains elusive, which greatly impedes functional genomics research on this species. In this study, transcriptome profiles from leaves and flowers of L. japonica were examined using next-generation sequencing technology. A total of 239.41 million clean reads were used for de novo assembly with Trinity software, which generated 150,523 unigenes with N50 containing 947 bp. All the unigenes were annotated using Nr, SwissProt, COGs (Clusters of Orthologous Groups), GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases. A total of 35,327 differentially expressed genes (DEGs, P ≤ 0.05) between leaves and flowers were detected. Among them, a total of 6602 DEGs were assigned with important biological processes including "Metabolic process," "Response to stimulus," "Cellular process," and etc. KEGG analysis showed that three possible enzymes involved in the biosynthesis of chlorogenic acid were up-regulated in flowers. Furthermore, the TF-based regulation network in L. japonica identified three differentially expressed transcription factors between leaves and flowers, suggesting distinct regulatory roles in L. japonica. Taken together, this study has provided a global picture of differential gene expression patterns between leaves and flowers in L japonica, providing a useful genomic resource that can also be used for functional genomics research on L. japonica in the future.
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Affiliation(s)
- Libin Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Yan Long
- Institute of Biotechnology, Chinese Academy of Agricultural SciencesBeijing, China
| | - Chunhua Fu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Jun Xiang
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Jianping Gan
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Gang Wu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Haibo Jia
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Longjiang Yu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
- *Correspondence: Maoteng Li
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Chen SF, Li MW, Jing HJ, Zhou RC, Yang GL, Wu W, Fan Q, Liao WB. De Novo Transcriptome Assembly in Firmiana danxiaensis, a Tree Species Endemic to the Danxia Landform. PLoS One 2015; 10:e0139373. [PMID: 26427005 PMCID: PMC4591120 DOI: 10.1371/journal.pone.0139373] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 09/11/2015] [Indexed: 11/19/2022] Open
Abstract
Many Firmiana species are locally endemic, providing an interesting system for studying adaptation and speciation. Among these species, F. danxiaensis is a tree species endemic to Mount Danxia in Guangdong, China, which is an area known for presenting the Danxia landform. How F. danxiaensis could have adapted to the stressful environment of rocky cliffs covered with barren soils in the Danxia landform is still unknown. In this study, we performed de novo assembly of the transcriptome of F. danxiaensis, obtaining 47,221 unigenes with an N50 value of 987 bp. Homology analysis showed that 32,318 of the unigenes presented hits in the NCBI non-redundant database, and 31,857 exhibited significant matches with the protein database of Theobroma cacao. Gene Ontology (GO) annotation showed that hundreds of unigenes participated in responses to various stresses or nutritional starvation, which may help us to understand the adaptation of F. danxiaensis to Danxia landform. Additionally, we found 263 genes related to responses to Cd, partially explaining the high accumulation of Cd observed in Firmiana species. The EuKaryotic Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations revealed many genes playing roles in the biosynthesis of secondary metabolites and environmental adaptation, which may also contribute to the survivor and success of Firmiana species in extreme environments. Based on the obtained transcriptome, we further identified a Firmiana-specific whole-genome duplication event that occurred approximately 20 Mya, which may have provided raw materials for the diversification of Firmiana species.
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Affiliation(s)
- Su-Fang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ming-Wan Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Hui-Juan Jing
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ren-Chao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Gui-Li Yang
- National Engineering Resarch Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Wei Wu
- South China Botanical Garden, Chinese Academy of Science, Guangzhou 510650, China
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- * E-mail: (QF); (WL)
| | - Wen-Bo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- * E-mail: (QF); (WL)
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Zhou SM, Chen LM, Liu SQ, Wang XF, Sun XD. De Novo Assembly and Annotation of the Chinese Chive (Allium tuberosum Rottler ex Spr.) Transcriptome Using the Illumina Platform. PLoS One 2015. [PMID: 26204518 PMCID: PMC4512717 DOI: 10.1371/journal.pone.0133312] [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] [Indexed: 11/19/2022] Open
Abstract
Chinese chive (A. tuberosum Rottler ex Spr.) is one of the most widely cultivated Allium species in China. However, minimal transcriptomic and genomic data are available to reveal its evolution and genetic diversity. In this study, de novo transcriptome sequencing was performed to produce large transcript sequences using an Illumina HiSeq 2000 instrument. We produced 51,968,882 high-quality clean reads and assembled them into 150,154 contigs. A total of 60,031 unigenes with an average length of 631 bp were identified. Of these, 36,523 unigenes were homologous to existing database sequences, 35,648 unigenes were annotated in the NCBI non-redundant (Nr) sequence database, and 23,509 unigenes were annotated in the Swiss-Prot database. A total of 26,798 unigenes were assigned to 57 Gene Ontology (GO) terms, and 13,378 unigenes were assigned to Cluster of Orthologous Group categories. Using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database, we mapped 21,361 unigenes onto 128 pathways. Furthermore, 2,125 sequences containing simple sequence repeats (SSRs) were identified. This new dataset provides the most comprehensive resource currently available for gene expression, gene discovery, and future genomic research on Chinese chive. The sequence resources developed in this study can be used to develop molecular markers that will facilitate further genetic research on Chinese chive and related species.
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Affiliation(s)
- Shu-Mei Zhou
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai’an, Shandong, People's Republic of China
| | - Li-Mei Chen
- State Key Laboratory of Crop Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, People's Republic of China
| | - Shi-Qi Liu
- State Key Laboratory of Crop Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, People's Republic of China
| | - Xiu-Feng Wang
- State Key Laboratory of Crop Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, People's Republic of China
| | - Xiu-Dong Sun
- State Key Laboratory of Crop Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, People's Republic of China
- * E-mail:
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Kong HJ, Lee IK, Kim J, Kim WJ, Kim HS, Cho WS, Kim DW, Park JY, An CM. RNA-Seq-based transcriptome analysis of Korean rose bitterling (Rhodeus uyekii) exposed to synthetic estrogen 17-α-ethinylestradiol (EE2). Mar Genomics 2015; 24 Pt 3:233-6. [PMID: 26112897 DOI: 10.1016/j.margen.2015.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/12/2015] [Accepted: 06/12/2015] [Indexed: 11/29/2022]
Abstract
The potential impact of natural and synthetic estrogens on aquatic ecosystems has become a subject of great interest in recent years. One synthetic estrogen, 17-alpha-ethinylestradiol (EE2), is present in municipal sewage discharges and causes gonad alterations in various fish species. To understand the possible damage caused by EE2, male Rhodeus uyekii were exposed to 100 ng/L EE2 for 7 days. RNA-Seq was performed to assess the effects of EE2 on gene expression in hepatic and skin tissues. The analysis revealed that EE2 induced the expression of various genes, including sex hormone genes, anti-Mullerian hormone, vitellogenin, and estrogen receptor alpha; cancer genes, breast cancer anti-estrogen resistance protein 3, caveolin 2, and Smad2; and apoptotic genes, p53, Bcl-2, TNF-α, and WDR36. These results suggest that the synthetic estrogen EE2 disturbs the endocrine system and regulates both carcinogenic and apoptotic gene expressions in R. uyekii.
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Affiliation(s)
- Hee Jeong Kong
- Biotechnology Research Division, National Fisheries Research and Development Institute, Busan 619-705, Republic of Korea.
| | - Il Kyu Lee
- All Bio Technology Co., LTD, Internet Business Incubation Center, Mokweon University, Daejeon 302-729, Republic of Korea
| | - Julan Kim
- Biotechnology Research Division, National Fisheries Research and Development Institute, Busan 619-705, Republic of Korea
| | - Woo-Jin Kim
- Biotechnology Research Division, National Fisheries Research and Development Institute, Busan 619-705, Republic of Korea
| | - Hyung Soo Kim
- Biotechnology Research Division, National Fisheries Research and Development Institute, Busan 619-705, Republic of Korea
| | - Wang Sik Cho
- All Bio Technology Co., LTD, Internet Business Incubation Center, Mokweon University, Daejeon 302-729, Republic of Korea
| | - Dong-Wook Kim
- All Bio Technology Co., LTD, Internet Business Incubation Center, Mokweon University, Daejeon 302-729, Republic of Korea
| | - Jung Youn Park
- Biotechnology Research Division, National Fisheries Research and Development Institute, Busan 619-705, Republic of Korea
| | - Cheul Min An
- Biotechnology Research Division, National Fisheries Research and Development Institute, Busan 619-705, Republic of Korea
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Witzel K, Neugart S, Ruppel S, Schreiner M, Wiesner M, Baldermann S. Recent progress in the use of 'omics technologies in brassicaceous vegetables. FRONTIERS IN PLANT SCIENCE 2015; 6:244. [PMID: 25926843 PMCID: PMC4396356 DOI: 10.3389/fpls.2015.00244] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 03/26/2015] [Indexed: 05/21/2023]
Abstract
Continuing advances in 'omics methodologies and instrumentation is enhancing the understanding of how plants cope with the dynamic nature of their growing environment. 'Omics platforms have been only recently extended to cover horticultural crop species. Many of the most widely cultivated vegetable crops belong to the genus Brassica: these include plants grown for their root (turnip, rutabaga/swede), their swollen stem base (kohlrabi), their leaves (cabbage, kale, pak choi) and their inflorescence (cauliflower, broccoli). Characterization at the genome, transcript, protein and metabolite levels has illustrated the complexity of the cellular response to a whole series of environmental stresses, including nutrient deficiency, pathogen attack, heavy metal toxicity, cold acclimation, and excessive and sub-optimal irradiation. This review covers recent applications of 'omics technologies to the brassicaceous vegetables, and discusses future scenarios in achieving improvements in crop end-use quality.
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Affiliation(s)
- Katja Witzel
- Leibniz-Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V.Großbeeren, Germany
| | - Susanne Neugart
- Leibniz-Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V.Großbeeren, Germany
| | - Silke Ruppel
- Leibniz-Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V.Großbeeren, Germany
| | - Monika Schreiner
- Leibniz-Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V.Großbeeren, Germany
| | - Melanie Wiesner
- Leibniz-Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V.Großbeeren, Germany
| | - Susanne Baldermann
- Leibniz-Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V.Großbeeren, Germany
- Institute of Nutritional Science, University of PotsdamNuthetal, Germany
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Wu G, Zhang L, Yin Y, Wu J, Yu L, Zhou Y, Li M. Sequencing, de novo assembly and comparative analysis of Raphanus sativus transcriptome. FRONTIERS IN PLANT SCIENCE 2015; 6:198. [PMID: 26029219 PMCID: PMC4428447 DOI: 10.3389/fpls.2015.00198] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 03/12/2015] [Indexed: 05/29/2023]
Abstract
Raphanus sativus is an important Brassicaceae plant and also an edible vegetable with great economic value. However, currently there is not enough transcriptome information of R. sativus tissues, which impedes further functional genomics research on R. sativus. In this study, RNA-seq technology was employed to characterize the transcriptome of leaf tissues. Approximately 70 million clean pair-end reads were obtained and used for de novo assembly by Trinity program, which generated 68,086 unigenes with an average length of 576 bp. All the unigenes were annotated against GO and KEGG databases. In the meanwhile, we merged leaf sequencing data with existing root sequencing data and obtained better de novo assembly of R. sativus using Oases program. Accordingly, potential simple sequence repeats (SSRs), transcription factors (TFs) and enzyme codes were identified in R. sativus. Additionally, we detected a total of 3563 significantly differentially expressed genes (DEGs, P = 0.05) and tissue-specific biological processes between leaf and root tissues. Furthermore, a TFs-based regulation network was constructed using Cytoscape software. Taken together, these results not only provide a comprehensive genomic resource of R. sativus but also shed light on functional genomic and proteomic research on R. sativus in the future.
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Affiliation(s)
- Gang Wu
- School of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Libin Zhang
- School of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Yongtai Yin
- School of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Jiangsheng Wu
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
| | - Longjiang Yu
- School of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Yanhong Zhou
- School of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Maoteng Li
- School of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
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Amar D, Frades I, Danek A, Goldberg T, Sharma SK, Hedley PE, Proux-Wera E, Andreasson E, Shamir R, Tzfadia O, Alexandersson E. Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case. BMC PLANT BIOLOGY 2014; 14:329. [PMID: 25476999 PMCID: PMC4274702 DOI: 10.1186/s12870-014-0329-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 11/10/2014] [Indexed: 05/08/2023]
Abstract
BACKGROUND For most organisms, even if their genome sequence is available, little functional information about individual genes or proteins exists. Several annotation pipelines have been developed for functional analysis based on sequence, 'omics', and literature data. However, researchers encounter little guidance on how well they perform. Here, we used the recently sequenced potato genome as a case study. The potato genome was selected since its genome is newly sequenced and it is a non-model plant even if there is relatively ample information on individual potato genes, and multiple gene expression profiles are available. RESULTS We show that the automatic gene annotations of potato have low accuracy when compared to a "gold standard" based on experimentally validated potato genes. Furthermore, we evaluate six state-of-the-art annotation pipelines and show that their predictions are markedly dissimilar (Jaccard similarity coefficient of 0.27 between pipelines on average). To overcome this discrepancy, we introduce a simple GO structure-based algorithm that reconciles the predictions of the different pipelines. We show that the integrated annotation covers more genes, increases by over 50% the number of highly co-expressed GO processes, and obtains much higher agreement with the gold standard. CONCLUSIONS We find that different annotation pipelines produce different results, and show how to integrate them into a unified annotation that is of higher quality than each single pipeline. We offer an improved functional annotation of both PGSC and ITAG potato gene models, as well as tools that can be applied to additional pipelines and improve annotation in other organisms. This will greatly aid future functional analysis of '-omics' datasets from potato and other organisms with newly sequenced genomes. The new potato annotations are available with this paper.
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Affiliation(s)
- David Amar
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
| | - Itziar Frades
- Deptartment of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
| | - Agnieszka Danek
- Institute of Informatics, Silesian University of Technology, Akademicka 2A, 44-100, Gliwice, Poland.
| | - Tatyana Goldberg
- Department for Bioinformatics and Computational Biology, Technical University of Munich, Arcisstraße 21, 80333, Munich, Germany.
| | - Sanjeev K Sharma
- Cell and Molecular Sciences, The James Hutton Institute, Aberdeen, Scotland, UK.
| | - Pete E Hedley
- Cell and Molecular Sciences, The James Hutton Institute, Aberdeen, Scotland, UK.
| | - Estelle Proux-Wera
- Deptartment of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
- Current affiliation: SciLifeLab, Stockholm University, Universitetsvägen 10, 114 18, Stockholm, Sweden.
| | - Erik Andreasson
- Deptartment of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
| | - Oren Tzfadia
- Department of Plant Science, The Weizmann Institute of Science, Rehovot, Israel.
| | - Erik Alexandersson
- Deptartment of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
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Guzman F, Kulcheski FR, Turchetto-Zolet AC, Margis R. De novo assembly of Eugenia uniflora L. transcriptome and identification of genes from the terpenoid biosynthesis pathway. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 229:238-246. [PMID: 25443850 DOI: 10.1016/j.plantsci.2014.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 10/07/2014] [Accepted: 10/10/2014] [Indexed: 05/06/2023]
Abstract
Pitanga (Eugenia uniflora L.) is a member of the Myrtaceae family and is of particular interest due to its medicinal properties that are attributed to specialized metabolites with known biological activities. Among these molecules, terpenoids are the most abundant in essential oils that are found in the leaves and represent compounds with potential pharmacological benefits. The terpene diversity observed in Myrtaceae is determined by the activity of different members of the terpene synthase and oxidosqualene cyclase families. Therefore, the aim of this study was to perform a de novo assembly of transcripts from E. uniflora leaves and to annotation to identify the genes potentially involved in the terpenoid biosynthesis pathway and terpene diversity. In total, 72,742 unigenes with a mean length of 1048bp were identified. Of these, 43,631 and 36,289 were annotated with the NCBI non-redundant protein and Swiss-Prot databases, respectively. The gene ontology categorized the sequences into 53 functional groups. A metabolic pathway analysis with KEGG revealed 8,625 unigenes assigned to 141 metabolic pathways and 40 unigenes predicted to be associated with the biosynthesis of terpenoids. Furthermore, we identified four putative full-length terpene synthase genes involved in sesquiterpenes and monoterpenes biosynthesis, and three putative full-length oxidosqualene cyclase genes involved in the triterpenes biosynthesis. The expression of these genes was validated in different E. uniflora tissues.
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Affiliation(s)
- Frank Guzman
- PPGGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil; PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Franceli Rodrigues Kulcheski
- PPGGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil; PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | | | - Rogerio Margis
- PPGGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil; PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil; Departamento de Biofisica, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil.
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26
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Jung WY, Lee SS, Kim CW, Kim HS, Min SR, Moon JS, Kwon SY, Jeon JH, Cho HS. RNA-seq analysis and de novo transcriptome assembly of Jerusalem artichoke (Helianthus tuberosus Linne). PLoS One 2014; 9:e111982. [PMID: 25375764 PMCID: PMC4222968 DOI: 10.1371/journal.pone.0111982] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 10/09/2014] [Indexed: 11/18/2022] Open
Abstract
Jerusalem artichoke (Helianthus tuberosus L.) has long been cultivated as a vegetable and as a source of fructans (inulin) for pharmaceutical applications in diabetes and obesity prevention. However, transcriptomic and genomic data for Jerusalem artichoke remain scarce. In this study, Illumina RNA sequencing (RNA-Seq) was performed on samples from Jerusalem artichoke leaves, roots, stems and two different tuber tissues (early and late tuber development). Data were used for de novo assembly and characterization of the transcriptome. In total 206,215,632 paired-end reads were generated. These were assembled into 66,322 loci with 272,548 transcripts. Loci were annotated by querying against the NCBI non-redundant, Phytozome and UniProt databases, and 40,215 loci were homologous to existing database sequences. Gene Ontology terms were assigned to 19,848 loci, 15,434 loci were matched to 25 Clusters of Eukaryotic Orthologous Groups classifications, and 11,844 loci were classified into 142 Kyoto Encyclopedia of Genes and Genomes pathways. The assembled loci also contained 10,778 potential simple sequence repeats. The newly assembled transcriptome was used to identify loci with tissue-specific differential expression patterns. In total, 670 loci exhibited tissue-specific expression, and a subset of these were confirmed using RT-PCR and qRT-PCR. Gene expression related to inulin biosynthesis in tuber tissue was also investigated. Exsiting genetic and genomic data for H. tuberosus are scarce. The sequence resources developed in this study will enable the analysis of thousands of transcripts and will thus accelerate marker-assisted breeding studies and studies of inulin biosynthesis in Jerusalem artichoke.
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Affiliation(s)
- Won Yong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea; Animal Material Engineering, Gyeongnam National University of Science and Technology, Jinju, Korea
| | - Sang Sook Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Chul Wook Kim
- Animal Material Engineering, Gyeongnam National University of Science and Technology, Jinju, Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Sung Ran Min
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Jae Sun Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Jae-Heung Jeon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
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Rastogi S, Meena S, Bhattacharya A, Ghosh S, Shukla RK, Sangwan NS, Lal RK, Gupta MM, Lavania UC, Gupta V, Nagegowda DA, Shasany AK. De novo sequencing and comparative analysis of holy and sweet basil transcriptomes. BMC Genomics 2014; 15:588. [PMID: 25015319 PMCID: PMC4125705 DOI: 10.1186/1471-2164-15-588] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 07/04/2014] [Indexed: 01/08/2023] Open
Abstract
Background Ocimum L. of family Lamiaceae is a well known genus for its ethnobotanical, medicinal and aromatic properties, which are attributed to innumerable phenylpropanoid and terpenoid compounds produced by the plant. To enrich genomic resources for understanding various pathways, de novo transcriptome sequencing of two important species, O. sanctum and O. basilicum, was carried out by Illumina paired-end sequencing. Results The sequence assembly resulted in 69117 and 130043 transcripts with an average length of 1646 ± 1210.1 bp and 1363 ± 1139.3 bp for O. sanctum and O. basilicum, respectively. Out of the total transcripts, 59648 (86.30%) and 105470 (81.10%) from O. sanctum and O. basilicum, and respectively were annotated by uniprot blastx against Arabidopsis, rice and lamiaceae. KEGG analysis identified 501 and 952 transcripts from O. sanctum and O. basilicum, respectively, related to secondary metabolism with higher percentage of transcripts for biosynthesis of terpenoids in O. sanctum and phenylpropanoids in O. basilicum. Higher digital gene expression in O. basilicum was validated through qPCR and correlated to higher essential oil content and chromosome number (O. sanctum, 2n = 16; and O. basilicum, 2n = 48). Several CYP450 (26) and TF (40) families were identified having probable roles in primary and secondary metabolism. Also SSR and SNP markers were identified in the transcriptomes of both species with many SSRs linked to phenylpropanoid and terpenoid pathway genes. Conclusion This is the first report of a comparative transcriptome analysis of Ocimum species and can be utilized to characterize genes related to secondary metabolism, their regulation, and breeding special chemotypes with unique essential oil composition in Ocimum. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-588) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Dinesh A Nagegowda
- Biotechnology Divison, CSIR-Central Institute of Medicinal and Aromatic Plants, P,O, CIMAP, 226015 Lucknow, U,P, India.
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