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Wang H, Liu S, Ma S, Wang Y, Yang H, Liu J, Li M, Cui X, Liang S, Cheng Q, Shen H. Characterization of the Molecular Events Underlying the Establishment of Axillary Meristem Region in Pepper. Int J Mol Sci 2023; 24:12718. [PMID: 37628899 PMCID: PMC10454251 DOI: 10.3390/ijms241612718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Plant architecture is a major motif of plant diversity, and shoot branching patterns primarily determine the aerial architecture of plants. In this study, we identified an inbred pepper line with fewer lateral branches, 20C1734, which was free of lateral branches at the middle and upper nodes of the main stem with smooth and flat leaf axils. Successive leaf axil sections confirmed that in normal pepper plants, for either node n, Pn (Primordium n) < 1 cm and Pn+1 < 1 cm were the critical periods between the identification of axillary meristems and the establishment of the region, whereas Pn+3 < 1 cm was fully developed and formed a completely new organ. In 20C1734, the normal axillary meristematic tissue region establishment and meristematic cell identity confirmation could not be performed on the axils without axillary buds. Comparative transcriptome analysis revealed that "auxin-activated signaling pathway", "response to auxin", "response to abscisic acid", "auxin biosynthetic process", and the biosynthesis of the terms/pathways, such as "secondary metabolites", were differentially enriched in different types of leaf axils at critical periods of axillary meristem development. The accuracy of RNA-seq was verified using RT-PCR for some genes in the pathway. Several differentially expressed genes (DEGs) related to endogenous phytohormones were targeted, including several genes of the PINs family. The endogenous hormone assay showed extremely high levels of IAA and ABA in leaf axils without axillary buds. ABA content in particular was unusually high. At the same time, there is no regular change in IAA level in this type of leaf axils (normal leaf axils will be accompanied by AM formation and IAA content will be low). Based on this, we speculated that the contents of endogenous hormones IAA and ABA in 20C1734 plant increased sharply, which led to the abnormal expression of genes in related pathways, which affected the formation of Ams in leaf axils in the middle and late vegetative growth period, and finally, nodes without axillary buds and side branches appeared.
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Affiliation(s)
- Haoran Wang
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Sujun Liu
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Shijie Ma
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Yun Wang
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Hanyu Yang
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Jiankun Liu
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Mingxuan Li
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Xiangyun Cui
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Sun Liang
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Sanya Institute, China Agricultural University, Sanya 572025, China
| | - Qing Cheng
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Sanya Institute, China Agricultural University, Sanya 572025, China
| | - Huolin Shen
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Sanya Institute, China Agricultural University, Sanya 572025, China
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Lara-Cabrera SI, Perez-Garcia MDLL, Maya-Lastra CA, Montero-Castro JC, Godden GT, Cibrian-Jaramillo A, Fisher AE, Porter JM. Phylogenomics of Salvia L. subgenus Calosphace (Lamiaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:725900. [PMID: 34721456 PMCID: PMC8554000 DOI: 10.3389/fpls.2021.725900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/07/2021] [Indexed: 05/13/2023]
Abstract
The evolutionary relationships of Salvia have been difficult to estimate. In this study, we used the Next Generation Sequencing method Hyb-Seq to evaluate relationships among 90 Lamiaceae samples, including representatives of Mentheae, Ocimeae, Salvia subgenera Audibertia, Leonia, Salvia, and 69 species of subgenus Calosphace, representing 32 of Epling's sections. A bait set was designed in MarkerMiner using available transcriptome data to enrich 119 variable nuclear loci. Nuclear and chloroplast loci were assembled with hybphylomaker (HPM), followed by coalescent approach analyses for nuclear data (ASTRAL, BEAST) and a concatenated Maximum Likelihood analysis of chloroplast loci. The HPM assembly had an average of 1,314,368 mapped reads for the sample and 527 putative exons. Phylogenetic inferences resolved strongly supported relationships for the deep-level nodes, agreeing with previous hypotheses which assumed that subgenus Audibertia is sister to subgenus Calosphace. Within subgenus Calosphace, we recovered eight monophyletic sections sensu Epling, Cardinalis, Hastatae, Incarnatae, and Uricae in all the analyses (nDNA and cpDNA), Biflorae, Lavanduloideae, and Sigmoideae in nuclear analyses (ASTRAL, BEAST) and Curtiflorae in ASTRAL trees. Network analysis supports deep node relationships, some of the main clades, and recovers reticulation within the core Calosphace. The chloroplast phylogeny resolved deep nodes and four monophyletic Calosphace sections. Placement of S. axillaris is distinct in nuclear evidence and chloroplast, as sister to the rest of the S. subg. Calosphace in chloroplast and a clade with "Hastatae clade" sister to the rest of the subgenus in nuclear evidence. We also tested the monophyly of S. hispanica, S. polystachia, S. purpurea, and S. tiliifolia, including two samples of each, and found that S. hispanica and S. purpurea are monophyletic. Our baits can be used in future studies of Lamiaceae phylogeny to estimate relationships between genera and among species. In this study, we presented a Hyb-Seq phylogeny for complex, recently diverged Salvia, which could be implemented in other Lamiaceae.
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Affiliation(s)
- Sabina Irene Lara-Cabrera
- Laboratorio de Sistemática Molecular de Plantas, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Maria de la Luz Perez-Garcia
- Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Mexico
| | - Carlos Alonso Maya-Lastra
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, United States
| | - Juan Carlos Montero-Castro
- Laboratorio de Sistemática Molecular de Plantas, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Grant T. Godden
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
| | - Angelica Cibrian-Jaramillo
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación y de Estudios Avanzados del instituto Politécnico Nacional, Irapuato, Mexico
| | - Amanda E. Fisher
- Department of Biological Sciences, California State University, Long Beach, CA, United States
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Gupta P, Geniza M, Naithani S, Phillips JL, Haq E, Jaiswal P. Chia ( Salvia hispanica) Gene Expression Atlas Elucidates Dynamic Spatio-Temporal Changes Associated With Plant Growth and Development. FRONTIERS IN PLANT SCIENCE 2021; 12:667678. [PMID: 34354718 PMCID: PMC8330693 DOI: 10.3389/fpls.2021.667678] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/09/2021] [Indexed: 06/12/2023]
Abstract
Chia (Salvia hispanica L.), now a popular superfood and a pseudocereal, is one of the richest sources of dietary nutrients such as protein, fiber, and polyunsaturated fatty acids (PUFAs). At present, the genomic and genetic information available in the public domain for this crop are scanty, which hinders an understanding of its growth and development and genetic improvement. We report an RNA-sequencing (RNA-Seq)-based comprehensive transcriptome atlas of Chia sampled from 13 tissue types covering vegetative and reproductive growth stages. We used ~355 million high-quality reads of total ~394 million raw reads from transcriptome sequencing to generate de novo reference transcriptome assembly and the tissue-specific transcript assemblies. After the quality assessment of the merged assemblies and implementing redundancy reduction methods, 82,663 reference transcripts were identified. About 65,587 of 82,663 transcripts were translated into 99,307 peptides, and we were successful in assigning InterPro annotations to 45,209 peptides and gene ontology (GO) terms to 32,638 peptides. The assembled transcriptome is estimated to have the complete sequence information for ~86% of the genes found in the Chia genome. Furthermore, the analysis of 53,200 differentially expressed transcripts (DETs) revealed their distinct expression patterns in Chia's vegetative and reproductive tissues; tissue-specific networks and developmental stage-specific networks of transcription factors (TFs); and the regulation of the expression of enzyme-coding genes associated with important metabolic pathways. In addition, we identified 2,411 simple sequence repeats (SSRs) as potential genetic markers from the transcripts. Overall, this study provides a comprehensive transcriptome atlas, and SSRs, contributing to building essential genomic resources to support basic research, genome annotation, functional genomics, and molecular breeding of Chia.
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Affiliation(s)
- Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Matthew Geniza
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR, United States
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jeremy L. Phillips
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Ebaad Haq
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
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Wu H, Ma PF, Li HT, Hu GX, Li DZ. Comparative plastomic analysis and insights into the phylogeny of Salvia (Lamiaceae). PLANT DIVERSITY 2021; 43:15-26. [PMID: 33778221 PMCID: PMC7987561 DOI: 10.1016/j.pld.2020.07.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 05/13/2023]
Abstract
Salvia is the largest genus of Lamiaceae, with almost 1000 species, and has been divided into 11 subgenera. Salvia subg. Glutinaria, native to East Asia, is particularly important because of its potential medicinal value. However, the interspecific relationships of this subgenus have not been resolved and the plastomes of Salvia have rarely been studied. In the current study, we compared plastid genome structure and organization of 19 species of Salvia (14 newly sequenced and 5 previously published). Our comparative analysis showed that all Salvia plastomes examined have a quadripartite structure typical of most angiosperms and contain an identical set of 114 unique genes (80 protein-coding genes, 4 rRNA genes, and 30 tRNA genes). The plastome structure of all Salvia species is highly conserved like other Lamiaceae plastomes. Gene content, gene order, and GC content were highly similar in these plastomes. The inverted repeats/single copy region (IR/SC) boundaries of Salvia are highly conserved, and IR contraction only occurred in two species (Salvia mekongensis and S. rosmarinus). In Salvia, sequence divergence was higher in non-coding regions than in coding regions. We found that using large single copy (LSC) and small single copy regions (SSC) with exclusion of the rapidly evolving sites produced the highest resolution in phylogenetic analysis of Salvia, suggesting that using suitable informative sites to build trees is more conducive in phylogenetic research. This study assembled a powerful matrix data set for studying the phylogeny of Salvia, resolving the interspecific relationship of Salvia subg. Glutinaria. The newly sequenced plastid genomes will also enrich the plastome database of Salvia, providing the scientific basis for the development and utilization of germplasm resources of this large and important genus.
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Affiliation(s)
- Hong Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Guo-Xiong Hu
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, 550025, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
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Jiao SQ, Dong AX, Shi TL, Liu H, Porth I, Xin HB, Mao JF. Development of a Large Gene-Associated SSR Marker Set and in-Depth Genetic Characterization in Scarlet Sage. Front Genet 2020; 11:504. [PMID: 32508885 PMCID: PMC7253628 DOI: 10.3389/fgene.2020.00504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/23/2020] [Indexed: 11/25/2022] Open
Abstract
Salvia splendens, scarlet or tropical sage, is a tender perennial herbaceous flowering plant popularly grown in public and private gardens all over the world. In this study, we developed a set of simple sequence repeats (SSRs) from genome-wide sequences to assess the genetic diversity and population structure among 112 cultivars. We obtained 364,379 SSRs by mining scarlet sage’s recently published whole genome sequence; 14,545 gene-associated SSR loci were identified in 2 kb gene flanking regions. Among the 768 gene-associated SSR primer sets we screened, 576 loci successfully amplified in DNA pools of 3–4 different cultivars, of which 271 remained polymorphic when tested across eight individual plants. We searched for the related gene functions attributable to these gene-associated SSRs using diverse databases, resulting in 259 Non-redundant matching sequences, 205 individual Gene Ontology (GO) terms, 236 assigned to eukaryotic orthologous groups, and 67 KEGG-annotated (Kyoto Encyclopedia of Genes and Genomes) sequences. We finally selected 41 polymorphic SSR loci to infer genetic diversity and population structure among 112 S. splendens accessions. Based on the developed gene-associated SSRs, clustering analyses consistently revealed two distinct genetic groups within the core collection of S. splendens cultivars. This work developed and characterized an exhaustive set of genome-wide gene-associated SSR markers for scarlet sage. These SSRs can provide species identification, genetic diversity and population structure information for S. splendens, and will therefore be important tools for the management and protection of S. splendens germplasm.
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Affiliation(s)
- Si-Qian Jiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Ai-Xiang Dong
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Institute of Landscape Architecture, Beijing, China
| | - Tian-Le Shi
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hui Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Ilga Porth
- Département des Sciences du Bois et de la Forêt, Pavillon Charles-Eugène-Marchand, Université Laval, Québec, QC, Canada
| | - Hai-Bo Xin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Beijing Key Laboratory of Greening Plants Breeding, Beijing Institute of Landscape Architecture, Beijing, China
| | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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Aminfar Z, Rabiei B, Tohidfar M, Mirjalili MH. Identification of key genes involved in the biosynthesis of triterpenic acids in the mint family. Sci Rep 2019; 9:15826. [PMID: 31676750 PMCID: PMC6825174 DOI: 10.1038/s41598-019-52090-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 10/14/2019] [Indexed: 01/11/2023] Open
Abstract
Triterpenic acids (TAs), a large group of natural compounds with diverse biological activity, are produced by several plant taxa. Betulinic, oleanolic, and ursolic acids are the most medicinally important TAs and are mainly found in plants of the mint family. Metabolic engineering is strongly dependent on identifying the key genes in biosynthetic pathways toward the products of interest. In this study, gene expression tracking was performed by transcriptome mining, co-expression network analysis, and tissue-specific metabolite-expression analysis in order to identify possible key genes involved in TAs biosynthetic pathways. To this end, taxa-specific degenerate primers of six important genes were designed using an effective method based on the MEME algorithm in a phylogenetically related group of sequences and successfully applied in three members of the Lamiaceae (Rosmarinus officinalis, Salvia officinalis, and Thymus persicus). Based on the results of in-depth data analysis, genes encoding squalene epoxidase and oxido squalene cyclases are proposed as targets for boosting triterpene production. The results emphasize the importance of identifying key genes in triterpene biosynthesis, which may facilitate genetic manipulation or overexpression of target genes.
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Affiliation(s)
- Zahra Aminfar
- Department of Agronomy and Plant Breeding, Faculty of Agricultural science, University of Guilan, Rasht, Iran
| | - Babak Rabiei
- Department of Agronomy and Plant Breeding, Faculty of Agricultural science, University of Guilan, Rasht, Iran.
| | - Masoud Tohidfar
- Department of Plant Biotechnology, Faculty of Sciences & Biotechnology, Shahid Beheshti University G.C., Tehran, Iran
| | - Mohammad Hossein Mirjalili
- Department of Agriculture, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, G. C., Tehran, Iran.
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Transcriptome Landscape Variation in the Genus Thymus. Genes (Basel) 2019; 10:genes10080620. [PMID: 31426352 PMCID: PMC6723042 DOI: 10.3390/genes10080620] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/31/2019] [Accepted: 08/12/2019] [Indexed: 12/13/2022] Open
Abstract
Among the Lamiaceae family, the genus Thymus is an economically important genera due to its medicinal and aromatic properties. Most Thymus molecular research has focused on the determining the phylogenetic relationships between different species, but no published work has focused on the evolution of the transcriptome across the genus to elucidate genes involved in terpenoid biosynthesis. Hence, in this study, the transcriptomes of five different Thymus species were generated and analyzed to mine putative genes involved in thymol and carvacrol biosynthesis. High-throughput sequencing produced ~43 million high-quality reads per sample, which were assembled de novo using several tools, then further subjected to a quality evaluation. The best assembly for each species was used as queries to search within the UniProt, KEGG (Kyoto Encyclopedia of Genes and Genomes), COG (Clusters of Orthologous Groups) and TF (Transcription Factors) databases. Mining the transcriptomes resulted in the identification of 592 single-copy orthogroups used for phylogenetic analysis. The data showed strongly support a close genetic relationship between Thymus vulgaris and Thymus daenensis. Additionally, this study dates the speciation events between 1.5–2.1 and 9–10.2 MYA according to different methodologies. Our study provides a global overview of genes related to the terpenoid pathway in Thymus, and can help establish an understanding of the relationship that exists among Thymus species.
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Ramya M, Park PH, Chuang YC, Kwon OK, An HR, Park PM, Baek YS, Kang BC, Tsai WC, Chen HH. RNA sequencing analysis of Cymbidium goeringii identifies floral scent biosynthesis related genes. BMC PLANT BIOLOGY 2019; 19:337. [PMID: 31375064 PMCID: PMC6679452 DOI: 10.1186/s12870-019-1940-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 07/17/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Cymbidium goeringii belongs to the Orchidaceae, which is one of the most abundant angiosperm families. Cymbidium goeringii consist with high economic value and characteristics include fragrance and multiple flower colors. Floral scent is one of the important strategies for ensuring fertilization. However, limited genetic data is available in this non-model plant, and little known about the molecular mechanism responsible for floral scent in this orchid. Transcriptome and expression profiling data are needed to identify genes and better understand the biological mechanisms of floral scents in this species. Present transcriptomic data provides basic information on the genes and enzymes related to and pathways involved in flower secondary metabolism in this plant. RESULTS In this study, RNA sequencing analyses were performed to identify changes in gene expression and biological pathways related scent metabolism. Three cDNA libraries were obtained from three developmental floral stages: closed bud, half flowering stage and full flowering stage. Using Illumina technique 159,616,374 clean reads were obtained and were assembled into 85,868 final unigenes (average length 1194 nt), 33.85% of which were annotated in the NCBI non redundant protein database. Among this unigenes 36,082 were assigned to gene ontology and 23,164 were combined with COG groups. Total 33,417 unigenes were assigned in 127 pathways according to the Kyoto Encyclopedia of Genes and Genomes pathway database. According these transcriptomic data we identified number of candidates genes which differentially expressed in different developmental stages of flower related to fragrance biosynthesis. In q-RT-PCR most of the fragrance related genes highly expressed in half flowering stage. CONCLUSIONS RNA-seq and DEG data provided comprehensive gene expression information at the transcriptional level that could be facilitate the molecular mechanisms of floral biosynthesis pathways in three developmental phase's flowers in Cymbidium goeringii, moreover providing useful information for further analysis on C. goeringii, and other plants of genus Cymbidium.
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Affiliation(s)
- Mummadireddy Ramya
- Floriculture Research Division, National Institute of Horticultural & Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju, 55365 South Korea
| | - Pue Hee Park
- Floriculture Research Division, National Institute of Horticultural & Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju, 55365 South Korea
- Department of Life Sciences, National Cheng Kung University (NCKU), Tainan, 701 Taiwan
- Department of Horticultural Science and Biotechnology, Seoul National University (SNU), Seoul, 08826 South Korea
| | - Yu-Chen Chuang
- Department of Life Sciences, National Cheng Kung University (NCKU), Tainan, 701 Taiwan
| | - Oh Keun Kwon
- Floriculture Research Division, National Institute of Horticultural & Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju, 55365 South Korea
| | - Hye Ryun An
- Floriculture Research Division, National Institute of Horticultural & Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju, 55365 South Korea
| | - Pil Man Park
- Floriculture Research Division, National Institute of Horticultural & Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju, 55365 South Korea
| | - Yun Su Baek
- Floriculture Research Division, National Institute of Horticultural & Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju, 55365 South Korea
| | - Byoung-Chorl Kang
- Department of Horticultural Science and Biotechnology, Seoul National University (SNU), Seoul, 08826 South Korea
| | - Wen-Chieh Tsai
- Department of Life Sciences, National Cheng Kung University (NCKU), Tainan, 701 Taiwan
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hong-Hwa Chen
- Department of Life Sciences, National Cheng Kung University (NCKU), Tainan, 701 Taiwan
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
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Dong A, Wang J, Zhang H, Xin H, Zhao Z, Liang F, Li Z, Cong R, Lin Y, Song L, Tan L, Zhang P, Cui R. Comparative transcriptomic analysis provides insights into the development of a Salvia splendens Ker-Gawler mutant, SX919M. PLoS One 2019; 14:e0213446. [PMID: 30870444 PMCID: PMC6417697 DOI: 10.1371/journal.pone.0213446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 02/21/2019] [Indexed: 11/28/2022] Open
Abstract
Salvia splendens is a perennial, ornamental herbaceous flower that is widely cultivated as a bedding plant in gardens. The development of novel S. splendens cultivars and investigating the relevant molecular mechanisms are of great significance. In this study, RNA-sequencing and real-time PCR methods were used to analyze the possible molecular mechanism of S. splendens mutant, SX919M. From the wild-type S. splendens 919CK, we firstly selected a natural mutant, SX919M, which displayed multiple branches, clustered spheroids, and radial symmetrical inflorescence with higher numbers of calyces, ovules, stamens, and perianth tubes. Further, the RNA-seq was used to identify the differentially expressed genes (DEGs) in the mutant which included a total of 3568 upregulated and 3290 downregulated unigenes. We further observed that the indole alkaloid biosynthesis pathway showed the highest DEG enrichment, which was supported by a significant increase in the IAA content in mutant SX919M. In addition, we validated three DEGs, namely, CL2200.Contig2_All encoding methyl IAA esterase, CL12462.Contig1_All and CL12462.Contig2_All, which encoded strictosidine synthase, upregulated in mutant SX919M. We selected a novel S. splendens germplasm SX919M with a high ornamental value and determined that the upregulation of IAA biogenesis may be associated with its development.
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Affiliation(s)
- Aixiang Dong
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Institute of Landscape Architecture, Beijing, People’s Republic of China
| | - Jingjing Wang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, People’s Republic of China
| | - Huali Zhang
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Institute of Landscape Architecture, Beijing, People’s Republic of China
| | - Haibo Xin
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Institute of Landscape Architecture, Beijing, People’s Republic of China
| | - Zhengnan Zhao
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Institute of Landscape Architecture, Beijing, People’s Republic of China
| | - Fang Liang
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Institute of Landscape Architecture, Beijing, People’s Republic of China
| | - Zijing Li
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Institute of Landscape Architecture, Beijing, People’s Republic of China
| | - Richen Cong
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Institute of Landscape Architecture, Beijing, People’s Republic of China
| | - Yan Lin
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Institute of Landscape Architecture, Beijing, People’s Republic of China
| | - Lina Song
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Institute of Landscape Architecture, Beijing, People’s Republic of China
| | - Lingling Tan
- School of life sciences, Qingdao Agricultural University, Qingdao, Shandong, People’s Republic of China
| | - Pengwei Zhang
- ShiJiaZhuang Academy of Agricultural and Forestry Sciences, Zhaoxian, Shijiazhuang, Hebei, People’s Republic of China
| | - Rongfeng Cui
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Institute of Landscape Architecture, Beijing, People’s Republic of China
- * E-mail:
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Rashmi D, Barvkar VT, Nadaf A, Mundhe S, Kadoo NY. Integrative omics analysis in Pandanus odorifer (Forssk.) Kuntze reveals the role of Asparagine synthetase in salinity tolerance. Sci Rep 2019; 9:932. [PMID: 30700750 PMCID: PMC6353967 DOI: 10.1038/s41598-018-37039-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 11/30/2018] [Indexed: 11/12/2022] Open
Abstract
Pandanus odorifer (Forssk) Kuntze grows naturally along the coastal regions and withstands salt-sprays as well as strong winds. A combination of omics approaches and enzyme activity studies was employed to comprehend the mechanistic basis of high salinity tolerance in P. odorifer. The young seedlings of P. odorifer were exposed to 1 M salt stress for up to three weeks and analyzed using RNAsequencing (RNAseq) and LC-MS. Integrative omics analysis revealed high expression of the Asparagine synthetase (AS) (EC 6.3.5.4) (8.95 fold) and remarkable levels of Asparagine (Asn) (28.5 fold). This indicated that salt stress promoted Asn accumulation in P. odorifer. To understand this further, the Asn biosynthesis pathway was traced out in P. odorifer. It was noticed that seven genes involved in Asn bisynthetic pathway namely glutamine synthetase (GS) (EC 6.3.1.2) glutamate synthase (GOGAT) (EC 1.4.1.14), aspartate kinase (EC 2.7.2.4), pyruvate kinase (EC 2.7.1.40), aspartate aminotransferase (AspAT) (EC 2.6.1.1), phosphoenolpyruvate carboxylase (PEPC) (EC 4.1.1.31) and AS were up-regulated under salt stress. AS transcripts were most abundant thereby showed its highest activity and thus were generating maximal Asn under salt stress. Also, an up-regulated Na+/H+ antiporter (NHX1) facilitated compartmentalization of Na+ into vacuoles, suggesting P. odorifer as salt accumulator species.
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Affiliation(s)
- Deo Rashmi
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India
| | - Vitthal T Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India.
| | - Altafhusain Nadaf
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India.
| | - Swapnil Mundhe
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, India
| | - Narendra Y Kadoo
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, India
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11
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Dong AX, Xin HB, Li ZJ, Liu H, Sun YQ, Nie S, Zhao ZN, Cui RF, Zhang RG, Yun QZ, Wang XN, Maghuly F, Porth I, Cong RC, Mao JF. High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant. Gigascience 2018; 7:5040257. [PMID: 29931210 PMCID: PMC6030905 DOI: 10.1093/gigascience/giy068] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 05/06/2018] [Accepted: 06/15/2018] [Indexed: 12/03/2022] Open
Abstract
Background Salvia splendens Ker-Gawler, scarlet or tropical sage, is a tender herbaceous perennial widely introduced and seen in public gardens all over the world. With few molecular resources, breeding is still restricted to traditional phenotypic selection, and the genetic mechanisms underlying phenotypic variation remain unknown. Hence, a high-quality reference genome will be very valuable for marker-assisted breeding, genome editing, and molecular genetics. Findings We generated 66 Gb and 37 Gb of raw DNA sequences, respectively, from whole-genome sequencing of a largely homozygous scarlet sage inbred line using Pacific Biosciences (PacBio) single-molecule real-time and Illumina HiSeq sequencing platforms. The PacBio de novo assembly yielded a final genome with a scaffold N50 size of 3.12 Mb and a total length of 808 Mb. The repetitive sequences identified accounted for 57.52% of the genome sequence, and 54,008 protein-coding genes were predicted collectively with ab initio and homology-based gene prediction from the masked genome. The divergence time between S. splendens and Salvia miltiorrhiza was estimated at 28.21 million years ago (Mya). Moreover, 3,797 species-specific genes and 1,187 expanded gene families were identified for the scarlet sage genome. Conclusions We provide the first genome sequence and gene annotation for the scarlet sage. The availability of these resources will be of great importance for further breeding strategies, genome editing, and comparative genomics among related species.
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Affiliation(s)
- Ai-Xiang Dong
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Institute of Landscape Architecture, Beijing, 100102, China
| | - Hai-Bo Xin
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Institute of Landscape Architecture, Beijing, 100102, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zi-Jing Li
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Institute of Landscape Architecture, Beijing, 100102, China
| | - Hui Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yan-Qiang Sun
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shuai Nie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zheng-Nan Zhao
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Institute of Landscape Architecture, Beijing, 100102, China
| | - Rong-Feng Cui
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Institute of Landscape Architecture, Beijing, 100102, China
| | - Ren-Gang Zhang
- Beijing Ori-Gene Science and Technology Co. Ltd, Beijing, 102206, China
| | - Quan-Zheng Yun
- Beijing Ori-Gene Science and Technology Co. Ltd, Beijing, 102206, China
| | - Xin-Ning Wang
- Beijing Ori-Gene Science and Technology Co. Ltd, Beijing, 102206, China
| | - Fatemeh Maghuly
- Plant Biotechnology Unit, Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Ilga Porth
- Département des sciences du bois et de la forêt, Pavillon Charles-Eugène-Marchand, 1030, Avenue de la Médecine, Université Laval, Québec (Québec) G1V 0A6, Canada
| | - Ri-Chen Cong
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Institute of Landscape Architecture, Beijing, 100102, China
| | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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12
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Cuong DM, Jeon J, Morgan AMA, Kim C, Kim JK, Lee SY, Park SU. Accumulation of Charantin and Expression of Triterpenoid Biosynthesis Genes in Bitter Melon (Momordica charantia). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:7240-7249. [PMID: 28737900 DOI: 10.1021/acs.jafc.7b01948] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Charantin, a natural cucurbitane type triterpenoid, has been reported to have beneficial pharmacological functions such as anticancer, antidiabetic, and antibacterial activities. However, accumulation of charantin in bitter melon has been little studied. Here, we performed a transcriptome analysis to identify genes involved in the triterpenoid biosynthesis pathway in bitter melon seedlings. A total of 88,703 transcripts with an average length of 898 bp were identified in bitter melon seedlings. On the basis of a functional annotation, we identified 15 candidate genes encoding enzymes related to triterpenoid biosynthesis and analyzed their expression in different organs of mature plants. Most genes were highly expressed in flowers and/or fruit from the ripening stages. An HPLC analysis confirmed that the accumulation of charantin was highest in fruits from the ripening stage, followed by male flowers. The accumulation patterns of charantin coincide with the expression pattern of McSE and McCAS1, indicating that these genes play important roles in charantin biosynthesis in bitter melon. We also investigated optimum light conditions for enhancing charantin biosynthesis in bitter melon and found that red light was the most effective wavelength.
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Affiliation(s)
- Do Manh Cuong
- Department of Crop Science, Chungnam National University , 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Jin Jeon
- Department of Crop Science, Chungnam National University , 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Abubaker M A Morgan
- Department of Crop Science, Chungnam National University , 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Changsoo Kim
- Department of Crop Science, Chungnam National University , 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Jae Kwang Kim
- Division of Life Sciences and Bio-Resource and Environmental Center, Incheon National University , Yeonsu-gu, Incheon 406-772, Korea
| | - Sook Young Lee
- Regional Innovation Center for Dental Science & Engineering, Chosun University , 309 Pilmun-daero, Dong-gu, Gwangju 501-759, Korea
| | - Sang Un Park
- Department of Crop Science, Chungnam National University , 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
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Liu C, Dou Y, Guan X, Fu Q, Zhang Z, Hu Z, Zheng J, Lu Y, Li W. De novo transcriptomic analysis and development of EST-SSRs for Sorbus pohuashanensis (Hance) Hedl. PLoS One 2017; 12:e0179219. [PMID: 28614366 PMCID: PMC5470691 DOI: 10.1371/journal.pone.0179219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 05/25/2017] [Indexed: 11/18/2022] Open
Abstract
Sorbus pohuashanensis is a native tree species of northern China that is used for a variety of ecological purposes. The species is often grown as an ornamental landscape tree because of its beautiful form, silver flowers in early summer, attractive pinnate leaves in summer, and red leaves and fruits in autumn. However, development and further utilization of the species are hindered by the lack of comprehensive genetic information, which impedes research into its genetics and molecular biology. Recent advances in de novo transcriptome sequencing (RNA-seq) technology have provided an effective means to obtain genomic information from non-model species. Here, we applied RNA-seq for sequencing S. pohuashanensis leaves and obtained a total of 137,506 clean reads. After assembly, 96,213 unigenes with an average length of 770 bp were obtained. We found that 64.5% of the unigenes could be annotated using bioinformatics tools to analyze gene function and alignment with the NCBI database. Overall, 59,089 unigenes were annotated using the Nr database(non-redundant protein database), 35,225 unigenes were annotated using the GO (Gene Ontology categories) database, and 33,168 unigenes were annotated using COG (Cluster of Orthologous Groups). Analysis of the unigenes using the KEGG (Kyoto Encyclopedia of Genes and Genomes) database indicated that 13,953 unigenes were involved in 322 metabolic pathways. Finally, simple sequence repeat (SSR) site detection identified 6,604 unigenes that included EST-SSRs and a total of 7,473 EST-SSRs in the unigene sequences. Fifteen polymorphic SSRs were screened and found to be of use for future genetic research. These unigene sequences will provide important genetic resources for genetic improvement and investigation of biochemical processes in S. pohuashanensis.
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Affiliation(s)
- Congcong Liu
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Ying Dou
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Xuelian Guan
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Qiang Fu
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Ze Zhang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Zenghui Hu
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Jian Zheng
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
- Beijing Collaborative Innovation Center for Eco-environmental Improvement with Forestry and Fruit Trees, Beijing, China
- Beijing Engineering Research Center of rural landscape planning and design, Beijing, China
- * E-mail:
| | - Yizeng Lu
- Shandong Provincial Center of Forest Tree Germplasm Resources, Jinan, Shandong Province, China
| | - Wei Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, China
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Spatial transcriptome analysis provides insights of key gene(s) involved in steroidal saponin biosynthesis in medicinally important herb Trillium govanianum. Sci Rep 2017; 7:45295. [PMID: 28349986 PMCID: PMC5368571 DOI: 10.1038/srep45295] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 02/23/2017] [Indexed: 01/29/2023] Open
Abstract
Trillium govanianum, an endangered medicinal herb native to the Himalaya, is less studied at the molecular level due to the non-availability of genomic resources. To facilitate the basic understanding of the key genes and regulatory mechanism of pharmaceutically important biosynthesis pathways, first spatial transcriptome sequencing of T. govanianum was performed. 151,622,376 (~11.5 Gb) high quality reads obtained using paired-end Illumina sequencing were de novo assembled into 69,174 transcripts. Functional annotation with multiple public databases identified array of genes involved in steroidal saponin biosynthesis and other secondary metabolite pathways including brassinosteroid, carotenoid, diterpenoid, flavonoid, phenylpropanoid, steroid and terpenoid backbone biosynthesis, and important TF families (bHLH, MYB related, NAC, FAR1, bZIP, B3 and WRKY). Differentially expressed large number of transcripts, together with CYPs and UGTs suggests involvement of these candidates in tissue specific expression. Combined transcriptome and expression analysis revealed that leaf and fruit tissues are the main site of steroidal saponin biosynthesis. In conclusion, comprehensive genomic dataset created in the current study will serve as a resource for identification of potential candidates for genetic manipulation of targeted bioactive metabolites and also contribute for development of functionally relevant molecular marker resource to expedite molecular breeding and conservation efforts in T. govanianum.
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15
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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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De novo assembly and characterization of leaf transcriptome for the development of EST-SSR markers of the non-model species Indigofera szechuensis. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Insights into biosynthetic genes involved in the secondary metabolism of Gardenia jasminoides Ellis using transcriptome sequencing. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.05.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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18
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De Novo Assembly and Comparative Transcriptome Analysis Provide Insight into Lysine Biosynthesis in Toona sinensis Roem. Int J Genomics 2016; 2016:6735209. [PMID: 27376077 PMCID: PMC4914729 DOI: 10.1155/2016/6735209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/07/2016] [Accepted: 05/05/2016] [Indexed: 11/17/2022] Open
Abstract
Toona sinensis Roem is a popular leafy vegetable in Chinese cuisine and is also used as a traditional Chinese medicine. In this study, leaf samples were collected from the same plant on two development stages and then used for high-throughput Illumina RNA-sequencing (RNA-Seq). 125,884 transcripts and 54,628 unigenes were obtained through de novo assembly. A total of 25,570 could be annotated with known biological functions, which indicated that the T. sinensis leaves and shoots were undergoing multiple developmental processes especially for active metabolic processes. Analysis of differentially expressed unigenes between the two libraries showed that the lysine biosynthesis was an enriched KEGG pathway, and candidate genes involved in the lysine biosynthesis pathway in T. sinensis leaves and shoots were identified. Our results provide a primary analysis of the gene expression files of T. sinensis leaf and shoot on different development stages and afford a valuable resource for genetic and genomic research on plant lysine biosynthesis.
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He W, Zhuang H, Fu Y, Guo L, Guo B, Guo L, Zhang X, Wei Y. De novo Transcriptome Assembly of a Chinese Locoweed (Oxytropis ochrocephala) Species Provides Insights into Genes Associated with Drought, Salinity, and Cold Tolerance. FRONTIERS IN PLANT SCIENCE 2015; 6:1086. [PMID: 26697040 PMCID: PMC4667070 DOI: 10.3389/fpls.2015.01086] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 11/19/2015] [Indexed: 05/29/2023]
Abstract
BACKGROUND Locoweeds (toxic Oxytropis and Astraglus species), containing the toxic agent swainsonine, pose serious threats to animal husbandry on grasslands in both China and the US. Some locoweeds have evolved adaptations in order to resist various stress conditions such as drought, salt and cold. As a result they replace other plants in their communities and become an ecological problem. Currently very limited genetic information of locoweeds is available and this hinders our understanding in the molecular basis of their environmental plasticity, and the interaction between locoweeds and their symbiotic swainsonine producing endophytes. Next-generation sequencing provides a means of obtaining transcriptomic sequences in a timely manner, which is particularly useful for non-model plants. In this study, we performed transcriptome sequencing of Oxytropis ochrocephala plants followed by a de nove assembly. Our primary aim was to provide an enriched pool of genetic sequences of an Oxytropis sp. for further locoweed research. RESULTS Transcriptomes of four different O. ochrocephala samples, from control (CK) plants, and those that had experienced either drought (20% PEG), salt (150 mM NaCl) or cold (4°C) stress were sequenced using an Illumina Hiseq 2000 platform. From 232,209,506 clean reads 23,220,950,600 (~23 G nucleotides), 182,430 transcripts and 88,942 unigenes were retrieved, with an N50 value of 1237. Differential expression analysis revealed putative genes encoding heat shock proteins (HSPs) and late embryogenesis abundant (LEA) proteins, enzymes in secondary metabolite and plant hormone biosyntheses, and transcription factors which are involved in stress tolerance in O. ochrocephala. In order to validate our sequencing results, we further analyzed the expression profiles of nine genes by quantitative real-time PCR. Finally, we discuss the possible mechanism of O. ochrocephala's adaptations to stress environment. CONCLUSION Our transcriptome sequencing data present useful genetic information of a locoweed species. This genetic information will underpin further research in elucidating the environmental acclimation mechanism in locoweeds and the endophyte-plant association.
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Affiliation(s)
- Wei He
- Department of Biology, Northwest UniversityXian, China
| | - Huihui Zhuang
- Department of Biology, Northwest UniversityXian, China
| | - Yanping Fu
- Department of Biology, Northwest UniversityXian, China
| | - Linwei Guo
- Department of Biology, Northwest UniversityXian, China
| | - Bin Guo
- Department of Biology, Northwest UniversityXian, China
| | - Lizhu Guo
- Department of Biology, Northwest UniversityXian, China
| | - Xiuhong Zhang
- Grassland Station, Agriculture and Animal Husbandry BureauZhongwei, China
| | - Yahui Wei
- Department of Biology, Northwest UniversityXian, China
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Castro JC, Maddox JD, Cobos M, Requena D, Zimic M, Bombarely A, Imán SA, Cerdeira LA, Medina AE. De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis. BMC Genomics 2015; 16:997. [PMID: 26602763 PMCID: PMC4658800 DOI: 10.1186/s12864-015-2225-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 11/17/2015] [Indexed: 01/13/2023] Open
Abstract
Background Myrciaria dubia is an Amazonian fruit shrub that produces numerous bioactive phytochemicals, but is best known by its high L-ascorbic acid (AsA) content in fruits. Pronounced variation in AsA content has been observed both within and among individuals, but the genetic factors responsible for this variation are largely unknown. The goals of this research, therefore, were to assemble, characterize, and annotate the fruit transcriptome of M. dubia in order to reconstruct metabolic pathways and determine if multiple pathways contribute to AsA biosynthesis. Results In total 24,551,882 high-quality sequence reads were de novo assembled into 70,048 unigenes (mean length = 1150 bp, N50 = 1775 bp). Assembled sequences were annotated using BLASTX against public databases such as TAIR, GR-protein, FB, MGI, RGD, ZFIN, SGN, WB, TIGR_CMR, and JCVI-CMR with 75.2 % of unigenes having annotations. Of the three core GO annotation categories, biological processes comprised 53.6 % of the total assigned annotations, whereas cellular components and molecular functions comprised 23.3 and 23.1 %, respectively. Based on the KEGG pathway assignment of the functionally annotated transcripts, five metabolic pathways for AsA biosynthesis were identified: animal-like pathway, myo-inositol pathway, L-gulose pathway, D-mannose/L-galactose pathway, and uronic acid pathway. All transcripts coding enzymes involved in the ascorbate-glutathione cycle were also identified. Finally, we used the assembly to identified 6314 genic microsatellites and 23,481 high quality SNPs. Conclusions This study describes the first next-generation sequencing effort and transcriptome annotation of a non-model Amazonian plant that is relevant for AsA production and other bioactive phytochemicals. Genes encoding key enzymes were successfully identified and metabolic pathways involved in biosynthesis of AsA, anthocyanins, and other metabolic pathways have been reconstructed. The identification of these genes and pathways is in agreement with the empirically observed capability of M. dubia to synthesize and accumulate AsA and other important molecules, and adds to our current knowledge of the molecular biology and biochemistry of their production in plants. By providing insights into the mechanisms underpinning these metabolic processes, these results can be used to direct efforts to genetically manipulate this organism in order to enhance the production of these bioactive phytochemicals. The accumulation of AsA precursor and discovery of genes associated with their biosynthesis and metabolism in M. dubia is intriguing and worthy of further investigation. The sequences and pathways produced here present the genetic framework required for further studies. Quantitative transcriptomics in concert with studies of the genome, proteome, and metabolome under conditions that stimulate production and accumulation of AsA and their precursors are needed to provide a more comprehensive view of how these pathways for AsA metabolism are regulated and linked in this species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2225-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan C Castro
- Unidad Especializada de Biotecnología, Centro de Investigaciones de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonía Peruana (UNAP), Pasaje Los Paujiles S/N, San Juan Bautista, Iquitos, Perú. .,Círculo de Investigación en Plantas con Efecto en Salud (FONDECYT N° 010-2014), Lima, Perú.
| | - J Dylan Maddox
- Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum of Natural History, Chicago, IL, USA.
| | - Marianela Cobos
- Laboratorio de Biotecnología y Bioenergética, Universidad Científica del Perú (UCP), Av. Abelardo Quiñones km 2.5, San Juan Bautista, Iquitos, Perú.
| | - David Requena
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo (LID), Facultad de Ciencias, Universidad Peruana Cayetano Heredia (UPCH), Av. Honorio Delgado 430, San Martín de Porres, Lima, Perú. .,FARVET S.A.C. Carretera Panamericana Sur N° 766 Km 198.5, Chincha Alta, Ica, Perú.
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo (LID), Facultad de Ciencias, Universidad Peruana Cayetano Heredia (UPCH), Av. Honorio Delgado 430, San Martín de Porres, Lima, Perú. .,FARVET S.A.C. Carretera Panamericana Sur N° 766 Km 198.5, Chincha Alta, Ica, Perú.
| | | | - Sixto A Imán
- Área de Conservación de Recursos Fitogenéticos, Instituto Nacional de Innovación Agraria (INIA), Calle San Roque 209, Iquitos, Perú.
| | - Luis A Cerdeira
- Unidad Especializada de Biotecnología, Centro de Investigaciones de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonía Peruana (UNAP), Pasaje Los Paujiles S/N, San Juan Bautista, Iquitos, Perú.
| | - Andersson E Medina
- Unidad Especializada de Biotecnología, Centro de Investigaciones de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonía Peruana (UNAP), Pasaje Los Paujiles S/N, San Juan Bautista, Iquitos, Perú.
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Zheng J, Hu Z, Guan X, Dou D, Bai G, Wang Y, Guo Y, Li W, Leng P. Transcriptome Analysis of Syringa oblata Lindl. Inflorescence Identifies Genes Associated with Pigment Biosynthesis and Scent Metabolism. PLoS One 2015; 10:e0142542. [PMID: 26587670 PMCID: PMC4654506 DOI: 10.1371/journal.pone.0142542] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/25/2015] [Indexed: 12/22/2022] Open
Abstract
Syringa oblata Lindl. is a woody ornamental plant with high economic value and characteristics that include early flowering, multiple flower colors, and strong fragrance. Despite a long history of cultivation, the genetics and molecular biology of S. oblata are poorly understood. Transcriptome and expression profiling data are needed to identify genes and to better understand the biological mechanisms of floral pigments and scents in this species. Nine cDNA libraries were obtained from three replicates of three developmental stages: inflorescence with enlarged flower buds not protruded, inflorescence with corolla lobes not displayed, and inflorescence with flowers fully opened and emitting strong fragrance. Using the Illumina RNA-Seq technique, 319,425,972 clean reads were obtained and were assembled into 104,691 final unigenes (average length of 853 bp), 41.75% of which were annotated in the NCBI non-redundant protein database. Among the annotated unigenes, 36,967 were assigned to gene ontology categories and 19,956 were assigned to eukaryoticorthologous groups. Using the Kyoto Encyclopedia of Genes and Genomes pathway database, 12,388 unigenes were sorted into 286 pathways. Based on these transcriptomic data, we obtained a large number of candidate genes that were differentially expressed at different flower stages and that were related to floral pigment biosynthesis and fragrance metabolism. This comprehensive transcriptomic analysis provides fundamental information on the genes and pathways involved in flower secondary metabolism and development in S. oblata, providing a useful database for further research on S. oblata and other plants of genus Syringa.
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Affiliation(s)
- Jian Zheng
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Engineering Research Center of rural landscape planning and design, Beijing, 102206, China
| | - Zenghui Hu
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Xuelian Guan
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Dequan Dou
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Guo Bai
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Yu Wang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Yingtian Guo
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Wei Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266100, China
| | - Pingsheng Leng
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
- * E-mail:
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Muriira NG, Xu W, Muchugi A, Xu J, Liu A. De novo sequencing and assembly analysis of transcriptome in the Sodom apple (Calotropis gigantea). BMC Genomics 2015; 16:723. [PMID: 26395839 PMCID: PMC4580217 DOI: 10.1186/s12864-015-1908-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/09/2015] [Indexed: 11/18/2022] Open
Abstract
Background The Sodom apple (Calotropis gigantea), a member of the Asclepiadaceae family, is a large evergreen shrub native to continental Asia and northern Africa. As an important medicinal shrub and a fiber resource plant, there is an urgent need for developing molecular markers to facilitate breeding and genetic improvement of varieties. Results In this study, using the Illumina high throughput sequencing technique we obtained about 45 million paired end sequencing reads, De novo assembled and generated a total of 133,634 transcripts with a mean of 1837.47 bp in length. Based on protein homology searches against available databases, a total of 21,851 unigenes were functionally annotated. In particular, many transcripts that encode for putative proteins involved in fiber and secondary metabolite biosynthesis were identified and analyzed. Key fiber genes identified were validated experimentally through Real-Time PCR technique. Various transcription factors involved in regulating plant response to abiotic stress were also identified. In addition, based on the unigene sequences assembled, 11,623 microsatellites loci were detected, which provide very useful resources for developing microsatellite molecular markers. Conclusion This study is the first report on transcriptome information in the Calotropis species and provides rich gene transcript resources for conducting further studies on understanding the molecular basis of fiber and secondary metabolite biosynthesis, serving the genetic improvement and resource utilization in Calotropis plants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1908-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nkatha G Muriira
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,World Agroforestry Centre, East and Central Asia Office, 132 Lanhei Road, Kunming, 650201, China. .,World Agroforestry Centre (ICRAF), P.O. Box 30677-00100, Nairobi, Kenya.
| | - Wei Xu
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Alice Muchugi
- World Agroforestry Centre (ICRAF), P.O. Box 30677-00100, Nairobi, Kenya.
| | - Jianchu Xu
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China. .,World Agroforestry Centre, East and Central Asia Office, 132 Lanhei Road, Kunming, 650201, China.
| | - Aizhong Liu
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China.
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Verbruggen B, Bickley LK, Santos EM, Tyler CR, Stentiford GD, Bateman KS, van Aerle R. De novo assembly of the Carcinus maenas transcriptome and characterization of innate immune system pathways. BMC Genomics 2015; 16:458. [PMID: 26076827 PMCID: PMC4469326 DOI: 10.1186/s12864-015-1667-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 05/29/2015] [Indexed: 11/25/2022] Open
Abstract
Background The European shore crab, Carcinus maenas, is used widely in biomonitoring, ecotoxicology and for studies into host-pathogen interactions. It is also an important invasive species in numerous global locations. However, the genomic resources for this organism are still sparse, limiting research progress in these fields. To address this resource shortfall we produced a C. maenas transcriptome, enabled by the progress in next-generation sequencing technologies, and applied this to assemble information on the innate immune system in this species. Results We isolated and pooled RNA for twelve different tissues and organs from C. maenas individuals and sequenced the RNA using next generation sequencing on an Illumina HiSeq 2500 platform. After de novo assembly a transcriptome was generated encompassing 212,427 transcripts (153,699 loci). The transcripts were filtered, annotated and characterised using a variety of tools (including BLAST, MEGAN and RSEM) and databases (including NCBI, Gene Ontology and KEGG). There were differential patterns of expression for between 1,223 and 2,741 transcripts across tissues and organs with over-represented Gene Ontology terms relating to their specific function. Based on sequence homology to immune system components in other organisms, we show both the presence of transcripts for a series of known pathogen recognition receptors and response proteins that form part of the innate immune system, and transcripts representing the RNAi, Toll-like receptor signalling, IMD and JAK/STAT pathways. Conclusions We have produced an assembled transcriptome for C. maenas that provides a significant molecular resource for wide ranging studies in this species. Analysis of the transcriptome has revealed the presence of a series of known targets and functional pathways that form part of their innate immune system and illustrate tissue specific differences in their expression patterns. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1667-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bas Verbruggen
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD, UK.
| | - Lisa K Bickley
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD, UK.
| | - Eduarda M Santos
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD, UK.
| | - Charles R Tyler
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD, UK.
| | - Grant D Stentiford
- European Union Reference Laboratory for Crustacean Diseases, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset, DT4 8UB, UK.
| | - Kelly S Bateman
- European Union Reference Laboratory for Crustacean Diseases, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset, DT4 8UB, UK.
| | - Ronny van Aerle
- Aquatic Health and Hygiene Division, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset, DT4 8UB, UK.
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R. V. S, Kumari P, Rupwate SD, Rajasekharan R, Srinivasan M. Exploring triacylglycerol biosynthetic pathway in developing seeds of Chia (Salvia hispanica L.): a transcriptomic approach. PLoS One 2015; 10:e0123580. [PMID: 25875809 PMCID: PMC4395390 DOI: 10.1371/journal.pone.0123580] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 03/04/2015] [Indexed: 11/18/2022] Open
Abstract
Chia (Salvia hispanica L.), a member of the mint family (Lamiaceae), is a rediscovered crop with great importance in health and nutrition and is also the highest known terrestrial plant source of heart-healthy omega-3 fatty acid, alpha linolenic acid (ALA). At present, there is no public genomic information or database available for this crop, hindering research on its genetic improvement through genomics-assisted breeding programs. The first comprehensive analysis of the global transcriptome profile of developing Salvia hispanica L. seeds, with special reference to lipid biosynthesis is presented in this study. RNA from five different stages of seed development was extracted and sequenced separately using the Illumina GAIIx platform. De novo assembly of processed reads in the pooled transcriptome using Trinity yielded 76,014 transcripts. The total transcript length was 66,944,462 bases (66.9 Mb), with an average length of approximately 880 bases. In the molecular functions category of Gene Ontology (GO) terms, ATP binding and nucleotide binding were found to be the most abundant and in the biological processes category, the metabolic process and the regulation of transcription-DNA-dependent and oxidation-reduction process were abundant. From the EuKaryotic Orthologous Groups of proteins (KOG) classification, the major category was “Metabolism” (31.97%), of which the most prominent class was ‘carbohydrate metabolism and transport’ (5.81% of total KOG classifications) followed by ‘secondary metabolite biosynthesis transport and catabolism’ (5.34%) and ‘lipid metabolism’ (4.57%). A majority of the candidate genes involved in lipid biosynthesis and oil accumulation were identified. Furthermore, 5596 simple sequence repeats (SSRs) were identified. The transcriptome data was further validated through confirmative PCR and qRT-PCR for select lipid genes. Our study provides insight into the complex transcriptome and will contribute to further genome-wide research and understanding of chia. The identified novel UniGenes will facilitate gene discovery and creation of genomic resource for this crop.
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Affiliation(s)
- Sreedhar R. V.
- CSIR-Lipidomic Centre (CSIR-LIPIC), CSIR-Central Food Technological Research Institute (CSIR-CFTRI) Resource Centre, Allalasandra, GKVK Post, Bangalore—560 065, Karnataka, India
| | - Priya Kumari
- CSIR-Lipidomic Centre (CSIR-LIPIC), CSIR-Central Food Technological Research Institute (CSIR-CFTRI) Resource Centre, Allalasandra, GKVK Post, Bangalore—560 065, Karnataka, India
- Academy of Scientific and Innovative Research, CSIR, New Delhi—110 025, India
| | - Sunny D. Rupwate
- CSIR-Lipidomic Centre (CSIR-LIPIC), CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysore—570 020, Karnataka, India
| | - Ram Rajasekharan
- CSIR-Lipidomic Centre (CSIR-LIPIC), CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysore—570 020, Karnataka, India
| | - Malathi Srinivasan
- CSIR-Lipidomic Centre (CSIR-LIPIC), CSIR-Central Food Technological Research Institute (CSIR-CFTRI) Resource Centre, Allalasandra, GKVK Post, Bangalore—560 065, Karnataka, India
- Academy of Scientific and Innovative Research, CSIR, New Delhi—110 025, India
- * E-mail:
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Bárta J, Stone JD, Pech J, Sirová D, Adamec L, Campbell MA, Štorchová H. The transcriptome of Utricularia vulgaris, a rootless plant with minimalist genome, reveals extreme alternative splicing and only moderate sequence similarity with Utricularia gibba. BMC PLANT BIOLOGY 2015; 15:78. [PMID: 25848894 PMCID: PMC4358910 DOI: 10.1186/s12870-015-0467-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/23/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND The species of Utricularia attract attention not only owing to their carnivorous lifestyle, but also due to an elevated substitution rate and a dynamic evolution of genome size leading to its dramatic reduction. To better understand the evolutionary dynamics of genome size and content as well as the great physiological plasticity in this mostly aquatic carnivorous genus, we analyzed the transcriptome of Utricularia vulgaris, a temperate species with well characterized physiology and ecology. We compared its transcriptome, namely gene content and overall transcript profile, with a previously described transcriptome of Utricularia gibba, a congener possessing one of the smallest angiosperm genomes. RESULTS We sequenced a normalized cDNA library prepared from total RNA extracted from shoots of U. vulgaris including leaves and traps, cultivated under sterile or outdoor conditions. 454 pyrosequencing resulted in more than 1,400,000 reads which were assembled into 41,407 isotigs in 19,522 isogroups. We observed high transcript variation in several isogroups explained by multiple loci and/or alternative splicing. The comparison of U. vulgaris and U. gibba transcriptomes revealed a similar distribution of GO categories among expressed genes, despite the differences in transcriptome preparation. We also found a strong correspondence in the presence or absence of root-associated genes between the U. vulgaris transcriptome and U. gibba genome, which indicated that the loss of some root-specific genes had occurred before the divergence of the two rootless species. CONCLUSIONS The species-rich genus Utricularia offers a unique opportunity to study adaptations related to the environment and carnivorous habit and also evolutionary processes responsible for considerable genome reduction. We show that a transcriptome may approximate the genome for gene content or gene duplication estimation. Our study is the first comparison of two global sequence data sets in Utricularia.
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Affiliation(s)
- Jiří Bárta
- />Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 37005 Czech Republic
| | - James D Stone
- />Institute of Experimental Botany CAS, Rozvojová 263 6- Lysolaje, Praha, 16502 Czech Republic
- />Institute of Botany CAS, Zámek 1, Průhonice, 25243 Czech Republic
| | - Jiří Pech
- />Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 37005 Czech Republic
| | - Dagmara Sirová
- />Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 37005 Czech Republic
| | - Lubomír Adamec
- />Institute of Botany CAS, Section of Plant Ecology, Dukelská 135, Treboň, 37982 Czech Republic
| | - Matthew A Campbell
- />Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North, 4442 New Zealand
| | - Helena Štorchová
- />Institute of Experimental Botany CAS, Rozvojová 263 6- Lysolaje, Praha, 16502 Czech Republic
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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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Exploring the genes of yerba mate (Ilex paraguariensis A. St.-Hil.) by NGS and de novo transcriptome assembly. PLoS One 2014; 9:e109835. [PMID: 25330175 PMCID: PMC4199719 DOI: 10.1371/journal.pone.0109835] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/31/2014] [Indexed: 12/28/2022] Open
Abstract
Yerba mate (Ilex paraguariensis A. St.-Hil.) is an important subtropical tree crop cultivated on 326,000 ha in Argentina, Brazil and Paraguay, with a total yield production of more than 1,000,000 t. Yerba mate presents a strong limitation regarding sequence information. The NCBI GenBank lacks an EST database of yerba mate and depicts only 80 DNA sequences, mostly uncharacterized. In this scenario, in order to elucidate the yerba mate gene landscape by means of NGS, we explored and discovered a vast collection of I. paraguariensis transcripts. Total RNA from I. paraguariensis was sequenced by Illumina HiSeq-2000 obtaining 72,031,388 pair-end 100 bp sequences. High quality reads were de novo assembled into 44,907 transcripts encompassing 40 million bases with an estimated coverage of 180X. Multiple sequence analysis allowed us to predict that yerba mate contains ∼ 32,355 genes and 12,551 gene variants or isoforms. We identified and categorized members of more than 100 metabolic pathways. Overall, we have identified ∼ 1,000 putative transcription factors, genes involved in heat and oxidative stress, pathogen response, as well as disease resistance and hormone response. We have also identified, based in sequence homology searches, novel transcripts related to osmotic, drought, salinity and cold stress, senescence and early flowering. We have also pinpointed several members of the gene silencing pathway, and characterized the silencing effector Argonaute1. We predicted a diverse supply of putative microRNA precursors involved in developmental processes. We present here the first draft of the transcribed genomes of the yerba mate chloroplast and mitochondrion. The putative sequence and predicted structure of the caffeine synthase of yerba mate is presented. Moreover, we provide a collection of over 10,800 SSR accessible to the scientific community interested in yerba mate genetic improvement. This contribution broadly expands the limited knowledge of yerba mate genes, and is presented as the first genomic resource of this important crop.
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