1
|
Chen L, Li L, Huang C, Cao X, Jiang Y. Dynamic mRNA network profiles in macrophages challenged with lipopolysaccharide. Am J Transl Res 2024; 16:1643-1659. [PMID: 38883351 PMCID: PMC11170596 DOI: 10.62347/kmaj3260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/18/2024] [Indexed: 06/18/2024]
Abstract
OBJECTIVES To elucidate the transcriptome of macrophages in an inflammation model induced by lipopolysaccharide (LPS), providing insight into the molecular basis of inflammation. METHODS We utilized RNA sequencing (RNA-seq) to analyze dynamic changes in gene expression in RAW264.7 macrophages treated with LPS at multiple time points. Differentially expressed genes (DEGs) were identified using the edgeR package. Short Time-series Expression Miner (STEM) and KEGG pathway enrichment analyses were conducted to determine temporal expression patterns during inflammation. RESULTS We identified 2,512 DEGs, with initial inflammatory responses occurring in two distinct phases at 1 h and 3 h. Venn diagram analysis revealed 78 consistently dysregulated genes throughout the inflammatory process. A key module of 18 dysregulated genes was identified, including Irg1, which may exert an inhibitory effect on inflammation. Further, a second metabolic shift in activated macrophages was observed at the late middle stage (12 h). Multi-omics analysis highlighted the ribosome's potential regulatory role in the inflammatory response. CONCLUSIONS This study provides a detailed view of the molecular mechanisms underlying inflammation in macrophages and reveals a dynamic genetic landscape crucial for further research. Our findings underscore the complex interaction between gene expression, metabolic shifts, and ribosomal functions in response to LPS-induced inflammation.
Collapse
Affiliation(s)
- Li Chen
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University Guangzhou 510515, Guangdong, China
- Department of Anesthesiology, The Third Affiliated Hospital of Southern Medical University, Southern Medical University Guangzhou 510630, Guangdong, China
| | - Lei Li
- Department of Neurology, Shenzhen Hospital of Southern Medical University Shenzhen 518000, Guangdong, China
| | - Chenyang Huang
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University Guangzhou 510515, Guangdong, China
| | - Xusong Cao
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University Guangzhou 510515, Guangdong, China
| | - Yong Jiang
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University Guangzhou 510515, Guangdong, China
- Department of Respiratory and Critical Care Medicine, The Tenth Affiliated Hospital, Guangdong Provincial Key Laboratory of Proteomics, Southern Medical University (Dongguan People's Hospital) Dongguan 523059, Guangdong, China
| |
Collapse
|
2
|
Ali S, Kucek LK, Riday H, Krom N, Krogman S, Cooper K, Jacobs L, Mehta P, Trammell M, Bhamidimarri S, Butler T, Saha MC, Monteros MJ. Transcript profiling of hairy vetch (Vicia villosa Roth) identified interesting genes for seed dormancy. THE PLANT GENOME 2023; 16:e20330. [PMID: 37125613 DOI: 10.1002/tpg2.20330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Hairy vetch, a diploid annual legume species, has a robust growth habit, high biomass yield, and winter hardy characteristics. Seed hardness is a major constraint for growing hairy vetch commercially. Hard seeded cultivars are valuable as forages, whereas soft seeded and shatter resistant cultivars have advantages for their use as a cover crop. Transcript analysis of hairy vetch was performed to understand the genetic mechanisms associated with important hairy vetch traits. RNA was extracted from leaves, flowers, immature pods, seed coats, and cotyledons of contrasting soft and hard seeded "AU Merit" plants. A range of 31.22-79.18 Gb RNA sequence data per tissue sample were generated with estimated coverage of 1040-2639×. RNA sequence assembly and mapping of the contigs against the Medicago truncatula (V4.0) genome identified 76,422 gene transcripts. A total of 24,254 transcripts were constitutively expressed in hairy vetch tissues. Key genes, such as KNOX4 (a class II KNOTTED-like homeobox KNOXII gene), qHs1 (endo-1,4-β-glucanase), GmHs1-1 (calcineurin-like metallophosphoesterase), chitinase, shatterproof 1 and 2 (SHP1, SHP2), shatter resistant 1-5 (SHAT1-5)(NAC transcription factor), PDH1 (prephenate dehydrogenase 1), and pectin methylesterases with a potential role in seed hardness and pod shattering, were further explored based on genes involved in seed hardness from other species to query the hairy vetch transcriptome data. Identification of interesting candidate genes in hairy vetch can facilitate the development of improved cultivars with desirable seed characteristics for use as a forage and as a cover crop.
Collapse
Affiliation(s)
- Shahjahan Ali
- USDA-ARS, US Dairy Forage Research Center, Madison, Wisconsin, USA
| | | | | | - Nick Krom
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | - Sarah Krogman
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | | | - Lynne Jacobs
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | - Perdeep Mehta
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | - Michael Trammell
- Oklahoma State University Cooperative Extension, Shawnee, Oklahoma, USA
| | | | - Twain Butler
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | - Malay C Saha
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | | |
Collapse
|
3
|
Kumar P, Singh J, Kaur G, Adunola PM, Biswas A, Bazzer S, Kaur H, Kaur I, Kaur H, Sandhu KS, Vemula S, Kaur B, Singh V, Tseng TM. OMICS in Fodder Crops: Applications, Challenges, and Prospects. Curr Issues Mol Biol 2022; 44:5440-5473. [PMID: 36354681 PMCID: PMC9688858 DOI: 10.3390/cimb44110369] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 09/08/2024] Open
Abstract
Biomass yield and quality are the primary targets in forage crop improvement programs worldwide. Low-quality fodder reduces the quality of dairy products and affects cattle's health. In multipurpose crops, such as maize, sorghum, cowpea, alfalfa, and oat, a plethora of morphological and biochemical/nutritional quality studies have been conducted. However, the overall growth in fodder quality improvement is not on par with cereals or major food crops. The use of advanced technologies, such as multi-omics, has increased crop improvement programs manyfold. Traits such as stay-green, the number of tillers per plant, total biomass, and tolerance to biotic and/or abiotic stresses can be targeted in fodder crop improvement programs. Omic technologies, namely genomics, transcriptomics, proteomics, metabolomics, and phenomics, provide an efficient way to develop better cultivars. There is an abundance of scope for fodder quality improvement by improving the forage nutrition quality, edible quality, and digestibility. The present review includes a brief description of the established omics technologies for five major fodder crops, i.e., sorghum, cowpea, maize, oats, and alfalfa. Additionally, current improvements and future perspectives have been highlighted.
Collapse
Affiliation(s)
- Pawan Kumar
- Agrotechnology Division, Council of Scientific and Industrial Research-Institute of Himalayan Bioresource Technology, Palampur 176061, India
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India
| | - Jagmohan Singh
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India
- Krishi Vigyan Kendra, Guru Angad Dev Veterinary and Animal Science University, Barnala 148107, India
| | - Gurleen Kaur
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | | | - Anju Biswas
- Agronomy Department, University of Florida, Gainesville, FL 32611, USA
| | - Sumandeep Bazzer
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, WA 57007, USA
| | - Harpreet Kaur
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88001, USA
| | - Ishveen Kaur
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Harpreet Kaur
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN 37209, USA
| | - Karansher Singh Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA
| | - Shailaja Vemula
- Agronomy Department, UF/IFAS Research and Education Center, Belle Glade, FL 33430, USA
| | - Balwinder Kaur
- Department of Entomology, UF/IFAS Research and Education Center, Belle Glade, FL 33430, USA
| | - Varsha Singh
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS 39759, USA
| | - Te Ming Tseng
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS 39759, USA
| |
Collapse
|
4
|
Wu L, Fredua-Agyeman R, Strelkov SE, Chang KF, Hwang SF. Identification of Novel Genes Associated with Partial Resistance to Aphanomyces Root Rot in Field Pea by BSR-Seq Analysis. Int J Mol Sci 2022; 23:9744. [PMID: 36077139 PMCID: PMC9456226 DOI: 10.3390/ijms23179744] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 12/04/2022] Open
Abstract
Aphanomyces root rot, caused by Aphanomyces euteiches, causes severe yield loss in field pea (Pisum sativum). The identification of a pea germplasm resistant to this disease is an important breeding objective. Polygenetic resistance has been reported in the field pea cultivar '00-2067'. To facilitate marker-assisted selection (MAS), bulked segregant RNA-seq (BSR-seq) analysis was conducted using an F8 RIL population derived from the cross of 'Carman' × '00-2067'. Root rot development was assessed under controlled conditions in replicated experiments. Resistant (R) and susceptible (S) bulks were constructed based on the root rot severity in a greenhouse study. The BSR-seq analysis of the R bulks generated 44,595,510~51,658,688 reads, of which the aligned sequences were linked to 44,757 genes in a reference genome. In total, 2356 differentially expressed genes were identified, of which 44 were used for gene annotation, including defense-related pathways (jasmonate, ethylene and salicylate) and the GO biological process. A total of 344.1 K SNPs were identified between the R and S bulks, of which 395 variants were located in 31 candidate genes. The identification of novel genes associated with partial resistance to Aphanomyces root rot in field pea by BSR-seq may facilitate efforts to improve management of this important disease.
Collapse
Affiliation(s)
| | | | | | | | - Sheau-Fang Hwang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| |
Collapse
|
5
|
Comparative transcriptome analysis provides novel insights into the molecular mechanism of the silver carp (Hypophthalmichthys molitrix) brain in response to hypoxia stress. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 41:100951. [PMID: 34923202 DOI: 10.1016/j.cbd.2021.100951] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 02/05/2023]
Abstract
The brain of fish plays an important role in regulating growth and adapting to environmental changes. However, few studies have been performed to address the changes in gene expression profiles in fish brains under hypoxic stress. In the present study, silver carp (Hypophthalmichthys molitrix) were kept under hypoxic experimental conditions by using the method of natural oxygen consumption, which resulted in a significant decrease in malondialdehyde (MDA) and glutathione (GSH) content and superoxide dismutase (SOD) activity in the brain. In addition, RNA sequencing (RNA-Seq) was performed to analyze transcriptional regulation in the brains of silver carp under normoxia (control group), hypoxia, semi-asphyxia, and asphyxia conditions. The results of KEGG enrichment pathway analysis showed that the immune system, such as antigen processing and presentation, natural killer cell-mediated cytotoxicity, was enriched in the hypoxia group; the nervous system (e.g., "glutamatergic synapse"), signal transduction (e.g., "calcium signaling pathway"; "foxo signaling pathway"), and signaling molecules and interactions (e.g., "neuroactive ligand-receptor interaction") were enriched in the semi-asphyxia group; and signaling molecules and interactions (e.g., "neuroactive ligand-receptor interaction") were enriched in the asphyxia group. These results provide novel insights into the molecular regulatory mechanism of the fish brain coping with hypoxia stress.
Collapse
|
6
|
Huo J, Wu Z, Sun W, Wang Z, Wu J, Huang M, Wang B, Sun B. Protective Effects of Natural Polysaccharides on Intestinal Barrier Injury: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:711-735. [PMID: 35078319 DOI: 10.1021/acs.jafc.1c05966] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Owing to their minimal side effects and effective protection from oxidative stress, inflammation, and malignant growth, natural polysaccharides (NPs) are a potential adjuvant therapy for several diseases caused by intestinal barrier injury (IBI). More studies are accumulating on the protective effects of NPs with respect to IBI, but the underlying mechanisms remain unclear. Thus, this review aims to represent current studies that investigate the protective effects of NPs on IBI by directly maintaining intestinal epithelial barrier integrity (inhibiting oxidative stress, regulating inflammatory cytokine expression, and increasing tight junction protein expression) and indirectly regulating intestinal immunity and microbiota. Furthermore, the mechanisms underlying IBI development are briefly introduced, and the structure-activity relationships of polysaccharides with intestinal barrier protection effects are discussed. Potential developments and challenges associated with NPs exhibiting protective effects against IBI have also been highlighted to guide the application of NPs in the treatment of intestinal diseases caused by IBI.
Collapse
Affiliation(s)
- Jiaying Huo
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing 100048, People's Republic of China
- Beijing Laboratory of Food Quality and Safety, Beijing Technology and Business University, Beijing 100048, People's Republic of China
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong 510640, People's Republic of China
| | - Ziyan Wu
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing 100048, People's Republic of China
- College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, People's Republic of China
| | - Weizheng Sun
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong 510640, People's Republic of China
| | - Zhenhua Wang
- Center for Mitochondria and Healthy Aging, College of Life Science, Yantai University, Yantai, Shandong 264005, People's Republic of China
| | - Jihong Wu
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing 100048, People's Republic of China
- College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, People's Republic of China
- Beijing Laboratory of Food Quality and Safety, Beijing Technology and Business University, Beijing 100048, People's Republic of China
| | - Mingquan Huang
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing 100048, People's Republic of China
- Beijing Laboratory of Food Quality and Safety, Beijing Technology and Business University, Beijing 100048, People's Republic of China
| | - Bowen Wang
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing 100048, People's Republic of China
- Beijing Laboratory of Food Quality and Safety, Beijing Technology and Business University, Beijing 100048, People's Republic of China
| | - Baoguo Sun
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing 100048, People's Republic of China
- Beijing Laboratory of Food Quality and Safety, Beijing Technology and Business University, Beijing 100048, People's Republic of China
| |
Collapse
|
7
|
RNA-Seq-Based Profiling of pl Mutant Reveals Transcriptional Regulation of Anthocyanin Biosynthesis in Rice ( Oryza sativa L.). Int J Mol Sci 2021; 22:ijms22189787. [PMID: 34575968 PMCID: PMC8466560 DOI: 10.3390/ijms22189787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 11/17/2022] Open
Abstract
Purple-colored leaves in plants attain much interest for their important biological functions and could be a potential source of phenotypic marker in selecting individuals in breeding. The transcriptional profiling helps to precisely identify mechanisms of leaf pigmentation in crop plants. In this study, two genetically unlike rice genotypes, the mutant purple leaf (pl) and wild (WT) were selected for RNA-sequencing and identifying the differentially expressed genes (DEGs) that are regulating purple leaf color. In total, 609 DEGs were identified, of which 513 and 96 genes were up- and down-regulated, respectively. The identified DEGs are categorized into metabolic process, carboxylic acid biosynthesis, phenylpropanoids, and phenylpropanoid biosynthesis process enrichment by GO analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) confirmed their association with phenylpropanoid synthesis, flavonoid synthesis, and phenylalanine metabolism. To explore molecular mechanism of purple leaf color, a set of anthocyanin biosynthetic and regulatory gene expression patterns were checked by qPCR. We found that OsPAL (Os02g0626100, Os02g0626400, Os04g0518400, Os05g0427400 and Os02g0627100), OsF3H (Os03g0122300), OsC4HL (Os05g0320700), and Os4CL5 (Os08g0448000) are associated with anthocyanin biosynthesis, and they were up-regulated in pl leaves. Two members of regulatory MYB genes (OsMYB55; Os05g0553400 and Os08g0428200), two bHLH genes (Os01g0196300 and Os04g0300600), and two WD40 genes (Os11g0132700 and Os11g0610700) also showed up-regulation in pl mutant. These genes might have significant and vital roles in pl leaf coloration and could provide reference materials for further experimentation to confirm the molecular mechanisms of anthocyanin biosynthesis in rice.
Collapse
|
8
|
A Review of Unreduced Gametes and Neopolyploids in Alfalfa: How to Fill the Gap between Well-Established Meiotic Mutants and Next-Generation Genomic Resources. PLANTS 2021; 10:plants10050999. [PMID: 34067689 PMCID: PMC8156078 DOI: 10.3390/plants10050999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/03/2021] [Accepted: 05/12/2021] [Indexed: 01/11/2023]
Abstract
The gene flow mediated by unreduced gametes between diploid and tetraploid plants of the Medicagosativa-coerulea-falcata complex is pivotal for alfalfa breeding. Sexually tetraploidized hybrids could represent the best way to exploit progressive heterosis simultaneously derived from gene diversity, heterozygosity, and polyploidy. Moreover, unreduced gametes combined with parthenogenesis (i.e., apomixis) would enable the cloning of plants through seeds, providing a unique opportunity for the selection of superior genotypes with permanently fixed heterosis. This reproductive strategy has never been detected in the genus Medicago, but features of apomixis, such as restitutional apomeiosis and haploid parthenogenesis, have been reported. By means of an original case study, we demonstrated that sexually tetraploidized plants maintain apomeiosis, but this trait is developmentally independent from parthenogenesis. Alfalfa meiotic mutants producing unreduced egg cells revealed a null or very low capacity for parthenogenesis. The overall achievements reached so far are reviewed and discussed along with the efforts and strategies made for exploiting reproductive mutants that express apomictic elements in alfalfa breeding programs. Although several studies have investigated the cytological mechanisms responsible for 2n gamete formation and the inheritance of this trait, only a very small number of molecular markers and candidate genes putatively linked to unreduced gamete formation have been identified. Furthermore, this scenario has remained almost unchanged over the last two decades. Here, we propose a reverse genetics approach, by exploiting the genomic and transcriptomic resources available in alfalfa. Through a comparison with 9 proteins belonging to Arabidopsis thaliana known for their involvement in 2n gamete production, we identified 47 orthologous genes and evaluated their expression in several tissues, paving the way for novel candidate gene characterization studies. An overall view on strategies suitable to fill the gap between well-established meiotic mutants and next-generation genomic resources is presented and discussed.
Collapse
|
9
|
Guo S, Wang D, Ma Y, Zhang Y, Zhao X. Combination of RNA-Seq transcriptomics and iTRAQ proteomics reveal the mechanism involved in fresh-cut yam yellowing. Sci Rep 2021; 11:7755. [PMID: 33833352 PMCID: PMC8032744 DOI: 10.1038/s41598-021-87423-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/23/2021] [Indexed: 01/22/2023] Open
Abstract
The aim of this study was to examine the regulation of transcriptomics and proteomics related to the yellowing of fresh-cut yams after storage. The comparison of yellow fresh-cut yam (YFY) vs. white fresh-cut yam (control) revealed 6894 upregulated and 6800 downregulated differentially expressed genes along with 1277 upregulated and 677 downregulated differentially expressed proteins. The results showed that the total carotenoids, flavonoids, and bisdemethoxycurcumin in YFY were higher than in the control due to the significant up-regulation of critical genes in the carotenoid biosynthesis pathway, flavonoid biosynthesis pathway, and stilbenoid, diarylheptanoid, and gingerol biosynthesis pathway. In addition, the tricarboxylic acid cycle and phenylpropanoid biosynthesis were both enhanced in YFY compared to the control, providing energy and precursors for the formation of yellow pigments. The results suggest that the synthesis of yellow pigments is regulated by critical genes, which might explain the yellowing of fresh-cut yam after storage.
Collapse
Affiliation(s)
- Shuang Guo
- College of Food Science, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Agricultural Products of Fruits and Vegetables Preservation and Processing, Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing, 100097, China
| | - Dan Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Agricultural Products of Fruits and Vegetables Preservation and Processing, Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing, 100097, China
| | - Yue Ma
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Agricultural Products of Fruits and Vegetables Preservation and Processing, Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing, 100097, China
| | - Yan Zhang
- Longda Food Group Co. LTD, Shandong, 265231, China
| | - Xiaoyan Zhao
- College of Food Science, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Agricultural Products of Fruits and Vegetables Preservation and Processing, Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing, 100097, China.
| |
Collapse
|
10
|
Dissanayake R, Braich S, Cogan NOI, Smith K, Kaur S. Characterization of Genetic and Allelic Diversity Amongst Cultivated and Wild Lentil Accessions for Germplasm Enhancement. Front Genet 2020; 11:546. [PMID: 32587602 PMCID: PMC7298104 DOI: 10.3389/fgene.2020.00546] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/06/2020] [Indexed: 12/13/2022] Open
Abstract
Intensive breeding of cultivated lentil has resulted in a relatively narrow genetic base, which limits the options to increase crop productivity through selection. Assessment of genetic diversity in the wild gene pool of lentil, as well as characterization of useful and novel alleles/genes that can be introgressed into elite germplasm, presents new opportunities and pathways for germplasm enhancement, followed by successful crop improvement. In the current study, a lentil collection consisting of 467 wild and cultivated accessions that originated from 10 diverse geographical regions was assessed, to understand genetic relationships among different lentil species/subspecies. A total of 422,101 high-confidence SNP markers were identified against the reference lentil genome (cv. CDC Redberry). Phylogenetic analysis clustered the germplasm collection into four groups, namely, Lens culinaris/Lens orientalis, Lens lamottei/Lens odemensis, Lens ervoides, and Lens nigricans. A weak correlation was observed between geographical origin and genetic relationship, except for some accessions of L. culinaris and L. ervoides. Genetic distance matrices revealed a comparable level of variation within the gene pools of L. culinaris (Nei’s coefficient 0.01468–0.71163), L. ervoides (Nei’s coefficient 0.01807–0.71877), and L. nigricans (Nei’s coefficient 0.02188–1.2219). In order to understand any genic differences at species/subspecies level, allele frequencies were calculated from a subset of 263 lentil accessions. Among all cultivated and wild lentil species, L. nigricans exhibited the greatest allelic differentiation across the genome compared to all other species/subspecies. Major differences were observed on six genomic regions with the largest being on Chromosome 1 (c. 1 Mbp). These results indicate that L. nigricans is the most distantly related to L. culinaris and additional structural variations are likely to be identified from genome sequencing studies. This would provide further insights into evolutionary relationships between cultivated and wild lentil germplasm, for germplasm improvement and introgression.
Collapse
Affiliation(s)
- Ruwani Dissanayake
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Shivraj Braich
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,School of Applied Systems Biology, La Trobe University, Melbourne, VIC, Australia
| | - Noel O I Cogan
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,School of Applied Systems Biology, La Trobe University, Melbourne, VIC, Australia
| | - Kevin Smith
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.,Agriculture Victoria, Hamilton, VIC, Australia
| | - Sukhjiwan Kaur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| |
Collapse
|
11
|
Afzal M, Alghamdi SS, Migdadi HH, Khan MA, Nurmansyah, Mirza SB, El-Harty E. Legume genomics and transcriptomics: From classic breeding to modern technologies. Saudi J Biol Sci 2019; 27:543-555. [PMID: 31889880 PMCID: PMC6933173 DOI: 10.1016/j.sjbs.2019.11.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/16/2019] [Accepted: 11/17/2019] [Indexed: 02/06/2023] Open
Abstract
Legumes are essential and play a significant role in maintaining food standards and augmenting physiochemical soil properties through the biological nitrogen fixation process. Biotic and abiotic factors are the main factors limiting legume production. Classical breeding methodologies have been explored extensively about the problem of truncated yield in legumes but have not succeeded at the desired rate. Conventional breeding improved legume genotypes but with more resources and time. Recently, the invention of next-generation sequencing (NGS) and high-throughput methods for genotyping have opened new avenues for research and developments in legume studies. During the last decade, genome sequencing for many legume crops documented. Sequencing and re-sequencing of important legume species have made structural variation and functional genomics conceivable. NGS and other molecular techniques such as the development of markers; genotyping; high density genetic linkage maps; quantitative trait loci (QTLs) identification, expressed sequence tags (ESTs), single nucleotide polymorphisms (SNPs); and transcription factors incorporated into existing breeding technologies have made possible the accurate and accelerated delivery of information for researchers. The application of genome sequencing, RNA sequencing (transcriptome sequencing), and DNA sequencing (re-sequencing) provide considerable insights for legume development and improvement programs. Moreover, RNA-Seq helps to characterize genes, including differentially expressed genes, and can be applied for functional genomics studies, especially when there is limited information available for the studied genomes. Genome-based crop development studies and the availability of genomics data as well as decision-making gears look be specific for breeding programs. This review mainly presents an overview of the path from classical breeding to new emerging genomics tools, which will trigger and accelerate genomics-assisted breeding for recognition of novel genes for yield and quality characters for sustainable legume crop production.
Collapse
Affiliation(s)
- Muhammad Afzal
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Salem S Alghamdi
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Hussein H Migdadi
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Altaf Khan
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Nurmansyah
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Shaher Bano Mirza
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey.,Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Chak Shahzad, Islamabad, Pakistan
| | - Ehab El-Harty
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
12
|
Li Y, Nan Z, Duan T. Rhizophagus intraradices promotes alfalfa (Medicago sativa) defense against pea aphids (Acyrthosiphon pisum) revealed by RNA-Seq analysis. MYCORRHIZA 2019; 29:623-635. [PMID: 31588522 DOI: 10.1007/s00572-019-00915-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 09/06/2019] [Indexed: 06/10/2023]
Abstract
Pea aphids (Acyrthosiphon pisum) are one of the most important insect pests of alfalfa (Medicago sativa). Arbuscular mycorrhizal (AM) fungi are important microorganisms of the agroecosystem that promote plant growth and improve plant resistance to abiotic and biotic stress. Little information is available on AM fungi-regulated defense responses of alfalfa to pea aphids. To better understand how alfalfa responds and to evaluate the impact of an AM fungus on aphid infestation, transcriptome sequencing was done and physiological parameters were analyzed. Our experiments showed that Rhizophagus intraradices can regulate plant response to aphids by promoting growth and increasing plant peroxidase (POD) and catalase (CAT) activities and salicylic acid (SA) concentration after aphid infestation. Transcriptome analysis showed that R. intraradices increased the expression of resistance-related genes, such as "WRKY transcription factor" and "Kunitz trypsin inhibitor." Additionally, GO terms "chitinase activity," "peroxidase activity," "defense response," and "response to biotic stimulus," and KEGG pathways "phenylpropanoid biosynthesis" and "phenylalanine metabolism" were significantly enriched in mycorrhizal fungus-inoculated plants and aphid-infested plants. These findings will improve our understanding about the impact of this AM fungus on alfalfa response to aphid feeding and will provide the basis for further research on plant defense against aphids.
Collapse
Affiliation(s)
- Yingde Li
- State Key Laboratory of Grassland Agro-Ecosystems Lanzhou Unviersity, Lanzhou, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, 768 Jiayuguan West Road, Lanzhou, 730020, NO, China
| | - Zhibiao Nan
- State Key Laboratory of Grassland Agro-Ecosystems Lanzhou Unviersity, Lanzhou, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, 768 Jiayuguan West Road, Lanzhou, 730020, NO, China
| | - Tingyu Duan
- State Key Laboratory of Grassland Agro-Ecosystems Lanzhou Unviersity, Lanzhou, China.
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, China.
- College of Pastoral Agriculture Science and Technology, Lanzhou University, 768 Jiayuguan West Road, Lanzhou, 730020, NO, China.
| |
Collapse
|
13
|
Zager JJ, Lange I, Srividya N, Smith A, Lange BM. Gene Networks Underlying Cannabinoid and Terpenoid Accumulation in Cannabis. PLANT PHYSIOLOGY 2019; 180:1877-1897. [PMID: 31138625 PMCID: PMC6670104 DOI: 10.1104/pp.18.01506] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 05/15/2019] [Indexed: 05/21/2023]
Abstract
Glandular trichomes are specialized anatomical structures that accumulate secretions with important biological roles in plant-environment interactions. These secretions also have commercial uses in the flavor, fragrance, and pharmaceutical industries. The capitate-stalked glandular trichomes of Cannabis sativa (cannabis), situated on the surfaces of the bracts of the female flowers, are the primary site for the biosynthesis and storage of resins rich in cannabinoids and terpenoids. In this study, we profiled nine commercial cannabis strains with purportedly different attributes, such as taste, color, smell, and genetic origin. Glandular trichomes were isolated from each of these strains, and cell type-specific transcriptome data sets were acquired. Cannabinoids and terpenoids were quantified in flower buds. Statistical analyses indicated that these data sets enable the high-resolution differentiation of strains by providing complementary information. Integrative analyses revealed a coexpression network of genes involved in the biosynthesis of both cannabinoids and terpenoids from imported precursors. Terpene synthase genes involved in the biosynthesis of the major monoterpenes and sesquiterpenes routinely assayed by cannabis testing laboratories were identified and functionally evaluated. In addition to cloning variants of previously characterized genes, specifically CsTPS14CT [(-)-limonene synthase] and CsTPS15CT (β-myrcene synthase), we functionally evaluated genes that encode enzymes with activities not previously described in cannabis, namely CsTPS18VF and CsTPS19BL (nerolidol/linalool synthases), CsTPS16CC (germacrene B synthase), and CsTPS20CT (hedycaryol synthase). This study lays the groundwork for developing a better understanding of the complex chemistry and biochemistry underlying resin accumulation across commercial cannabis strains.
Collapse
Affiliation(s)
- Jordan J Zager
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Iris Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Narayanan Srividya
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | | | - B Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| |
Collapse
|
14
|
Pan L, Yu X, Shao J, Liu Z, Gao T, Zheng Y, Zeng C, Liang C, Chen C. Transcriptomic profiling and analysis of differentially expressed genes in asparagus bean (Vigna unguiculata ssp. sesquipedalis) under salt stress. PLoS One 2019; 14:e0219799. [PMID: 31299052 PMCID: PMC6625716 DOI: 10.1371/journal.pone.0219799] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/01/2019] [Indexed: 01/17/2023] Open
Abstract
Asparagus bean (Vigna unguiculata ssp. sesquipedalis) is a warm season legume which is widely distributed over subtropical regions and semiarid areas. It is mainly grown as a significant protein source in developing countries. Salinity, as one of the main abiotic stress factors, constrains the normal growth and yield of asparagus bean. This study used two cultivars (a salt-sensitive genotype and a salt-tolerant genotype) under salt stress vs. control to identify salt-stress-induced genes in asparagus bean using RNA sequencing. A total of 692,086,838 high-quality clean reads, assigned to 121,138 unigenes, were obtained from control and salt-treated libraries. Then, 216 root-derived DEGs (differentially expressed genes) and 127 leaf-derived DEGs were identified under salt stress between the two cultivars. Of these DEGs, thirteen were assigned to six transcription factors (TFs), including AP2/EREBP, CCHC(Zn), C2H2, WRKY, WD40-like and LIM. GO analysis indicated four DEGs might take effects on the "oxidation reduction", "transport" and "signal transduction" process. Moreover, expression of nine randomly-chosen DEGs was verified by quantitative real-time-PCR (qRT-PCR) analysis. Predicted function of the nine tested DEGs was mainly involved in the KEGG pathway of cation transport, response to osmotic stress, and phosphorelay signal transduction system. A salt-stress-related pathway of "SNARE interactions in vesicular transport" was concerned. As byproducts, 15, 321 microsatellite markers were found in all the unigenes, and 17 SNP linked to six salt-stress induced DEGs were revealed. These candidate genes provide novel insights for understanding the salt tolerance mechanism of asparagus bean in the future.
Collapse
Affiliation(s)
- Lei Pan
- Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan, China
- Computational Biology Institute and Center for Biomolecular Sciences, Department of Physics, The George Washington University, Washington, DC, United States of America
| | - Xiaolu Yu
- Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan, China
| | - Jingjie Shao
- Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan, China
| | - Zhichao Liu
- Computational Biology Institute and Center for Biomolecular Sciences, Department of Physics, The George Washington University, Washington, DC, United States of America
| | - Tong Gao
- Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan, China
| | - Yu Zheng
- Institute for Interdisciplinary Research, Jianghan University, Wuhan, China
| | - Chen Zeng
- Computational Biology Institute and Center for Biomolecular Sciences, Department of Physics, The George Washington University, Washington, DC, United States of America
| | - Chengzhi Liang
- Institute of Genetics and Development, Chinese Academy of Sciences, Beijing, China
| | - Chanyou Chen
- Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan, China
| |
Collapse
|
15
|
Akhter D, Qin R, Nath UK, Eshag J, Jin X, Shi C. Transcriptional Profile Corroborates that bml Mutant Plays likely Role in Premature Leaf Senescence of Rice ( Oryza sativa L.). Int J Mol Sci 2019; 20:ijms20071708. [PMID: 30959810 PMCID: PMC6480502 DOI: 10.3390/ijms20071708] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 02/06/2023] Open
Abstract
Leaf senescence is the last period of leaf growth and a dynamic procedure associated with its death. The adaptability of the plants to changing environments occurs thanks to leaf senescence. Hence, transcriptional profiling is important to figure out the exact mechanisms of inducing leaf senescence in a particular crop, such as rice. From this perspective, leaf samples of two different rice genotypes, the brown midrib leaf (bml) mutant and its wild type (WT) were sampled for transcriptional profiling to identify differentially-expressed genes (DEGs). We identified 2670 DEGs, among which 1657 genes were up- and 1013 genes were down-regulated. These DEGs were enriched in binding and catalytic activity, followed by the single organism process and metabolic process through gene ontology (GO), while the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the DEGs were related to the plant hormone signal transduction and photosynthetic pathway enrichment. The expression pattern and the clustering of DEGs revealed that the WRKY and NAC family, as well as zinc finger transcription factors, had greater effects on early-senescence of leaf compared to other transcription factors. These findings will help to elucidate the precise functional role of bml rice mutant in the early-leaf senescence.
Collapse
Affiliation(s)
- Delara Akhter
- Department of Agronomy, Zhejiang University, Hangzhou 310027, China.
- Department of Genetics and Plant Breeding, Sylhet Agricultural University, Sylhet 3100, Bangladesh.
| | - Ran Qin
- Department of Agronomy, Zhejiang University, Hangzhou 310027, China.
| | - Ujjal Kumar Nath
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh.
| | - Jamal Eshag
- Department of Agronomy, Zhejiang University, Hangzhou 310027, China.
| | - Xiaoli Jin
- Department of Agronomy, Zhejiang University, Hangzhou 310027, China.
| | - Chunhai Shi
- Department of Agronomy, Zhejiang University, Hangzhou 310027, China.
| |
Collapse
|
16
|
Pokou DN, Fister AS, Winters N, Tahi M, Klotioloma C, Sebastian A, Marden JH, Maximova SN, Guiltinan MJ. Resistant and susceptible cacao genotypes exhibit defense gene polymorphism and unique early responses to Phytophthora megakarya inoculation. PLANT MOLECULAR BIOLOGY 2019; 99:499-516. [PMID: 30739243 DOI: 10.1007/s11103-019-00832-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 01/24/2019] [Indexed: 05/26/2023]
Abstract
Key genes potentially involved in cacao disease resistance were identified by transcriptomic analysis of important cacao cultivars. Defense gene polymorphisms were identified which could contribute to pathogen recognition capacity. Cacao suffers significant annual losses to the water mold Phytophthora spp. (Oomycetes). In West Africa, P. megakarya poses a major threat to farmer livelihood and the stability of cocoa production. As part of a long-term goal to define key disease resistance genes in cacao, here we use a transcriptomic analysis of the disease-resistant cacao clone SCA6 and the susceptible clone NA32 to characterize basal differences in gene expression, early responses to infection, and polymorphisms in defense genes. Gene expression measurements by RNA-seq along a time course revealed the strongest transcriptomic response 24 h after inoculation in the resistant genotype. We observed strong regulation of several pathogenesis-related genes, pattern recognition receptors, and resistance genes, which could be critical for the ability of SCA6 to combat infection. These classes of genes also showed differences in basal expression between the two genotypes prior to infection, suggesting that prophylactic expression of defense-associated genes could contribute to SCA6's broad-spectrum disease resistance. Finally, we analyzed polymorphism in a set of defense-associated receptors, identifying coding variants between SCA6 and NA32 which could contribute to unique capacities for pathogen recognition. This work is an important step toward characterizing genetic differences underlying a successful defense response in cacao.
Collapse
Affiliation(s)
- Désiré N Pokou
- Centre National de Recherche Agronomique, Laboratoire Central de Biotechnologie, 01 BP 1740, Abidjan 01, Côte d'Ivoire
| | - Andrew S Fister
- Department of Plant Sciences, Life Sciences Building, Pennsylvania State University, University Park, PA, 16802, USA
| | - Noah Winters
- Intercollege Graduate Degree Program in Ecology, Pennsylvania State University, University Park, PA, 16802, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Mathias Tahi
- Centre National de Recherche Agronomique, Laboratoire Central de Biotechnologie, 01 BP 1740, Abidjan 01, Côte d'Ivoire
| | - Coulibaly Klotioloma
- Centre National de Recherche Agronomique, Laboratoire Central de Biotechnologie, 01 BP 1740, Abidjan 01, Côte d'Ivoire
| | - Aswathy Sebastian
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - James H Marden
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Siela N Maximova
- Department of Plant Sciences, Life Sciences Building, Pennsylvania State University, University Park, PA, 16802, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Mark J Guiltinan
- Department of Plant Sciences, Life Sciences Building, Pennsylvania State University, University Park, PA, 16802, USA.
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
| |
Collapse
|
17
|
Zhou Q, Luo D, Chai X, Wu Y, Wang Y, Nan Z, Yang Q, Liu W, Liu Z. Multiple Regulatory Networks Are Activated during Cold Stress in Medicago sativa L. Int J Mol Sci 2018; 19:ijms19103169. [PMID: 30326607 PMCID: PMC6214131 DOI: 10.3390/ijms19103169] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/07/2018] [Accepted: 10/10/2018] [Indexed: 12/18/2022] Open
Abstract
Cultivated alfalfa (Medicago sativa L.) is one of the most important perennial legume forages in the world, and it has considerable potential as a valuable forage crop for livestock. However, the molecular mechanisms underlying alfalfa responses to cold stress are largely unknown. In this study, the transcriptome changes in alfalfa under cold stress at 4 °C for 2, 6, 24, and 48 h (three replicates for each time point) were analyzed using the high-throughput sequencing platform, BGISEQ-500, resulting in the identification of 50,809 annotated unigenes and 5283 differentially expressed genes (DEGs). Metabolic pathway enrichment analysis demonstrated that the DEGs were involved in carbohydrate metabolism, photosynthesis, plant hormone signal transduction, and the biosynthesis of amino acids. Moreover, the physiological changes of glutathione and proline content, catalase, and peroxidase activity were in accordance with dynamic transcript profiles of the relevant genes. Additionally, some transcription factors might play important roles in the alfalfa response to cold stress, as determined by the expression pattern of the related genes during 48 h of cold stress treatment. These findings provide valuable information for identifying and characterizing important components in the cold signaling network in alfalfa and enhancing the understanding of the molecular mechanisms underlying alfalfa responses to cold stress.
Collapse
Affiliation(s)
- Qiang Zhou
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Dong Luo
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Xutian Chai
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Yuguo Wu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Yanrong Wang
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Zhibiao Nan
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Qingchuan Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100000, China.
| | - Wenxian Liu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Zhipeng Liu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| |
Collapse
|
18
|
Li J, Guo H, Wang Y, Zong J, Chen J, Li D, Li L, Wang J, Liu J. High-throughput SSR marker development and its application in a centipedegrass (Eremochloa ophiuroides (Munro) Hack.) genetic diversity analysis. PLoS One 2018; 13:e0202605. [PMID: 30133524 PMCID: PMC6105027 DOI: 10.1371/journal.pone.0202605] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 08/05/2018] [Indexed: 11/18/2022] Open
Abstract
Centipedegrass (Eremochloa ophiuroides (Munro) Hack.) is a perennial, warm-season C4 grass species that shows great potential for use as a low-maintenance turfgrass species in tropical and subtropical regions. However, limited genetic and genomic information is available for this species, which has impeded systematic studies on the enhancement of its turf quality and resistance against biotic and abiotic stress. In this study, Illumina HiSeq high-throughput sequencing technology was performed to generate centipedegrass transcriptome sequences. A total of 352,513 assembled sequences were used to search for simple sequence repeat (SSR) loci, and 64,470 SSR loci were detected in 47,638 SSR containing sequences. The tri-nucleotides were the most frequent repeat motif, followed by di-nucleotides, tetra-nucleotides hexnucleotides, and pentanucleotides. A total of 48,061 primer pairs were successfully designed in the flanking sequences of the SSRs, and 100 sets of primers were randomly selected for the initial validation in four centipedegrass accessions. In total, 56 (56.0%) of the 100 primer pairs tested successfully amplified alleles from all four centipedegrass accessions, while 50 were identified as polymorphic markers and were then used to assess the level of genetic diversity among 43 centipedegrass core collections. The genetic diversity analysis exhibited that the number of alleles (Na) per locus ranged from 3 to 13, and the observed heterozygosity (Ho) ranged from 0.17 to 0.83. The polymorphism information content (PIC) value of the markers ranged from 0.15 to 0.78, and the genetic distances (coefficient Nei72) between the accessions varied from 0.07 to 0.48. The UPGMA-based dendrogram clustered all 43 core collections into two main groups and six subgroups, which further validated the effectiveness of these newly developed SSR markers. Hence, these newly developed SSR markers will be valuable and potentially useful for future genetic and genomic studies of E. ophiuroides.
Collapse
Affiliation(s)
- Jianjian Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Hailin Guo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Yi Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Junqin Zong
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Jingbo Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Dandan Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Ling Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Jingjing Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
- * E-mail:
| |
Collapse
|
19
|
Jia J, Liu X, Li L, Lei C, Dong Y, Wu G, Hu G. Transcriptional and Translational Relationship in Environmental Stress: RNAseq and ITRAQ Proteomic Analysis Between Sexually Reproducing and Parthenogenetic Females in Moina micrura. Front Physiol 2018; 9:812. [PMID: 30013488 PMCID: PMC6036137 DOI: 10.3389/fphys.2018.00812] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 06/08/2018] [Indexed: 11/13/2022] Open
Abstract
Moina micrura is a kind of small-bodied water flea within the family Moinidae. Similar to Daphnia, M. micrura could also switch its reproduction mode from parthenogenetic female (PF) to sexual female (SF) to adapt to the external environment. To uncover the mechanisms of reproductive switching in M. micrura, we used both RNA-Seq and iTRAQ analyses to investigate the differentially expressed genes (DEGs) and their protein products between SF and PF in M. micrura. A total of 1665 DEGs (702 up-regulated, 963 down-regulated) and 600 differentially expressed proteins (DEPs) (102 up-regulated, 498 down-regulated) were detected in SF. Correlation analyses indicated that 31 genes were expressed significantly differentially at both transcriptomic and proteomic levels, including 15 up-regulated genes and 16 down-regulated genes in SF. Meanwhile, our data also showed that 528 DEPs have discordant expression at transcript level, implying post-transcriptional (including translational) regulation. These top up-regulated genes and their protein products in SF were mainly grouped into the globin-related family, vitellogenin-related family, cuticle-related family, Hsp-related family and methyltransferases-related family, which were all involved in the reproductive switching in Daphnia. In contrast, a cluster of orthologous groups revealed that up-regulated genes and their protein products in PF were strongly associated with the metabolic process, which may be responsible for rapid population proliferation in M. micrura.
Collapse
|
20
|
Mei C, Li S, Abbas SH, Tian W, Wang H, Li Y, Gui L, Zhang Y, Wu X, Zan L. Performance Measurement and Comparative Transcriptome Analysis Revealed the Efforts on Hybrid Improvement of Qinchuan Cattle. Anim Biotechnol 2018; 30:13-20. [PMID: 29402192 DOI: 10.1080/10495398.2017.1420662] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Crossbreeding can provide productive gains through heterosis, however, surveys about the effects of crossbreeding through global transcriptomic sequencing are few. This study revealed that Angus × Qinchuan cattle (AQF) have improved performance characteristics compared to Qinchuan cattle (QCF). We performed RNA-seq on the subcutaneous fat tissue of QCF and AQF. More than 42.2 million clean reads were obtained in each sample. We detected 40 and 21 breed-specific highly expressed genes (FPKM > 500) in QCF and AQF, respectively. Furthermore, a total of 353 differentially expressed genes (DEGs, |log2 ratio| ≥ 1 and Probability ≥ 0.8) were found between these two groups, of which 227 genes were upregulated in AQF and 126 genes were upregulated in QCF. Functional enrichment analyses showed that breed-specific highly expressed genes and DEGs were closely related to terms such as development in AQF, and adaption or immune in QCF. In addition, we also identified the novel transcript units, alternative splicing events, single-nucleotide polymorphisms and Indels. Our results revealed differences in inherent characteristics and genetic differences when comparing QCF with AQF.
Collapse
Affiliation(s)
- Chugang Mei
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Shijun Li
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Sayed Haidar Abbas
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Wanqiang Tian
- b Yangling Vocational & Technical College , Yangling , China
| | - Hongcheng Wang
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Yaokun Li
- c College of Animal Science and Technology , South China Agricultural University , Guangzhou , China
| | - Linsheng Gui
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Yingying Zhang
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | | | - Linsen Zan
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China.,e National Beef Cattle Improvement Center , Yangling , China
| |
Collapse
|
21
|
Transcriptome Analysis of the Thymus in Short-Term Calorie-Restricted Mice Using RNA-seq. Int J Genomics 2018; 2018:7647980. [PMID: 29511668 PMCID: PMC5817327 DOI: 10.1155/2018/7647980] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/09/2017] [Accepted: 12/03/2017] [Indexed: 12/14/2022] Open
Abstract
Calorie restriction (CR), which is a factor that expands lifespan and an important player in immune response, is an effective protective method against cancer development. Thymus, which plays a critical role in the development of the immune system, reacts to nutrition deficiency quickly. RNA-seq-based transcriptome sequencing was performed to thymus tissues of MMTV-TGF-α mice subjected to ad libitum (AL), chronic calorie restriction (CCR), and intermittent calorie restriction (ICR) diets in this study. Three cDNA libraries were sequenced using Illumina HiSeq™ 4000 to produce 100 base pair-end reads. On average, 105 million clean reads were mapped and in total 6091 significantly differentially expressed genes (DEGs) were identified (p < 0.05). These DEGs were clustered into Gene Ontology (GO) categories. The expression pattern revealed by RNA-seq was validated by quantitative real-time PCR (qPCR) analysis of four important genes, which are leptin, ghrelin, Igf1, and adinopectin. RNA-seq data has been deposited in NCBI Gene Expression Omnibus (GEO) database (GSE95371). We report the use of RNA sequencing to find DEGs that are affected by different feeding regimes in the thymus.
Collapse
|
22
|
Wang J, Islam F, Li L, Long M, Yang C, Jin X, Ali B, Mao B, Zhou W. Complementary RNA-Sequencing Based Transcriptomics and iTRAQ Proteomics Reveal the Mechanism of the Alleviation of Quinclorac Stress by Salicylic Acid in Oryza sativa ssp. japonica. Int J Mol Sci 2017; 18:ijms18091975. [PMID: 28906478 PMCID: PMC5618624 DOI: 10.3390/ijms18091975] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 09/08/2017] [Accepted: 09/12/2017] [Indexed: 12/16/2022] Open
Abstract
To uncover the alleviation mechanism of quinclorac stress by salicylic acid (SA), leaf samples of Oryza sativa ssp. Japonica under quinclorac stress with and without SA pre-treatment were analyzed for transcriptional and proteomic profiling to determine the differentially expressed genes (DEGs) and proteins (DEPs), respectively. Results showed that quinclorac stress altered the expression of 2207 DEGs (1427 up-regulated, 780 down-regulated) and 147 DEPs (98 down-regulated, 49 up-regulated). These genes and proteins were enriched in glutathione (GSH) metabolism, porphyrin and chlorophyll metabolism, the biosynthesis of secondary metabolites, glyoxylate and dicarboxylate metabolism, and so on. It also influenced apetala2- ethylene-responsive element binding protein (AP2-EREBP) family, myeloblastosis (MYB) family and WRKY family transcription factors. After SA pre-treatment, 697 genes and 124 proteins were differentially expressed. Pathway analysis showed similar enrichments in GSH, glyoxylate and dicarboxylate metabolism. Transcription factors were distributed in basic helix-loop-helix (bHLH), MYB, Tify and WRKY families. Quantitative real-time PCR results revealed that quinclorac stress induced the expression of glutathion reductase (GR) genes (OsGR2, OsGR3), which was further pronounced by SA pre-treatment. Quinclorac stress further mediated the accumulation of acetaldehyde in rice, while SA enhanced the expression of OsALDH2B5 and OsALDH7 to accelerate the metabolism of herbicide quinclorac for the protection of rice. Correlation analysis between transcriptome and proteomics demonstrated that, under quinclorac stress, correlated proteins/genes were mainly involved in the inhibition of intermediate steps in the biosynthesis of chlorophyll. Other interesting proteins/genes and pathways regulated by herbicide quinclorac and modulated by SA pre-treatment were also discussed, based on the transcriptome and proteomics results.
Collapse
Affiliation(s)
- Jian Wang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
| | - Faisal Islam
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
| | - Lan Li
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
| | - Meijuan Long
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
| | - Chong Yang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
| | - Xiaoli Jin
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
| | - Basharat Ali
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
- Institute of Crop Science and Resource Conservation (INRES), Abiotic Stress Tolerance in Crops, University of Bonn, 53115 Bonn, Germany.
| | - Bizeng Mao
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Weijun Zhou
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
23
|
Baldé A, Neves D, García-Breijo FJ, Pais MS, Cravador A. De novo assembly of Phlomis purpurea after challenging with Phytophthora cinnamomi. BMC Genomics 2017; 18:700. [PMID: 28877668 PMCID: PMC5585901 DOI: 10.1186/s12864-017-4042-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 08/09/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phlomis plants are a source of biological active substances with potential applications in the control of phytopathogens. Phlomis purpurea (Lamiaceae) is autochthonous of southern Iberian Peninsula and Morocco and was found to be resistant to Phytophthora cinnamomi. Phlomis purpurea has revealed antagonistic effect in the rhizosphere of Quercus suber and Q. ilex against P. cinnamomi. Phlomis purpurea roots produce bioactive compounds exhibiting antitumor and anti-Phytophthora activities with potential to protect susceptible plants. Although these important capacities of P. purpurea have been demonstrated, there is no transcriptomic or genomic information available in public databases that could bring insights on the genes underlying this anti-oomycete activity. RESULTS Using Illumina technology we obtained a de novo assembly of P. purpurea transcriptome and differential transcript abundance to identify putative defence related genes in challenged versus non-challenged plants. A total of 1,272,600,000 reads from 18 cDNA libraries were merged and assembled into 215,739 transcript contigs. BLASTX alignment to Nr NCBI database identified 124,386 unique annotated transcripts (57.7%) with significant hits. Functional annotation identified 83,550 out of 124,386 unique transcripts, which were mapped to 141 pathways. 39% of unigenes were assigned GO terms. Their functions cover biological processes, cellular component and molecular functions. Genes associated with response to stimuli, cellular and primary metabolic processes, catalytic and transporter functions were among those identified. Differential transcript abundance analysis using DESeq revealed significant differences among libraries depending on post-challenge times. Comparative cyto-histological studies of P. purpurea roots challenged with P. cinnamomi zoospores and controls revealed specific morphological features (exodermal strips and epi-cuticular layer), that may provide a constitutive efficient barrier against pathogen penetration. Genes involved in cutin biosynthesis and in exodermal Casparian strips formation were up-regulated. CONCLUSIONS The de novo assembly of transcriptome using short reads for a non-model plant, P. purpurea, revealed many unique transcripts useful for further gene expression, biological function, genomics and functional genomics studies. The data presented suggest a combination of a constitutive resistance and an increased transcriptional response from P. purpurea when challenged with the pathogen. This knowledge opens new perspectives for the understanding of defence responses underlying pathogenic oomycete/plant interaction upon challenge with P. cinnamomi.
Collapse
Affiliation(s)
- Aladje Baldé
- Plant Molecular Biology and Biotechnology Lab, Center for Biosystems (BioSys), Functional and Integrative Genomics (BioFIG), Edifício C2, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal
- Present Address: Universidade Jean Piaget, Bissau, Guinea-Bissau
| | - Dina Neves
- Faculdade de Ciências e Tecnologia, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Francisco J. García-Breijo
- Departamento de Ecosistemas Agroforestales, Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Maria Salomé Pais
- Plant Molecular Biology and Biotechnology Lab, Center for Biosystems (BioSys), Functional and Integrative Genomics (BioFIG), Edifício C2, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal
| | - Alfredo Cravador
- Centre for Mediterranean Bioresources and Food (MeditBio), FCT, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| |
Collapse
|
24
|
Al-Tobasei R, Ali A, Leeds TD, Liu S, Palti Y, Kenney B, Salem M. Identification of SNPs associated with muscle yield and quality traits using allelic-imbalance analyses of pooled RNA-Seq samples in rainbow trout. BMC Genomics 2017; 18:582. [PMID: 28784089 PMCID: PMC5547479 DOI: 10.1186/s12864-017-3992-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 08/01/2017] [Indexed: 12/22/2022] Open
Abstract
Background Coding/functional SNPs change the biological function of a gene and, therefore, could serve as “large-effect” genetic markers. In this study, we used two bioinformatics pipelines, GATK and SAMtools, for discovering coding/functional SNPs with allelic-imbalances associated with total body weight, muscle yield, muscle fat content, shear force, and whiteness. Phenotypic data were collected for approximately 500 fish, representing 98 families (5 fish/family), from a growth-selected line, and the muscle transcriptome was sequenced from 22 families with divergent phenotypes (4 low- versus 4 high-ranked families per trait). Results GATK detected 59,112 putative SNPs; of these SNPs, 4798 showed allelic imbalances (>2.0 as an amplification and <0.5 as loss of heterozygosity). SAMtools detected 87,066 putative SNPs; and of them, 4962 had allelic imbalances between the low- and high-ranked families. Only 1829 SNPs with allelic imbalances were common between the two datasets, indicating significant differences in algorithms. The two datasets contained 7930 non-redundant SNPs of which 4439 mapped to 1498 protein-coding genes (with 6.4% non-synonymous SNPs) and 684 mapped to 295 lncRNAs. Validation of a subset of 92 SNPs revealed 1) 86.7–93.8% success rate in calling polymorphic SNPs and 2) 95.4% consistent matching between DNA and cDNA genotypes indicating a high rate of identifying SNPs with allelic imbalances. In addition, 4.64% SNPs revealed random monoallelic expression. Genome distribution of the SNPs with allelic imbalances exhibited high density for all five traits in several chromosomes, especially chromosome 9, 20 and 28. Most of the SNP-harboring genes were assigned to important growth-related metabolic pathways. Conclusion These results demonstrate utility of RNA-Seq in assessing phenotype-associated allelic imbalances in pooled RNA-Seq samples. The SNPs identified in this study were included in a new SNP-Chip design (available from Affymetrix) for genomic and genetic analyses in rainbow trout. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3992-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Rafet Al-Tobasei
- Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Ali Ali
- Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Timothy D Leeds
- National Center for Cool and Cold Water Aquaculture, ARS-USDA, Kearneysville, WV, 25430, USA
| | - Sixin Liu
- National Center for Cool and Cold Water Aquaculture, ARS-USDA, Kearneysville, WV, 25430, USA
| | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, ARS-USDA, Kearneysville, WV, 25430, USA
| | - Brett Kenney
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Mohamed Salem
- Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, 37132, USA. .,Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, 37132, USA.
| |
Collapse
|
25
|
Xiang QD, Yu Q, Wang H, Zhao MM, Liu SY, Nie SP, Xie MY. Immunomodulatory Activity of Ganoderma atrum Polysaccharide on Purified T Lymphocytes through Ca 2+/CaN and Mitogen-Activated Protein Kinase Pathway Based on RNA Sequencing. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:5306-5315. [PMID: 28608696 DOI: 10.1021/acs.jafc.7b01763] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Our previous study has demonstrated that Ganoderma atrum polysaccharide (PSG-1) has immunomodulatory activity on spleen lymphocytes. However, how PSG-1 exerts its effect on purified lymphocytes is still obscure. Thus, this study aimed to investigate the immunomodulatory activity of PSG-1 on purified T lymphocytes and further elucidate the underlying mechanism based on RNA sequencing (RNA-seq). Our results showed that PSG-1 promoted T lymphocytes proliferation and increased the production of IL-2, IFN-γ, and IL-12. Meanwhile, RNA-seq analysis found 394 differentially expressed genes. KEGG pathway analysis identified 20 significant canonical pathways and seven biological functions. Furthermore, PSG-1 elevated intracellular Ca2+ concentration and calcineurin (CaN) activity and raised the p-ERK, p-JNK, and p-p38 expression levels. T lymphocytes proliferation and the production of IL-2, IFN-γ, and IL-12 were decreased by the inhibitors of calcium channel and mitogen-activated protein kinases (MAPKs). These results indicated that PSG-1 possesses immunomodulatory activity on purified T lymphocytes, in which Ca2+/CaN and MAPK pathways play essential roles.
Collapse
Affiliation(s)
- Quan-Dan Xiang
- State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang 330047, China
| | - Qiang Yu
- State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang 330047, China
| | - Hui Wang
- Institute of Life Science & College of Life Sciences, Nanchang University , Nanchang 330031, China
| | - Ming-Ming Zhao
- State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang 330047, China
| | - Shi-Yu Liu
- State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang 330047, China
| | - Shao-Ping Nie
- State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang 330047, China
| | - Ming-Yong Xie
- State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang 330047, China
| |
Collapse
|
26
|
Li J, Liu H, Xia W, Mu J, Feng Y, Liu R, Yan P, Wang A, Lin Z, Guo Y, Zhu J, Chen X. De Novo Transcriptome Sequencing and the Hypothetical Cold Response Mode of Saussurea involucrata in Extreme Cold Environments. Int J Mol Sci 2017; 18:E1155. [PMID: 28590406 PMCID: PMC5485979 DOI: 10.3390/ijms18061155] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/18/2017] [Accepted: 05/23/2017] [Indexed: 11/16/2022] Open
Abstract
Saussurea involucrata grows in high mountain areas covered by snow throughout the year. The temperature of this habitat can change drastically in one day. To gain a better understanding of the cold response signaling pathways and molecular metabolic reactions involved in cold stress tolerance, genome-wide transcriptional analyses were performed using RNA-Seq technologies. A total of 199,758 transcripts were assembled, producing 138,540 unigenes with 46.8 Gb clean data. Overall, 184,416 (92.32%) transcripts were successfully annotated. The 365 transcription factors identified (292 unigenes) belonged to 49 transcription factor families associated with cold stress responses. A total of 343 transcripts on the signal transduction (132 upregulated and 212 downregulated in at least any one of the conditions) were strongly affected by cold temperature, such as the CBL-interacting serine/threonine-protein kinase (CIPKs), receptor-like protein kinases, and protein kinases. The circadian rhythm pathway was activated by cold adaptation, which was necessary to endure the severe temperature changes within a day. There were 346 differentially expressed genes (DEGs) related to transport, of which 138 were upregulated and 22 were downregulated in at least any one of the conditions. Under cold stress conditions, transcriptional regulation, molecular transport, and signal transduction were involved in the adaptation to low temperature in S. involucrata. These findings contribute to our understanding of the adaptation of plants to harsh environments and the survival traits of S. involucrata. In addition, the present study provides insight into the molecular mechanisms of chilling and freezing tolerance.
Collapse
Affiliation(s)
- Jin Li
- College of Life Sciences, Shihezi University, Shihezi 832000, China.
| | - Hailiang Liu
- Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai 200065, China.
| | - Wenwen Xia
- College of Life Sciences, Shihezi University, Shihezi 832000, China.
| | - Jianqiang Mu
- College of Life Sciences, Shihezi University, Shihezi 832000, China.
| | - Yujie Feng
- College of Life Sciences, Shihezi University, Shihezi 832000, China.
| | - Ruina Liu
- College of Life Sciences, Shihezi University, Shihezi 832000, China.
| | - Panyao Yan
- ShengTing Bioinformatics Institute, Christiansburg, VA 24073, USA.
| | - Aiying Wang
- College of Life Sciences, Shihezi University, Shihezi 832000, China.
| | - Zhongping Lin
- College of Life Sciences, Shihezi University, Shihezi 832000, China.
- College of Life Sciences, Perking University, Beijing 100871, China.
| | - Yong Guo
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jianbo Zhu
- College of Life Sciences, Shihezi University, Shihezi 832000, China.
| | - Xianfeng Chen
- College of Life Sciences, Shihezi University, Shihezi 832000, China.
- ShengTing Bioinformatics Institute, Christiansburg, VA 24073, USA.
| |
Collapse
|
27
|
Transcriptomic and physiological analyses of Medicago sativa L. roots in response to lead stress. PLoS One 2017; 12:e0175307. [PMID: 28388670 PMCID: PMC5384761 DOI: 10.1371/journal.pone.0175307] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 03/23/2017] [Indexed: 12/16/2022] Open
Abstract
Lead (Pb) is one of the nonessential and toxic metals that threaten the environment and human health. Medicago sativa L. is a legume with high salt tolerance and high biomass production. It is not only a globally important forage crop but is also an ideal plant for phytoremediation. However, the biological and molecular mechanisms that respond to heavy metals are still not well defined in M. sativa. In this study, de novo and strand-specific RNA-sequencing was performed to identify genes involved in the Pb stress response in M. sativa roots. A total of 415,350 unigenes were obtained from the assembled cDNA libraries, among which 5,416 were identified as significantly differentially expressed genes (DEGs) (false discovery rate < 0.005) between cDNA libraries from control and Pb-treated plants. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the DEGs showed they mainly clustered with terms associated with binding, transport, membranes, and the pathways related to signal and energy metabolism. Moreover, a number of candidate genes included antioxidant enzymes, metal transporters, and transcription factors involved in heavy metal response were upregulated under Pb stress. Quantitative real-time PCR(qRT-PCR) validation of the expression patterns of 10 randomly selected candidate DEGs were consistent with the transcriptome analysis results. Thus, this study offers new information towards the investigation of biological changes and molecular mechanisms related to Pb stress response in plants.
Collapse
|
28
|
In Silico identification and annotation of non-coding RNAs by RNA-seq and De Novo assembly of the transcriptome of Tomato Fruits. PLoS One 2017; 12:e0171504. [PMID: 28187155 PMCID: PMC5302821 DOI: 10.1371/journal.pone.0171504] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 01/21/2017] [Indexed: 12/12/2022] Open
Abstract
The complexity of the tomato (Solanum lycopersicum) transcriptome has not yet been fully elucidated. To gain insights into the diversity and features of coding and non-coding RNA molecules of tomato fruits, we generated strand-specific libraries from berries of two tomato cultivars grown in two open-field conditions with different soil type. Following high-throughput Illumina RNA-sequencing (RNA-seq), more than 90% of the reads (over one billion, derived from twelve dataset) were aligned to the tomato reference genome. We report a comprehensive analysis of the transcriptome, improved with 39,095 transcripts, which reveals previously unannotated novel transcripts, natural antisense transcripts, long non-coding RNAs and alternative splicing variants. In addition, we investigated the sequence variants between the cultivars under investigation to highlight their genetic difference. Our strand-specific analysis allowed us to expand the current tomato transcriptome annotation and it is the first to reveal the complexity of the poly-adenylated RNA world in tomato. Moreover, our work demonstrates the usefulness of strand specific RNA-seq approach for the transcriptome-based genome annotation and provides a resource valuable for further functional studies.
Collapse
|
29
|
Scheben A, Batley J, Edwards D. Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:149-161. [PMID: 27696619 PMCID: PMC5258866 DOI: 10.1111/pbi.12645] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/24/2016] [Accepted: 09/28/2016] [Indexed: 05/18/2023]
Abstract
In the last decade, the revolution in sequencing technologies has deeply impacted crop genotyping practice. New methods allowing rapid, high-throughput genotyping of entire crop populations have proliferated and opened the door to wider use of molecular tools in plant breeding. These new genotyping-by-sequencing (GBS) methods include over a dozen reduced-representation sequencing (RRS) approaches and at least four whole-genome resequencing (WGR) approaches. The diversity of methods available, each often producing different types of data at different cost, can make selection of the best-suited method seem a daunting task. We review the most common genotyping methods used today and compare their suitability for linkage mapping, genomewide association studies (GWAS), marker-assisted and genomic selection and genome assembly and improvement in crops with various genome sizes and complexity. Furthermore, we give an outline of bioinformatics tools for analysis of genotyping data. WGR is well suited to genotyping biparental cross populations with complex, small- to moderate-sized genomes and provides the lowest cost per marker data point. RRS approaches differ in their suitability for various tasks, but demonstrate similar costs per marker data point. These approaches are generally better suited for de novo applications and more cost-effective when genotyping populations with large genomes or high heterozygosity. We expect that although RRS approaches will remain the most cost-effective for some time, WGR will become more widespread for crop genotyping as sequencing costs continue to decrease.
Collapse
Affiliation(s)
- Armin Scheben
- School of Plant Biology and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
| | - Jacqueline Batley
- School of Plant Biology and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
| | - David Edwards
- School of Plant Biology and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
| |
Collapse
|
30
|
Yu L, Zheng P, Zhang T, Rodringuez J, Main D. Genotyping-by-sequencing-based genome-wide association studies on Verticillium wilt resistance in autotetraploid alfalfa (Medicago sativa L.). MOLECULAR PLANT PATHOLOGY 2017; 18:187-194. [PMID: 26933934 PMCID: PMC6638244 DOI: 10.1111/mpp.12389] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Verticillium wilt (VW) is a fungal disease that causes severe yield losses in alfalfa. The most effective method to control the disease is through the development and use of resistant varieties. The identification of marker loci linked to VW resistance can facilitate breeding for disease-resistant alfalfa. In the present investigation, we applied an integrated framework of genome-wide association with genotyping-by-sequencing (GBS) to identify VW resistance loci in a panel of elite alfalfa breeding lines. Phenotyping was performed by manual inoculation of the pathogen to healthy seedlings, and scoring for disease resistance was carried out according to the standard test of the North America Alfalfa Improvement Conference (NAAIC). Marker-trait association by linkage disequilibrium identified 10 single nucleotide polymorphism (SNP) markers significantly associated with VW resistance. Alignment of the SNP marker sequences to the M. truncatula genome revealed multiple quantitative trait loci (QTLs). Three, two, one and five markers were located on chromosomes 5, 6, 7 and 8, respectively. Resistance loci found on chromosomes 7 and 8 in the present study co-localized with the QTLs reported previously. A pairwise alignment (blastn) using the flanking sequences of the resistance loci against the M. truncatula genome identified potential candidate genes with putative disease resistance function. With further investigation, these markers may be implemented into breeding programmes using marker-assisted selection, ultimately leading to improved VW resistance in alfalfa.
Collapse
Affiliation(s)
- Long‐Xi Yu
- United States Department of Agriculture‐Agricultural Research ServicePlant Germplasm Introduction and Testing Research24106 N Bunn RoadProsserWA99350 USA
| | - Ping Zheng
- Department of HorticultureWashington State UniversityPullmanWA99164 USA
| | - Tiejun Zhang
- United States Department of Agriculture‐Agricultural Research ServicePlant Germplasm Introduction and Testing Research24106 N Bunn RoadProsserWA99350 USA
- Present address:
Institute of Animal ScienceChinese Academy of Agricultural SciencesBeijing100193 China
| | - Jonas Rodringuez
- Forage Genetics International, Inc.7661 Becker RoadDavisCA95618 USA
| | - Dorrie Main
- Department of HorticultureWashington State UniversityPullmanWA99164 USA
| |
Collapse
|
31
|
Fu YB, Yang MH, Zeng F, Biligetu B. Searching for an Accurate Marker-Based Prediction of an Individual Quantitative Trait in Molecular Plant Breeding. FRONTIERS IN PLANT SCIENCE 2017; 8:1182. [PMID: 28729875 PMCID: PMC5498511 DOI: 10.3389/fpls.2017.01182] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/20/2017] [Indexed: 05/09/2023]
Abstract
Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades. Many marker-based predictions for quantitative traits have been made to enhance parental selection, but the trait prediction accuracy remains generally low, even with the aid of dense, genome-wide SNP markers. To search for more accurate trait-specific prediction with informative SNP markers, we conducted a literature review on the prediction issues in molecular plant breeding and on the applicability of an RNA-Seq technique for developing function-associated specific trait (FAST) SNP markers. To understand whether and how FAST SNP markers could enhance trait prediction, we also performed a theoretical reasoning on the effectiveness of these markers in a trait-specific prediction, and verified the reasoning through computer simulation. To the end, the search yielded an alternative to regular genomic selection with FAST SNP markers that could be explored to achieve more accurate trait-specific prediction. Continuous search for better alternatives is encouraged to enhance marker-based predictions for an individual quantitative trait in molecular plant breeding.
Collapse
Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, SaskatoonSK, Canada
- *Correspondence: Yong-Bi Fu,
| | - Mo-Hua Yang
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, SaskatoonSK, Canada
- College of Forestry, Central South University of Forestry and TechnologyChangsha, China
| | - Fangqin Zeng
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, SaskatoonSK, Canada
| | - Bill Biligetu
- Department of Plant Sciences, University of Saskatchewan, SaskatoonSK, Canada
| |
Collapse
|
32
|
Gruber MY, Xia J, Yu M, Steppuhn H, Wall K, Messer D, Sharpe AG, Acharya SN, Wishart DS, Johnson D, Miller DR, Taheri A. Transcript analysis in two alfalfa salt tolerance selected breeding populations relative to a non-tolerant population. Genome 2016; 60:104-127. [PMID: 28045337 DOI: 10.1139/gen-2016-0111] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
With the growing limitations on arable land, alfalfa (a widely cultivated, low-input forage) is now being selected to extend cultivation into saline lands for low-cost biofeedstock purposes. Here, minerals and transcriptome profiles were compared between two new salinity-tolerant North American alfalfa breeding populations and a more salinity-sensitive western Canadian alfalfa population grown under hydroponic saline conditions. All three populations accumulated two-fold higher sodium in roots than shoots as a function of increased electrical conductivity. At least 50% of differentially expressed genes (p < 0.05) were down-regulated in the salt-sensitive population growing under high salinity, while expression remained unchanged in the saline-tolerant populations. In particular, most reduction in transcript levels in the salt-sensitive population was observed in genes specifying cell wall structural components, lipids, secondary metabolism, auxin and ethylene hormones, development, transport, signalling, heat shock, proteolysis, pathogenesis-response, abiotic stress, RNA processing, and protein metabolism. Transcript diversity for transcription factors, protein modification, and protein degradation genes was also more strongly affected in salt-tolerant CW064027 than in salt-tolerant Bridgeview and salt-sensitive Rangelander, while both saline-tolerant populations showed more substantial up-regulation in redox-related genes and B-ZIP transcripts. The report highlights the first use of bulked genotypes as replicated samples to compare the transcriptomes of obligate out-cross breeding populations in alfalfa.
Collapse
Affiliation(s)
- M Y Gruber
- a Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7J 0X2, Canada.,b Department of Computing Science, University of Alberta, 2-21 Athabasca Hall, Edmonton, AB T6G 2R3, Canada
| | - J Xia
- b Department of Computing Science, University of Alberta, 2-21 Athabasca Hall, Edmonton, AB T6G 2R3, Canada
| | - M Yu
- a Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7J 0X2, Canada
| | - H Steppuhn
- c Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, P.O. Box 1030, Swift Current, SK S9H 3X2, Canada
| | - K Wall
- c Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, P.O. Box 1030, Swift Current, SK S9H 3X2, Canada
| | - D Messer
- c Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, P.O. Box 1030, Swift Current, SK S9H 3X2, Canada
| | - A G Sharpe
- d National Research Council, 110 Gymnasium Pl., Saskatoon, SK S7N 0W9, Canada
| | - S N Acharya
- e AAFC Lethbridge Research Centre, Agriculture and Agri-Food Canada, 5403 - 1st Avenue S., Lethbridge, AB T1J 4B1, Canada
| | - D S Wishart
- b Department of Computing Science, University of Alberta, 2-21 Athabasca Hall, Edmonton, AB T6G 2R3, Canada.,f Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2R3, Canada
| | - D Johnson
- g Alforex Seeds, an affiliate of Dow AgroSciences, N4505 CTH M, West Salem, WI 54669, USA
| | - D R Miller
- g Alforex Seeds, an affiliate of Dow AgroSciences, N4505 CTH M, West Salem, WI 54669, USA
| | - A Taheri
- a Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7J 0X2, Canada
| |
Collapse
|
33
|
Mora-Ortiz M, Swain MT, Vickers MJ, Hegarty MJ, Kelly R, Smith LMJ, Skøt L. De-novo transcriptome assembly for gene identification, analysis, annotation, and molecular marker discovery in Onobrychis viciifolia. BMC Genomics 2016; 17:756. [PMID: 27671367 PMCID: PMC5037894 DOI: 10.1186/s12864-016-3083-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 09/13/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Sainfoin (Onobrychis viciifolia) is a highly nutritious tannin-containing forage legume. In the diet of ruminants sainfoin can have anti-parasitic effects and reduce methane emissions under in vitro conditions. Many of these benefits have been attributed to condensed tannins or proanthocyanidins in sainfoin. A combination of increased use of industrially produced nitrogen fertilizer, issues with establishment and productivity in the first year and more reliable alternatives, such as red clover led to a decline in the use of sainfoin since the middle of the last century. In recent years there has been a resurgence of interest in sainfoin due to its potential beneficial nutraceutical and environmental attributes. However, genomic resources are scarce, thus hampering progress in genetic analysis and improvement. To address this we have used next generation RNA sequencing technology to obtain the first transcriptome of sainfoin. We used the library to identify gene-based simple sequence repeats (SSRs) and potential single nucleotide polymorphisms (SNPs). RESULTS One genotype from each of five sainfoin accessions was sequenced. Paired-end (PE) sequences were generated from cDNA libraries of RNA extracted from 7 day old seedlings. A combined assembly of 92,772 transcripts was produced de novo using the Trinity programme. About 18,000 transcripts were annotated with at least one GO (gene ontology) term. A total of 63 transcripts were annotated as involved in the tannin biosynthesis pathway. We identified 3786 potential SSRs. SNPs were identified by mapping the reads of the individual assemblies against the combined assembly. After stringent filtering a total of 77,000 putative SNPs were identified. A phylogenetic analysis of single copy number genes showed that sainfoin was most closely related to red clover and Medicago truncatula, while Lotus japonicus, bean and soybean are more distant relatives. CONCLUSIONS This work describes the first transcriptome assembly in sainfoin. The 92 K transcripts provide a rich source of SNP and SSR polymorphisms for future use in genetic studies of this crop. Annotation of genes involved in the condensed tannin biosynthesis pathway has provided the basis for further studies of the genetic control of this important trait in sainfoin.
Collapse
Affiliation(s)
- Marina Mora-Ortiz
- National Institute of Agricultural Botany, Huntingdon Road, Cambridge, CB3 OLE, UK.,Present Address: School of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights Campus, Reading, RG6 6AP, UK
| | - Martin T Swain
- Aberystwyth University, IBERS, Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - Martin J Vickers
- Aberystwyth University, IBERS, Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK.,Present Address: The Department of Cell and Developmental Biology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Matthew J Hegarty
- Aberystwyth University, IBERS, Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - Rhys Kelly
- Aberystwyth University, IBERS, Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - Lydia M J Smith
- National Institute of Agricultural Botany, Huntingdon Road, Cambridge, CB3 OLE, UK
| | - Leif Skøt
- Aberystwyth University, IBERS, Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK.
| |
Collapse
|
34
|
Han J, Thamilarasan SK, Natarajan S, Park JI, Chung MY, Nou IS. De Novo Assembly and Transcriptome Analysis of Bulb Onion (Allium cepa L.) during Cold Acclimation Using Contrasting Genotypes. PLoS One 2016; 11:e0161987. [PMID: 27627679 PMCID: PMC5023330 DOI: 10.1371/journal.pone.0161987] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/16/2016] [Indexed: 12/03/2022] Open
Abstract
Bulb onion (Allium cepa) is the second most widely cultivated and consumed vegetable crop in the world. During winter, cold injury can limit the production of bulb onion. Genomic resources available for bulb onion are still very limited. To date, no studies on heritably durable cold and freezing tolerance have been carried out in bulb onion genotypes. We applied high-throughput sequencing technology to cold (2°C), freezing (-5 and -15°C), and control (25°C)-treated samples of cold tolerant (CT) and cold susceptible (CS) genotypes of A. cepa lines. A total of 452 million paired-end reads were de novo assembled into 54,047 genes with an average length of 1,331 bp. Based on similarity searches, these genes were aligned with entries in the public non-redundant (nr) database, as well as KEGG and COG database. Differentially expressed genes (DEGs) were identified using log10 values with the FPKM method. Among 5,167DEGs, 491 genes were differentially expressed at freezing temperature compared to the control temperature in both CT and CS libraries. The DEG results were validated with qRT-PCR. We performed GO and KEGG pathway enrichment analyses of all DEGs and iPath interactive analysis found 31 pathways including those related to metabolism of carbohydrate, nucleotide, energy, cofactors and vitamins, other amino acids and xenobiotics biodegradation. Furthermore, a large number of molecular markers were identified from the assembled genes, including simple sequence repeats (SSRs) 4,437 and SNP substitutions of transition and transversion types of CT and CS. Our study is the first to provide a transcriptome sequence resource for Allium spp. with regard to cold and freezing stress. We identified a large set of genes and determined their DEG profiles under cold and freezing conditions using two different genotypes. These data represent a valuable resource for genetic and genomic studies of Allium spp.
Collapse
Affiliation(s)
- Jeongsukhyeon Han
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea
| | | | - Sathishkumar Natarajan
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea
| | - Mi-Young Chung
- Department of Agricultural Education, Sunchon National University, Suncheon, Jeonnam, Republic of Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea
- * E-mail:
| |
Collapse
|
35
|
Song L, Jiang L, Chen Y, Shu Y, Bai Y, Guo C. Deep-sequencing transcriptome analysis of field-grown Medicago sativa L. crown buds acclimated to freezing stress. Funct Integr Genomics 2016; 16:495-511. [PMID: 27272950 DOI: 10.1007/s10142-016-0500-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 05/18/2016] [Accepted: 05/27/2016] [Indexed: 12/01/2022]
Abstract
Medicago sativa L. (alfalfa) 'Zhaodong' is an important forage legume that can safely survive in northern China where winter temperatures reach as low as -30 °C. Survival of alfalfa following freezing stress depends on the amount and revival ability of crown buds. In order to investigate the molecular mechanisms of frost tolerance in alfalfa, we used transcriptome sequencing technology and bioinformatics strategies to analyze crown buds of field-grown alfalfa during winter. We statistically identified a total of 5605 differentially expressed genes (DEGs) involved in freezing stress including 1900 upregulated and 3705 downregulated DEGs. We validated 36 candidate DEGs using qPCR to confirm the accuracy of the RNA-seq data. Unlike other recent studies, this study employed alfalfa plants grown in the natural environment. Our results indicate that not only the CBF orthologs but also membrane proteins, hormone signal transduction pathways, and ubiquitin-mediated proteolysis pathways indicate the presence of a special freezing adaptation mechanism in alfalfa. The antioxidant defense system may rapidly confer freezing tolerance to alfalfa. Importantly, biosynthesis of secondary metabolites and phenylalanine metabolism, which is of potential importance in coordinating freezing tolerance with growth and development, were downregulated in subzero temperatures. The adaptive mechanism for frost tolerance is a complex multigenic process that is not well understood. This systematic analysis provided an in-depth view of stress tolerance mechanisms in alfalfa.
Collapse
Affiliation(s)
- Lili Song
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, Heilongjiang, China
| | - Lin Jiang
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, Heilongjiang, China
| | - Yue Chen
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, Heilongjiang, China
| | - Yongjun Shu
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, Heilongjiang, China
| | - Yan Bai
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, Heilongjiang, China
| | - Changhong Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, Heilongjiang, China.
| |
Collapse
|
36
|
Li M, Liang Z, Zeng Y, Jing Y, Wu K, Liang J, He S, Wang G, Mo Z, Tan F, Li S, Wang L. De novo analysis of transcriptome reveals genes associated with leaf abscission in sugarcane (Saccharum officinarum L.). BMC Genomics 2016; 17:195. [PMID: 26946183 PMCID: PMC4779555 DOI: 10.1186/s12864-016-2552-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/28/2016] [Indexed: 01/01/2023] Open
Abstract
Background Sugarcane (Saccharum officinarum L.) is an important sugar crop which belongs to the grass family and can be used for fuel ethanol production. The growing demands for sugar and biofuel is asking for breeding a sugarcane variety that can shed their leaves during the maturity time due to the increasing cost on sugarcane harvest. Results To determine leaf abscission related genes in sugarcane, we generated 524,328,950 paired reads with RNA-Seq and profiled the transcriptome of new born leaves of leaf abscission sugarcane varieties (Q1 and T) and leaf packaging sugarcane varieties (Q2 and B). Initially, 275,018 transcripts were assembled with N50 of 1,177 bp. Next, the transcriptome was annotated by mapping them to NR, UniProtKB/Swiss-Prot, Gene Ontology and KEGG pathway databases. Further, we used TransDecoder and Trinotate to obtain the likely proteins and annotate them in terms of known proteins, protein domains, signal peptides, transmembrane regions and rRNA transcripts. Different expression analysis showed 1,202 transcripts were up regulated in leaf abscission sugarcane varieties, relatively to the leaf packaging sugarcane varieties. Functional analysis told us 62, 38 and 10 upregulated transcripts were involved in plant-pathogen interaction, response to stress and abscisic acid associated pathways, respectively. The upregulation of transcripts encoding 4 disease resistance proteins (RPM1, RPP13, RGA2, and RGA4), 6 ABC transporter G family members and 16 transcription factors including WRK33 and heat stress transcription factors indicate they may be used as candidate genes for sugarcane breeding. The expression levels of transcripts were validated by qRT-PCR. In addition, we characterized 3,722 SNPs between leaf abscission and leaf packaging sugarcane plants. Conclusion Our results showed leaf abscission associated genes in sugarcane during the maturity period. The output of this study provides a valuable resource for future genetic and genomic studies in sugarcane. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2552-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ming Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Zhaoxu Liang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Yuan Zeng
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Yan Jing
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Kaichao Wu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Jun Liang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Shanshan He
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Guanyu Wang
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Zhanghong Mo
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Fang Tan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Song Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| | - Lunwang Wang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China.
| |
Collapse
|
37
|
Liu W, Zhang Z, Chen S, Ma L, Wang H, Dong R, Wang Y, Liu Z. Global transcriptome profiling analysis reveals insight into saliva-responsive genes in alfalfa. PLANT CELL REPORTS 2016; 35:561-571. [PMID: 26645698 DOI: 10.1007/s00299-015-1903-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 10/25/2015] [Accepted: 11/17/2015] [Indexed: 06/05/2023]
Abstract
We studied the genome-wide multiple time-course transcriptome dynamics after saliva deposition in alfalfa and demonstrate that saliva deposition functions as a stress that negatively affects the regrowth of alfalfa. Saliva deposition is one of the key factors influencing plant-herbivore interactions during grazing. Although many studies have focused on the effects of saliva deposition on plant regrowth, no consistent conclusions have been reached. Alfalfa is the most extensively cultivated forage legume, yet most alfalfa cultivars, thus far, are not grazing-tolerant. To better understand the underlying mechanism, we undertook a study to evaluate the global changes in the transcriptome of alfalfa after cow saliva deposition treatment. In this study, cDNA libraries from alfalfa seedlings at 0, 4, 8, and 24 h after cow saliva deposition were constructed and sequenced, resulting in the identification of 53,195 annotated unigenes, from which 4,814 unigenes were significantly differentially expressed. A metabolic pathway enrichment analysis demonstrated that saliva deposition functions as a stress that negatively affects the regrowth of alfalfa by modifying jasmonic acid synthesis, enhancing the susceptibility to pathogens and reducing the expression levels of ribosomal protein genes. In the present study, we demonstrate the potential effects of saliva deposition on alfalfa regrowth at the transcriptome level. These fundamental and important findings could facilitate further investigations into the molecular mechanisms underlying the responses of alfalfa and other related species to herbivore grazing.
Collapse
Affiliation(s)
- Wenxian Liu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhengshe Zhang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Shuangyan Chen
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
| | - Lichao Ma
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Hucheng Wang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Rui Dong
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhipeng Liu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China.
| |
Collapse
|
38
|
Wang J, Zhao Y, Ray I, Song M. Transcriptome responses in alfalfa associated with tolerance to intensive animal grazing. Sci Rep 2016; 6:19438. [PMID: 26763747 PMCID: PMC4725929 DOI: 10.1038/srep19438] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 12/02/2015] [Indexed: 01/15/2023] Open
Abstract
Tolerance of alfalfa (Medicago sativa L.) to animal grazing varies widely within the species. However, the molecular mechanisms influencing the grazing tolerant phenotype remain uncharacterized. The objective of this study was to identify genes and pathways that control grazing response in alfalfa. We analyzed whole-plant de novo transcriptomes from grazing tolerant and intolerant populations of M. sativa ssp. falcata subjected to grazing by sheep. Among the Gene Ontology terms which were identified as grazing responsive in the tolerant plants and differentially enriched between the tolerant and intolerant populations (both grazed), most were associated with the ribosome and translation-related activities, cell wall processes, and response to oxygen levels. Twenty-one grazing responsive pathways were identified that also exhibited differential expression between the tolerant and intolerant populations. These pathways were associated with secondary metabolite production, primary carbohydrate metabolic pathways, shikimate derivative dependent pathways, ribosomal subunit composition, hormone signaling, wound response, cell wall formation, and anti-oxidant defense. Sequence polymorphisms were detected among several differentially expressed homologous transcripts between the tolerant and intolerant populations. These differentially responsive genes and pathways constitute potential response mechanisms for grazing tolerance in alfalfa. They also provide potential targets for molecular breeding efforts to develop grazing-tolerant cultivars of alfalfa.
Collapse
Affiliation(s)
- Junjie Wang
- College of Ecology and Environmental Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yan Zhao
- College of Ecology and Environmental Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Ian Ray
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, USA
| | - Mingzhou Song
- Department of Computer Science, New Mexico State University, Las Cruces, NM, USA
| |
Collapse
|
39
|
Zhang L, Long Y, Fu C, Xiang J, Gan J, Wu G, Jia H, Yu L, Li M. Different Gene Expression Patterns between Leaves and Flowers in Lonicera japonica Revealed by Transcriptome Analysis. FRONTIERS IN PLANT SCIENCE 2016; 7:637. [PMID: 27242839 PMCID: PMC4861853 DOI: 10.3389/fpls.2016.00637] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/25/2016] [Indexed: 05/20/2023]
Abstract
The perennial and evergreen twining vine, Lonicera japonica is an important herbal medicine with great economic value. However, gene expression information for flowers and leaves of L. japonica remains elusive, which greatly impedes functional genomics research on this species. In this study, transcriptome profiles from leaves and flowers of L. japonica were examined using next-generation sequencing technology. A total of 239.41 million clean reads were used for de novo assembly with Trinity software, which generated 150,523 unigenes with N50 containing 947 bp. All the unigenes were annotated using Nr, SwissProt, COGs (Clusters of Orthologous Groups), GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases. A total of 35,327 differentially expressed genes (DEGs, P ≤ 0.05) between leaves and flowers were detected. Among them, a total of 6602 DEGs were assigned with important biological processes including "Metabolic process," "Response to stimulus," "Cellular process," and etc. KEGG analysis showed that three possible enzymes involved in the biosynthesis of chlorogenic acid were up-regulated in flowers. Furthermore, the TF-based regulation network in L. japonica identified three differentially expressed transcription factors between leaves and flowers, suggesting distinct regulatory roles in L. japonica. Taken together, this study has provided a global picture of differential gene expression patterns between leaves and flowers in L japonica, providing a useful genomic resource that can also be used for functional genomics research on L. japonica in the future.
Collapse
Affiliation(s)
- Libin Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Yan Long
- Institute of Biotechnology, Chinese Academy of Agricultural SciencesBeijing, China
| | - Chunhua Fu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Jun Xiang
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Jianping Gan
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Gang Wu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Haibo Jia
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Longjiang Yu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
- *Correspondence: Maoteng Li
| |
Collapse
|
40
|
Yang J, Chen X, Zhu C, Peng X, He X, Fu J, Ouyang L, Bian J, Hu L, Sun X, Xu J, He H. Using RNA-seq to Profile Gene Expression of Spikelet Development in Response to Temperature and Nitrogen during Meiosis in Rice (Oryza sativa L.). PLoS One 2015; 10:e0145532. [PMID: 26714321 PMCID: PMC4694716 DOI: 10.1371/journal.pone.0145532] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 12/04/2015] [Indexed: 11/18/2022] Open
Abstract
Rice reproductive development is sensitive to high temperature and soil nitrogen supply, both of which are predicted to be increased threats to rice crop yield. Rice spikelet development is a critical process that determines yield, yet little is known about the transcriptional regulation of rice spikelet development in response to the combination of heat stress and low nitrogen availability. Here, we profiled gene expression of rice spikelet development during meiosis under heat stress and different nitrogen levels using RNA-seq. We subjected plants to four treatments: 1) NN: normal nitrogen level (165 kg ha-1) with normal temperature (30°C); 2) HH: high nitrogen level (264 kg ha-1) with high temperature (37°C); 3) NH: normal nitrogen level and high temperature; and 4) HN: high nitrogen level and normal temperature. The de novo transcriptome assembly resulted in 52,250,482 clean reads aligned with 76,103 unigenes, which were then used to compare differentially expressed genes (DEGs) in the different treatments. Comparing gene expression in samples with the same nitrogen levels but different temperatures, we identified 70 temperature-responsive DEGs in normal nitrogen levels (NN vs NH) and 135 DEGs in high nitrogen levels (HN vs HH), with 27 overlapping DEGs. We identified 17 and seven nitrogen-responsive DEGs by comparing changes in nitrogen levels in lower temperature (NN vs HN) and higher temperature (NH vs HH), with one common DEG. The temperature-responsive genes were principally associated with cytochrome, heat shock protein, peroxidase, and ubiquitin, while the nitrogen-responsive genes were mainly involved in glutamine synthetase, amino acid transporter, pollen development, and plant hormone. Rice spikelet fertility was significantly reduced under high temperature, but less reduced under high-nitrogen treatment. In the high temperature treatments, we observed downregulation of genes involved in spikelet development, such as pollen tube growth, pollen maturation, especially sporopollenin biosynthetic process, and pollen exine formation. Moreover, we observed higher expression levels of the co-expressed DEGs in HN vs HH compared to NN vs NH. These included the six downregulated genes (one pollen maturation and five pollen exine formation genes), as well as the four upregulated DEGs in response to heat. This suggests that high-nitrogen treatment may enhance the gene expression levels to mitigate aspects of heat-stress. The spikelet genes identified in this study may play important roles in response to the combined effects of high temperature and high nitrogen, and may serve as candidates for crop improvement.
Collapse
Affiliation(s)
- Jun Yang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaorong Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha, 410128, China
| | - Changlan Zhu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha, 410128, China
| | - Xiaosong Peng
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha, 410128, China
| | - Xiaopeng He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha, 410128, China
| | - Junru Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha, 410128, China
| | - Linjuan Ouyang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha, 410128, China
| | - Jianmin Bian
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha, 410128, China
| | - Lifang Hu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha, 410128, China
| | - Xiaotang Sun
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha, 410128, China
| | - Jie Xu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha, 410128, China
- * E-mail:
| |
Collapse
|
41
|
Lin R, Du X, Peng S, Yang L, Ma Y, Gong Y, Li S. Discovering All Transcriptome Single-Nucleotide Polymorphisms and Scanning for Selection Signatures in Ducks (Anas platyrhynchos). Evol Bioinform Online 2015; 11:67-76. [PMID: 26819540 PMCID: PMC4721680 DOI: 10.4137/ebo.s21545] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 11/02/2015] [Accepted: 11/08/2015] [Indexed: 12/21/2022] Open
Abstract
The duck is one of the most economically important waterfowl as a source of meat, eggs, and feathers. Characterizing the genetic variation in duck species is an important step toward linking genes or genomic regions with phenotypes. Human-driven selection during duck domestication and subsequent breed formation has likely left detectable signatures in duck genome. In this study, we employed a panel of >1.4 million single-nucleotide polymorphisms (SNPs) identified from the RNA sequencing (RNA-seq) data of 15 duck individuals. The density of the resulting SNPs is significantly positively correlated with the density of genes across the duck genome, which demonstrates that the usage of the RNA-seq data allowed us to enrich variant functional categories, such as coding exons, untranslated regions (UTRs), introns, and downstream/upstream. We performed a complete scan of selection signatures in the ducks using the composite likelihood ratio (CLR) and found 76 candidate regions of selection, many of which harbor genes related to phenotypes relevant to the function of the digestive system and fat metabolism, including TCF7L2, EIF2AK3, ELOVL2, and fatty acid-binding protein family. This study illustrates the potential of population genetic approaches for identifying genomic regions affecting domestication-related phenotypes and further helps to increase the known genetic information about this economically important animal.
Collapse
Affiliation(s)
- Ruiyi Lin
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xiaoyong Du
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China.; College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Sixue Peng
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Liubin Yang
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yunlong Ma
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yanzhang Gong
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shijun Li
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| |
Collapse
|
42
|
Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement. Sci Rep 2015; 5:17394. [PMID: 26617401 PMCID: PMC4663792 DOI: 10.1038/srep17394] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/29/2015] [Indexed: 01/19/2023] Open
Abstract
Red clover (Trifolium pratense L.) is a globally significant forage legume in pastoral livestock farming systems. It is an attractive component of grassland farming, because of its high yield and protein content, nutritional value and ability to fix atmospheric nitrogen. Enhancing its role further in sustainable agriculture requires genetic improvement of persistency, disease resistance, and tolerance to grazing. To help address these challenges, we have assembled a chromosome-scale reference genome for red clover. We observed large blocks of conserved synteny with Medicago truncatula and estimated that the two species diverged ~23 million years ago. Among the 40,868 annotated genes, we identified gene clusters involved in biochemical pathways of importance for forage quality and livestock nutrition. Genotyping by sequencing of a synthetic population of 86 genotypes show that the number of markers required for genomics-based breeding approaches is tractable, making red clover a suitable candidate for association studies and genomic selection.
Collapse
|
43
|
Summers CF, Gulliford CM, Carlson CH, Lillis JA, Carlson MO, Cadle-Davidson L, Gent DH, Smart CD. Identification of Genetic Variation between Obligate Plant Pathogens Pseudoperonospora cubensis and P. humuli Using RNA Sequencing and Genotyping-By-Sequencing. PLoS One 2015; 10:e0143665. [PMID: 26599440 PMCID: PMC4658093 DOI: 10.1371/journal.pone.0143665] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/06/2015] [Indexed: 12/29/2022] Open
Abstract
RNA sequencing (RNA-seq) and genotyping-by-sequencing (GBS) were used for single nucleotide polymorphism (SNP) identification from two economically important obligate plant pathogens, Pseudoperonospora cubensis and P. humuli. Twenty isolates of P. cubensis and 19 isolates of P. humuli were genotyped using RNA-seq and GBS. Principle components analysis (PCA) of each data set showed genetic separation between the two species. Additionally, results supported previous findings that P. cubensis isolates from squash are genetically distinct from cucumber and cantaloupe isolates. A PCA-based procedure was used to identify SNPs correlated with the separation of the two species, with 994 and 4,231 PCA-correlated SNPs found within the RNA-seq and GBS data, respectively. The corresponding unigenes (n = 800) containing these potential species-specific SNPs were then annotated and 135 putative pathogenicity genes, including 3 effectors, were identified. The characterization of genes containing SNPs differentiating these two closely related downy mildew species may contribute to the development of improved detection and diagnosis strategies and improve our understanding of host specificity pathways.
Collapse
Affiliation(s)
- Carly F. Summers
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America
| | - Colwyn M. Gulliford
- Cornell Laboratory for Accelerator-based Sciences and Education, Cornell University, Ithaca, New York, United States of America
| | - Craig H. Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America
| | - Jacquelyn A. Lillis
- United States Department of Agriculture Agricultural Research Service, Grape Genetics Research Unit, Geneva, New York, United States of America
| | - Maryn O. Carlson
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America
| | - Lance Cadle-Davidson
- United States Department of Agriculture Agricultural Research Service, Grape Genetics Research Unit, Geneva, New York, United States of America
| | - David H. Gent
- United States Department of Agriculture Agricultural Research Service, Forage Seed and Cereal Research Unit and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Christine D. Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America
| |
Collapse
|
44
|
Miao Z, Xu W, Li D, Hu X, Liu J, Zhang R, Tong Z, Dong J, Su Z, Zhang L, Sun M, Li W, Du Z, Hu S, Wang T. De novo transcriptome analysis of Medicago falcata reveals novel insights about the mechanisms underlying abiotic stress-responsive pathway. BMC Genomics 2015; 16:818. [PMID: 26481731 PMCID: PMC4615886 DOI: 10.1186/s12864-015-2019-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 10/07/2015] [Indexed: 11/21/2022] Open
Abstract
Background The entire world is facing a deteriorating environment. Understanding the mechanisms underlying plant responses to external abiotic stresses is important for breeding stress-tolerant crops and herbages. Phytohormones play critical regulatory roles in plants in the response to external and internal cues to regulate growth and development. Medicago falcata is one of the stress-tolerant candidate leguminous species and is able to fix atmospheric nitrogen. This ability allows leguminous plants to grow in nitrogen deficient soils. Methods We performed Illumina sequencing of cDNA prepared from abiotic stress treated M. falcata. Sequencedreads were assembled to provide a transcriptome resource. Transcripts were annotated using BLASTsearches against the NCBI non-redundant database and gene ontology definitions were assigned. Acomparison among the three abiotic stress treated samples was carried out. The expression of transcriptswas confirmed with qRT-PCR. Results We present an abiotic stress-responsive M. falcata transcriptome using next-generation sequencing data from samples grown under standard, dehydration, high salinity, and cold conditions. We combined reads from all samples and de novo assembled 98,515 transcripts to build the M. falcata gene index. A comprehensive analysis of the transcriptome revealed abiotic stress-responsive mechanisms underlying the metabolism and core signalling components of major phytohormones. We identified nod factor signalling pathways during early symbiotic nodulation that are modified by abiotic stresses. Additionally, a global comparison of homology between the M. falcata and M. truncatula transcriptomes, along with five other leguminous species, revealed a high level of global sequence conservation within the family. Conclusions M. falcata is shown to be a model candidate for studying abiotic stress-responsive mechanisms in legumes. This global gene expression analysis provides new insights into the biochemical and molecular mechanisms involved in the acclimation to abiotic stresses. Our data provides many gene candidates that might be used for herbage and crop breeding. Additionally, FalcataBase (http://bioinformatics.cau.edu.cn/falcata/) was built for storing these data. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2019-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Zhenyan Miao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China. .,Present address: Department of Agronomy, Purdue University, West Lafayette, IN, USA.
| | - Wei Xu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China.
| | - Daofeng Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China. .,Present address: Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Xiaona Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Jiaxing Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Rongxue Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Zongyong Tong
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Jiangli Dong
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Liwei Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Min Sun
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China.
| | - Wenjie Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China.
| | - Zhenglin Du
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China.
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China.
| | - Tao Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
45
|
Galeano E, Vasconcelos TS, Vidal M, Mejia-Guerra MK, Carrer H. Large-scale transcriptional profiling of lignified tissues in Tectona grandis. BMC PLANT BIOLOGY 2015; 15:221. [PMID: 26369560 PMCID: PMC4570228 DOI: 10.1186/s12870-015-0599-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 09/02/2015] [Indexed: 05/06/2023]
Abstract
BACKGROUND Currently, Tectona grandis is one of the most valuable trees in the world and no transcript dataset related to secondary xylem is available. Considering how important the secondary xylem and sapwood transition from young to mature trees is, little is known about the expression differences between those successional processes and which transcription factors could regulate lignin biosynthesis in this tropical tree. Although MYB transcription factors are one of the largest superfamilies in plants related to secondary metabolism, it has not yet been characterized in teak. These results will open new perspectives for studies of diversity, ecology, breeding and genomic programs aiming to understand deeply the biology of this species. RESULTS We present a widely expressed gene catalog for T. grandis using Illumina technology and the de novo assembly. A total of 462,260 transcripts were obtained, with 1,502 and 931 genes differentially expressed for stem and branch secondary xylem, respectively, during age transition. Analysis of stem and branch secondary xylem indicates substantial similarity in gene ontologies including carbohydrate enzymes, response to stress, protein binding, and allowed us to find transcription factors and heat-shock proteins differentially expressed. TgMYB1 displays a MYB domain and a predicted coiled-coil (CC) domain, while TgMYB2, TgMYB3 and TgMYB4 showed R2R3-MYB domain and grouped with MYBs from several gymnosperms and flowering plants. TgMYB1, TgMYB4 and TgCES presented higher expression in mature secondary xylem, in contrast with TgMYB2, TgHsp1, TgHsp2, TgHsp3, and TgBi whose expression is higher in young lignified tissues. TgMYB3 is expressed at lower level in secondary xylem. CONCLUSIONS Expression patterns of MYB transcription factors and heat-shock proteins in lignified tissues are dissimilar when tree development was evaluated, obtaining more expression of TgMYB1 and TgMYB4 in lignified tissues of 60-year-old trees, and more expression in TgHsp1, TgHsp2, TgHsp3 and TgBi in stem secondary xylem of 12-year-old trees. We are opening a door for further functional characterization by reverse genetics and marker-assisted selection with those genes. Investigation of some of the key regulators of lignin biosynthesis in teak, however, could be a valuable step towards understanding how rigidity of teak wood and extractives content are different from most other woods. The obtained transcriptome data represents new sequences of T. grandis deposited in public databases, representing an unprecedented opportunity to discover several related-genes associated with secondary xylem such as transcription factors and stress-related genes in a tropical tree.
Collapse
Affiliation(s)
- Esteban Galeano
- Laboratório de Biotecnologia Agrícola (CEBTEC), Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias, 11, Piracicaba, São Paulo, 13418-900, Brazil.
| | - Tarcísio Sales Vasconcelos
- Laboratório de Biotecnologia Agrícola (CEBTEC), Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias, 11, Piracicaba, São Paulo, 13418-900, Brazil.
| | - Mabel Vidal
- CAPS Computational Biology Laboratory (CCBL), Center for Applied Plant Sciences, Ohio State University, 206 Rightmire Hall, 1060 Carmack Road, Columbus, Ohio, 43210, United States.
| | - Maria Katherine Mejia-Guerra
- CAPS Computational Biology Laboratory (CCBL), Center for Applied Plant Sciences, Ohio State University, 206 Rightmire Hall, 1060 Carmack Road, Columbus, Ohio, 43210, United States.
| | - Helaine Carrer
- Laboratório de Biotecnologia Agrícola (CEBTEC), Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias, 11, Piracicaba, São Paulo, 13418-900, Brazil.
| |
Collapse
|
46
|
Printz B, Guerriero G, Sergeant K, Renaut J, Lutts S, Hausman JF. Ups and downs in alfalfa: Proteomic and metabolic changes occurring in the growing stem. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 238:13-25. [PMID: 26259170 DOI: 10.1016/j.plantsci.2015.05.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/16/2015] [Indexed: 05/05/2023]
Abstract
The expanding interest for using lignocellulosic biomass in industry spurred the study of the mechanisms underlying plant cell-wall synthesis. Efforts using genetic approaches allowed the disentanglement of major steps governing stem fibre synthesis. Nonetheless, little is known about the relations between the stem maturation and the evolution of its proteome. During Medicago sativa L. maturation, the different internodes grow asynchronously allowing the discrimination of various developmental stages on a same stem. In this study, the proteome of three selected regions of the stem of alfalfa (apical, intermediate and basal) was analyzed and combined with a compositional analysis of the different stem parts. Interestingly, the apical and the median regions share many similarities: high abundance of chloroplast- and mitochondrial-related proteins together with the accumulation of proteins acting in the early steps of fibre production. In the mature basal region, forisomes and stress-related proteins accumulate. The RT-qPCR assessment of the expression of genes coding for members of the cellulose synthase family likewise indicates that fibres and the machinery responsible for the deposition of secondary cell walls are predominantly formed in the apical section. Altogether, this study reflects the metabolic change from the fibre production in the upper stem regions to the acquisition of defence-related functions in the fibrous basal part.
Collapse
Affiliation(s)
- Bruno Printz
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5, Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg; Groupe de Recherche en Physiologie végétale (GRPV), Earth and Life Institute Agronomy (ELI-A), Université catholique de Louvain, 5 (bte 7.07.13) Place Croix du Sud, B-1348 Louvain-la-Neuve, Belgium
| | - Gea Guerriero
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5, Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg
| | - Kjell Sergeant
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5, Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg.
| | - Jenny Renaut
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5, Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg
| | - Stanley Lutts
- Groupe de Recherche en Physiologie végétale (GRPV), Earth and Life Institute Agronomy (ELI-A), Université catholique de Louvain, 5 (bte 7.07.13) Place Croix du Sud, B-1348 Louvain-la-Neuve, Belgium
| | - Jean-Francois Hausman
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5, Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg
| |
Collapse
|
47
|
Vicentini R, Bottcher A, Brito MDS, dos Santos AB, Creste S, Landell MGDA, Cesarino I, Mazzafera P. Large-Scale Transcriptome Analysis of Two Sugarcane Genotypes Contrasting for Lignin Content. PLoS One 2015; 10:e0134909. [PMID: 26241317 PMCID: PMC4524650 DOI: 10.1371/journal.pone.0134909] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 07/15/2015] [Indexed: 12/16/2022] Open
Abstract
Sugarcane is an important crop worldwide for sugar and first generation ethanol production. Recently, the residue of sugarcane mills, named bagasse, has been considered a promising lignocellulosic biomass to produce the second-generation ethanol. Lignin is a major factor limiting the use of bagasse and other plant lignocellulosic materials to produce second-generation ethanol. Lignin biosynthesis pathway is a complex network and changes in the expression of genes of this pathway have in general led to diverse and undesirable impacts on plant structure and physiology. Despite its economic importance, sugarcane genome was still not sequenced. In this study a high-throughput transcriptome evaluation of two sugarcane genotypes contrasting for lignin content was carried out. We generated a set of 85,151 transcripts of sugarcane using RNA-seq and de novo assembling. More than 2,000 transcripts showed differential expression between the genotypes, including several genes involved in the lignin biosynthetic pathway. This information can give valuable knowledge on the lignin biosynthesis and its interactions with other metabolic pathways in the complex sugarcane genome.
Collapse
Affiliation(s)
- Renato Vicentini
- Systems Biology Laboratory, Centre for Molecular Biology and Genetic Engineering, State University of Campinas, Campinas, SP, Brazil
- * E-mail:
| | - Alexandra Bottcher
- Department of Plant Biology, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
| | - Michael dos Santos Brito
- Department of Plant Biology, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
- Sugarcane Center, Agronomic Institute of Campinas, Ribeirão Preto, SP, Brazil
| | | | - Silvana Creste
- Sugarcane Center, Agronomic Institute of Campinas, Ribeirão Preto, SP, Brazil
| | | | - Igor Cesarino
- Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Paulo Mazzafera
- Department of Plant Biology, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
| |
Collapse
|
48
|
O'Rourke JA, Fu F, Bucciarelli B, Yang SS, Samac DA, Lamb JFS, Monteros MJ, Graham MA, Gronwald JW, Krom N, Li J, Dai X, Zhao PX, Vance CP. The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies. BMC Genomics 2015; 16:502. [PMID: 26149169 PMCID: PMC4492073 DOI: 10.1186/s12864-015-1718-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/24/2015] [Indexed: 11/19/2022] Open
Abstract
Background Alfalfa (Medicago sativa L.) is the primary forage legume crop species in the United States and plays essential economic and ecological roles in agricultural systems across the country. Modern alfalfa is the result of hybridization between tetraploid M. sativa ssp. sativa and M. sativa ssp. falcata. Due to its large and complex genome, there are few genomic resources available for alfalfa improvement. Results A de novo transcriptome assembly from two alfalfa subspecies, M. sativa ssp. sativa (B47) and M. sativa ssp. falcata (F56) was developed using Illumina RNA-seq technology. Transcripts from roots, nitrogen-fixing root nodules, leaves, flowers, elongating stem internodes, and post-elongation stem internodes were assembled into the Medicago sativa Gene Index 1.2 (MSGI 1.2) representing 112,626 unique transcript sequences. Nodule-specific and transcripts involved in cell wall biosynthesis were identified. Statistical analyses identified 20,447 transcripts differentially expressed between the two subspecies. Pair-wise comparisons of each tissue combination identified 58,932 sequences differentially expressed in B47 and 69,143 sequences differentially expressed in F56. Comparing transcript abundance in floral tissues of B47 and F56 identified expression differences in sequences involved in anthocyanin and carotenoid synthesis, which determine flower pigmentation. Single nucleotide polymorphisms (SNPs) unique to each M. sativa subspecies (110,241) were identified. Conclusions The Medicago sativa Gene Index 1.2 increases the expressed sequence data available for alfalfa by ninefold and can be expanded as additional experiments are performed. The MSGI 1.2 transcriptome sequences, annotations, expression profiles, and SNPs were assembled into the Alfalfa Gene Index and Expression Database (AGED) at http://plantgrn.noble.org/AGED/, a publicly available genomic resource for alfalfa improvement and legume research. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1718-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jamie A O'Rourke
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA.
| | - Fengli Fu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
| | | | - S Sam Yang
- USDA-ARS-Plant Science Research Unit, St. Paul, MN, 55108, USA. .,Present Address: Monsanto Company, Molecular Breeding Technology, Chesterfield, MO, 63167, USA.
| | - Deborah A Samac
- USDA-ARS-Plant Science Research Unit, St. Paul, MN, 55108, USA.
| | - JoAnn F S Lamb
- USDA-ARS-Plant Science Research Unit, St. Paul, MN, 55108, USA.
| | | | - Michelle A Graham
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA.
| | - John W Gronwald
- USDA-ARS-Plant Science Research Unit, St. Paul, MN, 55108, USA.
| | - Nick Krom
- Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA.
| | - Jun Li
- Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA.
| | - Xinbin Dai
- Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA.
| | - Patrick X Zhao
- Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA.
| | - Carroll P Vance
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA. .,USDA-ARS-Plant Science Research Unit, St. Paul, MN, 55108, USA.
| |
Collapse
|
49
|
Transcriptome Sequencing and Analysis of Wild Pear (Pyrus hopeiensis) Using the Illumina Platform. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2015. [DOI: 10.1007/s13369-015-1725-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
50
|
Mehr S, Verdes A, DeSalle R, Sparks J, Pieribone V, Gruber DF. Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae). BMC Genomics 2015; 16:445. [PMID: 26059236 PMCID: PMC4462082 DOI: 10.1186/s12864-015-1565-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background The amphinomid polychaete Hermodice carunculata is a cosmopolitan and ecologically important omnivore in coral reef ecosystems, preying on a diverse suite of reef organisms and potentially acting as a vector for coral disease. While amphinomids are a key group for determining the root of the Annelida, their phylogenetic position has been difficult to resolve, and their publically available genomic data was scarce. Results We performed deep transcriptome sequencing (Illumina HiSeq) and profiling on Hermodice carunculata collected in the Western Atlantic Ocean. We focused this study on 58,454 predicted Open Reading Frames (ORFs) of genes longer than 200 amino acids for our homology search, and Gene Ontology (GO) terms and InterPro IDs were assigned to 32,500 of these ORFs. We used this de novo assembled transcriptome to recover major signaling pathways and housekeeping genes. We also identify a suite of H. carunculata genes related to reproduction and immune response. Conclusions We provide a comprehensive catalogue of annotated genes for Hermodice carunculata and expand the knowledge of reproduction and immune response genes in annelids, in general. Overall, this study vastly expands the available genomic data for H. carunculata, of which previously consisted of only 279 nucleotide sequences in NCBI. This underscores the utility of Illumina sequencing for de novo transcriptome assembly in non-model organisms as a cost-effective and efficient tool for gene discovery and downstream applications, such as phylogenetic analysis and gene expression profiling. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1565-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Shaadi Mehr
- Biological Science Department, State University of New York, College at Old Westbury, Old Westbury, NY, 11568, USA. .,American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park W at 79th St, New York, NY, 10024, USA.
| | - Aida Verdes
- Baruch College and The Graduate Center, Department of Natural Sciences, City University of New York, New York, NY, 10010, USA.
| | - Rob DeSalle
- American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park W at 79th St, New York, NY, 10024, USA.
| | - John Sparks
- American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park W at 79th St, New York, NY, 10024, USA. .,American Museum of Natural History, Department of Ichthyology, American Museum of Natural History, Division of Vertebrate Zoology, New York, NY, 10024, USA.
| | - Vincent Pieribone
- John B. Pierce Laboratory, Cellular and Molecular Physiology, Yale University, New Haven, CT 06519, USA.
| | - David F Gruber
- American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park W at 79th St, New York, NY, 10024, USA. .,Baruch College and The Graduate Center, Department of Natural Sciences, City University of New York, New York, NY, 10010, USA.
| |
Collapse
|