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Sadeghpour N, Asadi-Gharneh HA, Nasr-Esfahani M, Rahimiardkapan B, Nasr-Esfahani A, Nasr-Esfahani A, Monazah M. Gene markers generating polygenic resistance in melon-Fusarium wilt-FOM1.2 interaction pathosystem. PLANT BIOLOGY (STUTTGART, GERMANY) 2025; 27:52-65. [PMID: 39404640 DOI: 10.1111/plb.13729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 10/12/2023] [Indexed: 12/20/2024]
Abstract
Developing melon genotypes with resistance to Fusarium oxysporum f. sp. Melonis-(FOM) race1.2 is a major goal in any breeding program. In this study, we identified the role of 11 gene markers that contribute to polygenic resistance during the FOM1.2-melon interaction. qRT-PCR analysis elucidated upregulation of candidate marker genes AMT, DXPR, Fom-2, GLUC, GalS, GRF3, MLO, PRK, RuBlsCo, TLP and WRKY in resistant 'Shante-F1' and 'Khatouni', and susceptible 'Shante-T' and 'Shahabadi' at 7, 14 and 21 days post-inoculation (dpi). We also studied changes in defence-related enzyme activity: chitinase (CHI), β-1,3-glucanase (GLU) and peroxidase (POX) in melon roots. AMT, GLUC and DXPR transcripts were upregulatied in leaf and root tissues of the resistant 'Shante-F1' and 'Shahabadi'. Transcript levels for GalS and GRF3 increased 6.77- and 6.83-fold in roots of 'Shante-F1' at 7 dpi, whereas in PRK, TLP and WRKY theye increased by 7.84-, 5.15- and 12.26-fold at 14 dpi, respectively. However, transcript levels increased by 5.18-fold for Fom-2 and 8.46-fold for MLO at 21 dpi. Also, RBC transcript level peaked at 14 dpi with 4.9-fold increase in leaves of resistant genotypes, whereas AMT increased 2.94-fold at 21 dpi, and GLUC and DXPR increased 7.11- and 2.91-fold at 14 dpi in 'Shante-F', respectively. Defence-related-enzyme activity was also upregulated three-fold in resistant varieties. The dynamic shifts in the melon transcriptome induced by FOM1.2 emphasize that resistance mechanisms are predominantly regulated through signalling pathways involving CHI, GLU, and POX defence response. Surprisingly, the AMT gene, basically resistant to downy mildew, Pseudoperonospora cubensis; GLUC, MLO and PRK resistant to powdery mildew (Sphaerotheca fusca); TLP and WRKY resistant to Phytophthora blight (Phytophthora capsici); and GRF3 and RBC resistant to root knot nematodes (Meloidogyne spp.) were upregulated in resistant genotypes, indicating a dual role of these genes in resistance to more than one disease at a time.
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Affiliation(s)
- N Sadeghpour
- Horticulture Department, College of Agriculture, Esfahan Branch (Khorasgan), Islamic Azad University, Isfahan, Iran
| | - H A Asadi-Gharneh
- Horticulture Department, College of Agriculture, Esfahan Branch (Khorasgan), Islamic Azad University, Isfahan, Iran
| | - M Nasr-Esfahani
- Plant Protection Research Department, Esfahan Agriculture and Natural Resource Research and Education Center, AREEO, Esfahan, Iran
| | - B Rahimiardkapan
- Horticulture Department, College of Agriculture, Esfahan Branch (Khorasgan), Islamic Azad University, Isfahan, Iran
| | - A Nasr-Esfahani
- Department of Mycology and Parasitology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - A Nasr-Esfahani
- Department of Mycology and Parasitology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - M Monazah
- Plant Protection Research Department, Esfahan Agriculture and Natural Resource Research and Education Center, AREEO, Esfahan, Iran
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Sørensen MD, Olsen RFS, Burton M, Kavan S, Petterson SA, Thomassen M, Kruse TA, Meyer M, Kristensen BW. Microglia induce an interferon-stimulated gene expression profile in glioblastoma and increase glioblastoma resistance to temozolomide. Neuropathol Appl Neurobiol 2024; 50:e13016. [PMID: 39558550 PMCID: PMC11618491 DOI: 10.1111/nan.13016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 10/22/2024] [Accepted: 10/25/2024] [Indexed: 11/20/2024]
Abstract
AIMS Glioblastoma is the most malignant primary brain tumour. Even with standard treatment comprising surgery followed by radiation and concomitant temozolomide (TMZ) chemotherapy, glioblastoma remains incurable. Almost all patients with glioblastoma relapse owing to various intrinsic and extrinsic resistance mechanisms of the tumour cells. Glioblastomas are densely infiltrated with tumour-associated microglia and macrophages (TAMs). These immune cells affect the tumour cells in experimental studies and are associated with poor patient survival in clinical studies. The aim of the study was to investigate the impact of microglia on glioblastoma chemo-resistance. METHODS We co-cultured patient-derived glioblastoma spheroids with microglia at different TMZ concentrations and analysed cell death. In addition, we used RNA sequencing to explore differentially expressed genes after co-culture. Immunostaining was used for validation. RESULTS Co-culture experiments showed that microglia significantly increased TMZ resistance in glioblastoma cells. RNA sequencing revealed upregulation of a clear interferon-stimulated gene (ISG) expression signature in the glioblastoma cells after co-culture with microglia, including genes such as IFI6, IFI27, BST2, MX1 and STAT1. This ISG expression signature is linked to STAT1 signalling, which was confirmed by immunostaining. The ISG expression profile observed in glioblastoma cells with enhanced TMZ resistance corresponded to the interferon-related DNA damage resistance signature (IRDS) described in different solid cancers. CONCLUSIONS Here, we show that the IRDS signature, linked to chemo-resistance in other cancers, can be induced in glioblastoma by microglia. ISG genes and the microglia inducing the ISG expression could be promising novel therapeutic targets in glioblastoma.
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Affiliation(s)
- Mia Dahl Sørensen
- Department of PathologyOdense University HospitalOdenseDenmark
- Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
| | | | - Mark Burton
- Department of Clinical GeneticsOdense University HospitalOdenseDenmark
- Clinical Genome Center, Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
| | - Stephanie Kavan
- Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
- Department of Clinical GeneticsOdense University HospitalOdenseDenmark
| | - Stine Asferg Petterson
- Department of PathologyOdense University HospitalOdenseDenmark
- Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
| | - Mads Thomassen
- Department of Clinical GeneticsOdense University HospitalOdenseDenmark
- Clinical Genome Center, Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
| | - Torben Arvid Kruse
- Department of Clinical GeneticsOdense University HospitalOdenseDenmark
- Clinical Genome Center, Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
| | - Morten Meyer
- Department of Neurobiology Research, Institute of Molecular MedicineUniversity of Southern DenmarkOdenseDenmark
- Brain Research Inter‐Disciplinary Guided Excellence (BRIDGE), Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
| | - Bjarne Winther Kristensen
- Department of PathologyOdense University HospitalOdenseDenmark
- Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
- Department of Pathology, The Bartholin Institute, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
- Department of Clinical Medicine and Biotech Research & Innovation Centre (BRIC)University of CopenhagenCopenhagenDenmark
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Teng X, Shang J, Du L, Huang W, Wang Y, Liu M, Ma Y, Wang M, Tang H, Bai L. RNA-binding protein Trx regulates alternative splicing and promotes metastasis of HCC via interacting with LINC00152. J Gastroenterol Hepatol 2024; 39:2892-2902. [PMID: 39343436 PMCID: PMC11660213 DOI: 10.1111/jgh.16735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 08/19/2024] [Accepted: 08/29/2024] [Indexed: 10/01/2024]
Abstract
BACKGROUND Epithelial-mesenchymal transition (EMT) is central to HCC metastasis, in which RNA-binding proteins (RBPs) play a key role. METHODS To explore the role of RBPs in metastasis of hepatocellular carcinoma (HCC), whole transcriptome sequencing was conducted to identify differential RBPs between HCC with metastasis and HCC without metastasis. The influence of RBPs on metastasis of HCC was verified by in vitro and in vivo experiments. The interaction of RBPs with non-coding RNAs was evaluated by RNA immunoprecipitation and pull-down assays. RNA sequencing, whole-genome sequencing, and alternative splicing analysis were further performed to clarify post-transcriptional regulation mechanisms. RESULTS Whole transcriptome sequencing results showed that expression of thioredoxin (Trx) was significantly upregulated in HCC patients with metastasis. Trx was also found to be associated with poor prognosis in HCC patients. Overexpression of Trx could promote migration and invasion of HCC cells in vitro and increase the rate of lung metastasis of HCC cells in vivo. Moreover, binding assays showed that Trx could bind to LINC00152. As a result, LINC00152 was verified to determine the pro-metastasis function of Trx by knockdown assay. Furthermore, we revealed that Trx could regulate metastasis-associated alternative splicing program. Specifically, angiopoietin 1 (ANGPT1) was the splicing target; the splicing isoform switching of ANGPT1 could activate the PI3K-Akt pathway, upregulate EMT-associated proteins, and promote migration and invasion of HCC cells. CONCLUSIONS We found that Trx could interact with LINC00152 and promote HCC metastasis via regulating alternative splicing, indicating that Trx may serve as a novel therapeutic target for HCC treatment.
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Affiliation(s)
- Xiangnan Teng
- Center of Infectious DiseasesWest China Hospital, Sichuan UniversityChengduChina
| | - Jin Shang
- Center of Infectious DiseasesWest China Hospital, Sichuan UniversityChengduChina
- Liver Transplantation Center and HBP Surgery, Sichuan Clinical Research Center for Cancer Sichuan Cancer Hospital & Institute, Sichuan Cancer CenterAffiliated Cancer Hospital of University of Electronic Science and Technology of ChinaChengduChina
| | - Lingyao Du
- Center of Infectious DiseasesWest China Hospital, Sichuan UniversityChengduChina
| | - Wei Huang
- Center of Infectious DiseasesWest China Hospital, Sichuan UniversityChengduChina
| | - Yonghong Wang
- Center of Infectious DiseasesWest China Hospital, Sichuan UniversityChengduChina
| | - Miao Liu
- Center of Infectious DiseasesWest China Hospital, Sichuan UniversityChengduChina
| | - Yuanji Ma
- Center of Infectious DiseasesWest China Hospital, Sichuan UniversityChengduChina
| | - Ming Wang
- Center of Infectious DiseasesWest China Hospital, Sichuan UniversityChengduChina
| | - Hong Tang
- Center of Infectious DiseasesWest China Hospital, Sichuan UniversityChengduChina
| | - Lang Bai
- Center of Infectious DiseasesWest China Hospital, Sichuan UniversityChengduChina
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Pola-Sánchez E, Hernández-Martínez KM, Pérez-Estrada R, Sélem-Mójica N, Simpson J, Abraham-Juárez MJ, Herrera-Estrella A, Villalobos-Escobedo JM. RNA-Seq Data Analysis: A Practical Guide for Model and Non-Model Organisms. Curr Protoc 2024; 4:e1054. [PMID: 38808970 DOI: 10.1002/cpz1.1054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
RNA sequencing (RNA-seq) has emerged as a powerful tool for assessing genome-wide gene expression, revolutionizing various fields of biology. However, analyzing large RNA-seq datasets can be challenging, especially for students or researchers lacking bioinformatics experience. To address these challenges, we present a comprehensive guide to provide step-by-step workflows for analyzing RNA-seq data, from raw reads to functional enrichment analysis, starting with considerations for experimental design. This is designed to aid students and researchers working with any organism, irrespective of whether an assembled genome is available. Within this guide, we employ various recognized bioinformatics tools to navigate the landscape of RNA-seq analysis and discuss the advantages and disadvantages of different tools for the same task. Our protocol focuses on clarity, reproducibility, and practicality to enable users to navigate the complexities of RNA-seq data analysis easily and gain valuable biological insights from the datasets. Additionally, all scripts and a sample dataset are available in a GitHub repository to facilitate the implementation of the analysis pipeline. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Analysis of data from a model plant with an available reference genome Basic Protocol 2: Gene ontology enrichment analysis Basic Protocol 3: De novo assembly of data from non-model plants.
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Affiliation(s)
- Enrique Pola-Sánchez
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV), Unidad Irapuato, Irapuato, México
| | | | - Rafael Pérez-Estrada
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México (UNAM), Morelia, México
| | - Nelly Sélem-Mójica
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México (UNAM), Morelia, México
- The LatAmBio Initiative, Irapuato, México
| | - June Simpson
- Departamento de Ingeniería Genética, CINVESTAV, Unidad Irapuato, Irapuato, México
| | - María Jazmín Abraham-Juárez
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV), Unidad Irapuato, Irapuato, México
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV), Unidad Irapuato, Irapuato, México
- The LatAmBio Initiative, Irapuato, México
| | - José Manuel Villalobos-Escobedo
- The LatAmBio Initiative, Irapuato, México
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, California, United States
- Institute for Obesity Research, Tecnológico de Monterrey, Monterrey, Mexico
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Kudapa H, Ghatak A, Barmukh R, Chaturvedi P, Khan A, Kale S, Fragner L, Chitikineni A, Weckwerth W, Varshney RK. Integrated multi-omics analysis reveals drought stress response mechanism in chickpea (Cicer arietinum L.). THE PLANT GENOME 2024; 17:e20337. [PMID: 37165696 DOI: 10.1002/tpg2.20337] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/04/2023] [Accepted: 03/09/2023] [Indexed: 05/12/2023]
Abstract
Drought is one of the major constraints limiting chickpea productivity. To unravel complex mechanisms regulating drought response in chickpea, we generated transcriptomics, proteomics, and metabolomics datasets from root tissues of four contrasting drought-responsive chickpea genotypes: ICC 4958, JG 11, and JG 11+ (drought-tolerant), and ICC 1882 (drought-sensitive) under control and drought stress conditions. Integration of transcriptomics and proteomics data identified enriched hub proteins encoding isoflavone 4'-O-methyltransferase, UDP-d-glucose/UDP-d-galactose 4-epimerase, and delta-1-pyrroline-5-carboxylate synthetase. These proteins highlighted the involvement of pathways such as antibiotic biosynthesis, galactose metabolism, and isoflavonoid biosynthesis in activating drought stress response mechanisms. Subsequently, the integration of metabolomics data identified six metabolites (fructose, galactose, glucose, myoinositol, galactinol, and raffinose) that showed a significant correlation with galactose metabolism. Integration of root-omics data also revealed some key candidate genes underlying the drought-responsive "QTL-hotspot" region. These results provided key insights into complex molecular mechanisms underlying drought stress response in chickpea.
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Affiliation(s)
- Himabindu Kudapa
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Rutwik Barmukh
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Aamir Khan
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sandip Kale
- The Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Lena Fragner
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Centre (VIME), University of Vienna, Vienna, Austria
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
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Du Y, Liu G, Chen D, Yang J, Wang J, Sun Y, Zhang Q, Liu Y. NQO1 regulates expression and alternative splicing of apoptotic genes associated with Alzheimer's disease in PC12 cells. Brain Behav 2023; 13:e2917. [PMID: 37002649 PMCID: PMC10175992 DOI: 10.1002/brb3.2917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/10/2022] [Accepted: 01/29/2023] [Indexed: 05/13/2023] Open
Abstract
PURPOSE Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive memory loss and cognitive dysfunction. Quinone oxidoreductase 1 (NQO1) is an antioxidant enzyme that plays an important role in controlling cellular redox state, whose expression is altered in the brain tissues of AD patients. In addition to its traditional antioxidant effects, NQO1 also acts as a multifunctional RNA-binding protein involved in posttranscriptional regulation. Whether the RNA-binding activity of NQO1 influences AD pathology has not been investigated yet. METHODS The RNA-binding functions of NQO1 in rat pheochromocytoma (PC12) cells were investigated using siRNA knockdown followed by total RNA sequencing. Reverse transcription quantitative polymerase chain reaction was performed to explore the impact of NQO1 on the transcription and alternative splicing of apoptotic genes. RESULTS NQO1 knockdown led to a significant increase in cellular apoptosis. Genes involved in certain apoptosis pathways, such as positive regulation of apoptotic processes and mitogen-activated protein kinase signaling, were under global transcriptional and alternative splicing regulation. NQO1 regulated the transcription of apoptotic genes Cryab, Lgmn, Ngf, Apoe, Brd7, and Stat3, as well as the alternative splicing of apoptotic genes BIN1, Picalm, and Fyn. CONCLUSION Our findings suggest that NQO1 participates in the pathology of AD by regulating the expression and alternative splicing of the genes involved in apoptosis. These results extend our understanding of NQO1 in apoptotic pathways at the posttranscriptional level in AD.
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Affiliation(s)
- Yingshi Du
- Section 1, Department of Geriatrics, The First Hospital of Lanzhou University, Lanzhou, China
| | - Gejing Liu
- Section 1, Department of Geriatrics, The First Hospital of Lanzhou University, Lanzhou, China
| | - Dong Chen
- Center for Genome Analysis, ABLife Inc., Wuhan, China
| | - Jinggang Yang
- Section 1, Department of Geriatrics, The First Hospital of Lanzhou University, Lanzhou, China
| | - Jing Wang
- Section 1, Department of Geriatrics, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yue Sun
- Center for Genome Analysis, ABLife Inc., Wuhan, China
| | - Qian Zhang
- Center for Genome Analysis, ABLife Inc., Wuhan, China
| | - Yongming Liu
- Section 1, Department of Geriatrics, The First Hospital of Lanzhou University, Lanzhou, China
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Li Q, Stroup EK, Ji Z. Rfoot-seq: Transcriptomic RNase Footprinting for Mapping Stable RNA-Protein Complexes and Rapid Ribosome Profiling. Curr Protoc 2023; 3:e761. [PMID: 37097194 PMCID: PMC10667019 DOI: 10.1002/cpz1.761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Ribosome profiling isolates ribosome-protected fragments for sequencing and is a valuable method for studying different aspects of RNA translation. However, conventional protocols require millions of input cells and time-consuming steps to isolate translating ribosome complexes using ultracentrifugation or immunoprecipitation. These limitations have prevented their application to rare physiological samples. To address these technical barriers, we developed an RNase footprinting approach named Rfoot-seq to map stable transcriptomic RNA-protein complexes that allows rapid ribosome profiling using low-input samples (Li, Yang, Stroup, Wang, & Ji, 2022). In this assay, we treat a cell lysate with concentrated RNase without complex crosslinking and retained only RNA footprints associated with stable complexes for sequencing. The footprints in coding regions represent ribosome-protected fragments and can be used to study cytosolic and mitochondrial translation simultaneously. Rfoot-seq achieves comparable results to conventional ribosome profiling to quantify ribosome occupancy and works robustly for various cultured cells and primary tissue samples. Moreover, Rfoot-seq maps RNA fragments associated with stable non-ribosomal RNA-protein complexes in noncoding domains of small noncoding RNAs and some long noncoding RNAs. Taken together, Rfoot-seq opens an avenue to quantify transcriptomic translation and characterize functional noncoding RNA domains using low-input samples. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Harvesting and lysing adherent cells Alternate Protocol 1: Harvesting and lysing suspension cells Alternate Protocol 2: Harvesting and lysing primary tissue samples Basic Protocol 2: RNase treatment and footprint purification for low-input samples Alternate Protocol 3: RNase treatment and footprint purification for ultra-low-input samples Basic Protocol 3: Library preparation for high-throughput sequencing Support Protocol: Preparation of dsDNA markers for library size selection Basic Protocol 4: Data analysis and quality control after sequencing.
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Affiliation(s)
- Qianru Li
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Emily K Stroup
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Zhe Ji
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, Illinois
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Jiang C, Wang G, Zhang J, Gu S, Wang X, Qin W, Chen K, Yuan D, Chai X, Yang M, Zhou F, Xiong J, Miao W. iGDP: An integrated genome decontamination pipeline for wild ciliated microeukaryotes. Mol Ecol Resour 2023. [PMID: 36912756 DOI: 10.1111/1755-0998.13782] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 02/25/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
Ciliates are a large group of ubiquitous and highly diverse single-celled eukaryotes that play an essential role in the functioning of microbial food webs. However, their genomic diversity is far from clear due to the need to develop cultivation methods for most species, so most research is based on wild organisms that almost invariably contain contaminants. Here we establish an integrated Genome Decontamination Pipeline (iGDP) that combines homology search, telomere reads-assisted and clustering approaches to filter contaminated ciliate genome assemblies from wild specimens. We benchmarked the performance of iGDP using genomic data from a contaminated ciliate culture and the results showed that iGDP could recall 91.9% of the target sequences with 96.9% precision. We also used a synthetic dataset to offer guidelines for the application of iGDP in the removal of various groups of contaminants. Compared with several popular metagenome binning tools, iGDP could show better performance. To further validate the effectiveness of iGDP on real-world data, we applied it to decontaminate genome assemblies of three wild ciliate specimens and obtained their genomes with high quality comparable to that of previously well-studied model ciliate genomes. It is anticipated that the newly generated genomes and the established iGDP method will be valuable community resources for detailed studies on ciliate biodiversity, phylogeny, ecology and evolution. The pipeline (https://github.com/GWang2022/iGDP) can be implemented automatically to reduce manual filtering and classification and may be further developed to apply to other microeukaryotes.
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Affiliation(s)
- Chuanqi Jiang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Guangying Wang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jing Zhang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Siyu Gu
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xueyan Wang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Weiwei Qin
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kai Chen
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Dongxia Yuan
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xiaocui Chai
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Mingkun Yang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Fang Zhou
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Wuhan, China
- CAS Center for Excellence in Animal Evolution and Genetics, Kunming, China
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Lu J, Sheng Y, Qian W, Pan M, Zhao X, Ge Q. scRNA-seq data analysis method to improve analysis performance. IET Nanobiotechnol 2023; 17:246-256. [PMID: 36727937 DOI: 10.1049/nbt2.12115] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/28/2022] [Accepted: 12/30/2022] [Indexed: 02/03/2023] Open
Abstract
With the development of single-cell RNA sequencing technology (scRNA-seq), we have the ability to study biological questions at the level of the individual cell transcriptome. Nowadays, many analysis tools, specifically suitable for single-cell RNA sequencing data, have been developed. In this review, the currently commonly used scRNA-seq protocols are discussed. The upstream processing flow pipeline of scRNA-seq data, including goals and popular tools for reads mapping and expression quantification, quality control, normalization, imputation, and batch effect removal is also introduced. Finally, methods to evaluate these tools in both cellular and genetic dimensions, clustering and differential expression analysis are presented.
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Affiliation(s)
- Junru Lu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, China
| | - Yuqi Sheng
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, China
| | - Weiheng Qian
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, China
| | - Min Pan
- School of Medicine, Southeast University, Nanjing, China
| | - Xiangwei Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, China
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10
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Basuroy T, Dreier M, Baum C, Blomquist T, Trumbly R, Filipp FV, de la Serna IL. Epigenetic and pharmacological control of pigmentation via Bromodomain Protein 9 (BRD9). Pigment Cell Melanoma Res 2023; 36:19-32. [PMID: 36112085 PMCID: PMC10091956 DOI: 10.1111/pcmr.13068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/01/2022] [Accepted: 09/14/2022] [Indexed: 12/31/2022]
Abstract
Lineage-specific differentiation programs are activated by epigenetic changes in chromatin structure. Melanin-producing melanocytes maintain a gene expression program ensuring appropriate enzymatic conversion of metabolites into the pigment, melanin, and transfer to surrounding cells. During neuroectodermal development, SMARCA4 (BRG1), the catalytic subunit of SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complexes, is essential for lineage specification. SMARCA4 is also required for development of multipotent neural crest precursors into melanoblasts, which differentiate into pigment-producing melanocytes. In addition to the catalytic domain, SMARCA4 and several SWI/SNF subunits contain bromodomains which are amenable to pharmacological inhibition. We investigated the effects of pharmacological inhibitors of SWI/SNF bromodomains on melanocyte differentiation. Strikingly, treatment of murine melanoblasts and human neonatal epidermal melanocytes with selected bromodomain inhibitors abrogated melanin synthesis and visible pigmentation. Using functional genomics, iBRD9, a small molecule selective for the bromodomain of BRD9 was found to repress pigmentation-specific gene expression. Depletion of BRD9 confirmed a requirement for expression of pigmentation genes in the differentiation program from melanoblasts into pigmented melanocytes and in melanoma cells. Chromatin immunoprecipitation assays showed that iBRD9 disrupts the occupancy of BRD9 and the catalytic subunit SMARCA4 at melanocyte-specific loci. These data indicate that BRD9 promotes melanocyte pigmentation whereas pharmacological inhibition of BRD9 is repressive.
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Affiliation(s)
- Tupa Basuroy
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Megan Dreier
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Caitlin Baum
- Department of Pathology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Thomas Blomquist
- Department of Pathology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Robert Trumbly
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA.,Department of Medical Education, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Fabian V Filipp
- Metaflux, Broadway, San Diego, California, USA.,Cancer Systems Biology, Institute for Diabetes and Cancer, Helmholtz Zentrum München, Munich, Germany.,School of Life Sciences Weihenstephan, Technical University München, Freising, Germany
| | - Ivana L de la Serna
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
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11
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Minden S, Aniolek M, Noorman H, Takors R. Performing in spite of starvation: How Saccharomyces cerevisiae maintains robust growth when facing famine zones in industrial bioreactors. Microb Biotechnol 2022; 16:148-168. [PMID: 36479922 PMCID: PMC9803336 DOI: 10.1111/1751-7915.14188] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/08/2022] [Accepted: 11/13/2022] [Indexed: 12/13/2022] Open
Abstract
In fed-batch operated industrial bioreactors, glucose-limited feeding is commonly applied for optimal control of cell growth and product formation. Still, microbial cells such as yeasts and bacteria are frequently exposed to glucose starvation conditions in poorly mixed zones or far away from the feedstock inlet point. Despite its commonness, studies mimicking related stimuli are still underrepresented in scale-up/scale-down considerations. This may surprise as the transition from glucose limitation to starvation has the potential to provoke regulatory responses with negative consequences for production performance. In order to shed more light, we performed gene-expression analysis of Saccharomyces cerevisiae grown in intermittently fed chemostat cultures to study the effect of limitation-starvation transitions. The resulting glucose concentration gradient was representative for the commercial scale and compelled cells to tolerate about 76 s with sub-optimal substrate supply. Special attention was paid to the adaptation status of the population by discriminating between first time and repeated entry into the starvation regime. Unprepared cells reacted with a transiently reduced growth rate governed by the general stress response. Yeasts adapted to the dynamic environment by increasing internal growth capacities at the cost of rising maintenance demands by 2.7%. Evidence was found that multiple protein kinase A (PKA) and Snf1-mediated regulatory circuits were initiated and ramped down still keeping the cells in an adapted trade-off between growth optimization and down-regulation of stress response. From this finding, primary engineering guidelines are deduced to optimize both the production host's genetic background and the design of scale-down experiments.
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Affiliation(s)
- Steven Minden
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Maria Aniolek
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Henk Noorman
- Royal DSMDelftThe Netherlands,Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
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12
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Long C, Liu H, Zhan W, Chen L, Yu Z, Tian S, Xiang Y, Chen S, Tian X. Chronological attenuation of NPRA/PKG/AMPK signaling promotes vascular aging and elevates blood pressure. Aging Cell 2022; 21:e13699. [PMID: 36016499 PMCID: PMC9470896 DOI: 10.1111/acel.13699] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/09/2022] [Accepted: 08/02/2022] [Indexed: 01/25/2023] Open
Abstract
Hypertension is common in elderly population. We designed to search comprehensively for genes that are chronologically shifted in their expressions and to define their contributions to vascular aging and hypertension. RNA sequencing was conducted to search for senescence-shifted transcripts in human umbilical vein endothelial cells (HUVECs). Small interfering RNA (siRNA), small-molecule drugs, CRISPR/Cas9 techniques, and imaging were used to determine genes' function and contributions to age-related phenotypes of the endothelial cell and blood vessel. Of 25 genes enriched in the term of "regulation of blood pressure," NPRA was changed most significantly. The decreased NPRA expression was replicated in aortas of aged mice. The knockdown of NPRA promoted HUVEC senescence and it decreased expressions of protein kinase cGMP-dependent 1 (PKG), sirtuin 1 (SIRT1), and endothelial nitric oxide synthase (eNOS). Suppression of NPRA also decreased the phosphorylation of AMP-activated protein kinase (AMPK) as well as the ratio of oxidized nicotinamide adenine dinucleotide (NAD+ )/reduced nicotinamide adenine dinucleotide (NADH) but increased the production of reactive oxygen species (ROS). 8-Br-cGMP (analog of cGMP), or AICAR (AMPK activator), counteracted the observed changes in HUVECs. The Npr1+/- mice presented an elevated systolic blood pressure and their vessels became insensitive to endothelial-dependent vasodilators. Further, vessels from Npr1+/- mice increased Cdkn1a but decreased eNos expressions. These phenotypes were rescued by intravenously administrated 8-Br-cGMP and viral overexpression of human PKG, respectively. In conclusion, we demonstrate NPRA/PKG/AMPK as a novel and critical signaling axis in the modulation of endothelial cell senescence, vascular aging, and hypertension.
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Affiliation(s)
- Changkun Long
- Vascular Function LaboratoryHuman Aging Research Institute and School of Life Science, Nanchang university, and Jiangxi Key Laboratory of Human AgingNanchangChina
| | - Hongfei Liu
- Vascular Function LaboratoryHuman Aging Research Institute and School of Life Science, Nanchang university, and Jiangxi Key Laboratory of Human AgingNanchangChina
| | - Wenxing Zhan
- Vascular Function LaboratoryHuman Aging Research Institute and School of Life Science, Nanchang university, and Jiangxi Key Laboratory of Human AgingNanchangChina
| | - Liping Chen
- Vascular Function LaboratoryHuman Aging Research Institute and School of Life Science, Nanchang university, and Jiangxi Key Laboratory of Human AgingNanchangChina
| | - Zhenping Yu
- Institute of Translational MedicineNanchang UniversityNanchangChina,School of Life Science, Nanchang UniversityNanchangChina
| | - Shane Tian
- Department of Biochemistry/ChemistryOhio State UniversityColumbusOhioUSA
| | - Yang Xiang
- Metabolic Control and AgingHuman Aging Research Institute and School of Life Science, Nanchang university, and Jiangxi Key Laboratory of Human AgingNanchangChina
| | - Shenghan Chen
- Vascular Function LaboratoryHuman Aging Research Institute and School of Life Science, Nanchang university, and Jiangxi Key Laboratory of Human AgingNanchangChina
| | - Xiao‐Li Tian
- Aging and Vascular DiseasesHuman Aging Research Institute and School of Life Science, Nanchang university, and Jiangxi Key Laboratory of Human AgingNanchangChina
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13
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Wu C, Chaw S. Evolution of mitochondrial RNA editing in extant gymnosperms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1676-1687. [PMID: 35877596 PMCID: PMC9545813 DOI: 10.1111/tpj.15916] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 06/01/2023]
Abstract
To unveil the evolution of mitochondrial RNA editing in gymnosperms, we characterized mitochondrial genomes (mitogenomes), plastid genomes, RNA editing sites, and pentatricopeptide repeat (PPR) proteins from 10 key taxa representing four of the five extant gymnosperm clades. The assembled mitogenomes vary in gene content due to massive gene losses in Gnetum and Conifer II clades. Mitochondrial gene expression levels also vary according to protein function, with the most highly expressed genes involved in the respiratory complex. We identified 9132 mitochondrial C-to-U editing sites, as well as 2846 P-class and 8530 PLS-class PPR proteins. Regains of editing sites were demonstrated in Conifer II rps3 transcripts whose corresponding mitogenomic sequences lack introns due to retroprocessing. Our analyses reveal that non-synonymous editing is efficient and results in more codons encoding hydrophobic amino acids. In contrast, synonymous editing, although performed with variable efficiency, can increase the number of U-ending codons that are preferentially utilized in gymnosperm mitochondria. The inferred loss-to-gain ratio of mitochondrial editing sites in gymnosperms is 2.1:1, of which losses of non-synonymous editing are mainly due to genomic C-to-T substitutions. However, such substitutions only explain a small fraction of synonymous editing site losses, indicating distinct evolutionary mechanisms. We show that gymnosperms have experienced multiple lineage-specific duplications in PLS-class PPR proteins. These duplications likely contribute to accumulated RNA editing sites, as a mechanistic correlation between RNA editing and PLS-class PPR proteins is statistically supported.
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Affiliation(s)
- Chung‐Shien Wu
- Biodiversity Research CenterAcademia SinicaTaipei11529Taiwan
| | - Shu‐Miaw Chaw
- Biodiversity Research CenterAcademia SinicaTaipei11529Taiwan
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14
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Junaid A, Singh NK, Gaikwad K. Evolutionary fates of gene-body methylation and its divergent association with gene expression in pigeonpea. THE PLANT GENOME 2022; 15:e20207. [PMID: 35790083 DOI: 10.1002/tpg2.20207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 05/07/2021] [Indexed: 06/15/2023]
Abstract
Pigeonpea (Cajanus cajan L. Huth) is an agronomically important legume cultivated worldwide. In this study, we extensively analyzed gene-body methylation (GbM) patterns in pigeonpea. We found a bimodal distribution of CG and CHG methylation patterns. GbM features- slow evolution rate and increased length remained conserved. Genes with moderate CG body methylation showed highest expression where as highly-methylated genes showed lowest expression. Transposable element (TE)-related genes were methylated in multiple contexts and hence classified as C-methylated genes. A low expression among C-methylated genes was associated with transposons insertion in gene-body and upstream regulatory regions. The CG methylation patterns were found to be conserved in orthologs compared with non-CG methylation. By comparing methylation patterns between differentially methylated regions (DMRs) of the three genotypes, we found that variably methylated marks are less likely to target evolutionary conserved sequences. Finally, our analysis showed enrichment of nitrogen-related genes in GbM orthologs of legumes, which could be promising candidates for generating epialleles for crop improvement.
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Affiliation(s)
- Alim Junaid
- National Institute of Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Nagendra Kumar Singh
- National Institute of Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Kishor Gaikwad
- National Institute of Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
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15
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Jenckel M, Hall RN, Strive T. Pathogen profiling of Australian rabbits by metatranscriptomic sequencing. Transbound Emerg Dis 2022; 69:e2629-e2640. [PMID: 35687756 PMCID: PMC9796941 DOI: 10.1111/tbed.14609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/04/2022] [Accepted: 05/30/2022] [Indexed: 01/07/2023]
Abstract
Australia is known for its long history of using biocontrol agents, such as myxoma virus (MYXV) and rabbit haemorrhagic disease virus (RHDV), to manage wild European rabbit populations. Interestingly, while undertaking RHDV surveillance of rabbits that were found dead, we observed that approximately 40% of samples were negative for RHDV. To investigate whether other infectious agents are responsible for killing rabbits in Australia, we subjected a subset of these RHDV-negative liver samples to metatranscriptomic sequencing. In addition, we investigated whether the host transcriptome data could provide additional differentiation between likely infectious versus non-infectious causes of death. We identified transcripts from several Clostridia species, Pasteurella multocida, Pseudomonas spp., and Eimeria stiedae, in liver samples of several rabbits that had died suddenly, all of which are known to infect rabbits and are capable of causing disease and mortality. In addition, we identified Hepatitis E virus and Cyniclomyces yeast in some samples, both of which are not usually associated with severe disease. In one-third of the sequenced total liver RNAs, no infectious agent could be identified. While metatranscriptomic sequencing cannot provide definitive evidence of causation, additional host transcriptome analysis provided further insights to distinguish between pathogenic microbes and commensals or environmental contaminants. Interestingly, three samples where no pathogen could be identified showed evidence of up-regulated host immune responses, while immune response pathways were not up-regulated when E. stiedae, Pseudomonas, or yeast were detected. In summary, although no new putative rabbit pathogens were identified, this study provides a robust workflow for future investigations into rabbit mortality events.
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Affiliation(s)
| | - Robyn N. Hall
- CSIRO Health and BiosecurityCanberraAustralia,Centre for Invasive Species SolutionsUniversity of CanberraBruceAustralia
| | - Tanja Strive
- CSIRO Health and BiosecurityCanberraAustralia,Centre for Invasive Species SolutionsUniversity of CanberraBruceAustralia
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16
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Berton MP, de Lemos MVA, Stafuzza NB, Simielli Fonseca LF, Silva DBDS, Peripolli E, Pereira ASC, Magalhães AFB, Albuquerque LG, Baldi F. Integration analyses of structural variations and differential gene expression associated with beef fatty acid profile in Nellore cattle. Anim Genet 2022; 53:570-582. [PMID: 35811456 DOI: 10.1111/age.13242] [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: 10/08/2022] [Revised: 06/06/2022] [Accepted: 06/22/2022] [Indexed: 11/26/2022]
Abstract
This study aimed to integrate analyses of structural variations and differentially expressed genes (DEGs) associated with the beef fatty acid (FA) profile in Nellore cattle. Copy numbers variation (CNV) detection was performed using the penncnv algorithm and CNVRuler software in 3794 genotyped animals through the High-Density Bovine BeadChip. In order to perform the genomic wide association study (GWAS), a total of 963 genotyped animals were selected to obtain the intramuscular lipid concentration and quantify the beef FA profile. A total of 48 animals belonging to the same farm and management lot were extracted from the 963 genotyped and phenotyped animals to carry out the transcriptomic and differentially expressed gene analyses. The GWAS with extreme groups of FA profiles was performed using a logistic model. A total of 43, 42, 66 and 35 significant CNV regions (p < 0.05) for saturated, monounsaturated, polyunsaturated and omega 3 and 6 fatty acids were identified respectively. The paired-end sequencing of 48 samples was performed using the Illumina HiSeq2500 platform. Real-time quantitative PCR was used to validate the DEGs identified by RNA-seq analysis. The results showed several DEGs associated with the FA profile of Longissimus thoracis, such as BSCL2 and SAMD8. Enriched terms as the cellular response to corticosteroid (GO:0071384) and glucocorticoid stimulus (GO:0071385) could be highlighted. The identification of structural variations harboring candidate genes for beef FA must contribute to the elucidation of the genetic basis that determines the beef FA composition of intramuscular fat in Nellore cattle. Our results will contribute to the identification of potential biomarkers for complex phenotypes, such as the FA profile, to improve the reliability of the genomic predictions including pre-selected variants using differentiated weighting in the genomic models.
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Affiliation(s)
- Mariana Piatto Berton
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Brazil
| | | | | | | | | | - Elisa Peripolli
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Brazil
| | - Angélica S C Pereira
- Departamento de Nutrição e Produção Animal, Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Pirassununga, Brazil
| | - Ana Fabricia Braga Magalhães
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Brazil
| | - Lucia G Albuquerque
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Brazil
| | - Fernando Baldi
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Brazil
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17
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Wei J, Yang XK, Zhang SK, Segraves KA, Xue HJ. Parallel meta-transcriptome analysis reveals degradation of plant secondary metabolites by beetles and their gut symbionts. Mol Ecol 2022; 31:3999-4016. [PMID: 35665559 DOI: 10.1111/mec.16557] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 03/10/2022] [Accepted: 04/14/2022] [Indexed: 11/28/2022]
Abstract
Switching to a new host plant is a driving force for divergence and speciation in herbivorous insects. This process of incorporating a novel host plant into the diet may require a number of adaptations in the insect herbivores that allow them to consume host plant tissue that may contain toxic secondary chemicals. As a result, herbivorous insects are predicted to have evolved efficient ways to detoxify major plant defenses and increase fitness by either relying on their own genomes or by recruiting other organisms such as microbial gut symbionts. In the present study we used parallel meta-transcriptomic analyses of Altica flea beetles and their gut symbionts to explore the contributions of beetle detoxification mechanisms versus detoxification by their gut consortium. We compared the gut meta-transcriptomes of two sympatric Altica species that feed exclusively on different host plant species as well as their F1 hybrids that were fed one of the two host plant species. These comparisons revealed that gene expression patterns of Altica are dependent on both beetle species identity and diet. The community structure of gut symbionts was also dependent on the identity of the beetle species, and the gene expression patterns of the gut symbionts were significantly correlated with beetle species and plant diet. Some of the enriched genes identified in the beetles and gut symbionts are involved in the degradation of secondary metabolites produced by plants, suggesting that Altica flea beetles may use their gut microbiota to help them feed on and adapt to their host plants.
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Affiliation(s)
- Jing Wei
- School of Life Sciences, Chongqing University, Chongqing 400044, China.,Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xing-Ke Yang
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shou-Ke Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China.,School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Kari A Segraves
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA.,Archbold Biological Station, 123 Main Drive, Venus, FL 33960, USA
| | - Huai-Jun Xue
- College of Life Sciences, Nankai University, Tianjin 300071, China.,Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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18
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Veltsos P, Porcelli D, Fang Y, Cossins AR, Ritchie MG, Snook RR. Experimental sexual selection reveals rapid evolutionary divergence in sex-specific transcriptomes and their interactions following mating. Mol Ecol 2022; 31:3374-3388. [PMID: 35437824 PMCID: PMC9325514 DOI: 10.1111/mec.16473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/31/2022] [Accepted: 04/11/2022] [Indexed: 11/27/2022]
Abstract
Post copulatory interactions between the sexes in internally fertilizing species elicits both sexual conflict and sexual selection. Macroevolutionary and comparative studies have linked these processes to rapid transcriptomic evolution in sex‐specific tissues and substantial transcriptomic post mating responses in females, patterns of which are altered when mating between reproductively isolated species. Here, we tested multiple predictions arising from sexual selection and conflict theory about the evolution of sex‐specific and tissue‐specific gene expression and the post mating response at the microevolutionary level. Following over 150 generations of experimental evolution under either reduced (enforced monogamy) or elevated (polyandry) sexual selection in Drosophila pseudoobscura, we found a substantial effect of sexual selection treatment on transcriptomic divergence in virgin male and female reproductive tissues (testes, male accessory glands, the female reproductive tract and ovaries). Sexual selection treatment also had a dominant effect on the post mating response, particularly in the female reproductive tract – the main arena for sexual conflict – compared to ovaries. This effect was asymmetric with monandry females typically showing more post mating responses than polyandry females, with enriched gene functions varying across treatments. The evolutionary history of the male partner had a larger effect on the post mating response of monandry females, but females from both sexual selection treatments showed unique patterns of gene expression and gene function when mating with males from the alternate treatment. Our microevolutionary results mostly confirm comparative macroevolutionary predictions on the role of sexual selection on transcriptomic divergence and altered gene regulation arising from divergent coevolutionary trajectories between sexual selection treatments.
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Affiliation(s)
- Paris Veltsos
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | - Damiano Porcelli
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Yongxiang Fang
- CGR, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Andrew R Cossins
- Centre for Genomic Research, Institute for Integrative Biology, University of Liverpool, Liverpool, UK
| | - Michael G Ritchie
- Centre for Biological Diversity, University of St Andrews, St Andrews, Fife, KY16 9TH, UK
| | - Rhonda R Snook
- Department of Zoology, Stockholm University, Stockholm, 106 91, Sweden
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19
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Zhang S, Xia Z, Li C, Wang X, Lu X, Zhang W, Ma H, Zhou X, Zhang W, Zhu T, Liu P, Liu G, Wang W, Xia T. Chromosome-Scale Genome Assembly Provides Insights into Speciation of Allotetraploid and Massive Biomass Accumulation of Elephant Grass (Pennisetum purpureum Schum.). Mol Ecol Resour 2022; 22:2363-2378. [PMID: 35347881 DOI: 10.1111/1755-0998.13612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/02/2022] [Accepted: 03/23/2022] [Indexed: 11/29/2022]
Abstract
Elephant grass (Pennisetum purpureum Schum) is an important forage, biofuels and industrial plant widely distributed in tropical and subtropical areas globally. It is characterized with robust growth and high biomass. We sequenced its allopolyploid genome and assembled 2.07 Gb into A' and B sub-genomes of 14 chromosomes with scaffold N50 of 8.47 Mb, yielding a total of 77,139 genes. The allotetraploid speciation occurred approximately 15 MYA after the divergence between Setaria italica and Pennisetum glaucum, according to a phylogenetic analysis of Pennisetum species. Double whole-genome duplication (WGD) and polyploidization events resulted in large scale gene expansion, especially in the key steps of growth and biomass accumulation. Integrated transcriptome profiling revealed the functional divergence between sub-genomes A' and B. A' sub-genome mainly contributed to plant growth, development and photosynthesis, whereas the B sub-genome was primarily responsible for effective transportation and resistance to stimulation. Some key gene families related to cellulose biosynthesis were expanded and highly expressed in stems, which could explain the high cellulose content in elephant grass. Our findings provide deep insights into genetic evolution of elephant grass and will aid future biological research and breeding, even for other grasses in the family Poaceae.
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Affiliation(s)
- Shengkui Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, 250353, Shandong, PR China.,School of Bioengineering, Qilu University of Technology, Jinan, 250353, Shandong, PR China
| | - Zhiqiang Xia
- College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, PR China
| | - Can Li
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, 250353, Shandong, PR China.,School of Bioengineering, Qilu University of Technology, Jinan, 250353, Shandong, PR China
| | - Xiaohan Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, 250353, Shandong, PR China.,School of Bioengineering, Qilu University of Technology, Jinan, 250353, Shandong, PR China
| | - Xianqin Lu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, 250353, Shandong, PR China.,School of Bioengineering, Qilu University of Technology, Jinan, 250353, Shandong, PR China
| | - Wenqing Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, 250353, Shandong, PR China.,School of Bioengineering, Qilu University of Technology, Jinan, 250353, Shandong, PR China
| | - Haizhen Ma
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, 250353, Shandong, PR China.,School of Bioengineering, Qilu University of Technology, Jinan, 250353, Shandong, PR China
| | - Xincheng Zhou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haiko, 571101, Hainan, PR China
| | - Weixiong Zhang
- Department of Computer Science and Engineering, Department of Genetics, Washington University, St. Louis, MO, USA
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Pandao Liu
- Institute of Tropical Crops Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571700, Hainan, PR China
| | - Guodao Liu
- Institute of Tropical Crops Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571700, Hainan, PR China
| | - Wenquan Wang
- College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, PR China.,Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haiko, 571101, Hainan, PR China
| | - Tao Xia
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, 250353, Shandong, PR China.,School of Bioengineering, Qilu University of Technology, Jinan, 250353, Shandong, PR China
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20
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He X, Wu R, Yun Y, Qin X, Chen L, Han Y, Wu J, Sha L, Borjigin G. Transcriptome analysis of messenger RNA and long noncoding RNA related to different developmental stages of tail adipose tissues of sunite sheep. Food Sci Nutr 2021; 9:5722-5734. [PMID: 34646540 PMCID: PMC8498062 DOI: 10.1002/fsn3.2537] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 08/03/2021] [Accepted: 08/09/2021] [Indexed: 12/18/2022] Open
Abstract
The tail fat of sheep is the most typical deposited fat, and it can be widely used in human daily life, such as diet, cosmetics, and industrial raw materials. To understand the potential regulatory mechanism of different growth stages of tail fat in Sunite sheep, we performed high-throughput RNA sequencing to characterize the long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression profiles of the sheep tail fat at the age of 6, 18, and 30 months. A total of 223 differentially expressed genes (DEGs) and 148 differentially expressed lncRNAs were found in the tail fat of 6-, 18-, and 30-month-old sheep. Based on functional analysis, we found that fat-related DEGs were mainly expressed at 6 months of age and gradually decreased at 18 and 30 months of age. The target gene prediction analysis shows that most of the lncRNAs target more than 20 mRNAs as their transregulators. Further, we obtained several fat-related differentially expressed target genes; these target genes interact with different differentially expressed lncRNAs at various ages and play an important role in the development of tail fat. Based on the DEGs and differentially expressed lncRNAs, we established three co-expression networks for each comparison group. Finally, we concluded that the development of the sheep tail fat is more active during the early stage of growth and gradually decreases with the increase in age. The mutual regulation of lncRNAs and mRNAs may play a key role in this complex biological process.
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Affiliation(s)
- Xige He
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Rihan Wu
- College of Biochemistry and EngineeringHohhot Vocational CollegeHohhotChina
| | - Yueying Yun
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
- School of Life Science and TechnologyInner Mongolia University of Science and TechnologyBaotouChina
| | - Xia Qin
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Lu Chen
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Yunfei Han
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Jindi Wu
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Lina Sha
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Gerelt Borjigin
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
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21
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Marx HE, Carboni M, Douzet R, Perrier C, Delbart F, Thuiller W, Lavergne S, Tank DC. Can functional genomic diversity provide novel insights into mechanisms of community assembly? A pilot study from an invaded alpine streambed. Ecol Evol 2021; 11:12075-12091. [PMID: 34522362 PMCID: PMC8427620 DOI: 10.1002/ece3.7973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/28/2021] [Accepted: 07/09/2021] [Indexed: 11/30/2022] Open
Abstract
An important focus of community ecology, including invasion biology, is to investigate functional trait diversity patterns to disentangle the effects of environmental and biotic interactions. However, a notable limitation is that studies usually rely on a small and easy-to-measure set of functional traits, which might not immediately reflect ongoing ecological responses to changing abiotic or biotic conditions, including those that occur at a molecular or physiological level. We explored the potential of using the diversity of expressed genes-functional genomic diversity (FGD)-to understand ecological dynamics of a recent and ongoing alpine invasion. We quantified FGD based on transcriptomic data measured for 26 plant species occurring along adjacent invaded and pristine streambeds. We used an RNA-seq approach to summarize the overall number of expressed transcripts and their annotations to functional categories, and contrasted this with functional trait diversity (FTD) measured from a suite of characters that have been traditionally considered in plant ecology. We found greater FGD and FTD in the invaded community, independent of differences in species richness. However, the magnitude of functional dispersion was greater from the perspective of FGD than from FTD. Comparing FGD between congeneric alien-native species pairs, we did not find many significant differences in the proportion of genes whose annotations matched functional categories. Still, native species with a greater relative abundance in the invaded community compared with the pristine tended to express a greater fraction of genes at significant levels in the invaded community, suggesting that changes in FGD may relate to shifts in community composition. Comparisons of diversity patterns from the community to the species level offer complementary insights into processes and mechanisms driving invasion dynamics. FGD has the potential to illuminate cryptic changes in ecological diversity, and we foresee promising avenues for future extensions across taxonomic levels and macro-ecosystems.
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Affiliation(s)
- Hannah E. Marx
- Department of Biology & Museum of Southwestern BiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | | | - Rolland Douzet
- CNRSLautaretJardin du LautaretUniversité Grenoble AlpesGrenobleFrance
| | | | - Franck Delbart
- CNRSLautaretJardin du LautaretUniversité Grenoble AlpesGrenobleFrance
| | - Wilfried Thuiller
- Laboratoire d'Ecologie Alpine (LECA)CNRSUniversité Grenoble AlpesUniversité Savoie Mont BlancGrenobleFrance
| | - Sébastien Lavergne
- Laboratoire d'Ecologie Alpine (LECA)CNRSUniversité Grenoble AlpesUniversité Savoie Mont BlancGrenobleFrance
| | - David C. Tank
- Department of Biological SciencesUniversity of IdahoMoscowIdahoUSA
- Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowIdahoUSA
- Stillinger HerbariumUniversity of IdahoMoscowIdahoUSA
- Present address:
Department of Botany and Rocky Mountain HerbariumUniversity of WyomingLaramieWY82072‐3165USA
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22
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Peng Y, Li H, Liu Z, Zhang C, Li K, Gong Y, Geng L, Su J, Guan X, Liu L, Zhou R, Zhao Z, Guo J, Liang Q, Li X. Chromosome-level genome assembly of the Arctic fox (Vulpes lagopus) using PacBio sequencing and Hi-C technology. Mol Ecol Resour 2021; 21:2093-2108. [PMID: 33829635 DOI: 10.1111/1755-0998.13397] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 03/28/2021] [Accepted: 03/30/2021] [Indexed: 10/21/2022]
Abstract
The Arctic fox (Vulpes lagopus) is the only fox species occurring in the Arctic and has adapted to its extreme climatic conditions. Currently, the molecular basis of its adaptation to the extreme climate has not been characterized. Here, we applied PacBio sequencing and chromosome structure capture technique to assemble the first V. lagopus genome assembly, which is assembled into chromosome fragments. The genome assembly has a total length of 2.345 Gb with a contig N50 of 31.848 Mb and a scaffold N50 of 131.537 Mb, consisting of 25 pseudochromosomal scaffolds. The V. lagopus genome had approximately 32.33% repeat sequences. In total, 21,278 protein-coding genes were predicted, of which 99.14% were functionally annotated. Compared with 12 other mammals, V. lagopus was most closely related to V. Vulpes with an estimated divergence time of ~7.1 Ma. The expanded gene families and positively selected genes potentially play roles in the adaptation of V. lagopus to Arctic extreme environment. This high-quality assembled genome will not only promote future studies of genetic diversity and evolution in foxes and other canids but also provide important resources for conservation of Arctic species.
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Affiliation(s)
- Yongdong Peng
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Hong Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Zhengzhu Liu
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Chuansheng Zhang
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Keqiang Li
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Mathematics and Information Science, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yuanfang Gong
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Liying Geng
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jingjing Su
- Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, China
| | - Xuemin Guan
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Lei Liu
- College of Animal Science and Technology, Shandong Agricultural University, Tai-an, China
| | - Ruihong Zhou
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Ziya Zhao
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jianxu Guo
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing, China
| | - Xianglong Li
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
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23
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Gage JL, Vaillancourt B, Hamilton JP, Manrique-Carpintero NC, Gustafson TJ, Barry K, Lipzen A, Tracy WF, Mikel MA, Kaeppler SM, Buell CR, de Leon N. Multiple Maize Reference Genomes Impact the Identification of Variants by Genome-Wide Association Study in a Diverse Inbred Panel. THE PLANT GENOME 2019; 12:180069. [PMID: 31290926 DOI: 10.3835/plantgenome2018.09.0069] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Use of a single reference genome for genome-wide association studies (GWAS) limits the gene space represented to that of a single accession. This limitation can complicate identification and characterization of genes located within presence-absence variations (PAVs). In this study, we present the draft de novo genome assembly of 'PHJ89', an 'Oh43'-type inbred line of maize ( L.). From three separate reference genome assemblies ('B73', 'PH207', and PHJ89) that represent the predominant germplasm groups of maize, we generated three separate whole-seedling gene expression profiles and single nucleotide polymorphism (SNP) matrices from a panel of 942 diverse inbred lines. We identified 34,447 (B73), 39,672 (PH207), and 37,436 (PHJ89) transcripts that are not present in the respective reference genome assemblies. Genome-wide association studies were conducted in the 942 inbred panel with both the SNP and expression data values to map (SCMV) resistance. Highlighting the impact of alternative reference genomes in gene discovery, the GWAS results for SCMV resistance with expression values as a surrogate measure of PAV resulted in robust detection of the physical location of a known resistance gene when the B73 reference that contains the gene was used, but not the PH207 reference. This study provides the valuable resource of the Oh43-type PHJ89 genome assembly as well as SNP and expression data for 942 individuals generated from three different reference genomes.
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24
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Million CR, Wijeratne S, Cassone BJ, Lee S, Rouf Mian MA, McHale LK, Dorrance AE. Hybrid Genome Assembly of a Major Quantitative Disease Resistance Locus in Soybean Toward Fusarium graminearum. THE PLANT GENOME 2019; 12. [PMID: 31290916 DOI: 10.3835/plantgenome2018.12.0102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 03/11/2019] [Indexed: 05/27/2023]
Abstract
Schwabe [teleomorph: Gibberella zeae (Schweintiz) Petch] has been identified as a pathogen of soybean [ (L.) Merr.] causing seed, seedling damping-off and root rot in North America. A major quantitative disease resistance locus (QDRL) that contributed 38.5% of the phenotypic variance toward in soybean was previously identified through mapping of a recombinant inbred line (RIL) population derived from a cross between 'Wyandot' and PI 567301B. This major QDRL mapped to chromosome 8 to a predicted 305 kb region harboring 36 genes. This locus maps near the locus for soybean cyst nematode (SCN) and the locus contributing to seed coat color. Long-read sequencing of the region was completed and variations in gene sequence and gene order compared with the 'Williams 82' reference were identified. Molecular markers were developed for genes within this region and mapped in the original population, slightly narrowing the region of interest. Analyses of the hybrid genome reassembly using three previously published bacterial artificial chromosome (BAC) sequences (BAC56G2, BAC104J7, and BAC77G7-a) combined with RNA-sequencing narrowed the region making candidate gene identification possible. The markers within this region may be used for marker-assisted selection (MAS). There were 10 differentially expressed genes between resistant and susceptible lines, with four of these candidates also located within the genomic interval defined by the flanking markers. These genes included an actin-related protein 2/3 complex subunit, an unknown protein, a hypothetical protein, and a chalcone synthase 3.
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25
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Waters AJ, Makarevitch I, Noshay J, Burghardt LT, Hirsch CN, Hirsch CD, Springer NM. Natural variation for gene expression responses to abiotic stress in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:706-717. [PMID: 28188666 DOI: 10.1111/tpj.13414] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 10/26/2016] [Accepted: 11/01/2016] [Indexed: 05/27/2023]
Abstract
Plants respond to abiotic stress through a variety of physiological, biochemical, and transcriptional mechanisms. Many genes exhibit altered levels of expression in response to abiotic stress, which requires concerted action of both cis- and trans-regulatory features. In order to study the variability in transcriptome response to abiotic stress, RNA sequencing was performed using 14-day-old maize seedlings of inbreds B73, Mo17, Oh43, PH207 and B37 under control, cold and heat conditions. Large numbers of genes that responded differentially to stress between parental inbred lines were identified. RNA sequencing was also performed on similar tissues of the F1 hybrids produced by crossing B73 and each of the three other inbred lines. By evaluating allele-specific transcript abundance in the F1 hybrids, we were able to measure the abundance of cis- and trans-regulatory variation between genotypes for both steady-state and stress-responsive expression differences. Although examples of trans-regulatory variation were observed, cis-regulatory variation was more common for both steady-state and stress-responsive expression differences. The genes with cis-allelic variation for response to cold or heat stress provided an opportunity to study the basis for regulatory diversity.
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Affiliation(s)
- Amanda J Waters
- Department of Plant Biology University of Minnesota, Microbial and Plant Genomics Institute, Saint Paul, MN, 55108, USA
| | - Irina Makarevitch
- Department of Biology, Hamline University, Saint Paul, MN, 55114, USA
| | - Jaclyn Noshay
- Department of Plant Biology University of Minnesota, Microbial and Plant Genomics Institute, Saint Paul, MN, 55108, USA
| | - Liana T Burghardt
- Department of Plant Biology University of Minnesota, Microbial and Plant Genomics Institute, Saint Paul, MN, 55108, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, Microbial and Plant Genomics Institute, St. Paul, MN, 55108, USA
| | - Cory D Hirsch
- Department of Plant Pathology, Microbial and Plant Genomics Institute, St. Paul, MN, 55108, USA
| | - Nathan M Springer
- Department of Plant Biology University of Minnesota, Microbial and Plant Genomics Institute, Saint Paul, MN, 55108, USA
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26
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Michael TP, Bryant D, Gutierrez R, Borisjuk N, Chu P, Zhang H, Xia J, Zhou J, Peng H, El Baidouri M, Ten Hallers B, Hastie AR, Liang T, Acosta K, Gilbert S, McEntee C, Jackson SA, Mockler TC, Zhang W, Lam E. Comprehensive definition of genome features in Spirodela polyrhiza by high-depth physical mapping and short-read DNA sequencing strategies. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:617-635. [PMID: 27754575 DOI: 10.1111/tpj.13400] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 10/05/2016] [Accepted: 10/07/2016] [Indexed: 05/15/2023]
Abstract
Spirodela polyrhiza is a fast-growing aquatic monocot with highly reduced morphology, genome size and number of protein-coding genes. Considering these biological features of Spirodela and its basal position in the monocot lineage, understanding its genome architecture could shed light on plant adaptation and genome evolution. Like many draft genomes, however, the 158-Mb Spirodela genome sequence has not been resolved to chromosomes, and important genome characteristics have not been defined. Here we deployed rapid genome-wide physical maps combined with high-coverage short-read sequencing to resolve the 20 chromosomes of Spirodela and to empirically delineate its genome features. Our data revealed a dramatic reduction in the number of the rDNA repeat units in Spirodela to fewer than 100, which is even fewer than that reported for yeast. Consistent with its unique phylogenetic position, small RNA sequencing revealed 29 Spirodela-specific microRNA, with only two being shared with Elaeis guineensis (oil palm) and Musa balbisiana (banana). Combining DNA methylation data and small RNA sequencing enabled the accurate prediction of 20.5% long terminal repeats (LTRs) that doubled the previous estimate, and revealed a high Solo:Intact LTR ratio of 8.2. Interestingly, we found that Spirodela has the lowest global DNA methylation levels (9%) of any plant species tested. Taken together our results reveal a genome that has undergone reduction, likely through eliminating non-essential protein coding genes, rDNA and LTRs. In addition to delineating the genome features of this unique plant, the methodologies described and large-scale genome resources from this work will enable future evolutionary and functional studies of this basal monocot family.
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Affiliation(s)
- Todd P Michael
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
- IBIS Bioscience, Carlsbad, CA, USA
| | - Douglas Bryant
- IBIS Bioscience, Carlsbad, CA, USA
- Donald Danforth Center for Plant Science, St. Louis, MO, USA
| | - Ryan Gutierrez
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
| | - Nikolai Borisjuk
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
| | - Philomena Chu
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
| | - Hanzhong Zhang
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
| | - Jing Xia
- Institute for Systems Biology, Jianghan University, Wuhan, China
- Department of Computer Science and Engineering, Washington University, St. Louis, MO, USA
| | - Junfei Zhou
- Institute for Systems Biology, Jianghan University, Wuhan, China
| | - Hai Peng
- Institute for Systems Biology, Jianghan University, Wuhan, China
| | - Moaine El Baidouri
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | | | | | | | - Kenneth Acosta
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
| | - Sarah Gilbert
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
| | | | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Todd C Mockler
- Donald Danforth Center for Plant Science, St. Louis, MO, USA
| | - Weixiong Zhang
- Institute for Systems Biology, Jianghan University, Wuhan, China
- Department of Computer Science and Engineering, Washington University, St. Louis, MO, USA
| | - Eric Lam
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
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Abstract
Abundant but short second-generation sequencing reads make assembly difficult, leading to fragmented genomes and gene annotations. Gene structure information from RNA sequences can be used to improve the completeness and contiguity of an assembly, but bioinformatics methods have been lacking. Rascaf is a highly efficient tool leveraging long-range continuity information from intron spanning RNA sequencing (RNA-seq) read pairs to detect new contig connections. It determines a heaviest path in an exon block graph that simultaneously represents a gene and the underlying contig relationships. Rascaf is more accurate than its competitors, highly precise, and finds thousands of new verifiable connections in several draft Rosaceae genomes. Lightweight and practical, it can be readily incorporated into sequencing pipelines to improve an assembly and its gene annotations.
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28
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Redekar NR, Clevinger EM, Laskar MA, Biyashev RM, Ashfield T, Jensen RV, Jeong SC, Tolin SA, Saghai Maroof MA. Candidate Gene Sequence Analyses toward Identifying -Type Resistance to. THE PLANT GENOME 2016; 9. [PMID: 27898808 DOI: 10.3835/plantgenome2015.09.0088] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/22/2016] [Indexed: 05/25/2023]
Abstract
is one of three genetic loci conferring strain-specific resistance to (SMV). The locus has been mapped to a 154-kb region on chromosome 14, containing a cluster of five nucleotide-binding leucine-rich repeat (NB-LRR) resistance genes. High sequence similarity between the candidate genes challenges fine mapping of the locus. Among the five, Glyma14g38533 showed the highest transcript abundance in 1 to 3 h of SMV-G7 inoculation. Comparative sequence analyses were conducted with the five candidate NB-LRR genes from susceptible (-type) soybean [ (L.) Merr.] cultivar Williams 82, resistant (-type) cultivar Hwangkeum, and resistant lines L29 and RRR. Sequence comparisons revealed that Glyma14g38533 had far more polymorphisms than the other candidate genes. Interestingly, Glyma14g38533 gene from -type lines exhibited 150 single-nucleotide polymorphism (SNP and six insertion-deletion (InDel) markers relative to -type line, Furthermore, the polymorphisms identified in three -type lines were highly conserved. Several polymorphisms were validated in 18 -type resistant and six -type susceptible lines and were found associated with their disease response. The majority of the polymorphisms were located in LRR domain encoding region, which is involved in pathogen recognition via protein-protein interactions. These findings associating Glyma14g38533 with -type resistance to SMV suggest it is the most likely candidate gene for .
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29
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Bakir Y, Eldem V, Zararsiz G, Unver T. Global Transcriptome Analysis Reveals Differences in Gene Expression Patterns Between Nonhyperhydric and Hyperhydric Peach Leaves. THE PLANT GENOME 2016; 9. [PMID: 27898837 DOI: 10.3835/plantgenome2015.09.0080] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Hyperhydricity is a morphophysiological disorder of plants in tissue culture characterized morphologically by the presence of translucent, thick, curled, and fragile leaves as a result of excessive water intake. Since clonal propagation is a major in vitro technique for multiplying plants vegetatively, the emergence of hyperhydricity-related symptoms causes significant economic losses to agriculture and horticulture. Although numerous efforts have been hitherto devoted to the morphological and anatomical responses of plants to hyperhydricity, the underlying molecular mechanism remains largely unknown. Here, a genome-wide transcriptome analysis was performed to identify differentially expressed genes in hyperhydric and nonhyperhydric leaves of peach [ (L.) Batsch]. The RNA sequencing (RNA-Seq) analysis showed that the expression of >300 transcripts was altered between control and hyperhydric leaf cells. The top 30 differentially expressed transcripts (DETs) were related to the posttranscriptional regulators of organelle gene expression and photosynthesis, cellular elimination, plant cuticle development, and abiotic stress response processes. The expression of 10 DETs was also conformed by quantitative real-time polymerase chain reaction (RT-qPCR) in hyperhydric and nonhyperhydric leaves. As a complex biological process, hyperhydricity alters the expression of various transcripts including transcription factor (), RNA binding protein (pentatricopeptide, ), transporter protein (), and . Thus, this genome-wide transcriptome profiling study may help elucidate the molecular mechanism of hyperhydricity.
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30
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Serba DD, Uppalapati SR, Mukherjee S, Krom N, Tang Y, Mysore KS, Saha MC. Transcriptome Profiling of Rust Resistance in Switchgrass Using RNA-Seq Analysis. THE PLANT GENOME 2015; 8:eplantgenome2014.10.0075. [PMID: 33228298 DOI: 10.3835/plantgenome2014.10.0075] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 12/23/2014] [Indexed: 06/11/2023]
Abstract
Switchgrass rust caused by Puccinia emaculata is a major limiting factor for switchgrass (Panicum virgatum L.) production, especially in monoculture. Natural populations of switchgrass displayed diverse reactions to P. emaculata when evaluated in an Ardmore, OK, field. To identify the differentially expressed genes during the rust infection process and the mechanisms of switchgrass rust resistance, transcriptome analysis using RNA-Seq was conducted in two pseudo-F1 parents ('PV281' and 'NFGA472'), and three moderately resistant and three susceptible progenies selected from a three-generation, four-founder switchgrass population (K5 × A4) × (AP13 × VS16). On average, 23.5 million reads per sample (leaf tissue was collected at 0, 24, and 60 h post-inoculation (hpi)) were obtained from paired-end (2 × 100 bp) sequencing on the Illumina HiSeq2000 platform. Mapping of the RNA-Seq reads to the switchgrass reference genome (AP13 ver. 1.1 assembly) constructed a total of 84,209 transcripts from 98,007 gene loci among all of the samples. Further analysis revealed that host defense-related genes, including the nucleotide binding site-leucine-rich repeat domain containing disease resistance gene analogs, play an important role in resistance to rust infection. Rust-induced gene (RIG) transcripts inherited across generations were identified. The rust-resistant gene transcripts can be a valuable resource for developing molecular markers for rust resistance. Furthermore, the rust-resistant genotypes and gene transcripts identified in this study can expedite rust-resistant cultivar development in switchgrass.
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Affiliation(s)
- Desalegn D Serba
- Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401
- Department of Energy, BioEnergy Science Center, Oak Ridge National Lab., Oak Ridge, TN, 37831
| | - Srinivasa Rao Uppalapati
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401
- Dupont Pioneer, Dupont Knowledge Center, Turakapally, Hyderabad, Telangana, India, 500 078
| | - Shreyartha Mukherjee
- Computing Services, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401
| | - Nick Krom
- Computing Services, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401
| | - Yuhong Tang
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401
- Department of Energy, BioEnergy Science Center, Oak Ridge National Lab., Oak Ridge, TN, 37831
| | - Kirankumar S Mysore
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401
| | - Malay C Saha
- Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401
- Department of Energy, BioEnergy Science Center, Oak Ridge National Lab., Oak Ridge, TN, 37831
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