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Maura F, Rajanna AR, Ziccheddu B, Poos AM, Derkach A, Maclachlan K, Durante M, Diamond B, Papadimitriou M, Davies F, Boyle EM, Walker B, Hultcrantz M, Silva A, Hampton O, Teer JK, Siegel EM, Bolli N, Jackson GH, Kaiser M, Pawlyn C, Cook G, Kazandjian D, Stein C, Chesi M, Bergsagel L, Mai EK, Goldschmidt H, Weisel KC, Fenk R, Raab MS, Van Rhee F, Usmani S, Shain KH, Weinhold N, Morgan G, Landgren O. Genomic Classification and Individualized Prognosis in Multiple Myeloma. J Clin Oncol 2024; 42:1229-1240. [PMID: 38194610 DOI: 10.1200/jco.23.01277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/08/2023] [Accepted: 10/23/2023] [Indexed: 01/11/2024] Open
Abstract
PURPOSE Outcomes for patients with newly diagnosed multiple myeloma (NDMM) are heterogenous, with overall survival (OS) ranging from months to over 10 years. METHODS To decipher and predict the molecular and clinical heterogeneity of NDMM, we assembled a series of 1,933 patients with available clinical, genomic, and therapeutic data. RESULTS Leveraging a comprehensive catalog of genomic drivers, we identified 12 groups, expanding on previous gene expression-based molecular classifications. To build a model predicting individualized risk in NDMM (IRMMa), we integrated clinical, genomic, and treatment variables. To correct for time-dependent variables, including high-dose melphalan followed by autologous stem-cell transplantation (HDM-ASCT), and maintenance therapy, a multi-state model was designed. The IRMMa model accuracy was significantly higher than all comparator prognostic models, with a c-index for OS of 0.726, compared with International Staging System (ISS; 0.61), revised-ISS (0.572), and R2-ISS (0.625). Integral to model accuracy was 20 genomic features, including 1q21 gain/amp, del 1p, TP53 loss, NSD2 translocations, APOBEC mutational signatures, and copy-number signatures (reflecting the complex structural variant chromothripsis). IRMMa accuracy and superiority compared with other prognostic models were validated on 256 patients enrolled in the GMMG-HD6 (ClinicalTrials.gov identifier: NCT02495922) clinical trial. Individualized patient risks were significantly affected across the 12 genomic groups by different treatment strategies (ie, treatment variance), which was used to identify patients for whom HDM-ASCT is particularly effective versus patients for whom the impact is limited. CONCLUSION Integrating clinical, demographic, genomic, and therapeutic data, to our knowledge, we have developed the first individualized risk-prediction model enabling personally tailored therapeutic decisions for patients with NDMM.
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Affiliation(s)
- Francesco Maura
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Arjun Raj Rajanna
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Bachisio Ziccheddu
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Alexandra M Poos
- Heidelberg Myeloma Center, Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit (CCU) Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andriy Derkach
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kylee Maclachlan
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael Durante
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Benjamin Diamond
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Marios Papadimitriou
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Faith Davies
- Myeloma Research Program, New York University Langone, Perlmutter Cancer Center, New York, NY
| | - Eileen M Boyle
- Myeloma Research Program, New York University Langone, Perlmutter Cancer Center, New York, NY
| | - Brian Walker
- Division of Hematology Oncology, Melvin and Bren Simon Comprehensive Cancer Center, Indiana University, Indianapolis, IN
| | - Malin Hultcrantz
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ariosto Silva
- Department of Malignant Hematology, Moffitt Cancer Center, Tampa, FL
| | | | - Jamie K Teer
- Department of Biostatistics & Bioinformatics, Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Erin M Siegel
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL
| | - Niccolò Bolli
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Oncology and Onco-Hematology, University of Milan, Milan, Italy
| | - Graham H Jackson
- Freeman Hospital, The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle, United Kingdom
| | - Martin Kaiser
- The Institute of Cancer Research, London, United Kingdom
| | - Charlotte Pawlyn
- Leeds Cancer Research UK Clinical Trials Unit, Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, United Kingdom
| | - Gordon Cook
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Dickran Kazandjian
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Caleb Stein
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Marta Chesi
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Leif Bergsagel
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Elias K Mai
- Heidelberg Myeloma Center, Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
| | - Hartmut Goldschmidt
- Heidelberg Myeloma Center, Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
| | - Katja C Weisel
- Department of Oncology, Hematology and Blood and Marrow Transplant, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Roland Fenk
- Department of Hematology, Oncology and Clinical Immunology, University-Hospital Duesseldorf, Duesseldorf, Germany
| | - Marc S Raab
- Heidelberg Myeloma Center, Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit (CCU) Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Fritz Van Rhee
- Myeloma Institute for Research & Therapy, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Saad Usmani
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kenneth H Shain
- Department of Malignant Hematology, Moffitt Cancer Center, Tampa, FL
| | - Niels Weinhold
- Heidelberg Myeloma Center, Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit (CCU) Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Gareth Morgan
- Myeloma Research Program, New York University Langone, Perlmutter Cancer Center, New York, NY
| | - Ola Landgren
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
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Ricciuti B, Lamberti G, Puchala SR, Mahadevan NR, Lin JR, Alessi JV, Chowdhury A, Li YY, Wang X, Spurr L, Pecci F, Di Federico A, Venkatraman D, Barrichello AP, Gandhi M, Vaz VR, Pangilinan AJ, Haradon D, Lee E, Gupta H, Pfaff KL, Welsh EL, Nishino M, Cherniack AD, Johnson BE, Weirather JL, Dryg ID, Rodig SJ, Sholl LM, Sorger P, Santagata S, Umeton R, Awad MM. Genomic and Immunophenotypic Landscape of Acquired Resistance to PD-(L)1 Blockade in Non-Small-Cell Lung Cancer. J Clin Oncol 2024; 42:1311-1321. [PMID: 38207230 DOI: 10.1200/jco.23.00580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 08/27/2023] [Accepted: 10/24/2023] [Indexed: 01/13/2024] Open
Abstract
PURPOSE Although immune checkpoint inhibitors (ICI) have extended survival in patients with non-small-cell lung cancer (NSCLC), acquired resistance (AR) to ICI frequently develops after an initial benefit. However, the mechanisms of AR to ICI in NSCLC are largely unknown. METHODS Comprehensive tumor genomic profiling, machine learning-based assessment of tumor-infiltrating lymphocytes, multiplexed immunofluorescence, and/or HLA-I immunohistochemistry (IHC) were performed on matched pre- and post-ICI tumor biopsies from patients with NSCLC treated with ICI at the Dana-Farber Cancer Institute who developed AR to ICI. Two additional cohorts of patients with intervening chemotherapy or targeted therapies between biopsies were included as controls. RESULTS We performed comprehensive genomic profiling and immunophenotypic characterization on samples from 82 patients with NSCLC and matched pre- and post-ICI biopsies and compared findings with a control cohort of patients with non-ICI intervening therapies between biopsies (chemotherapy, N = 32; targeted therapies, N = 89; both, N = 17). Putative resistance mutations were identified in 27.8% of immunotherapy-treated cases and included acquired loss-of-function mutations in STK11, B2M, APC, MTOR, KEAP1, and JAK1/2; these acquired alterations were not observed in the control groups. Immunophenotyping of matched pre- and post-ICI samples demonstrated significant decreases in intratumoral lymphocytes, CD3e+ and CD8a+ T cells, and PD-L1-PD1 engagement, as well as increased distance between tumor cells and CD8+PD-1+ T cells. There was a significant decrease in HLA class I expression in the immunotherapy cohort at the time of AR compared with the chemotherapy (P = .005) and the targeted therapy (P = .01) cohorts. CONCLUSION These findings highlight the genomic and immunophenotypic heterogeneity of ICI resistance in NSCLC, which will need to be considered when developing novel therapeutic strategies aimed at overcoming resistance.
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Affiliation(s)
- Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Giuseppe Lamberti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Sreekar R Puchala
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA
| | | | - Jia-Ren Lin
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA
| | - Joao V Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Alexander Chowdhury
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA
| | - Yvonne Y Li
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Xinan Wang
- Harvard School of Public Health, Boston, MA
| | - Liam Spurr
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Federica Pecci
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Deepti Venkatraman
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Malini Gandhi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Victor R Vaz
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Andy J Pangilinan
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Danielle Haradon
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Elinton Lee
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Hersh Gupta
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA
| | - Kathleen L Pfaff
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Emma L Welsh
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Mizuki Nishino
- Department of Radiology, Brigham and Women's Hospital, Boston, MA
| | - Andrew D Cherniack
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA
| | - Bruce E Johnson
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Jason L Weirather
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Ian D Dryg
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Peter Sorger
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA
| | - Sandro Santagata
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA
| | - Renato Umeton
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA
| | - Mark M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
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153
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Williams A. Multiomics data integration, limitations, and prospects to reveal the metabolic activity of the coral holobiont. FEMS Microbiol Ecol 2024; 100:fiae058. [PMID: 38653719 PMCID: PMC11067971 DOI: 10.1093/femsec/fiae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/25/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024] Open
Abstract
Since their radiation in the Middle Triassic period ∼240 million years ago, stony corals have survived past climate fluctuations and five mass extinctions. Their long-term survival underscores the inherent resilience of corals, particularly when considering the nutrient-poor marine environments in which they have thrived. However, coral bleaching has emerged as a global threat to coral survival, requiring rapid advancements in coral research to understand holobiont stress responses and allow for interventions before extensive bleaching occurs. This review encompasses the potential, as well as the limits, of multiomics data applications when applied to the coral holobiont. Synopses for how different omics tools have been applied to date and their current restrictions are discussed, in addition to ways these restrictions may be overcome, such as recruiting new technology to studies, utilizing novel bioinformatics approaches, and generally integrating omics data. Lastly, this review presents considerations for the design of holobiont multiomics studies to support lab-to-field advancements of coral stress marker monitoring systems. Although much of the bleaching mechanism has eluded investigation to date, multiomic studies have already produced key findings regarding the holobiont's stress response, and have the potential to advance the field further.
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Affiliation(s)
- Amanda Williams
- Microbial Biology Graduate Program, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, United States
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, United States
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154
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Zhang Q, Feng X, Wang X, Liu F, Zhou B, Zhang C, Wang Y, Shi J, Hao S, Hui L, Yi B. [Clinical and genetic analysis of two pedigrees affected with Carnitine-acylcarnitine translocase deficiency due to variant of SLC25A20 gene]. Zhonghua Yi Xue Yi Chuan Xue Za Zhi 2024; 41:467-472. [PMID: 38565514 DOI: 10.3760/cma.j.cn511374-20220721-00482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
OBJECTIVE To analyze the clinical phenotype and genotypes of two children with Carnitine-acylcarnitine translocase deficiency (CACTD). METHODS Two children diagnosed with CACTD at the Gansu Provincial Maternal and Child Health Care Hospital respectively on January 3 and November 19, 2018 were selected as the study subjects. Trio-whole exome sequencing (trio-WES) was carried out, and candidate variants were validated through Sanger sequencing and pathogenicity analysis. RESULTS Both children were males and had manifested mainly with hypoglycemia. Trio-WES and Sanger sequencing showed that child 1 had harbored compound heterozygous variants of the SLC25A20 gene, namely c.49G>C (p.Gly17Arg) and c.106-2A>G, which were inherited from his father and mother, respectively. Child 2 had harbored homozygous c.199-10T>G variants of the SLC25A20 gene, which were inherited from both of his parents. Among these, the c.106-2A>G and c.49G>C variants were unreported previously. Based on the guidelines from the American College of Medical Genetics and Genomics (ACMG), the c.49G>C (p.Gly17Arg), c.106-2A>G, and c.199-10T>G variants were classified as likely pathogenic (PM2_supporting+PP3+PM3_strong+PP4), pathogenic (PVS1+PM2_supporting+PM5+PP3), and pathogenic (PVS1+PM2_supporting+PP3+PP5), respectively. CONCLUSION Combined with their clinical phenotype and genetic analysis, both children were diagnosed with CACTD. Above finding has provided a basis for their treatment as well as genetic counseling and prenatal diagnosis for their families.
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Affiliation(s)
- Qinghua Zhang
- Medical Genetic Center, Gansu Provincial Maternal and Child Health Care Hospital (Gansu Province Central Hospital), Lanzhou, Gansu 730050, China.
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155
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Taylor JY, Jones-Patten A, Prescott L, Potts-Thompson S, Joyce C, Tayo B, Saban K. The race-based stress reduction intervention (RiSE) study on African American women in NYC and Chicago: Design and methods for complex genomic analysis. PLoS One 2024; 19:e0295293. [PMID: 38598554 PMCID: PMC11006145 DOI: 10.1371/journal.pone.0295293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/19/2023] [Indexed: 04/12/2024] Open
Abstract
RiSE study aims to evaluate a race-based stress-reduction intervention as an effective strategy to improve coping and decrease stress-related symptoms, inflammatory burden, and modify DNA methylation of stress response-related genes in older AA women. This article will describe genomic analytic methods to be utilized in this longitudinal, randomized clinical trial of older adult AA women in Chicago and NYC that examines the effect of the RiSE intervention on DNAm pre- and post-intervention, and its overall influence on inflammatory burden. Salivary DNAm will be measured at baseline and 6 months following the intervention, using the Oragene-DNA kit. Measures of perceived stress, depressive symptoms, fatigue, sleep, inflammatory burden, and coping strategies will be assessed at 4 time points including at baseline, 4 weeks, 8 weeks, and 6 months. Genomic data analysis will include the use of pre-processed and quality-controlled methylation data expressed as beta (β) values. Association analyses will be performed to detect differentially methylated sites on the targeted candidate genes between the intervention and non-intervention groups using the Δβ (changes in methylation) with adjustment for age, health behaviors, early life adversity, hybridization batch, and top principal components of the probes as covariates. To account for multiple testing, we will use FDR adjustment with a corrected p-value of <0.05 regarded as statistically significant. To assess the relationship between inflammatory burden and Δβ among the study samples, we will repeat association analyses with the inclusion of individual inflammation protein measures. ANCOVA will be used because it is more statistically powerful to detect differences.
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Affiliation(s)
- Jacquelyn Y. Taylor
- Center for Research on People of Color, Columbia University School of Nursing, New York, New York, United States of America
| | - Alexandria Jones-Patten
- Center for Research on People of Color, Columbia University School of Nursing, New York, New York, United States of America
| | - Laura Prescott
- Center for Research on People of Color, Columbia University School of Nursing, New York, New York, United States of America
| | - Stephanie Potts-Thompson
- Center for Research on People of Color, Columbia University School of Nursing, New York, New York, United States of America
| | - Cara Joyce
- Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Bamidele Tayo
- Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Karen Saban
- Marcella Niehoff School of Nursing, Center for Translational Research and Education, Loyola University Chicago, Maywood, Illinois, United States of America
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156
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Peng Y, Williams MM, Xiaoli L, Simon A, Fueston H, Tondella ML, Weigand MR. Strengthening Bordetella pertussis genomic surveillance by direct sequencing of residual positive specimens. J Clin Microbiol 2024; 62:e0165323. [PMID: 38445858 PMCID: PMC11005353 DOI: 10.1128/jcm.01653-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/12/2024] [Indexed: 03/07/2024] Open
Abstract
Whole-genome sequencing (WGS) of microbial pathogens recovered from patients with infectious disease facilitates high-resolution strain characterization and molecular epidemiology. However, increasing reliance on culture-independent methods to diagnose infectious diseases has resulted in few isolates available for WGS. Here, we report a novel culture-independent approach to genome characterization of Bordetella pertussis, the causative agent of pertussis and a paradigm for insufficient genomic surveillance due to limited culture of clinical isolates. Sequencing libraries constructed directly from residual pertussis-positive diagnostic nasopharyngeal specimens were hybridized with biotinylated RNA "baits" targeting B. pertussis fragments within complex mixtures that contained high concentrations of host and microbial background DNA. Recovery of B. pertussis genome sequence data was evaluated with mock and pooled negative clinical specimens spiked with reducing concentrations of either purified DNA or inactivated cells. Targeted enrichment increased the yield of B. pertussis sequencing reads up to 90% while simultaneously decreasing host reads to less than 10%. Filtered sequencing reads provided sufficient genome coverage to perform characterization via whole-genome single nucleotide polymorphisms and whole-genome multilocus sequencing typing. Moreover, these data were concordant with sequenced isolates recovered from the same specimens such that phylogenetic reconstructions from either consistently clustered the same putatively linked cases. The optimized protocol is suitable for nasopharyngeal specimens with diagnostic IS481 Ct < 35 and >10 ng DNA. Routine implementation of these methods could strengthen surveillance and study of pertussis resurgence by capturing additional cases with genomic characterization.
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Affiliation(s)
- Yanhui Peng
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Margaret M. Williams
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Ashley Simon
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Heather Fueston
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maria L. Tondella
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael R. Weigand
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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157
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Langedijk AC, Vrancken B, Lebbink RJ, Wilkins D, Kelly EJ, Baraldi E, Mascareñas de Los Santos AH, Danilenko DM, Choi EH, Palomino MA, Chi H, Keller C, Cohen R, Papenburg J, Pernica J, Greenough A, Richmond P, Martinón-Torres F, Heikkinen T, Stein RT, Hosoya M, Nunes MC, Verwey C, Evers A, Kragten-Tabatabaie L, Suchard MA, Kosakovsky Pond SL, Poletto C, Colizza V, Lemey P, Bont LJ. The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus. Nat Commun 2024; 15:3083. [PMID: 38600104 PMCID: PMC11006891 DOI: 10.1038/s41467-024-47118-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 03/14/2024] [Indexed: 04/12/2024] Open
Abstract
Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infection in young children and the second leading cause of infant death worldwide. While global circulation has been extensively studied for respiratory viruses such as seasonal influenza, and more recently also in great detail for SARS-CoV-2, a lack of global multi-annual sampling of complete RSV genomes limits our understanding of RSV molecular epidemiology. Here, we capitalise on the genomic surveillance by the INFORM-RSV study and apply phylodynamic approaches to uncover how selection and neutral epidemiological processes shape RSV diversity. Using complete viral genome sequences, we show similar patterns of site-specific diversifying selection among RSVA and RSVB and recover the imprint of non-neutral epidemic processes on their genealogies. Using a phylogeographic approach, we provide evidence for air travel governing the global patterns of RSVA and RSVB spread, which results in a considerable degree of phylogenetic mixing across countries. Our findings highlight the potential of systematic global RSV genomic surveillance for transforming our understanding of global RSV spread.
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Affiliation(s)
- Annefleur C Langedijk
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Lundlaan 6, 3584 EA, Utrecht, the Netherlands
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Herestraat 49, 3000, Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
| | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - Deidre Wilkins
- Translational Medicine, Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, 1 MedImmune Way, Gaithersburg, MD, USA
| | - Elizabeth J Kelly
- Translational Medicine, Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, 1 MedImmune Way, Gaithersburg, MD, USA
| | - Eugenio Baraldi
- Department of Woman's and Child's Health, University Hospital of Padova, Padova, Italy
- ReSViNET Foundation, Zeist, the Netherlands
- Institute of Pediatric Research "Città della Speranza", Padova, Italy
| | | | - Daria M Danilenko
- Smorodintsev Research Institute of Influenza, St. Petersburg, Russia
| | - Eun Hwa Choi
- Seoul National University Children's Hospital, Seoul, South Korea
| | | | - Hsin Chi
- MacKay Children's Hospital, New Taipei, Taiwan, ROC
| | - Christian Keller
- Institute of Virology, University Hospital Giessen and Marburg, Marburg, Germany
| | | | | | | | - Anne Greenough
- ReSViNET Foundation, Zeist, the Netherlands
- King's College London, London, UK
| | | | - Federico Martinón-Torres
- ReSViNET Foundation, Zeist, the Netherlands
- Hospital Clínico Universitario de Santiago, Galicia, Spain
| | - Terho Heikkinen
- ReSViNET Foundation, Zeist, the Netherlands
- University of Turku and Turku University Hospital, Turku, Finland
| | - Renato T Stein
- ReSViNET Foundation, Zeist, the Netherlands
- Pontificia Universidade Catolica de Rio Grande do Sul, Porto Alegre, Brazil
| | - Mitsuaki Hosoya
- Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Marta C Nunes
- ReSViNET Foundation, Zeist, the Netherlands
- Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- South African Medical Research Council, Vaccines & Infectious Diseases Analytics Research Unit, and Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Charl Verwey
- Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Hospices Civils de Lyon and the Centre International de Recherche en Infectiologie (CIRI) Inserm U1111, CNRS UMR5308, ENS de Lyon, UCBL1, Lyon, France
| | - Anouk Evers
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | | | - Marc A Suchard
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Sergei L Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, 801 N Broad St, Philadelphia, PA, 19122, USA
| | - Chiara Poletto
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, F75012, Paris, France
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, F75012, Paris, France
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Herestraat 49, 3000, Leuven, Belgium
| | - Louis J Bont
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Lundlaan 6, 3584 EA, Utrecht, the Netherlands.
- ReSViNET Foundation, Zeist, the Netherlands.
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158
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Wu C, Xiong L, Liao Q, Zhang W, Xiao Y, Xie Y. Clinical manifestations, antimicrobial resistance and genomic feature analysis of multidrug-resistant Elizabethkingia strains. Ann Clin Microbiol Antimicrob 2024; 23:32. [PMID: 38600542 PMCID: PMC11007976 DOI: 10.1186/s12941-024-00691-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 03/26/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Elizabethkingia is emerging as an opportunistic pathogen in humans. The aim of this study was to investigate the clinical epidemiology, antimicrobial susceptibility, virulence factors, and genome features of Elizabethkingia spp. METHODS Clinical data from 71 patients who were diagnosed with Elizabethkingia-induced pneumonia and bacteremia between August 2019 and September 2021 were analyzed. Whole-genome sequencing was performed on seven isolates, and the results were compared with a dataset of 83 available Elizabethkingia genomes. Genomic features, Kyoto Encyclopedia of Genes and Genomes (KEGG) results and clusters of orthologous groups (COGs) were analyzed. RESULTS The mean age of the patients was 56.9 ± 20.7 years, and the in-hospital mortality rate was 29.6% (21/71). Elizabethkingia strains were obtained mainly from intensive care units (36.6%, 26/71) and emergency departments (32.4%, 23/71). The majority of the strains were isolated from respiratory tract specimens (85.9%, 61/71). All patients had a history of broad-spectrum antimicrobial exposure. Hospitalization for invasive mechanical ventilation or catheter insertion was found to be a risk factor for infection. The isolates displayed a high rate of resistance to cephalosporins and carbapenems, but all were susceptible to minocycline and colistin. Genomic analysis identified five β-lactamase genes (blaGOB, blaBlaB, blaCME, blaOXA, and blaTEM) responsible for β-lactam resistance and virulence genes involved in stress adaptation (ureB/G, katA/B, and clpP), adherence (groEL, tufA, and htpB) and immune modulation (gmd, tviB, cps4J, wbtIL, cap8E/D/G, and rfbC). Functional analysis of the COGs revealed that "metabolism" constituted the largest category within the core genome, while "information storage and processing" was predominant in both the accessory and unique genomes. The unique genes in our 7 strains were mostly enriched in KEGG pathways related to microRNAs in cancer, drug resistance (β-lactam and vancomycin), ABC transporters, biological metabolism and biosynthesis, and nucleotide excision repair mechanisms. CONCLUSION The Elizabethkingia genus exhibits multidrug resistance and carries carbapenemase genes. This study presents a comparative genomic analysis of Elizabethkingia, providing knowledge that facilitates a better understanding of this microorganism.
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Affiliation(s)
- Chongyang Wu
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, Sichuan, 610041, China
| | - Li Xiong
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, Sichuan, 610041, China
| | - Quanfeng Liao
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, Sichuan, 610041, China
| | - Weili Zhang
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yuling Xiao
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yi Xie
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, Sichuan, 610041, China.
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159
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de Jong TV, Pan Y, Rastas P, Munro D, Tutaj M, Akil H, Benner C, Chen D, Chitre AS, Chow W, Colonna V, Dalgard CL, Demos WM, Doris PA, Garrison E, Geurts AM, Gunturkun HM, Guryev V, Hourlier T, Howe K, Huang J, Kalbfleisch T, Kim P, Li L, Mahaffey S, Martin FJ, Mohammadi P, Ozel AB, Polesskaya O, Pravenec M, Prins P, Sebat J, Smith JR, Solberg Woods LC, Tabakoff B, Tracey A, Uliano-Silva M, Villani F, Wang H, Sharp BM, Telese F, Jiang Z, Saba L, Wang X, Murphy TD, Palmer AA, Kwitek AE, Dwinell MR, Williams RW, Li JZ, Chen H. A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats. Cell Genom 2024; 4:100527. [PMID: 38537634 PMCID: PMC11019364 DOI: 10.1016/j.xgen.2024.100527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/26/2023] [Accepted: 02/29/2024] [Indexed: 04/09/2024]
Abstract
The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.
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Affiliation(s)
- Tristan V de Jong
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Yanchao Pan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Daniel Munro
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA; Department of Integrative Structural and Computational Biology, Scripps Research, San Diego, CA, USA
| | - Monika Tutaj
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Huda Akil
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Chris Benner
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Denghui Chen
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - William Chow
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Vincenza Colonna
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Wendy M Demos
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Peter A Doris
- The Brown Foundation Institute of Molecular Medicine, Center for Human Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Aron M Geurts
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Hakan M Gunturkun
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Victor Guryev
- Genome Structure and Ageing, University of Groningen, UMC, Groningen, the Netherlands
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Jun Huang
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ted Kalbfleisch
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Louisville, KY, USA
| | - Panjun Kim
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ling Li
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Spencer Mahaffey
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK
| | - Pejman Mohammadi
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Ayse Bilge Ozel
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, Prague, Czechia
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Jennifer R Smith
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | | | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hongyang Wang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Burt M Sharp
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Francesca Telese
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Laura Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Xusheng Wang
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Anne E Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
| | - Hao Chen
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
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Brindisi LJ, Mattera R, Mudiyala S, Honig J, Simon JE. Genetic linkage mapping and quantitative trait locus (QTL) analysis of sweet basil (Ocimum basilicum L.) to identify genomic regions associated with cold tolerance and major volatiles. PLoS One 2024; 19:e0299825. [PMID: 38593174 PMCID: PMC11003626 DOI: 10.1371/journal.pone.0299825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/15/2024] [Indexed: 04/11/2024] Open
Abstract
Chilling sensitivity is one of the greatest challenges affecting the marketability and profitability of sweet basil (Ocimum basilicum L.) in the US and worldwide. Currently, there are no sweet basils commercially available with significant chilling tolerance and traditional aroma profiles. This study was conducted to identify quantitative trait loci (QTLs) responsible for chilling tolerance and aroma compounds in a biparental mapping population, including the Rutgers advanced breeding line that served as a chilling tolerant parent, 'CB15', the chilling sensitive parent, 'Rutgers Obsession DMR' and 200 F2 individuals. Chilling tolerance was assessed by percent necrosis using machine learning and aroma profiling was evaluated using gas chromatography (GC) mass spectrometry (MS). Single nucleotide polymorphism (SNP) markers were generated from genomic sequences derived from double digestion restriction-site associated DNA sequencing (ddRADseq) and converted to genotype data using a reference genome alignment. A genetic linkage map was constructed and five statistically significant QTLs were identified in response to chilling temperatures with possible interactions between QTLs. The QTL on LG24 (qCH24) demonstrated the largest effect for chilling response and was significant in all three replicates. No QTLs were identified for linalool, as the population did not segregate sufficiently to detect this trait. Two significant QTLs were identified for estragole (also known as methyl chavicol) with only qEST1 on LG1 being significant in the multiple-QTL model (MQM). QEUC26 was identified as a significant QTL for eucalyptol (also known as 1,8-cineole) on LG26. These QTLs may represent key mechanisms for chilling tolerance and aroma in basil, providing critical knowledge for future investigation of these phenotypic traits and molecular breeding.
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Affiliation(s)
- Lara J. Brindisi
- New Use Agriculture and Natural Plant Products Program, Department of Plant Biology, Rutgers University, New Jersey, United States of America
| | - Robert Mattera
- New Use Agriculture and Natural Plant Products Program, Department of Plant Biology, Rutgers University, New Jersey, United States of America
| | - Sonika Mudiyala
- New Use Agriculture and Natural Plant Products Program, Department of Plant Biology, Rutgers University, New Jersey, United States of America
| | - Joshua Honig
- New Use Agriculture and Natural Plant Products Program, Department of Plant Biology, Rutgers University, New Jersey, United States of America
| | - James E. Simon
- New Use Agriculture and Natural Plant Products Program, Department of Plant Biology, Rutgers University, New Jersey, United States of America
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161
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Naghavi AO, Bryant JM, Kim Y, Weygand J, Redler G, Sim AJ, Miller J, Coucoules K, Michael LT, Gloria WE, Yang G, Rosenberg SA, Ahmed K, Bui MM, Henderson-Jackson EB, Lee A, Lee CD, Gonzalez RJ, Feygelman V, Eschrich SA, Scott JG, Torres-Roca J, Latifi K, Parikh N, Costello J. Habitat escalated adaptive therapy (HEAT): a phase 2 trial utilizing radiomic habitat-directed and genomic-adjusted radiation dose (GARD) optimization for high-grade soft tissue sarcoma. BMC Cancer 2024; 24:437. [PMID: 38594603 PMCID: PMC11003059 DOI: 10.1186/s12885-024-12151-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 03/20/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND Soft tissue sarcomas (STS), have significant inter- and intra-tumoral heterogeneity, with poor response to standard neoadjuvant radiotherapy (RT). Achieving a favorable pathologic response (FPR ≥ 95%) from RT is associated with improved patient outcome. Genomic adjusted radiation dose (GARD), a radiation-specific metric that quantifies the expected RT treatment effect as a function of tumor dose and genomics, proposed that STS is significantly underdosed. STS have significant radiomic heterogeneity, where radiomic habitats can delineate regions of intra-tumoral hypoxia and radioresistance. We designed a novel clinical trial, Habitat Escalated Adaptive Therapy (HEAT), utilizing radiomic habitats to identify areas of radioresistance within the tumor and targeting them with GARD-optimized doses, to improve FPR in high-grade STS. METHODS Phase 2 non-randomized single-arm clinical trial includes non-metastatic, resectable high-grade STS patients. Pre-treatment multiparametric MRIs (mpMRI) delineate three distinct intra-tumoral habitats based on apparent diffusion coefficient (ADC) and dynamic contrast enhanced (DCE) sequences. GARD estimates that simultaneous integrated boost (SIB) doses of 70 and 60 Gy in 25 fractions to the highest and intermediate radioresistant habitats, while the remaining volume receives standard 50 Gy, would lead to a > 3 fold FPR increase to 24%. Pre-treatment CT guided biopsies of each habitat along with clip placement will be performed for pathologic evaluation, future genomic studies, and response assessment. An mpMRI taken between weeks two and three of treatment will be used for biological plan adaptation to account for tumor response, in addition to an mpMRI after the completion of radiotherapy in addition to pathologic response, toxicity, radiomic response, disease control, and survival will be evaluated as secondary endpoints. Furthermore, liquid biopsy will be performed with mpMRI for future ancillary studies. DISCUSSION This is the first clinical trial to test a novel genomic-based RT dose optimization (GARD) and to utilize radiomic habitats to identify and target radioresistance regions, as a strategy to improve the outcome of RT-treated STS patients. Its success could usher in a new phase in radiation oncology, integrating genomic and radiomic insights into clinical practice and trial designs, and may reveal new radiomic and genomic biomarkers, refining personalized treatment strategies for STS. TRIAL REGISTRATION NCT05301283. TRIAL STATUS The trial started recruitment on March 17, 2022.
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Affiliation(s)
- Arash O Naghavi
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
| | - J M Bryant
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Youngchul Kim
- Department of Bioinformatics and Biostatistics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Joseph Weygand
- Department of Radiation Oncology and Applied Sciences, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Gage Redler
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Austin J Sim
- Department of Radiation Oncology, James Cancer Hospital, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Justin Miller
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Kaitlyn Coucoules
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Lauren Taylor Michael
- Clinical Trials Office, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Warren E Gloria
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - George Yang
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Stephen A Rosenberg
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Kamran Ahmed
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Marilyn M Bui
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | | | - Andrew Lee
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Caitlin D Lee
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Ricardo J Gonzalez
- Department of Sarcoma, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Vladimir Feygelman
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Steven A Eschrich
- Department of Bioinformatics and Biostatistics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jacob G Scott
- Translational Hematology and Oncology Research, Radiation Oncology Department, Cleveland Clinic, Cleveland, OH, USA
| | - Javier Torres-Roca
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Kujtim Latifi
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Nainesh Parikh
- Department of Diagnostic Imaging and Interventional Radiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - James Costello
- Department of Diagnostic Imaging and Interventional Radiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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162
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Price MN, Arkin AP. A fast comparative genome browser for diverse bacteria and archaea. PLoS One 2024; 19:e0301871. [PMID: 38593165 PMCID: PMC11003636 DOI: 10.1371/journal.pone.0301871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/22/2024] [Indexed: 04/11/2024] Open
Abstract
Genome sequencing has revealed an incredible diversity of bacteria and archaea, but there are no fast and convenient tools for browsing across these genomes. It is cumbersome to view the prevalence of homologs for a protein of interest, or the gene neighborhoods of those homologs, across the diversity of the prokaryotes. We developed a web-based tool, fast.genomics, that uses two strategies to support fast browsing across the diversity of prokaryotes. First, the database of genomes is split up. The main database contains one representative from each of the 6,377 genera that have a high-quality genome, and additional databases for each taxonomic order contain up to 10 representatives of each species. Second, homologs of proteins of interest are identified quickly by using accelerated searches, usually in a few seconds. Once homologs are identified, fast.genomics can quickly show their prevalence across taxa, view their neighboring genes, or compare the prevalence of two different proteins. Fast.genomics is available at https://fast.genomics.lbl.gov.
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Affiliation(s)
- Morgan N. Price
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Lab, Berkeley, California, United States of America
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Lab, Berkeley, California, United States of America
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163
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Baharav TZ, Tse D, Salzman J. OASIS: An interpretable, finite-sample valid alternative to Pearson's X2 for scientific discovery. Proc Natl Acad Sci U S A 2024; 121:e2304671121. [PMID: 38564640 PMCID: PMC11009617 DOI: 10.1073/pnas.2304671121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 02/08/2024] [Indexed: 04/04/2024] Open
Abstract
Contingency tables, data represented as counts matrices, are ubiquitous across quantitative research and data-science applications. Existing statistical tests are insufficient however, as none are simultaneously computationally efficient and statistically valid for a finite number of observations. In this work, motivated by a recent application in reference-free genomic inference [K. Chaung et al., Cell 186, 5440-5456 (2023)], we develop Optimized Adaptive Statistic for Inferring Structure (OASIS), a family of statistical tests for contingency tables. OASIS constructs a test statistic which is linear in the normalized data matrix, providing closed-form P-value bounds through classical concentration inequalities. In the process, OASIS provides a decomposition of the table, lending interpretability to its rejection of the null. We derive the asymptotic distribution of the OASIS test statistic, showing that these finite-sample bounds correctly characterize the test statistic's P-value up to a variance term. Experiments on genomic sequencing data highlight the power and interpretability of OASIS. Using OASIS, we develop a method that can detect SARS-CoV-2 and Mycobacterium tuberculosis strains de novo, which existing approaches cannot achieve. We demonstrate in simulations that OASIS is robust to overdispersion, a common feature in genomic data like single-cell RNA sequencing, where under accepted noise models OASIS provides good control of the false discovery rate, while Pearson's [Formula: see text] consistently rejects the null. Additionally, we show in simulations that OASIS is more powerful than Pearson's [Formula: see text] in certain regimes, including for some important two group alternatives, which we corroborate with approximate power calculations.
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Affiliation(s)
- Tavor Z. Baharav
- Eric and Wendy Schmidt Center, Broad Institute, Cambridge, MA02142
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA02115
| | - David Tse
- Department of Electrical Engineering, Stanford University, Stanford, CA94305
| | - Julia Salzman
- Department of Biomedical Data Science, Stanford University, Stanford, CA94305
- Department of Biochemistry, Stanford University, Stanford, CA94305
- Department of Statistics (by courtesy), Stanford University, Stanford, CA94305
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164
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Rubin R. All of Us Program Illustrates What Less-Diverse Genomics Studies Might Be Missing. JAMA 2024; 331:1167-1168. [PMID: 38477926 DOI: 10.1001/jama.2024.2976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
This Medical News story discusses new findings from genomics studies involving diverse cohorts.
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165
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Broman MT, Nadadur RD, Perez-Cervantes C, Burnicka-Turek O, Lazarevic S, Gams A, Laforest B, Steimle JD, Iddir S, Wang Z, Smith L, Mazurek SR, Olivey HE, Zhou P, Gadek M, Shen KM, Khan Z, Theisen JWM, Yang XH, Ikegami K, Efimov IR, Pu WT, Weber CR, McNally EM, Svensson EC, Moskowitz IP. A Genomic Link From Heart Failure to Atrial Fibrillation Risk: FOG2 Modulates a TBX5/GATA4-Dependent Atrial Gene Regulatory Network. Circulation 2024; 149:1205-1230. [PMID: 38189150 DOI: 10.1161/circulationaha.123.066804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/11/2023] [Indexed: 01/09/2024]
Abstract
BACKGROUND The relationship between heart failure (HF) and atrial fibrillation (AF) is clear, with up to half of patients with HF progressing to AF. The pathophysiological basis of AF in the context of HF is presumed to result from atrial remodeling. Upregulation of the transcription factor FOG2 (friend of GATA2; encoded by ZFPM2) is observed in human ventricles during HF and causes HF in mice. METHODS FOG2 expression was assessed in human atria. The effect of adult-specific FOG2 overexpression in the mouse heart was evaluated by whole animal electrophysiology, in vivo organ electrophysiology, cellular electrophysiology, calcium flux, mouse genetic interactions, gene expression, and genomic function, including a novel approach for defining functional transcription factor interactions based on overlapping effects on enhancer noncoding transcription. RESULTS FOG2 is significantly upregulated in the human atria during HF. Adult cardiomyocyte-specific FOG2 overexpression in mice caused primary spontaneous AF before the development of HF or atrial remodeling. FOG2 overexpression generated arrhythmia substrate and trigger in cardiomyocytes, including calcium cycling defects. We found that FOG2 repressed atrial gene expression promoted by TBX5. FOG2 bound a subset of GATA4 and TBX5 co-bound genomic locations, defining a shared atrial gene regulatory network. FOG2 repressed TBX5-dependent transcription from a subset of co-bound enhancers, including a conserved enhancer at the Atp2a2 locus. Atrial rhythm abnormalities in mice caused by Tbx5 haploinsufficiency were rescued by Zfpm2 haploinsufficiency. CONCLUSIONS Transcriptional changes in the atria observed in human HF directly antagonize the atrial rhythm gene regulatory network, providing a genomic link between HF and AF risk independent of atrial remodeling.
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Affiliation(s)
- Michael T Broman
- Department of Medicine, Section of Cardiology (M.T.B., B.L., S.R.M.), University of Chicago, IL
| | - Rangarajan D Nadadur
- Departments of Pediatrics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
- Pathology (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., C.R.W., I.P.M.), University of Chicago, IL
- Human Genetics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
| | - Carlos Perez-Cervantes
- Departments of Pediatrics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
- Pathology (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., C.R.W., I.P.M.), University of Chicago, IL
- Human Genetics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
| | - Ozanna Burnicka-Turek
- Departments of Pediatrics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
- Pathology (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., C.R.W., I.P.M.), University of Chicago, IL
- Human Genetics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
| | - Sonja Lazarevic
- Departments of Pediatrics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
- Pathology (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., C.R.W., I.P.M.), University of Chicago, IL
- Human Genetics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
| | - Anna Gams
- Department of Biomedical Engineering, George Washington University (A.G., I.R.E.), Washington, DC
| | - Brigitte Laforest
- Department of Medicine, Section of Cardiology (M.T.B., B.L., S.R.M.), University of Chicago, IL
| | - Jeffrey D Steimle
- Pathology (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., C.R.W., I.P.M.), University of Chicago, IL
- Human Genetics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
| | - Sabrina Iddir
- Pathology (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., C.R.W., I.P.M.), University of Chicago, IL
- Human Genetics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
| | - Zhezhen Wang
- Departments of Pediatrics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
- Pathology (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., C.R.W., I.P.M.), University of Chicago, IL
- Human Genetics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
| | - Linsin Smith
- Departments of Pediatrics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
- Pathology (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., C.R.W., I.P.M.), University of Chicago, IL
- Human Genetics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
| | - Stefan R Mazurek
- Department of Medicine, Section of Cardiology (M.T.B., B.L., S.R.M.), University of Chicago, IL
| | - Harold E Olivey
- Department of Biology, Indiana University Northwest, Gary (H.E.O.)
| | - Pingzhu Zhou
- School of Medicine, Shanghai University, China (P.Z.)
| | - Margaret Gadek
- Departments of Pediatrics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
- Pathology (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., C.R.W., I.P.M.), University of Chicago, IL
- Human Genetics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
| | - Kaitlyn M Shen
- Departments of Pediatrics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
- Pathology (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., C.R.W., I.P.M.), University of Chicago, IL
- Human Genetics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
| | - Zoheb Khan
- Departments of Pediatrics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
- Pathology (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., C.R.W., I.P.M.), University of Chicago, IL
- Human Genetics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
| | - Joshua W M Theisen
- Departments of Pediatrics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
- Pathology (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., C.R.W., I.P.M.), University of Chicago, IL
- Human Genetics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
| | - Xinan H Yang
- Departments of Pediatrics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
- Pathology (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., C.R.W., I.P.M.), University of Chicago, IL
- Human Genetics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
| | - Kohta Ikegami
- Division of Molecular and Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, OH (K.I.)
| | - Igor R Efimov
- Department of Biomedical Engineering, George Washington University (A.G., I.R.E.), Washington, DC
| | - William T Pu
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA (W.T.P.)
- Department of Cardiology, Boston Children's Hospital, MA (W.T.P.)
| | - Christopher R Weber
- Pathology (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., C.R.W., I.P.M.), University of Chicago, IL
| | | | | | - Ivan P Moskowitz
- Departments of Pediatrics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
- Pathology (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., C.R.W., I.P.M.), University of Chicago, IL
- Human Genetics (R.D.N., C.P.-C., O.B.-T., S.L., J.D.S., S.I., Z.W., L.S., M.G., K.M.S., Z.K., J.W.M.T., X.H.Y., I.P.M.), University of Chicago, IL
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Bernal-Gallardo JJ, de Folter S. Plant genome information facilitates plant functional genomics. Planta 2024; 259:117. [PMID: 38592421 PMCID: PMC11004055 DOI: 10.1007/s00425-024-04397-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/20/2024] [Indexed: 04/10/2024]
Abstract
MAIN CONCLUSION In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. Plant genome sequence information greatly facilitates the studies of plant biology, functional genomics, evolution of genomes and genes, domestication processes, phylogenetic relationships, among many others. More than two decades of sequencing efforts have boosted the number of available sequenced plant genomes. The first plant genome, of Arabidopsis, was published in the year 2000 and currently, 4604 plant genomes from 1482 plant species have been published. Various large sequence initiatives are running, which are planning to produce tens of thousands of sequenced plant genomes in the near future. In this review, we give an overview on the status of sequenced plant genomes and on the use of genome information in different research areas.
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Affiliation(s)
- Judith Jazmin Bernal-Gallardo
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico.
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167
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Kyung SM, Lee JH, Lee ES, Xiang XR, Yoo HS. Emergence and genomic chion of Proteus mirabilis harboring bla NDM-1 in Korean companion dogs. Vet Res 2024; 55:50. [PMID: 38594755 PMCID: PMC11005143 DOI: 10.1186/s13567-024-01306-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/26/2024] [Indexed: 04/11/2024] Open
Abstract
Proteus mirabilis is a commensal bacterium dwelling in the gastrointestinal (GI) tract of humans and animals. Although New Delhi metallo-β-lactamase 1 (NDM-1) producing P. mirabilis is emerging as a threat, its epidemiology in our society remains largely unknown. LHPm1, the first P. mirabilis isolate harboring NDM-1, was detected from a companion dog that resides with a human owner. The whole-genome study revealed 20 different antimicrobial resistance (AMR) genes against various classes of antimicrobial agents, which corresponded to the MIC results. Genomic regions, including MDR genes, were identified with multiple variations and visualized in a comparative manner. In the whole-genome epidemiological analysis, multiple phylogroups were identified, revealing the genetic relationship of LHPm1 with other P. mirabilis strains carrying various AMR genes. These genetic findings offer comprehensive insights into NDM-1-producing P. mirabilis, underscoring the need for urgent control measures and surveillance programs using a "one health approach".
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Affiliation(s)
- Su Min Kyung
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jun Ho Lee
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Eun-Seo Lee
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Xi-Rui Xiang
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Han Sang Yoo
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.
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168
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Berg T, Jensen MB, Celik A, Talman ML, Misiakou MA, Knoop AS, Nielsen FC, Ejlertsen B, Rossing M. Molecular subtyping improves breast cancer diagnosis in the Copenhagen Breast Cancer Genomics Study. JCI Insight 2024; 9:e178114. [PMID: 38587073 DOI: 10.1172/jci.insight.178114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/16/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUNDIntrinsic molecular subtypes define distinct biological breast cancers and can be used to further improve diagnosis and risk allocation.METHODSThe Copenhagen Breast Cancer Genomics Study (CBCGS) prospectively included women diagnosed with breast cancer at Rigshospitalet from 2014 to 2021. Eligible patients were females with a primary invasive breast cancer (T1c, if N0M0; otherwise, any T, any N, or any M stage) and no prior malignancy. All patients underwent molecular profiling with the CIT256 and PAM50 molecular profile.RESULTSIn the study period, 2,816 patients were included in the CBCGS. Molecular subtyping showed an increase in nonluminal (molecular-apocrine, luminal C, and Basal-like) as compared with luminal (luminal A, luminal B, and Normal-like) subtypes with increasing stage from I to IV. Across all stages, we found a significant difference in survival among subtypes; 91% of patients with LumA were alive at 5 years compared with 91% for LumB, 84% for LumC, 82% for mApo, and 80% for Basal-like. We identified 442 tumors (16%) that were discordant in subtype between CIT256 and IHC. Discordant subtype proved to be a risk factor of death among patients with IHC luminal breast cancer (hazard ratio [HR], 2.08; 95% CI, 1.51-2.86) in a multivariable Cox regression analysis. Discordance occurred more often among patients with N3, stage IV, or grade III disease.CONCLUSIONOur findings indicate that molecular subtypes are a predominant classification for survival. Assessment is particularly crucial for patients with IHC luminal breast cancer with known high-risk factors, since they are at an increased risk of harboring an aggressive molecular subtype.
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Affiliation(s)
- Tobias Berg
- Danish Breast Cancer Group
- Department of Clinical Oncology
- Center for Genomic Medicine, and
| | | | | | - Maj-Lis Talman
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | | | - Finn Cilius Nielsen
- Center for Genomic Medicine, and
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Bent Ejlertsen
- Danish Breast Cancer Group
- Department of Clinical Oncology
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Maria Rossing
- Center for Genomic Medicine, and
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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169
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Gu J, Guan Z, Jiao Y, Liu K, Hong D. The story of a decade: Genomics, functional genomics, and molecular breeding in Brassica napus. Plant Commun 2024; 5:100884. [PMID: 38494786 PMCID: PMC11009362 DOI: 10.1016/j.xplc.2024.100884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/01/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Rapeseed (Brassica napus L.) is one of the major global sources of edible vegetable oil and is also used as a feed and pioneer crop and for sightseeing and industrial purposes. Improvements in genome sequencing and molecular marker technology have fueled a boom in functional genomic studies of major agronomic characters such as yield, quality, flowering time, and stress resistance. Moreover, introgression and pyramiding of key functional genes have greatly accelerated the genetic improvement of important traits. Here we summarize recent progress in rapeseed genomics and genetics, and we discuss effective molecular breeding strategies by exploring these findings in rapeseed. These insights will extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture throughout the world.
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Affiliation(s)
- Jianwei Gu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Life Science and Technology, Hubei Engineering University, Xiaogan 432100 Hubei, China
| | - Zhilin Guan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074 Hubei, China
| | - Yushun Jiao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Yazhouwan National Laboratory, Sanya 572024 Hainan, China.
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Hao Y, Wang XF, Guo Y, Li TY, Yang J, Ainouche ML, Salmon A, Ju RT, Wu JH, Li LF, Li B. Genomic and phenotypic signatures provide insights into the wide adaptation of a global plant invader. Plant Commun 2024; 5:100820. [PMID: 38221758 PMCID: PMC11009367 DOI: 10.1016/j.xplc.2024.100820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 01/16/2024]
Abstract
Invasive alien species are primary drivers of biodiversity loss and species extinction. Smooth cordgrass (Spartina alterniflora) is one of the most aggressive invasive plants in coastal ecosystems around the world. However, the genomic bases and evolutionary mechanisms underlying its invasion success have remained largely unknown. Here, we assembled a chromosome-level reference genome and performed phenotypic and population genomic analyses between native US and introduced Chinese populations. Our phenotypic comparisons showed that introduced Chinese populations have evolved competitive traits, such as early flowering time and greater plant biomass, during secondary introductions along China's coast. Population genomic and transcriptomic inferences revealed distinct evolutionary trajectories of low- and high-latitude Chinese populations. In particular, genetic mixture among different source populations, together with independent natural selection acting on distinct target genes, may have resulted in high genome dynamics of the introduced Chinese populations. Our study provides novel phenotypic and genomic evidence showing how smooth cordgrass rapidly adapts to variable environmental conditions in its introduced ranges. Moreover, candidate genes related to flowering time, fast growth, and stress tolerance (i.e., salinity and submergence) provide valuable genetic resources for future improvement of cereal crops.
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Affiliation(s)
- Yan Hao
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xin-Feng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yaolin Guo
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Tian-Yang Li
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ji Yang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Malika L Ainouche
- UMR CNRS 6553, Université of Rennes, Campus de Beaulieu, 35042 Rennes Cedex Paris, France
| | - Armel Salmon
- UMR CNRS 6553, Université of Rennes, Campus de Beaulieu, 35042 Rennes Cedex Paris, France
| | - Rui-Ting Ju
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ji-Hua Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China.
| | - Lin-Feng Li
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China; State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Bo Li
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China; Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan 650504, China.
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171
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Bao Y, Zhang Q, Huang J, Zhang S, Yao W, Yu Z, Deng Z, Yu J, Kong W, Yu X, Lu S, Wang Y, Li R, Song Y, Zou C, Xu Y, Liu Z, Yu F, Song J, Huang Y, Zhang J, Wang H, Chen B, Zhang X, Zhang M. A chromosomal-scale genome assembly of modern cultivated hybrid sugarcane provides insights into origination and evolution. Nat Commun 2024; 15:3041. [PMID: 38589412 PMCID: PMC11001919 DOI: 10.1038/s41467-024-47390-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 03/31/2024] [Indexed: 04/10/2024] Open
Abstract
Sugarcane is a vital crop with significant economic and industrial value. However, the cultivated sugarcane's ultra-complex genome still needs to be resolved due to its high ploidy and extensive recombination between the two subgenomes. Here, we generate a chromosomal-scale, haplotype-resolved genome assembly for a hybrid sugarcane cultivar ZZ1. This assembly contains 10.4 Gb genomic sequences and 68,509 annotated genes with defined alleles in two sub-genomes distributed in 99 original and 15 recombined chromosomes. RNA-seq data analysis shows that sugar accumulation-associated gene families have been primarily expanded from the ZZSO subgenome. However, genes responding to pokkah boeng disease susceptibility have been derived dominantly from the ZZSS subgenome. The region harboring the possible smut resistance genes has expanded significantly. Among them, the expansion of WAK and FLS2 families is proposed to have occurred during the breeding of ZZ1. Our findings provide insights into the complex genome of hybrid sugarcane cultivars and pave the way for future genomics and molecular breeding studies in sugarcane.
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Affiliation(s)
- Yixue Bao
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Qing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Jiangfeng Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Shengcheng Zhang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Wei Yao
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Zehuai Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Zuhu Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Jiaxin Yu
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Weilong Kong
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Xikai Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Shan Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Yibin Wang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Ru Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Yuhan Song
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Chengwu Zou
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Yuzhi Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Zongling Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Fan Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Jiaming Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Youzong Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Jisen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Haifeng Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China.
| | - Xingtan Zhang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China.
| | - Muqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China.
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172
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Zhu Y, Wang Z, Zhou Z, Liu Y, Gao X, Guo W, Shi J. HEMU: An integrated comparative genomics database and analysis platform for Andropogoneae grasses. Plant Commun 2024; 5:100786. [PMID: 38155575 PMCID: PMC11009152 DOI: 10.1016/j.xplc.2023.100786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/05/2023] [Accepted: 12/26/2023] [Indexed: 12/30/2023]
Abstract
This study reports an online database and analysis platform HEMU, which integrates 75 genome assemblies from 20 unique species, large amounts of multi-omics data, and six sophisticated analysis toolkits. HEMU will facilitate comparative genomics analysis within the tribe Andropogoneae.
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Affiliation(s)
- Yuzhi Zhu
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Zijie Wang
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Zanchen Zhou
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Yuting Liu
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Xiang Gao
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Junpeng Shi
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China.
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173
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Louie TS, Kumar A, Bini E, Häggblom MM. Mo than meets the eye: genomic insights into molybdoenzyme diversity of Seleniivibrio woodruffii strain S4T. Lett Appl Microbiol 2024; 77:ovae038. [PMID: 38573838 DOI: 10.1093/lambio/ovae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/12/2024] [Accepted: 04/03/2024] [Indexed: 04/06/2024]
Abstract
Seleniivibrio woodruffii strain S4T is an obligate anaerobe belonging to the phylum Deferribacterota. It was isolated for its ability to respire selenate and was also found to respire arsenate. The high-quality draft genome of this bacterium is 2.9 Mbp, has a G+C content of 48%, 2762 predicted genes of which 2709 are protein-coding, and 53 RNA genes. An analysis of the genome focusing on the genes encoding for molybdenum-containing enzymes (molybdoenzymes) uncovered a remarkable number of genes encoding for members of the dimethylsulfoxide reductase family of proteins (DMSOR), including putative reductases for selenate and arsenate respiration, as well as genes for nitrogen fixation. Respiratory molybdoenzymes catalyze redox reactions that transfer electrons to a variety of substrates that can act as terminal electron acceptors for energy generation. Seleniivibrio woodruffii strain S4T also has essential genes for molybdate transporters and the biosynthesis of the molybdopterin guanine dinucleotide cofactors characteristic of the active centers of DMSORs. Phylogenetic analysis revealed candidate respiratory DMSORs spanning nine subfamilies encoded within the genome. Our analysis revealed the untapped potential of this interesting microorganism and expanded our knowledge of molybdoenzyme co-occurrence.
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Affiliation(s)
- Tiffany S Louie
- Department of Biochemistry and Microbiology Rutgers, The State University of New Jersey, School of Environmental and Biological Sciences, 76 Lipman Drive, New Brunswick, NJ 08901, United States
| | - Anil Kumar
- Department of Biochemistry and Microbiology Rutgers, The State University of New Jersey, School of Environmental and Biological Sciences,, 76 Lipman Drive, New Brunswick, NJ 08901, United States
| | - Elisabetta Bini
- Department of Biochemistry and Microbiology Rutgers, The State University of New Jersey, School of Environmental and Biological Sciences,, 76 Lipman Drive, New Brunswick, NJ 08901, United States
| | - Max M Häggblom
- Department of Biochemistry and Microbiology Rutgers, The State University of New Jersey, School of Environmental and Biological Sciences,, 76 Lipman Drive, New Brunswick, NJ 08901, United States
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Lin CJ, Jin X, Ma D, Chen C, Ou-Yang Y, Pei YC, Zhou CZ, Qu FL, Wang YJ, Liu CL, Fan L, Hu X, Shao ZM, Jiang YZ. Genetic interactions reveal distinct biological and therapeutic implications in breast cancer. Cancer Cell 2024; 42:701-719.e12. [PMID: 38593782 DOI: 10.1016/j.ccell.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 01/16/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024]
Abstract
Co-occurrence and mutual exclusivity of genomic alterations may reflect the existence of genetic interactions, potentially shaping distinct biological phenotypes and impacting therapeutic response in breast cancer. However, our understanding of them remains limited. Herein, we investigate a large-scale multi-omics cohort (n = 873) and a real-world clinical sequencing cohort (n = 4,405) including several clinical trials with detailed treatment outcomes and perform functional validation in patient-derived organoids, tumor fragments, and in vivo models. Through this comprehensive approach, we construct a network comprising co-alterations and mutually exclusive events and characterize their therapeutic potential and underlying biological basis. Notably, we identify associations between TP53mut-AURKAamp and endocrine therapy resistance, germline BRCA1mut-MYCamp and improved sensitivity to PARP inhibitors, and TP53mut-MYBamp and immunotherapy resistance. Furthermore, we reveal that precision treatment strategies informed by co-alterations hold promise to improve patient outcomes. Our study highlights the significance of genetic interactions in guiding genome-informed treatment decisions beyond single driver alterations.
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Affiliation(s)
- Cai-Jin Lin
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xi Jin
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ding Ma
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Chao Chen
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yang Ou-Yang
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yu-Chen Pei
- Precision Cancer Medical Center, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Chao-Zheng Zhou
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Fei-Lin Qu
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yun-Jin Wang
- Precision Cancer Medical Center, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Cheng-Lin Liu
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lei Fan
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xin Hu
- Precision Cancer Medical Center, Fudan University Shanghai Cancer Center, Shanghai 200032, China.
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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175
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Pierreux J, Bottieau E, Florence E, Maniewski U, Bruggemans A, Malotaux J, Martin C, Cox J, Konopnicki D, Guetens P, Verschueren J, Coppens J, Van Esbroeck M, Mutsaers M, Rosanas-Urgell A. Failure of artemether-lumefantrine therapy in travellers returning to Belgium with Plasmodium falciparum malaria: an observational case series with genomic analysis. J Travel Med 2024; 31:taad165. [PMID: 38157311 DOI: 10.1093/jtm/taad165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Failure of artemisinin-based combination therapy is increasingly reported in patients with Plasmodium falciparum malaria in sub-Saharan Africa. We aimed to describe the clinical and genomic characteristics of recent cases of P. falciparum malaria failing artemether-lumefantrine in Belgium. METHODS Travel-related cases of malaria confirmed at the national reference laboratory of the Institute of Tropical Medicine, Antwerp, Belgium, were reviewed. All cases for which attending clinicians reported persistence (beyond Day 3 post-treatment initiation, i.e. early failure) or recrudescence (from Day 7 to 42, i.e. late failure) of P. falciparum parasites despite adequate drug intake were analysed. Both initial and persistent/recurrent samples were submitted to next generation sequencing to investigate resistance-conferring mutations. RESULTS From July 2022 to June 2023, eight P. falciparum cases of failure with artemether-lumefantrine therapy were reported (early failure = 1; late failure = 7). All travellers were returning from sub-Saharan Africa, most (6/8) after a trip to visit friends and relatives. PfKelch13 (PF3D7_1343700) mutations associated with resistance to artemisinin were found in two travellers returning from East Africa, including the validated marker R561H in the patient with early failure and the candidate marker A675V in a patient with late failure. Additional mutations were detected that could contribute to decreased susceptibility to artemisinin in another three cases, lumefantrine in six cases and proguanil in all eight participants. Various regimens were used to treat the persistent/recrudescent cases, with favourable outcome. CONCLUSION Within a 12-month period, we investigated eight travellers returning from sub-Saharan Africa with P. falciparum malaria and in whom artemether-lumefantrine failure was documented. Mutations conferring resistance to antimalarials were found in all analysed blood samples, especially against lumefantrine and proguanil, but also artemisinin. There is a pressing need for systematic genomic surveillance of resistance to antimalarials in international travellers with P. falciparum malaria, especially those experiencing treatment failure.
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Affiliation(s)
- Jan Pierreux
- Infectious Diseases Department, Saint-Pierre University Hospital, Université Libre de Bruxelles, Brussels 1000, Belgium
| | - Emmanuel Bottieau
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
| | - Eric Florence
- Department of General Internal Medicine and Infectious Diseases, University Hospital of Antwerp, Antwerp 2000, Belgium
| | - Ula Maniewski
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
| | - Anne Bruggemans
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
| | - Jiska Malotaux
- Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Ghent 9000, Belgium
| | - Charlotte Martin
- Infectious Diseases Department, Saint-Pierre University Hospital, Université Libre de Bruxelles, Brussels 1000, Belgium
| | - Janneke Cox
- Department of Infectious Diseases and Immunity, Jessa Hospital, Hasselt 3500, Belgium
- Faculty of Medicine and Life Sciences, University of Hasselt, Hasselt 3500, Belgium
| | - Deborah Konopnicki
- Infectious Diseases Department, Saint-Pierre University Hospital, Université Libre de Bruxelles, Brussels 1000, Belgium
| | - Pieter Guetens
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
| | - Jacob Verschueren
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
| | - Jasmine Coppens
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
| | - Marjan Van Esbroeck
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
| | - Mathijs Mutsaers
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
| | - Anna Rosanas-Urgell
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
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Rider DF, Wolf ACE, Murray J, de Flamingh A, dos Santos ALC, Lanoë F, Zedeño MN, DeGiorgio M, Lindo J, Malhi RS. Genomic analyses correspond with deep persistence of peoples of Blackfoot Confederacy from glacial times. Sci Adv 2024; 10:eadl6595. [PMID: 38569022 PMCID: PMC10990285 DOI: 10.1126/sciadv.adl6595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/28/2024] [Indexed: 04/05/2024]
Abstract
Mutually beneficial partnerships between genomics researchers and North American Indigenous Nations are rare yet becoming more common. Here, we present one such partnership that provides insight into the peopling of the Americas and furnishes another line of evidence that can be used to further treaty and Indigenous rights. We show that the genomics of sampled individuals from the Blackfoot Confederacy belong to a previously undescribed ancient lineage that diverged from other genomic lineages in the Americas in Late Pleistocene times. Using multiple complementary forms of knowledge, we provide a scenario for Blackfoot population history that fits with oral tradition and provides a plausible model for the evolutionary process of the peopling of the Americas.
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Affiliation(s)
| | | | - John Murray
- Blackfeet Tribal Historic Preservation Office, Browning, MT 59417, USA
| | - Alida de Flamingh
- Center for Indigenous Science, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | | | - François Lanoë
- Bureau of Applied Research in Anthropology, School of Anthropology, The University of Arizona, Tucson, AZ 85721, USA
| | - Maria N. Zedeño
- Bureau of Applied Research in Anthropology, School of Anthropology, The University of Arizona, Tucson, AZ 85721, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - John Lindo
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Ripan S. Malhi
- Center for Indigenous Science, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
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177
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Chen L, Yu XY, Zhang F, Zhang HM, Guo LX, Ren L, Hong XY, Sun JT. A chromosome-level genome assembly of the spider mite Tetranychus piercei McGregor. Sci Data 2024; 11:340. [PMID: 38580722 PMCID: PMC10997676 DOI: 10.1038/s41597-024-03189-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/25/2024] [Indexed: 04/07/2024] Open
Abstract
Despite the rapid advances in sequencing technology, limited genomic resources are currently available for phytophagous spider mites, which include many important agricultural pests. One of these pests is Tetranychus piercei (McGregor), a serious banana pest in East Asia exhibiting remarkable tolerance to high temperature. In this study, we assembled a high-quality genome of T. piercei using a combination of PacBio long reads and Illumina short reads sequencing. With the assistance of chromatin conformation capture technology, 99.9% of the contigs were anchored into three pseudochromosomes with a total size of 86.02 Mb. Repetitive elements, accounting for 14.16% of this genome (12.20 Mb), are predominantly composed of long-terminal repeats (30.7%). By combining evidence of ab initio prediction, transcripts, and homologous proteins, we annotated 11,881 protein-coding genes. Both the genome and proteins have high BUSCO completeness scores (>94%). This high-quality genome, along with reliable annotation, provides a valuable resource for investigating the high-temperature tolerance of this species and exploring the genomic basis that underlies the host range evolution of spider mites.
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Affiliation(s)
- Lei Chen
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xin-Yue Yu
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Feng Zhang
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Hua-Meng Zhang
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Li-Xue Guo
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Lu Ren
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
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178
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Peralta DM, Túnez JI, Rodríguez Cruz UE, Ceballos SG. A rapid approach for sex assignment by RAD-seq using a reference genome. PLoS One 2024; 19:e0297987. [PMID: 38578816 PMCID: PMC10997085 DOI: 10.1371/journal.pone.0297987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 01/14/2024] [Indexed: 04/07/2024] Open
Abstract
Sex identification is a common objective in molecular ecology. While many vertebrates display sexual dimorphism, determining the sex can be challenging in certain situations, such as species lacking clear sex-related phenotypic characteristics or in studies using non-invasive methods. In these cases, DNA analyses serve as valuable tools not only for sex determination but also for validating sex assignment based on phenotypic traits. In this study, we developed a bioinformatic framework for sex assignment using genomic data obtained through GBS, and having an available closely related genome assembled at the chromosome level. Our method consists of two ad hoc indexes that rely on the different properties of the mammalian heteromorphic sex chromosomes. For this purpose, we mapped RAD-seq loci to a reference genome and then obtained missingness and coverage depth values for the autosomes and X and Y chromosomes of each individual. Our methodology successfully determined the sex of 165 fur seals that had been phenotypically sexed in a previous study and 40 sea lions sampled in a non-invasive way. Additionally, we evaluated the accuracy of each index in sequences with varying average coverage depths, with Index Y proving greater reliability and robustness in assigning sex to individuals with low-depth coverage. We believe that the approach presented here can be extended to any animal taxa with known heteromorphic XY/ZW sex chromosome systems and that it can tolerate various qualities of GBS sequencing data.
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Affiliation(s)
- Diego M. Peralta
- Grupo de Investigación en Ecología Molecular, Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu-CIC), Luján, Argentina
- Departamento de Ecología de la Diversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Juan I. Túnez
- Grupo de Investigación en Ecología Molecular, Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu-CIC), Luján, Argentina
- Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
| | - Ulises E. Rodríguez Cruz
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Santiago G. Ceballos
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales, Universidad Nacional de Tierra del Fuego, Ushuaia, Argentina
- Centro Austral de Investigaciones Científicas (CADIC-CONICET), Ushuaia, Argentina
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179
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Carroll RA, Rice ES, Murphy WJ, Lyons LA, Thibaud-Nissen F, Coghill LM, Swanson WF, Terio KA, Boyd T, Warren WC. A chromosome-scale fishing cat reference genome for the evaluation of potential germline risk variants. Sci Rep 2024; 14:8073. [PMID: 38580653 PMCID: PMC10997796 DOI: 10.1038/s41598-024-56003-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/29/2024] [Indexed: 04/07/2024] Open
Abstract
The fishing cat, Prionailurus viverrinus, faces a population decline, increasing the importance of maintaining healthy zoo populations. Unfortunately, zoo-managed individuals currently face a high prevalence of transitional cell carcinoma (TCC), a form of bladder cancer. To investigate the genetics of inherited diseases among captive fishing cats, we present a chromosome-scale assembly, generate the pedigree of the zoo-managed population, reaffirm the close genetic relationship with the Asian leopard cat (Prionailurus bengalensis), and identify 7.4 million single nucleotide variants (SNVs) and 23,432 structural variants (SVs) from whole genome sequencing (WGS) data of healthy and TCC cats. Only BRCA2 was found to have a high recurrent number of missense mutations in fishing cats diagnosed with TCC when compared to inherited human cancer risk variants. These new fishing cat genomic resources will aid conservation efforts to improve their genetic fitness and enhance the comparative study of feline genomes.
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Affiliation(s)
- Rachel A Carroll
- Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA
| | - Edward S Rice
- Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A and M University, College Station, TX, 77843-4458, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Lyndon M Coghill
- Bioinformatics and Analytics Core, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA
| | - William F Swanson
- Center for Conservation and Research of Endangered Wildlife, Cincinnati Zoo and Botanical Garden, 3400 Vine St., Cincinnati, OH, 45220, USA
| | - Karen A Terio
- Zoological Pathology Program, University of Illinois, 3300 Golf Rd, Brookfield, IL, 60513, USA
| | - Tyler Boyd
- Oklahoma City Zoo and Botanical Garden, 2000 Remington Pl., Oklahoma, OK, 73111, USA
| | - Wesley C Warren
- Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA.
- Department of Surgery, Bond Life Sciences Center, Institute of Data Science and Informatics, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA.
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180
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Yesaya A, Zhang L, Wu C, Fu Y, Zhang J, An J, Xiao Y. The chromosomal-scale genome sequencing and assembly of Athetis lepigone. Sci Data 2024; 11:338. [PMID: 38580759 PMCID: PMC10997617 DOI: 10.1038/s41597-024-03136-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/11/2024] [Indexed: 04/07/2024] Open
Abstract
Athetis lepigone is an emerging highly polyphagous insect pest reported to cause crop damage in several European and Asian countries. However, our understanding of its genetic adaptation mechanisms has been limited due to lack of high-quality genetic resources. In this study, we present a chromosomal-level genome of A. lepigone, representing the first species in the genus of Athetis. We employed PacBio long-read sequencing and Hi-C technologies to generate 612.49 Mb genome assembly which contains 42.43% repeat sequences with a scaffold N50 of 20.9 Mb. The contigs were successfully clustered into 31 chromosomal-size scaffolds with 37% GC content. BUSCO assessment revealed a genome completeness of 97.4% with 96.3 identified as core Arthropoda single copy orthologs. Among the 17,322 genes that were predicted, 15,965 genes were functionally annotated, representing a coverage of 92.17%. Furthermore, we revealed 106 P450, 37 GST, 27 UGT, and 74 COE gene families in the genome of A. lepigone. This genome provides a significant and invaluable genomic resource for further research across the entire genus of Athetis.
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Affiliation(s)
- Alexander Yesaya
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Lei Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Chao Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Yiheng Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, 530005, Nanning, China
| | - Ji Zhang
- Sanya Nanfan Research Institute and College of Tropical Crops, Hainan University, Sanya, 572025, China
| | - Jingjie An
- Plant Protection Institute, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs, IPM Innovation Canter of Hebei Province, International Science and Technology Joint Research Canter on IPM of Hebei Province, Baoding, China
| | - Yutao Xiao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China.
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181
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Tergas A, Byron S, Zhang G, Izatt T, Zhang J, Schork N, Rodriguez L. YIA24-007: Genetic Ancestry and Genomic Alterations of Cervical Cancer in a Diverse Patient Population. J Natl Compr Canc Netw 2024; 22:YIA24-007. [PMID: 38579857 DOI: 10.6004/jnccn.2023.7125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
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182
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Choi TY, Lee SR. Complete plastid genome of Iris orchioides and comparative analysis with 19 Iris plastomes. PLoS One 2024; 19:e0301346. [PMID: 38578735 PMCID: PMC10997070 DOI: 10.1371/journal.pone.0301346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 03/14/2024] [Indexed: 04/07/2024] Open
Abstract
Iris is a cosmopolitan genus comprising approximately 280 species distributed throughout the Northern Hemisphere. Although Iris is the most diverse group in the Iridaceae, the number of taxa is debatable owing to various taxonomic issues. Plastid genomes have been widely used for phylogenetic research in plants; however, only limited number of plastid DNA markers are available for phylogenetic study of the Iris. To understand the genomic features of plastids within the genus, including its structural and genetic variation, we newly sequenced and analyzed the complete plastid genome of I. orchioides and compared it with those of 19 other Iris taxa. Potential plastid markers for phylogenetic research were identified by computing the sequence divergence and phylogenetic informativeness. We then tested the utility of the markers with the phylogenies inferred from the markers and whole-plastome data. The average size of the plastid genome was 152,926 bp, and the overall genomic content and organization were nearly identical among the 20 Iris taxa, except for minor variations in the inverted repeats. We identified 10 highly informative regions (matK, ndhF, rpoC2, ycf1, ycf2, rps15-ycf, rpoB-trnC, petA-psbJ, ndhG-ndhI and psbK-trnQ) and inferred a phylogeny from each region individually, as well as from their concatenated data. Remarkably, the phylogeny reconstructed from the concatenated data comprising three selected regions (rpoC2, ycf1 and ycf2) exhibited the highest congruence with the phylogeny derived from the entire plastome dataset. The result suggests that this subset of data could serve as a viable alternative to the complete plastome data, especially for molecular diagnoses among closely related Iris taxa, and at a lower cost.
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Affiliation(s)
- Tae-Young Choi
- Department of Biology Education, Chosun University, Gwangju, South Korea
| | - Soo-Rang Lee
- Department of Biology Education, Chosun University, Gwangju, South Korea
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183
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Ding W, Li X, Zhang J, Ji M, Zhang M, Zhong X, Cao Y, Liu X, Li C, Xiao C, Wang J, Li T, Yu Q, Mo F, Zhang B, Qi J, Yang JC, Qi J, Tian L, Xu X, Peng Q, Zhou WZ, Liu Z, Fu A, Zhang X, Zhang JJ, Sun Y, Hu B, An NA, Zhang L, Li CY. Adaptive functions of structural variants in human brain development. Sci Adv 2024; 10:eadl4600. [PMID: 38579006 DOI: 10.1126/sciadv.adl4600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/01/2024] [Indexed: 04/07/2024]
Abstract
Quantifying the structural variants (SVs) in nonhuman primates could provide a niche to clarify the genetic backgrounds underlying human-specific traits, but such resource is largely lacking. Here, we report an accurate SV map in a population of 562 rhesus macaques, verified by in-house benchmarks of eight macaque genomes with long-read sequencing and another one with genome assembly. This map indicates stronger selective constrains on inversions at regulatory regions, suggesting a strategy for prioritizing them with the most important functions. Accordingly, we identified 75 human-specific inversions and prioritized them. The top-ranked inversions have substantially shaped the human transcriptome, through their dual effects of reconfiguring the ancestral genomic architecture and introducing regional mutation hotspots at the inverted regions. As a proof of concept, we linked APCDD1, located on one of these inversions and down-regulated specifically in humans, to neuronal maturation and cognitive ability. We thus highlight inversions in shaping the human uniqueness in brain development.
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Affiliation(s)
- Wanqiu Ding
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Xiangshang Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jie Zhang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Mingjun Ji
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Mengling Zhang
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Xiaoming Zhong
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yong Cao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119S Fourth Ring Rd W, Fengtai District, Beijing, China
| | - Xiaoge Liu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Chunqiong Li
- Chinese Institute for Brain Research, Beijing, China
| | - Chunfu Xiao
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jiaxin Wang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Ting Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Qing Yu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Fan Mo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Boya Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jianhuan Qi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jie-Chun Yang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Juntian Qi
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Lu Tian
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Xinwei Xu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Qi Peng
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Wei-Zhen Zhou
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhijin Liu
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Aisi Fu
- Wuhan Dgensee Clinical Laboratory, Wuhan, China
| | - Xiuqin Zhang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jian-Jun Zhang
- Shanxi Key Laboratory of Chinese Medicine Encephalopathy, National International Joint Research Center for Molecular Chinese Medicine, Shanxi University of Chinese Medicine, Jinzhong, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Baoyang Hu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Ni A An
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- National Biomedical Imaging Center, College of Future Technology, Peking University, Beijing, China
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, China
| | - Chuan-Yun Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
- National Biomedical Imaging Center, College of Future Technology, Peking University, Beijing, China
- Southwest United Graduate School, Kunming 650092, China
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184
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de Moraes Pires WM, Cruz ACR, de Souza AJS, Silva SP, Souza Barbosa Coelho TF, Dias DD, Rosa Júnior JW, Mendes SB, da Costa Fraga E, Barros MC, Sampaio I. Genomic characterization of a novel Hepatovirus identified in Maranhão state, Brazil. Sci Rep 2024; 14:7981. [PMID: 38575654 PMCID: PMC10995186 DOI: 10.1038/s41598-024-58171-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
Bats are efficient reservoirs of a number of viruses with zoonotic potential, and are involved directly in the transmission cycle of many zoonoses. In the present study, which is part of a larger project that is documenting the viromes of the bat species found in the Mid-North states of Maranhão and Piauí, we analyzed 16 pooled samples obtained from four species of bat of the genus Artibeus-Artibeus obscurus, Artibeus cinereus, Artibeus lituratus and Artibeus planirostris. We describe and identify a Hepatovirus, denominated Hepatovirus H isolate sotense, which was found in a pool of internal organs (liver and lungs) extracted from a specimen of A. planirostris, a frugivorous bat, collected in the Cerrado biome of Maranhão state. This material was analyzed using new generation sequencing, which produced a contig of 7390 nucleotides and presented a degree of identity with a number of existing Hepatovirus sequences available for bats (amino acid identity of 61.5% with Bat hepatovirus C of Miniopterus cf. manavi, 66.6% with Bat hepatovirus G of Coleura afra, 67.4% with Hepatovirus G2 of Rhinolophus landeri, and 75.3% with Hepatovirus H2 of Rhinolophus landeri). The analysis of the functional domains of this contig confirmed a pattern consistent with the characteristics of the genus Hepatovirus (Picornaviridae). In the phylogenetic tree with several other Hepatovirus species, this genome also grouped in a monophyletic clade with Hepatovirus H (HepV-H1; HepV-H2, and HepV-H3) albeit on an external branch, which suggests that it may be a distinct genotype within this species. This is the first isolate of Hepatovirus H identified in bats from South America, and represents an important discovery, given that most studies of viruses associated with bats in the state of Maranhão have focused on the family Rhabdoviridae.
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Affiliation(s)
| | - Ana Cecília Ribeiro Cruz
- Department of Arbovirology and Hemorrhagic Fevers, Instituto Evandro Chagas IEC/SVS/MS, Ananindeua, Pará, 67030-000, Brazil
| | - Alex Junior Souza de Souza
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo (USP), São Paulo, Brazil
| | - Sandro Patroca Silva
- Department of Arbovirology and Hemorrhagic Fevers, Instituto Evandro Chagas IEC/SVS/MS, Ananindeua, Pará, 67030-000, Brazil
| | | | - Daniel Damous Dias
- Laboratory of Medical Entomology, Instituto Evandro Chagas IEC/SVS/MS, Ananindeua, Pará, 67030-000, Brazil
| | - José Wilson Rosa Júnior
- Department of Arbovirology and Hemorrhagic Fevers, Instituto Evandro Chagas IEC/SVS/MS, Ananindeua, Pará, 67030-000, Brazil
| | - Samira Brito Mendes
- Graduate Program in Biodiversity and Biotechnology-Bionorte Network, Laboratory of Genetics and Molecular Biology, Universidade Estadual do Maranhão, São Luís, Maranhão, 65055-310, Brazil
| | - Elmary da Costa Fraga
- Laboratory of Genetics and Molecular Biology-GENBIMOL, Universidade Estadual Do Maranhão-Campus Caxias, Caxias, Maranhão, 65604-380, Brazil
| | - Maria Claudene Barros
- Laboratory of Genetics and Molecular Biology-GENBIMOL, Universidade Estadual Do Maranhão-Campus Caxias, Caxias, Maranhão, 65604-380, Brazil
| | - Iracilda Sampaio
- Laboratory of Evolution, Institute of Coastal Studies, Universidade Federal do Pará-UFPA-UFPA, Bragança, Pará, 68600-000, Brazil
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185
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Mikhaylova V, Rzepka M, Kawamura T, Xia Y, Chang PL, Zhou S, Paasch A, Pham L, Modi N, Yao L, Perez-Agustin A, Pagans S, Boles TC, Lei M, Wang Y, Garcia-Bassets I, Chen Z. Targeted phasing of 2-200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method. Sci Rep 2024; 14:7988. [PMID: 38580715 PMCID: PMC10997766 DOI: 10.1038/s41598-024-58733-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 04/02/2024] [Indexed: 04/07/2024] Open
Abstract
In the human genome, heterozygous sites refer to genomic positions with a different allele or nucleotide variant on the maternal and paternal chromosomes. Resolving these allelic differences by chromosomal copy, also known as phasing, is achievable on a short-read sequencer when using a library preparation method that captures long-range genomic information. TELL-Seq is a library preparation that captures long-range genomic information with the aid of molecular identifiers (barcodes). The same barcode is used to tag the reads derived from the same long DNA fragment within a range of up to 200 kilobases (kb), generating linked-reads. This strategy can be used to phase an entire genome. Here, we introduce a TELL-Seq protocol developed for targeted applications, enabling the phasing of enriched loci of varying sizes, purity levels, and heterozygosity. To validate this protocol, we phased 2-200 kb loci enriched with different methods: CRISPR/Cas9-mediated excision coupled with pulse-field electrophoresis for the longest fragments, CRISPR/Cas9-mediated protection from exonuclease digestion for mid-size fragments, and long PCR for the shortest fragments. All selected loci have known clinical relevance: BRCA1, BRCA2, MLH1, MSH2, MSH6, APC, PMS2, SCN5A-SCN10A, and PKI3CA. Collectively, the analyses show that TELL-Seq can accurately phase 2-200 kb targets using a short-read sequencer.
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Affiliation(s)
| | - Madison Rzepka
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | | | - Yu Xia
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | - Peter L Chang
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | | | - Amber Paasch
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | - Long Pham
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | - Naisarg Modi
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | - Likun Yao
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Adrian Perez-Agustin
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - Sara Pagans
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | | | - Ming Lei
- Universal Sequencing Technology Corp., Canton, MA, 02021, USA
| | - Yong Wang
- Universal Sequencing Technology Corp., Canton, MA, 02021, USA
| | | | - Zhoutao Chen
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA.
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186
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Rajawat D, Ghildiyal K, Sonejita Nayak S, Sharma A, Parida S, Kumar S, Ghosh AK, Singh U, Sivalingam J, Bhushan B, Dutt T, Panigrahi M. Genome-wide mining of diversity and evolutionary signatures revealed selective hotspots in Indian Sahiwal cattle. Gene 2024; 901:148178. [PMID: 38242377 DOI: 10.1016/j.gene.2024.148178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
The Sahiwal cattle breed is the best indigenous dairy cattle breed, and it plays a pivotal role in the Indian dairy industry. This is due to its exceptional milk-producing potential, adaptability to local tropical conditions, and its resilience to ticks and diseases. The study aimed to identify selective sweeps and estimate intrapopulation genetic diversity parameters in Sahiwal cattle using ddRAD sequencing-based genotyping data from 82 individuals. After applying filtering criteria, 78,193 high-quality SNPs remained for further analysis. The population exhibited an average minor allele frequency of 0.221 ± 0.119. Genetic diversity metrics, including observed (0.597 ± 0.196) and expected heterozygosity (0.433 ± 0.096), nucleotide diversity (0.327 ± 0.114), the proportion of polymorphic SNPs (0.726), and allelic richness (1.323 ± 0.134), indicated ample genomic diversity within the breed. Furthermore, an effective population size of 74 was observed in the most recent generation. The overall mean linkage disequilibrium (r2) for pairwise SNPs was 0.269 ± 0.057. Moreover, a greater proportion of short Runs of Homozygosity (ROH) segments were observed suggesting that there may be low levels of recent inbreeding in this population. The genomic inbreeding coefficients, computed using different inbreeding estimates (FHOM, FUNI, FROH, and FGROM), ranged from -0.0289 to 0.0725. Subsequently, we found 146 regions undergoing selective sweeps using five distinct statistical tests: Tajima's D, CLR, |iHS|, |iHH12|, and ROH. These regions, located in non-overlapping 500 kb windows, were mapped and revealed various protein-coding genes associated with enhanced immune systems and disease resistance (IFNL3, IRF8, BLK), as well as production traits (NRXN1, PLCE1, GHR). Notably, we identified interleukin 2 (IL2) on Chr17: 35217075-35223276 as a gene linked to tick resistance and uncovered a cluster of genes (HSPA8, UBASH3B, ADAMTS18, CRTAM) associated with heat stress. These findings indicate the evolutionary impact of natural and artificial selection on the environmental adaptation of the Sahiwal cattle population.
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Affiliation(s)
- Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Subhashree Parida
- Pharmacology & Toxicology Division, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Shive Kumar
- Department of Animal Genetics and Breeding, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - A K Ghosh
- Department of Animal Genetics and Breeding, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Umesh Singh
- ICAR Central Institute for Research on Cattle, Meerut, UP, India
| | | | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
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187
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Bastian L, Beder T, Barz MJ, Bendig S, Bartsch L, Walter W, Wolgast N, Brändl B, Rohrandt C, Hansen BT, Hartmann AM, Iben K, Das Gupta D, Denker M, Zimmermann J, Wittig M, Chitadze G, Neumann M, Schneller F, Fiedler W, Steffen B, Stelljes M, Faul C, Schwartz S, Müller FJ, Cario G, Harder L, Haferlach C, Pfeifer H, Gökbuget N, Brüggemann M, Baldus CD. Developmental trajectories and cooperating genomic events define molecular subtypes of BCR::ABL1-positive ALL. Blood 2024; 143:1391-1398. [PMID: 38153913 PMCID: PMC11033585 DOI: 10.1182/blood.2023021752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/30/2023] Open
Abstract
ABSTRACT Distinct diagnostic entities within BCR::ABL1-positive acute lymphoblastic leukemia (ALL) are currently defined by the International Consensus Classification of myeloid neoplasms and acute leukemias (ICC): "lymphoid only", with BCR::ABL1 observed exclusively in lymphatic precursors, vs "multilineage", where BCR::ABL1 is also present in other hematopoietic lineages. Here, we analyzed transcriptomes of 327 BCR::ABL1-positive patients with ALL (age, 2-84 years; median, 46 years) and identified 2 main gene expression clusters reproducible across 4 independent patient cohorts. Fluorescence in situ hybridization analysis of fluorescence-activated cell-sorted hematopoietic compartments showed distinct BCR::ABL1 involvement in myeloid cells for these clusters (n = 18/18 vs n = 3/16 patients; P < .001), indicating that a multilineage or lymphoid BCR::ABL1 subtype can be inferred from gene expression. Further subclusters grouped samples according to cooperating genomic events (multilineage: HBS1L deletion or monosomy 7; lymphoid: IKZF1-/- or CDKN2A/PAX5 deletions/hyperdiploidy). A novel HSB1L transcript was highly specific for BCR::ABL1 multilineage cases independent of HBS1L genomic aberrations. Treatment on current German Multicenter Study Group for Adult ALL (GMALL) protocols resulted in comparable disease-free survival (DFS) for multilineage vs lymphoid cluster patients (3-year DFS: 70% vs 61%; P = .530; n = 91). However, the IKZF1-/- enriched lymphoid subcluster was associated with inferior DFS, whereas hyperdiploid cases showed a superior outcome. Thus, gene expression clusters define underlying developmental trajectories and distinct patterns of cooperating events in BCR::ABL1-positive ALL with prognostic relevance.
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Affiliation(s)
- Lorenz Bastian
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit “CATCH ALL” (KFO 5010/1), Kiel, Germany
| | - Thomas Beder
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Malwine J. Barz
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit “CATCH ALL” (KFO 5010/1), Kiel, Germany
| | - Sonja Bendig
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit “CATCH ALL” (KFO 5010/1), Kiel, Germany
| | - Lorenz Bartsch
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit “CATCH ALL” (KFO 5010/1), Kiel, Germany
| | | | - Nadine Wolgast
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit “CATCH ALL” (KFO 5010/1), Kiel, Germany
| | - Björn Brändl
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Psychiatry and Psychotherapy, University Hospital Schleswig Holstein, Kiel, Germany
| | - Christian Rohrandt
- Department of Psychiatry and Psychotherapy, University Hospital Schleswig Holstein, Kiel, Germany
| | - Björn-Thore Hansen
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Alina M. Hartmann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit “CATCH ALL” (KFO 5010/1), Kiel, Germany
| | - Katharina Iben
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit “CATCH ALL” (KFO 5010/1), Kiel, Germany
| | - Dennis Das Gupta
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit “CATCH ALL” (KFO 5010/1), Kiel, Germany
| | - Miriam Denker
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Johannes Zimmermann
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian Albrechts University, Kiel, Germany
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Guranda Chitadze
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit “CATCH ALL” (KFO 5010/1), Kiel, Germany
| | - Martin Neumann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit “CATCH ALL” (KFO 5010/1), Kiel, Germany
| | - Folker Schneller
- Medical Clinic and Polyclinic of Klinikum rechts der Isar of Technical University Munich, Munich, Germany
| | - Walter Fiedler
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald University Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Björn Steffen
- Department of Medicine II, Hematology/Oncology, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - Matthias Stelljes
- Department of Medicine A–Hematology, Hemostaseology, Oncology, Pulmonology, University Hospital Muenster, Munster, Germany
| | - Christoph Faul
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Stefan Schwartz
- Department of Hematology, Oncology and Tumor Immunology (Campus Benjamin Franklin), Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
| | - Franz-Josef Müller
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Psychiatry and Psychotherapy, University Hospital Schleswig Holstein, Kiel, Germany
| | - Gunnar Cario
- Clinical Research Unit “CATCH ALL” (KFO 5010/1), Kiel, Germany
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Lana Harder
- Institut für Tumorgenetik Nord, Kiel, Germany
| | | | - Heike Pfeifer
- Department of Medicine II, Hematology/Oncology, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - Nicola Gökbuget
- Department of Medicine II, Hematology/Oncology, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - Monika Brüggemann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit “CATCH ALL” (KFO 5010/1), Kiel, Germany
| | - Claudia D. Baldus
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit “CATCH ALL” (KFO 5010/1), Kiel, Germany
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188
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Leader AE, McNair CM, Johnson JM. From Base Pairs to City Squares: Comprehensive Precision Oncology for the Future. Cancer Discov 2024; 14:569-572. [PMID: 38571420 DOI: 10.1158/2159-8290.cd-24-0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
SUMMARY An increased understanding of the role of the social determinants of health in cancer prevention, cancer care, and outcomes can lead to their integration into genetics and genomics as well as informing interventions and clinical trials, creating a comprehensive precision oncology framework.
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Affiliation(s)
- Amy E Leader
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Christopher M McNair
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Jennifer M Johnson
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
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189
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Aloryi KD, Okpala NE, Guo H, Karikari B, Amo A, Bello SF, Saini DK, Akaba S, Tian X. Integrated meta-analysis and transcriptomics pinpoint genomic loci and novel candidate genes associated with submergence tolerance in rice. BMC Genomics 2024; 25:338. [PMID: 38575927 PMCID: PMC10993490 DOI: 10.1186/s12864-024-10219-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Due to rising costs, water shortages, and labour shortages, farmers across the globe now prefer a direct seeding approach. However, submergence stress remains a major bottleneck limiting the success of this approach in rice cultivation. The merger of accumulated rice genetic resources provides an opportunity to detect key genomic loci and candidate genes that influence the flooding tolerance of rice. RESULTS In the present study, a whole-genome meta-analysis was conducted on 120 quantitative trait loci (QTL) obtained from 16 independent QTL studies reported from 2004 to 2023. These QTL were confined to 18 meta-QTL (MQTL), and ten MQTL were successfully validated by independent genome-wide association studies from diverse natural populations. The mean confidence interval (CI) of the identified MQTL was 3.44 times narrower than the mean CI of the initial QTL. Moreover, four core MQTL loci with genetic distance less than 2 cM were obtained. By combining differentially expressed genes (DEG) from two transcriptome datasets with 858 candidate genes identified in the core MQTL regions, we found 38 common differentially expressed candidate genes (DECGs). In silico expression analysis of these DECGs led to the identification of 21 genes with high expression in embryo and coleoptile under submerged conditions. These DECGs encode proteins with known functions involved in submergence tolerance including WRKY, F-box, zinc fingers, glycosyltransferase, protein kinase, cytochrome P450, PP2C, hypoxia-responsive family, and DUF domain. By haplotype analysis, the 21 DECGs demonstrated distinct genetic differentiation and substantial genetic distance mainly between indica and japonica subspecies. Further, the MQTL7.1 was successfully validated using flanked marker S2329 on a set of genotypes with phenotypic variation. CONCLUSION This study provides a new perspective on understanding the genetic basis of submergence tolerance in rice. The identified MQTL and novel candidate genes lay the foundation for marker-assisted breeding/engineering of flooding-tolerant cultivars conducive to direct seeding.
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Grants
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- Key R&D Project in Hubei Province, China
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Affiliation(s)
- Kelvin Dodzi Aloryi
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Nnaemeka Emmanuel Okpala
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Hong Guo
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Benjamin Karikari
- Département de phytologie, Université Laval, Québec, QC, Canada
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Aduragbemi Amo
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, USA
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, USA
| | - Semiu Folaniyi Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA
| | - Selorm Akaba
- School of Agriculture, University of Cape Coast, Cape Coast, Ghana
| | - Xiaohai Tian
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China.
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190
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Kim R, Clappier E. Uncovering new layers of Ph+ ALL biology. Blood 2024; 143:1322-1323. [PMID: 38573608 DOI: 10.1182/blood.2023023583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
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191
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Wilson S, Zheng C, Maliepaard C, Mulder HA, Visser RGF, van Eeuwijk F. Multienvironment genomic prediction in tetraploid potato. G3 (Bethesda) 2024; 14:jkae011. [PMID: 38243613 PMCID: PMC10989893 DOI: 10.1093/g3journal/jkae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 10/06/2023] [Accepted: 10/20/2023] [Indexed: 01/21/2024]
Abstract
Multienvironment genomic prediction was applied to tetraploid potato using 147 potato varieties, tested for 2 years, in 3 locations representative of 3 distinct regions in Europe. Different prediction scenarios were investigated to help breeders predict genotypic performance in the regions from one year to the next, for genotypes that were tested this year (scenario 1), as well as new genotypes (scenario 3). In scenario 2, we predicted new genotypes for any one of the 6 trials, using all the information that is available. The choice of prediction model required assessment of the variance-covariance matrix in a mixed model that takes into account heterogeneity of genetic variances and correlations. This was done for each analyzed trait (tuber weight, tuber length, and dry matter) where examples of both limited and higher degrees of heterogeneity was observed. This explains why dry matter did not need complex multienvironment modeling to combine environments and increase prediction ability, while prediction in tuber weight, improved only when models were flexible enough to capture the heterogeneous variances and covariances between environments. We also found that the prediction abilities in a target trial condition decreased, if trials with a low genetic correlation to the target were included when training the model. Genomic prediction in tetraploid potato can work once there is clarity about the prediction scenario, a suitable training set is created, and a multienvironment prediction model is chosen based on the patterns of G×E indicated by the genetic variances and covariances.
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Affiliation(s)
- Stefan Wilson
- Biometris, Wageningen University & Research Centre, Wageningen, PB 6708, The Netherlands
| | - Chaozhi Zheng
- Biometris, Wageningen University & Research Centre, Wageningen, PB 6708, The Netherlands
| | - Chris Maliepaard
- Plant Breeding, Wageningen University and Research, Wageningen, PB 6708, The Netherlands
| | - Han A Mulder
- Wageningen University and Research Animal Breeding and Genomics, Wageningen, AH 6700, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University and Research, Wageningen, PB 6708, The Netherlands
| | - Fred van Eeuwijk
- Biometris, Wageningen University & Research Centre, Wageningen, PB 6708, The Netherlands
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192
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Brault C, Segura V, Roques M, Lamblin P, Bouckenooghe V, Pouzalgues N, Cunty C, Breil M, Frouin M, Garcin L, Camps L, Ducasse MA, Romieu C, Masson G, Julliard S, Flutre T, Le Cunff L. Enhancing grapevine breeding efficiency through genomic prediction and selection index. G3 (Bethesda) 2024; 14:jkae038. [PMID: 38401528 PMCID: PMC10989862 DOI: 10.1093/g3journal/jkae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/09/2024] [Accepted: 02/18/2024] [Indexed: 02/26/2024]
Abstract
Grapevine (Vitis vinifera) breeding reaches a critical point. New cultivars are released every year with resistance to powdery and downy mildews. However, the traditional process remains time-consuming, taking 20-25 years, and demands the evaluation of new traits to enhance grapevine adaptation to climate change. Until now, the selection process has relied on phenotypic data and a limited number of molecular markers for simple genetic traits such as resistance to pathogens, without a clearly defined ideotype, and was carried out on a large scale. To accelerate the breeding process and address these challenges, we investigated the use of genomic prediction, a methodology using molecular markers to predict genotypic values. In our study, we focused on 2 existing grapevine breeding programs: Rosé wine and Cognac production. In these programs, several families were created through crosses of emblematic and interspecific resistant varieties to powdery and downy mildews. Thirty traits were evaluated for each program, using 2 genomic prediction methods: Genomic Best Linear Unbiased Predictor and Least Absolute Shrinkage Selection Operator. The results revealed substantial variability in predictive abilities across traits, ranging from 0 to 0.9. These discrepancies could be attributed to factors such as trait heritability and trait characteristics. Moreover, we explored the potential of across-population genomic prediction by leveraging other grapevine populations as training sets. Integrating genomic prediction allowed us to identify superior individuals for each program, using multivariate selection index method. The ideotype for each breeding program was defined collaboratively with representatives from the wine-growing sector.
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Affiliation(s)
- Charlotte Brault
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, Montpellier 34398, France
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
| | - Vincent Segura
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, Montpellier 34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier 34398, France
| | - Maryline Roques
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, Montpellier 34398, France
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
| | - Pauline Lamblin
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
| | - Virginie Bouckenooghe
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, Montpellier 34398, France
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
| | | | - Constance Cunty
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
- Centre du Rosé, Vidauban 83550, France
| | - Matthieu Breil
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, Montpellier 34398, France
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
| | - Marina Frouin
- Conservatoire du Vignoble Charentais, Institut de Formation de Richemont, Cherves-Richemont 16370, France
| | - Léa Garcin
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
- Conservatoire du Vignoble Charentais, Institut de Formation de Richemont, Cherves-Richemont 16370, France
| | - Louise Camps
- Conservatoire du Vignoble Charentais, Institut de Formation de Richemont, Cherves-Richemont 16370, France
| | - Marie-Agnès Ducasse
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
| | - Charles Romieu
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, Montpellier 34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier 34398, France
| | - Gilles Masson
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
- Centre du Rosé, Vidauban 83550, France
| | - Sébastien Julliard
- Conservatoire du Vignoble Charentais, Institut de Formation de Richemont, Cherves-Richemont 16370, France
| | - Timothée Flutre
- INRAE, CNRS, AgroParisTech, Université Paris-Saclay, GQE—Le Moulon, Gif-sur-Yvette 91190, France
| | - Loïc Le Cunff
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, Montpellier 34398, France
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
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193
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Lunke S, Bouffler SE, Downie L, Caruana J, Amor DJ, Archibald A, Bombard Y, Christodoulou J, Clausen M, De Fazio P, Greaves RF, Hollizeck S, Kanga-Parabia A, Lang N, Lynch F, Peters R, Sadedin S, Tutty E, Eggers S, Lee C, Wall M, Yeung A, Gaff C, Gyngell C, Vears DF, Best S, Goranitis I, Stark Z. Prospective cohort study of genomic newborn screening: BabyScreen+ pilot study protocol. BMJ Open 2024; 14:e081426. [PMID: 38569677 DOI: 10.1136/bmjopen-2023-081426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
INTRODUCTION Newborn bloodspot screening (NBS) is a highly successful public health programme that uses biochemical and other assays to screen for severe but treatable childhood-onset conditions. Introducing genomic sequencing into NBS programmes increases the range of detectable conditions but raises practical and ethical issues. Evidence from prospectively ascertained cohorts is required to guide policy and future implementation. This study aims to develop, implement and evaluate a genomic NBS (gNBS) pilot programme. METHODS AND ANALYSIS The BabyScreen+ study will pilot gNBS in three phases. In the preimplementation phase, study materials, including education resources, decision support and data collection tools, will be designed. Focus groups and key informant interviews will also be undertaken to inform delivery of the study and future gNBS programmes. During the implementation phase, we will prospectively recruit birth parents in Victoria, Australia, to screen 1000 newborns for over 600 severe, treatable, childhood-onset conditions. Clinically accredited whole genome sequencing will be performed following standard NBS using the same sample. High chance results will be returned by genetic healthcare professionals, with follow-on genetic and other confirmatory testing and referral to specialist services as required. The postimplementation phase will evaluate the feasibility of gNBS as the primary aim, and assess ethical, implementation, psychosocial and health economic factors to inform future service delivery. ETHICS AND DISSEMINATION This project received ethics approval from the Royal Children's Hospital Melbourne Research Ethics Committee: HREC/91500/RCHM-2023, HREC/90929/RCHM-2022 and HREC/91392/RCHM-2022. Findings will be disseminated to policy-makers, and through peer-reviewed journals and conferences.
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Affiliation(s)
- Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- University of Melbourne, Melbourne, Victoria, Australia
| | - Sophie E Bouffler
- Australian Genomics Health Alliance, Parkville, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Lilian Downie
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- University of Melbourne, Melbourne, Victoria, Australia
| | - Jade Caruana
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - David J Amor
- University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Alison Archibald
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- University of Melbourne, Melbourne, Victoria, Australia
| | - Yvonne Bombard
- Genomics Health Services Research Program, St Michael's Hospital, Toronto, Ontario, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - John Christodoulou
- University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Marc Clausen
- Genomics Health Services Research Program, St Michael's Hospital, Toronto, Ontario, Canada
| | - Paul De Fazio
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Ronda F Greaves
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- University of Melbourne, Melbourne, Victoria, Australia
| | - Sebastian Hollizeck
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Anaita Kanga-Parabia
- University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Nitzan Lang
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Fiona Lynch
- University of Melbourne, Melbourne, Victoria, Australia
| | | | - Simon Sadedin
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Erin Tutty
- University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Stefanie Eggers
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Crystle Lee
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Meaghan Wall
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- University of Melbourne, Melbourne, Victoria, Australia
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- University of Melbourne, Melbourne, Victoria, Australia
| | - Clara Gaff
- University of Melbourne, Melbourne, Victoria, Australia
- Melbourne Genomics Health Alliance, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Christopher Gyngell
- University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Danya F Vears
- University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Stephanie Best
- Australian Genomics Health Alliance, Parkville, Victoria, Australia
- Department of Health Services Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Ilias Goranitis
- University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics Health Alliance, Parkville, Victoria, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics Health Alliance, Parkville, Victoria, Australia
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194
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Joubert PM, Krasileva KV. Distinct genomic contexts predict gene presence-absence variation in different pathotypes of Magnaporthe oryzae. Genetics 2024; 226:iyae012. [PMID: 38290434 PMCID: PMC10990425 DOI: 10.1093/genetics/iyae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 11/28/2023] [Accepted: 12/19/2023] [Indexed: 02/01/2024] Open
Abstract
Fungi use the accessory gene content of their pangenomes to adapt to their environments. While gene presence-absence variation contributes to shaping accessory gene reservoirs, the genomic contexts that shape these events remain unclear. Since pangenome studies are typically species-wide and do not analyze different populations separately, it is yet to be uncovered whether presence-absence variation patterns and mechanisms are consistent across populations. Fungal plant pathogens are useful models for studying presence-absence variation because they rely on it to adapt to their hosts, and members of a species often infect distinct hosts. We analyzed gene presence-absence variation in the blast fungus, Magnaporthe oryzae (syn. Pyricularia oryzae), and found that presence-absence variation genes involved in host-pathogen and microbe-microbe interactions may drive the adaptation of the fungus to its environment. We then analyzed genomic and epigenomic features of presence-absence variation and observed that proximity to transposable elements, gene GC content, gene length, expression level in the host, and histone H3K27me3 marks were different between presence-absence variation genes and conserved genes. We used these features to construct a model that was able to predict whether a gene is likely to experience presence-absence variation with high precision (86.06%) and recall (92.88%) in M. oryzae. Finally, we found that presence-absence variation genes in the rice and wheat pathotypes of M. oryzae differed in their number and their genomic context. Our results suggest that genomic and epigenomic features of gene presence-absence variation can be used to better understand and predict fungal pangenome evolution. We also show that substantial intra-species variation can exist in these features.
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Affiliation(s)
- Pierre M Joubert
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Center for Computational Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Center for Computational Biology, University of California-Berkeley, Berkeley, CA 94720, USA
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195
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Tumas H, Ilska JJ, Gérardi S, Laroche J, A’Hara S, Boyle B, Janes M, McLean P, Lopez G, Lee SJ, Cottrell J, Gorjanc G, Bousquet J, Woolliams JA, MacKay JJ. High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers. G3 (Bethesda) 2024; 14:jkae020. [PMID: 38366548 PMCID: PMC10989875 DOI: 10.1093/g3journal/jkae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/03/2024] [Indexed: 02/18/2024]
Abstract
In species with large and complex genomes such as conifers, dense linkage maps are a useful resource for supporting genome assembly and laying the genomic groundwork at the structural, populational, and functional levels. However, most of the 600+ extant conifer species still lack extensive genotyping resources, which hampers the development of high-density linkage maps. In this study, we developed a linkage map relying on 21,570 single nucleotide polymorphism (SNP) markers in Sitka spruce (Picea sitchensis [Bong.] Carr.), a long-lived conifer from western North America that is widely planted for productive forestry in the British Isles. We used a single-step mapping approach to efficiently combine RAD-seq and genotyping array SNP data for 528 individuals from 2 full-sib families. As expected for spruce taxa, the saturated map contained 12 linkages groups with a total length of 2,142 cM. The positioning of 5,414 unique gene coding sequences allowed us to compare our map with that of other Pinaceae species, which provided evidence for high levels of synteny and gene order conservation in this family. We then developed an integrated map for P. sitchensis and Picea glauca based on 27,052 markers and 11,609 gene sequences. Altogether, these 2 linkage maps, the accompanying catalog of 286,159 SNPs and the genotyping chip developed, herein, open new perspectives for a variety of fundamental and more applied research objectives, such as for the improvement of spruce genome assemblies, or for marker-assisted sustainable management of genetic resources in Sitka spruce and related species.
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Affiliation(s)
- Hayley Tumas
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Joana J Ilska
- The Roslin Institute, Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Sebastien Gérardi
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC GIV 0A6, Canada
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC GIV 0A6, Canada
| | - Jerome Laroche
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC GIV 0A6, Canada
| | - Stuart A’Hara
- Forest Research, Northern Research Station, Midlothian EH25 9SY, UK
| | - Brian Boyle
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC GIV 0A6, Canada
| | - Mateja Janes
- The Roslin Institute, Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Paul McLean
- Forest Research, Northern Research Station, Midlothian EH25 9SY, UK
| | - Gustavo Lopez
- Forest Research, Northern Research Station, Midlothian EH25 9SY, UK
| | - Steve J Lee
- Forest Research, Northern Research Station, Midlothian EH25 9SY, UK
| | - Joan Cottrell
- Forest Research, Northern Research Station, Midlothian EH25 9SY, UK
| | - Gregor Gorjanc
- The Roslin Institute, Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC GIV 0A6, Canada
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC GIV 0A6, Canada
| | - John A Woolliams
- The Roslin Institute, Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, UK
| | - John J MacKay
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK
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196
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Fang Y, Wu D, Gao N, Lv M, Zhou M, Ma C, Sun Y, Cui B. Whole-genome sequencing and comparative genomic analyses of the medicinal fungus Sanguinoderma infundibulare in Ganodermataceae. G3 (Bethesda) 2024; 14:jkae005. [PMID: 38366555 PMCID: PMC10989896 DOI: 10.1093/g3journal/jkae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/05/2024] [Indexed: 02/18/2024]
Abstract
Sanguinoderma infundibulare is a newly discovered species of Ganodermataceae known to have high medicinal and ecological values. In this study, the whole-genome sequencing and comparative genomic analyses were conducted to further understand Ganodermataceae's genomic structural and functional characteristics. Using the Illumina NovaSeq and PacBio Sequel platforms, 88 scaffolds were assembled to obtain a 48.99-Mb high-quality genome of S. infundibulare. A total of 14,146 protein-coding genes were annotated in the whole genome, with 98.6% of complete benchmarking universal single-copy orthologs (BUSCO) scores. Comparative genomic analyses were conducted among S. infundibulare, Sanguinoderma rugosum, Ganoderma lucidum, and Ganoderma sinense to determine their intergeneric differences. The 4 species were found to share 4,011 orthogroups, and 24 specific gene families were detected in the genus Sanguinoderma. The gene families associated with carbohydrate esterase in S. infundibulare were significantly abundant, which was reported to be involved in hemicellulose degradation. One specific gene family in Sanguinoderma was annotated with siroheme synthase, which may be related to the typical characteristics of fresh pore surface changing to blood red when bruised. This study enriched the available genome data for the genus Sanguinoderma, elucidated the differences between Ganoderma and Sanguinoderma, and provided insights into the characteristics of the genome structure and function of S. infundibulare.
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Affiliation(s)
- Yuxuan Fang
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Dongmei Wu
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832061, China
| | - Neng Gao
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832061, China
| | - Mengxue Lv
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Miao Zhou
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Chuangui Ma
- Beijing Jingcheng Biotechnology Co., Ltd, Beijing 100083, China
| | - Yifei Sun
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Baokai Cui
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
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197
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Bhadauria V, Zhao W. The Molecular Genetics and Genomics of Plant-Pathogen Interactions. Int J Mol Sci 2024; 25:3970. [PMID: 38612780 PMCID: PMC11012200 DOI: 10.3390/ijms25073970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
Plants have evolved an intricate immune system to protect themselves from potential pathogens [...].
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Affiliation(s)
- Vijai Bhadauria
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
- Ministry of Agriculture and Rural Affairs—Key Laboratory for Crop Pest Monitoring and Green Control, China Agricultural University, Beijing 100193, China
| | - Wensheng Zhao
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
- Ministry of Agriculture and Rural Affairs—Key Laboratory for Crop Pest Monitoring and Green Control, China Agricultural University, Beijing 100193, China
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198
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Rodrigues MF, Kern AD, Ralph PL. Shared evolutionary processes shape landscapes of genomic variation in the great apes. Genetics 2024; 226:iyae006. [PMID: 38242701 PMCID: PMC10990428 DOI: 10.1093/genetics/iyae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 10/26/2023] [Accepted: 01/03/2024] [Indexed: 01/21/2024] Open
Abstract
For at least the past 5 decades, population genetics, as a field, has worked to describe the precise balance of forces that shape patterns of variation in genomes. The problem is challenging because modeling the interactions between evolutionary processes is difficult, and different processes can impact genetic variation in similar ways. In this paper, we describe how diversity and divergence between closely related species change with time, using correlations between landscapes of genetic variation as a tool to understand the interplay between evolutionary processes. We find strong correlations between landscapes of diversity and divergence in a well-sampled set of great ape genomes, and explore how various processes such as incomplete lineage sorting, mutation rate variation, GC-biased gene conversion and selection contribute to these correlations. Through highly realistic, chromosome-scale, forward-in-time simulations, we show that the landscapes of diversity and divergence in the great apes are too well correlated to be explained via strictly neutral processes alone. Our best fitting simulation includes both deleterious and beneficial mutations in functional portions of the genome, in which 9% of fixations within those regions is driven by positive selection. This study provides a framework for modeling genetic variation in closely related species, an approach which can shed light on the complex balance of forces that have shaped genetic variation.
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Affiliation(s)
- Murillo F Rodrigues
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
- Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - Andrew D Kern
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
- Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - Peter L Ralph
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
- Department of Biology, University of Oregon, Eugene, OR 97403, USA
- Department of Mathematics, University of Oregon, Eugene, OR 97403, USA
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199
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Saunders CJ, Brunelli L, Deem MJ, Farrow EG, Hegde M, Stark Z. More Than a Decade of Rapid Genomic Sequencing: Where Are We Now? Clin Chem 2024; 70:577-583. [PMID: 38565214 PMCID: PMC10987227 DOI: 10.1093/clinchem/hvae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 02/07/2024] [Indexed: 04/04/2024]
Affiliation(s)
- Carol J Saunders
- Director, Division of Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Mercy-Kansas City, Professor of Pediatrics and Pathology, University of Missouri-Kansas City School of Medicine, Kansas City, MO, United States
| | - Luca Brunelli
- Professor of Pediatrics, Division of Neonatology, Department of Pediatrics, University of Utah Spencer Fox Eccles School of Medicine, Salt Lake City, UT, United States
| | - Michael J Deem
- Associate Professor, Department of Human Genetics, Core Faculty, Center for Bioethics & Health Law, University of Pittsburgh, Pittsburgh, PA, United States
| | - Emily G Farrow
- Director of Genomics Operations, Division of Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Mercy-Kansas City, Associate Professor of Pediatrics and Pathology, University of Missouri-Kansas City School of Medicine, Kansas City, MO, United States
| | - Madhuri Hegde
- Vice President and Chief Scientific Officer, Revvity Inc., Waltham, MA, United States
| | - Zornitza Stark
- Professor, Department of Paediatrics, University of Melbourne; Australian Genomics; Victorian Clinical Genetics Services, Melbourne, Victoria, Australia
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200
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Christinaki AC, Myridakis AI, Kouvelis VN. Genomic insights into the evolution and adaptation of secondary metabolite gene clusters in fungicolous species Cladobotryum mycophilum ATHUM6906. G3 (Bethesda) 2024; 14:jkae006. [PMID: 38214578 PMCID: PMC10989895 DOI: 10.1093/g3journal/jkae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/01/2023] [Accepted: 11/29/2023] [Indexed: 01/13/2024]
Abstract
Mycophilic or fungicolous fungi can be found wherever fungi exist since they are able to colonize other fungi, which occupy a diverse range of habitats. Some fungicolous species cause important diseases on Basidiomycetes, and thus, they are the main reason for the destruction of mushroom cultivations. Nonetheless, despite their ecological significance, their genomic data remain limited. Cladobotryum mycophilum is one of the most aggressive species of the genus, destroying the economically important Agaricus bisporus cultivations. The 40.7 Mb whole genome of the Greek isolate ATHUM6906 is assembled in 16 fragments, including the mitochondrial genome and 2 small circular mitochondrial plasmids, in this study. This genome includes a comprehensive set of 12,282 protein coding, 56 rRNA, and 273 tRNA genes. Transposable elements, CAZymes, and pathogenicity related genes were also examined. The genome of C. mycophilum contained a diverse arsenal of genes involved in secondary metabolism, forming 106 biosynthetic gene clusters, which renders this genome as one of the most BGC abundant among fungicolous species. Comparative analyses were performed for genomes of species of the family Hypocreaceae. Some BGCs identified in C. mycophilum genome exhibited similarities to clusters found in the family Hypocreaceae, suggesting vertical heritage. In contrast, certain BGCs showed a scattered distribution among Hypocreaceae species or were solely found in Cladobotryum genomes. This work provides evidence of extensive BGC losses, horizontal gene transfer events, and formation of novel BGCs during evolution, potentially driven by neutral or even positive selection pressures. These events may increase Cladobotryum fitness under various environmental conditions and potentially during host-fungus interaction.
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Affiliation(s)
- Anastasia C Christinaki
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Antonis I Myridakis
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Vassili N Kouvelis
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, Athens 15771, Greece
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