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Japuntich SJ, Dunbar MS, Predmore Z, Bloom EL, Fang P, Basile S, Rindal DB, Waiwaiole LA, Carpenter MJ, Kopycka-Kedzierawski DT, Dahne J, Lischka TR, Richardson P. Dental staff and patient attitudes about nicotine replacement therapy samples in dental care: A National Dental Practice-Based Research Network study. Community Dent Oral Epidemiol 2023:10.1111/cdoe.12937. [PMID: 38095239 PMCID: PMC11176262 DOI: 10.1111/cdoe.12937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 09/26/2023] [Accepted: 11/29/2023] [Indexed: 05/24/2024]
Abstract
OBJECTIVES Cigarette smoking negatively affects oral health. Nicotine replacement therapies (NRT; e.g. nicotine patch or lozenge) and brief interventions (e.g. Ask-Advise-Refer; AAR) can improve cessation outcomes but are underutilized. NRT sampling (NRTS) increases NRT utilization by providing patients with samples of NRT as part of routine healthcare. Ask-Advise-Refer is a brief intervention where practitioners: ask patients about tobacco use, advise those using tobacco to quit and refer to the state quit line. The objective of this qualitative study was to explore dental care practitioners' and patients' attitudes and experiences regarding tobacco cessation treatment and perceptions of two brief intervention models, assessed separately: NRTS and AAR. METHODS Twenty-four dental care practitioners and nine patients, recruited through the National Dental Practice-Based Research Network, participated in semi-structured telephone interviews. Interviews assessed experiences with tobacco use intervention and attitudes towards NRTS and AAR. Thematic analysis identified emergent themes related to feasibility and acceptability of NRTS and AAR. RESULTS Practitioners varied on how they address tobacco use, from systematically to idiosyncratically. Some practitioners recommend NRT; few had prescribed it. Practitioners had favourable attitudes towards AAR and NRTS, with most believing that both interventions would be acceptable and feasible to implement. Concerns regarding AAR were time and patient resistance to discussing tobacco use. Concerns regarding NRTS were patient resistance to using NRT, side effects or medication interactions, and capacity to provide follow-up. Patients reported that oral health practitioners generally ask about tobacco use but do not provide interventions. Patients were open to discussing their tobacco use with practitioners and had favourable attitudes about NRTS. CONCLUSIONS This formative work suggests that NRTS and AAR may be feasible to implement in dental care settings. Future studies are needed to assess the effectiveness and implementation potential of NRTS in dental care settings.
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Affiliation(s)
- Sandra J Japuntich
- Hennepin Healthcare Research Institute, Minneapolis, Minnesota, USA
- Department of Psychiatry, Hennepin Healthcare, Minneapolis, Minnesota, USA
- Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Michael S Dunbar
- Health Care Division, RAND Corporation, Pittsburgh, Pennsylvania, USA
| | - Zachary Predmore
- Health Care Division, RAND Corporation, Boston, Massachusetts, USA
| | | | - Pearl Fang
- Hennepin Healthcare Research Institute, Minneapolis, Minnesota, USA
| | - Sarah Basile
- Health Partners Institute, Bloomington, Minnesota, USA
| | - D Brad Rindal
- Health Partners Institute, Bloomington, Minnesota, USA
| | - Lisa A Waiwaiole
- Kaiser Permanente Center for Health Research, Portland, Oregon, USA
| | - Matthew J Carpenter
- Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Dorota T Kopycka-Kedzierawski
- Department of Dentistry, Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, New York, USA
| | - Jennifer Dahne
- Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Tamara R Lischka
- Kaiser Permanente Center for Health Research, Portland, Oregon, USA
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Gebreslassie M, Galanti MR, Feldman I, Lager A. Should Nicotine Replacement Therapy be Provided Free of Charge? A Cost-Utility Analysis in Sweden. Nicotine Tob Res 2023; 25:1762-1769. [PMID: 37367182 DOI: 10.1093/ntr/ntad103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 06/07/2023] [Accepted: 06/26/2023] [Indexed: 06/28/2023]
Abstract
INTRODUCTION Treatment with nicotine replacement therapy (NRT) during an attempt to quit smoking increases the likelihood of success by about 55%. However, out-of-pocket payment for NRT can hinder its use. AIMS AND METHODS This study aims therefore to assess the cost-effectiveness of subsidizing NRT in Sweden. A homogeneous cohort-based Markov model was used to assess the lifetime costs and effects of subsidized NRT from a payer and societal perspective. Data to populate the model were retrieved from the literature, and selected parameters were varied in deterministic and probabilistic sensitivity analyses to assess robustness of model outputs. Costs are presented in USD, year 2021. RESULTS A 12-week treatment with NRT was estimated to cost USD 632 (474-790) per person. From a societal perspective, subsidized NRT was a cost-saving alternative in 98.5% of the simulations. NRT is cost-saving across all ages, but the health and economic gains are somewhat larger among younger smokers from a societal perspective. When a payer perspective was used, the incremental cost-effectiveness ratio was estimated at 14 480 (11 721-18 515) USD per QALY which was cost-effective at a willingness to pay of 50 000 USD per QALY in 100 % of the simulations. Results were robust with realistic changes in the inputs during scenario and sensitivity analyses. CONCLUSIONS Subsidizing NRT is potentially a cost-saving smoking cessation strategy from a societal perspective and cost-effective from a payer perspective. IMPLICATIONS This study found that subsidizing NRT is potentially a cost-saving smoking cessation policy alternative compared to current practice from a societal perspective. From a healthcare payer perspective, subsidizing NRT is estimated to cost USD 14 480 to gain an extra QALY. NRT is cost-saving across all ages, but the health and economic gains are somewhat larger among younger smokers from a societal perspective. Moreover, subsidizing NRT removes the financial barriers that are mostly faced by socioeconomically disadvantaged smokers which might reduce health inequalities. Thus, future economic evaluations should further investigate the health inequality impacts with methods that are more suitable for this.
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Affiliation(s)
| | - Maria Rosaria Galanti
- Centre for Epidemiology and Community Medicine, Stockholm, Sweden
- Department of Global Public Health, Karolinska Institute, Stockholm, Sweden
| | - Inna Feldman
- Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Anton Lager
- Centre for Epidemiology and Community Medicine, Stockholm, Sweden
- Department of Global Public Health, Karolinska Institute, Stockholm, Sweden
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Carpenter MJ, Wahlquist AE, Dahne J, Gray KM, Cummings KM, Warren G, Wagener TL, Goniewicz ML, Smith TT. Effect of unguided e-cigarette provision on uptake, use, and smoking cessation among adults who smoke in the USA: a naturalistic, randomised, controlled clinical trial. EClinicalMedicine 2023; 63:102142. [PMID: 37753443 PMCID: PMC10518503 DOI: 10.1016/j.eclinm.2023.102142] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 09/28/2023] Open
Abstract
Background As summarised in the most recent Cochrane review, the few clinical trials on e-cigarettes are largely focused on smoking cessation. We aimed to determine the naturalistic uptake, use, and impact of e-cigarettes among adults who may or may not want to stop smoking. Methods In this naturalistic, randomised, controlled clinical trial, adult smokers, across the motivational spectrum and with minimal history of e-cigarette use, were recruited online from the general community within 11 cities across the USA. Participants were randomly assigned (2:1) to either receive either a free 4-week supply of flavoured, tank-style e-cigarette, or not. E-cigarette group participants received a battery and device with up to 30 pre-filled tanks, offered among five flavours, with minimal instructions on use. The study's primary purpose was to descriptively assess naturalistic uptake and usage of the e-cigarette, and to secondarily assess its impact on smoking behavior. The latter, assessed through six months of follow-up, included: a) self-reported 7-day point prevalence abstinence, b) incidence of quit attempts, and c) smoking reduction. This trial is registered at ClinicalTrials.gov, NCT03453385. Findings Between 5/2018 and 3/2022, 638 adult smokers were enrolled and randomly assigned (427 in the e-cigarette group and 211 in the no-product control group). Uptake of e-cigarettes was robust: approximately 70% of participants used the product, with average usage exceeding 4 days per week during the initial 30 days. Based on an intent-to-treat approach where missing data is imputed as smoking, almost all behavioral outcomes favored the e-cigarette group relative to no-product control, including point prevalence abstinence at six months (Odds Ratio [OR] = 1.8; 95% Confidence Interval [CI] = 1.0-3.1), cumulative incidence of 24-hr quit attempts (OR = 1.5; 95% CI = 1.0-2.2), and having reduced smoking by at least 50% since baseline (OR = 1.8; 95% CI = 1.2-2.7). Results were similar under an alternative imputation. Interpretation Complementing cessation-focused trials, results suggest that unguided e-cigarette use also leads to smoking cessation, allaying the notion that causal effects of e-cigarettes on cessation are not reflective of real-world scenario of self-determined use. For smokers who may not be able to quit using existing pharmacologic approaches, e-cigarettes may be considered to achive that purpose. Funding National Cancer Institute.
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Affiliation(s)
- Matthew J. Carpenter
- Department of Psychiatry & Behavioral Sciences, Medical University of South Carolina (MUSC), Charleston, SC, USA
- Department of Public Health Sciences, MUSC, Charleston, SC, USA
- Hollings Cancer Center, MUSC, Charleston, SC, USA
| | - Amy E. Wahlquist
- Center for Rural Health Research, East Tennessee State University, Johnson City, TN, USA
| | - Jennifer Dahne
- Department of Psychiatry & Behavioral Sciences, Medical University of South Carolina (MUSC), Charleston, SC, USA
- Hollings Cancer Center, MUSC, Charleston, SC, USA
| | - Kevin M. Gray
- Department of Psychiatry & Behavioral Sciences, Medical University of South Carolina (MUSC), Charleston, SC, USA
- Hollings Cancer Center, MUSC, Charleston, SC, USA
| | - K. Michael Cummings
- Department of Psychiatry & Behavioral Sciences, Medical University of South Carolina (MUSC), Charleston, SC, USA
- Department of Public Health Sciences, MUSC, Charleston, SC, USA
- Hollings Cancer Center, MUSC, Charleston, SC, USA
| | - Graham Warren
- Hollings Cancer Center, MUSC, Charleston, SC, USA
- Department of Radiation Oncology, MUSC, Charleston, SC, USA
| | - Theodore L. Wagener
- Department of Internal Medicine, Ohio State University (OSU), Columbus, OH, USA
- Center for Tobacco Research, OSU Comprehensive Cancer Center, Columbus, OH, USA
| | - Maciej L. Goniewicz
- Department of Health Behavior, Roswell Park Comprehensive Cancer Center, Buffalo, USA
| | - Tracy T. Smith
- Department of Psychiatry & Behavioral Sciences, Medical University of South Carolina (MUSC), Charleston, SC, USA
- Hollings Cancer Center, MUSC, Charleston, SC, USA
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Wang H, Wu Y, He Y, Li G, Ma L, Li S, Huang J, Yang G. High-quality chromosome-level de novo assembly of the Trifolium repens. BMC Genomics 2023; 24:326. [PMID: 37312068 DOI: 10.1186/s12864-023-09437-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/08/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND White clover (Trifolium repens L.), an excellent perennial legume forage, is an allotetraploid native to southeastern Europe and southern Asia. It has high nutritional, ecological, genetic breeding, and medicinal values and exhibits excellent resistance to cold, drought, trample, and weed infestation. Thus, white clover is widely planted in Europe, America, and China; however, the lack of reference genome limits its breeding and cultivation. This study generated a white clover de novo genome assembly at the chromosomal level and annotated its components. RESULTS The PacBio third-generation Hi-Fi assembly and sequencing methods generated a 1096 Mb genome size of T. repens, with contigs of N50 = 14 Mb, scaffolds of N50 = 65 Mb, and BUSCO value of 98.5%. The newly assembled genome has better continuity and integrity than the previously reported white clover reference genome; thus provides important resources for the molecular breeding and evolution of white clover and other forage. Additionally, we annotated 90,128 high-confidence gene models from the genome. White clover was closely related to Trifolium pratense and Trifolium medium but distantly related to Glycine max, Vigna radiata, Medicago truncatula, and Cicer arietinum. The expansion, contraction, and GO functional enrichment analysis of the gene families showed that T. repens gene families were associated with biological processes, molecular function, cellular components, and environmental resistance, which explained its excellent agronomic traits. CONCLUSIONS This study reports a high-quality de novo assembly of white clover genome obtained at the chromosomal level using PacBio Hi-Fi sequencing, a third-generation sequencing. The generated high-quality genome assembly of white clover provides a key basis for accelerating the research and molecular breeding of this important forage crop. The genome is also valuable for future studies on legume forage biology, evolution, and genome-wide mapping of quantitative trait loci associated with the relevant agronomic traits.
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Affiliation(s)
- Hongjie Wang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Yongqiang Wu
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Yong He
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Guoyu Li
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lichao Ma
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Shuo Li
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | | | - Guofeng Yang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China.
- Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China.
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Kruse GR, Joyce A, Yu L, Park ER, Neil J, Chang Y, Rigotti NA. A pilot adaptive trial of text messages, mailed nicotine replacement therapy, and telephone coaching among primary care patients who smoke. JOURNAL OF SUBSTANCE USE AND ADDICTION TREATMENT 2023; 145:208930. [PMID: 36880910 PMCID: PMC10016234 DOI: 10.1016/j.josat.2022.208930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 07/01/2022] [Accepted: 10/31/2022] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Sequential multiple assignment randomized trials (SMART) inform the design of adaptive treatment interventions. We tested the feasibility of a SMART to deliver a stepped-care intervention among primary care patients who smoked daily. METHODS In a 12-week pilot SMART (NCT04020718), we tested the feasibility of recruiting and retaining (>80 %) participants to an adaptive intervention starting with cessation text messages (SMS). The study randomly assigned participants (R1) to assessment of quit status, the tailoring variable, after either 4 or 8 weeks of SMS. The study offered continued SMS alone to those reporting abstinence. Those reporting smoking were randomized (R2) to SMS + mailed NRT or SMS + NRT + brief telephone coaching. RESULTS During Jan-March and July-Aug 2020, we enrolled 35 patients (>18 years) from a primary care network in Massachusetts. Two (6 %) of 31 participants reported seven-day point prevalence abstinence at their tailoring variable assessment. The 29 participants who continued to smoke at 4 or 8 weeks were randomized (R2) to SMS + NRT (n = 16) or SMS + NRT + coaching (n = 13). Thirty of 35 participants (86 %) completed 12-weeks; 13 % (2/15) of those in 4-week group and 27 % (4/15) of those in 8-week group had CO < 6 ppm at 12-weeks (p = 0.65). Among 29 participants in R2, one was lost to follow-up, 19 % (3/16) of the SMS + NRT group had CO < 6 ppm vs. 17 % (2/12) of SMS + NRT + coaching (p = 1.00). Treatment satisfaction was high (93 %, 28 of 30 who completed 12-weeks). CONCLUSIONS A SMART exploring a stepped-care adaptive intervention combining SMS, NRT, and coaching for primary care patients was feasible. Retention and satisfaction were high and quit rates were promising.
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Affiliation(s)
- G R Kruse
- Division of General Internal Medicine, Department of Medicine, Massachusetts General Hospital, United States of America; Tobacco Research and Treatment Center, Massachusetts General Hospital, United States of America; Harvard Medical School, United States of America.
| | - A Joyce
- Division of General Internal Medicine, Department of Medicine, Massachusetts General Hospital, United States of America; Tobacco Research and Treatment Center, Massachusetts General Hospital, United States of America
| | - L Yu
- Division of General Internal Medicine, Department of Medicine, Massachusetts General Hospital, United States of America
| | - E R Park
- Tobacco Research and Treatment Center, Massachusetts General Hospital, United States of America; Harvard Medical School, United States of America; Department of Psychiatry, Massachusetts General Hospital, United States of America; Health Policy Research Center, Massachusetts General Hospital, United States of America
| | - J Neil
- Tobacco Research and Treatment Center, Massachusetts General Hospital, United States of America; Harvard Medical School, United States of America; Health Policy Research Center, Massachusetts General Hospital, United States of America; Health Promotion Research Center, Stephenson Cancer Center, University of Oklahoma Health Sciences Center, United States of America
| | - Y Chang
- Division of General Internal Medicine, Department of Medicine, Massachusetts General Hospital, United States of America; Tobacco Research and Treatment Center, Massachusetts General Hospital, United States of America; Harvard Medical School, United States of America
| | - N A Rigotti
- Division of General Internal Medicine, Department of Medicine, Massachusetts General Hospital, United States of America; Tobacco Research and Treatment Center, Massachusetts General Hospital, United States of America; Harvard Medical School, United States of America; Health Policy Research Center, Massachusetts General Hospital, United States of America
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Prasitwarachot R, Thavorn K, Patikorn C, Wattanasirichaigoon S, Rungruanghiranya S, Thongphiew A, Chaiyakunapruk N. A cost-effectiveness analysis of national smoking cessation services among chronic obstructive pulmonary disease patients in Thailand. J Med Econ 2023; 26:1377-1385. [PMID: 37818930 DOI: 10.1080/13696998.2023.2269748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/09/2023] [Indexed: 10/13/2023]
Abstract
AIMS Thailand's national smoking cessation services (FAH-SAI clinics) were founded in 2010. A cost-effectiveness analysis (CEA) is needed to inform policymakers of the allocation and prioritization of the limited budget to maximize the value for money of reimbursing these services. Chronic obstructive pulmonary disease (COPD) patients would benefit from smoking cessation services. Therefore, this study aimed to assess the cost-effectiveness of these multidisciplinary services compared to the usual care among COPD patients in Thailand from a societal perspective. METHODS We conducted a CEA from a societal perspective using a Markov model to simulate lifetime costs and quality-adjusted life years (QALYs) gained by each smoking cessation intervention over the patient's lifetime. We derived the effectiveness of the smoking cessation services from a multicenter, longitudinal study of smoking cessation services in Thailand and estimated the natural quit rate, transition probabilities, health utility, and cost data from the published literature. Costs and outcomes were discounted at 3%. Sensitivity analyses were performed. RESULTS Compared to the usual care, FAH-SAI clinics were associated with higher costs (4,207 THB (US$133)) and improved QALYs (0.11), with an incremental cost-effectiveness ratio of 37,675 THB/QALY (US$1,187/QALY). The effectiveness of FAH-SAI clinics was a key driver of the cost-effectiveness results. At the willingness-to-pay (WTP) threshold of 160,000 THB (US$5,042) per QALY gained, the probability of being cost-effective was 96.5%. CONCLUSIONS FAH-SAI clinics were cost-effective under Thailand's WTP threshold. Our results could inform policymakers in allocating resources to support smoking cessation services for COPD patients in Thailand.
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Affiliation(s)
- Ratthanon Prasitwarachot
- Department of Pharmacotherapy, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
- Department of Pharmacy Technicians, Sirindhorn College of Public Health Suphanburi, Suphanburi, Thailand
| | - Kednapa Thavorn
- Ottawa Hospital Research Institute, Ottawa Hospital, Ottawa, Canada
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Chanthawat Patikorn
- Department of Pharmacotherapy, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
- Department of Social and Administrative Pharmacy, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Somkiat Wattanasirichaigoon
- Division of Information Technology Management, Faculty of Engineering, Mahidol University, Nakhon Pathom, Thailand
- Thai Health Professional Alliance Against Tobacco, Bangkok, Thailand
| | - Suthat Rungruanghiranya
- Thai Health Professional Alliance Against Tobacco, Bangkok, Thailand
- Department of Internal Medicine, Faculty of Medicine, Srinakharinwirot University, Nakhon Nayok, Thailand
| | - Araya Thongphiew
- Thai Health Professional Alliance Against Tobacco, Bangkok, Thailand
- Diabetes Mellitus and Endocrine Center, Paolo Phaholyothin Hospital, Bangkok, Thailand
| | - Nathorn Chaiyakunapruk
- Department of Pharmacotherapy, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
- IDEAS Center, Veterans Affairs Salt Lake City Healthcare System, Salt Lake City, UT, USA
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Yan Z, Sang L, Ma Y, He Y, Sun J, Ma L, Li S, Miao F, Zhang Z, Huang J, Wang Z, Yang G. A de novo assembled high-quality chromosome-scale Trifolium pratense genome and fine-scale phylogenetic analysis. BMC PLANT BIOLOGY 2022; 22:332. [PMID: 35820796 PMCID: PMC9277957 DOI: 10.1186/s12870-022-03707-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/20/2022] [Indexed: 05/12/2023]
Abstract
BACKGROUND Red clover (Trifolium pratense L.) is a diploid perennial temperate legume with 14 chromosomes (2n = 14) native to Europe and West Asia, with high nutritional and economic value. It is a very important forage grass and is widely grown in marine climates, such as the United States and Sweden. Genetic research and molecular breeding are limited by the lack of high-quality reference genomes. In this study, we used Illumina, PacBio HiFi, and Hi-C to obtain a high-quality chromosome-scale red clover genome and used genome annotation results to analyze evolutionary relationships among related species. RESULTS The red clover genome obtained by PacBio HiFi assembly sequencing was 423 M. The assembly quality was the highest among legume genome assemblies published to date. The contig N50 was 13 Mb, scaffold N50 was 55 Mb, and BUSCO completeness was 97.9%, accounting for 92.8% of the predicted genome. Genome annotation revealed 44,588 gene models with high confidence and 52.81% repetitive elements in red clover genome. Based on a comparison of genome annotation results, red clover was closely related to Trifolium medium and distantly related to Glycine max, Vigna radiata, Medicago truncatula, and Cicer arietinum among legumes. Analyses of gene family expansions and contractions and forward gene selection revealed gene families and genes related to environmental stress resistance and energy metabolism. CONCLUSIONS We report a high-quality de novo genome assembly for the red clover at the chromosome level, with a substantial improvement in assembly quality over those of previously published red clover genomes. These annotated gene models can provide an important resource for molecular genetic breeding and legume evolution studies. Furthermore, we analyzed the evolutionary relationships among red clover and closely related species, providing a basis for evolutionary studies of clover leaf and legumes, genomics analyses of forage grass, the improvement of agronomic traits.
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Affiliation(s)
- Zhenfei Yan
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Lijun Sang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Yue Ma
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Yong He
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Juan Sun
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Lichao Ma
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Shuo Li
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Fuhong Miao
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Zixin Zhang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
| | | | - Zengyu Wang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China.
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China.
| | - Guofeng Yang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China.
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China.
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