Publications by authors named "Sook Jung"

85 Publications

The Breeding Information Management System (BIMS): an online resource for crop breeding.

Database (Oxford) 2021 08;2021

Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA.

In this era of big data, breeding programs are producing ever larger amounts of data. This necessitates access to efficient management systems to keep track of cross, performance, pedigree, geographical and image-based data, as well as genotyping data. In this article, we report the progress on the Breeding Information Management System (BIMS), a free, secure and online breeding management system that allows breeders to store, manage, archive and analyze their private breeding data. BIMS is the first publicly available database system that enables individual breeders to integrate their private phenotypic and genotypic data with public data and, at the same time, have complete control of their own breeding data along with access to tools such as data import/export, data analysis and data archiving. The integration of breeding data with publicly available genomic and genetic data enhances genetic understanding of important traits and maximizes the marker-assisted breeding utility for breeders and allied scientists. BIMS incorporates the use of the Android App Field Book, open-source phenotype data collection software for phones and tablets that allows breeders to replace hard copy field books, thus alleviating the possibility of transcription errors while providing faster access to the collected data. BIMS comes with training materials and support for individual or small group training and is currently implemented in the Genome Database for Rosaceae, CottonGEN, the Citrus Genome Database, the Pulse Crop Database, and the Genome Database for Vaccinium. Database URLs: (https://www.rosaceae.org/), (https://www.cottongen.org/), (https://www.citrusgenomedb.org/), (https://www.pulsedb.org/) and (https://www.vaccinium.org/).
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http://dx.doi.org/10.1093/database/baab054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8378516PMC
August 2021

Comparison of RT-PCR, RT-nested PCRs, and real-time PCR for diagnosis of severe fever with thrombocytopenia syndrome: a prospective study.

Sci Rep 2021 08 18;11(1):16764. Epub 2021 Aug 18.

Department of Internal Medicine, School of Medicine, Pusan National University, Pusan, Republic of Korea.

We designed a highly sensitive reverse transcription nested polymerase chain reaction targeting the M-segment (NPCR-M) of severe fever with thrombocytopenia syndrome (SFTS) virus. NPCR-M was performed in parallel with three other referenced PCR assays QPCR-S, PCR-M, and NPCR-S to assess their clinical usefulness as routine diagnostic techniques for SFTS. In this multi-centered prospective study, 122 blood samples from 38 laboratory-confirmed SFTS patients and 85 control samples were used. The results demonstrated that QPCR-S and NPCR-S had better sensitivity rate up to 21 days after symptom onset however, the PCR-M showed poor sensitivity after 7 days of symptom onset. Our designed NPCR-M had a higher detection rate up to 40 days from symptom onset and revealed the persistence of SFTSV RNA in the early convalescent phase. No false-positive results were seen for the control samples. Additionally, NPCR-M showed positive results for a sample that initially showed negative results from other PCRs and for many other samples collected in the convalescent phase of SFTS. Our designed nested PCR is suitable for SFTSV detection in patients' blood collected in the acute and early convalescent phase of SFTS, and shows better sensitivity and high specificity even up to 40 days after symptom onset.
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http://dx.doi.org/10.1038/s41598-021-96066-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8373928PMC
August 2021

Successful control of COVID-19 outbreak through tracing, testing, and isolation: Lessons learned from the outbreak control efforts made in a metropolitan city of South Korea.

J Infect Public Health 2021 Sep 13;14(9):1151-1154. Epub 2021 Jul 13.

Department of Preventive Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea; Gwangju Center for Infectious Disease Control and Prevention, Gwangju, Republic of Korea. Electronic address:

The first surge of coronavirus disease 2019 (COVID-19) cases began on June 27, 2020 in Gwangju metropolitan city, located in the southwestern part of South Korea, with a population of 1,501,000. Local governments and the Korean Center for Disease Control and Prevention immediately started an epidemiologic investigation and traced the contacts of patients using a wide variety of data sources, including location data from mobile devices, credit card transaction, and closed-circuit television footage. Until July 16, 2020, 138 community transmission cases and 10 infection clusters were identified across the city. Through contact tracing, epidemiologic relatedness was found in 136 (98.6%) of 138 cases. Our investigation showed how the extensive and meticulous contact tracing suppressed COVID-19 outbreak in a populated city.
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http://dx.doi.org/10.1016/j.jiph.2021.07.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8276554PMC
September 2021

Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases.

Brief Bioinform 2021 Jul 12. Epub 2021 Jul 12.

Washington State University, Pullman, WA USA.

Online, open access databases for biological knowledge serve as central repositories for research communities to store, find and analyze integrated, multi-disciplinary datasets. With increasing volumes, complexity and the need to integrate genomic, transcriptomic, metabolomic, proteomic, phenomic and environmental data, community databases face tremendous challenges in ongoing maintenance, expansion and upgrades. A common infrastructure framework using community standards shared by many databases can reduce development burden, provide interoperability, ensure use of common standards and support long-term sustainability. Tripal is a mature, open source platform built to meet this need. With ongoing improvement since its first release in 2009, Tripal provides full functionality for searching, browsing, loading and curating numerous types of data and is a primary technology powering at least 31 publicly available databases spanning plants, animals and human data, primarily storing genomics, genetics and breeding data. Tripal software development is managed by a shared, inclusive governance structure including both project management and advisory teams. Here, we report on the most important and innovative aspects of Tripal after 11 years development, including integration of diverse types of biological data, successful collaborative projects across member databases, and support for implementing FAIR principles.
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http://dx.doi.org/10.1093/bib/bbab238DOI Listing
July 2021

Source Analysis and Effective Control of a COVID-19 Outbreak in a University Teaching Hospital during a Period of Increasing Community Prevalence of COVID-19.

J Korean Med Sci 2021 Jun 21;36(24):e179. Epub 2021 Jun 21.

Department of Infectious Diseases, Chonnam National University Medical School, Gwangju, Korea.

Background: South Korea has been experiencing a third wave of coronavirus disease 2019 (COVID-19) since mid-November 2020. Our hospital in Gwangju metropolitan city experienced a healthcare-associated COVID-19 outbreak early in the third wave. The first confirmed COVID-19 patient was a symptomatic neurosurgery resident with high mobility throughout the hospital. We analyzed the transmission routes of nosocomial COVID-19 and discussed infection control strategies.

Methods: We retrospectively analyzed the severe acute respiratory syndrome coronavirus 2 reverse transcription-polymerase chain reaction (RT-PCR) testing results according to time point and evaluated transmission routes.

Results: Since COVID-19 was first confirmed in a healthcare worker (HCW) on 11/13/2020, we performed RT-PCR tests for all patients and caregivers and four complete enumeration surveys for all HCWs. We detected three clusters of nosocomial spread and several sporadic cases. The first cluster originated from the community outbreak spot, where an asymptomatic HCW visited, which led to a total of 22 cases. The second cluster, which included patient-to-patient transmission, originated from a COVID-19 positive caregiver before diagnosis and the third cluster involved a radiologist and a banker. We took measures to isolate Building 1 of the hospital for 17 days and controlled the outbreak during a period of increasing community COVID-19 prevalence. Universal screening of all inpatients upon admission and resident caregivers was made mandatory and hospital-related employees are now screened monthly.

Conclusion: Infection control strategies to prevent the nosocomial transmission of emerging infectious diseases must correspond with community disease prevalence. Our data reinforce the importance of multi-time point surveillance of asymptomatic HCWs and routine surveillance of patients and caregivers during an epidemic.
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http://dx.doi.org/10.3346/jkms.2021.36.e179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8216991PMC
June 2021

Tripal MegaSearch: a tool for interactive and customizable query and download of big data.

Database (Oxford) 2021 04;2021

Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA.

Tripal MegaSearch is a Tripal module for querying and downloading biological data stored in Chado. This module allows site users to select data types, restrict the dataset by applying various filters and then customizing fields to view and download through a single interface. Set by site administrators, example data types include gene, germplasm, marker, map, QTL, genotype, phenotype and expression data. When querying for genes, users can restrict the gene dataset using various filters such as name, chromosome position and functional annotation. They can then customize fields to download, such as name, organism, type, chromosome position, various functional annotations such as BLAST, KEGG, InterPro and GO term. FASTA files can also be downloaded for the sequence data. Site administrators can choose from two different data sources to serve data: Tripal MegaSearch materialized views or Chado tables. If neither data source is desired, administrators may also create their own materialized views and serve them through the flexible dynamic Tripal MegaSearch query form. Tripal MegaSearch is currently implemented in several databases including the Genome Database for Rosaceae www.rosaceae.org and TreeGenes www.https://treegenesdb.org/.
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http://dx.doi.org/10.1093/database/baab023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8074878PMC
April 2021

Effects of steroid therapy in patients with severe fever with Thrombocytopenia syndrome: A multicenter clinical cohort study.

PLoS Negl Trop Dis 2021 02 19;15(2):e0009128. Epub 2021 Feb 19.

Department of Internal Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea.

Background: Severe fever with thrombocytopenia syndrome (SFTS) is an acute, febrile, and potentially fatal tick-borne disease caused by the SFTS Phlebovirus. Here, we evaluated the effects of steroid therapy in Korean patients with SFTS.

Methods: A retrospective study was performed in a multicenter SFTS clinical cohort from 13 Korean university hospitals between 2013 and 2017. We performed survival analysis using propensity score matching of 142 patients with SFTS diagnosed by genetic or antibody tests.

Results: Overall fatality rate was 23.2%, with 39.7% among 58 patients who underwent steroid therapy. Complications were observed in 37/58 (63.8%) and 25/83 (30.1%) patients in the steroid and non-steroid groups, respectively (P < .001). Survival analysis after propensity score matching showed a significant difference in mean 30-day survival time between the non-steroid and steroid groups in patients with a mild condition [Acute Physiology and Chronic Health Evaluation II (APACHE II) score <14; 29.2 (95% CI 27.70-30.73] vs. 24.9 (95% CI 21.21-28.53], P = .022]. Survival times for the early steroid (≤5 days from the start of therapy after symptom onset), late steroid (>5 days), and non-steroid groups, were 18.4, 22.4, and 27.3 days, respectively (P = .005).

Conclusions: After steroid therapy, an increase in complications was observed among patients with SFTS. Steroid therapy should be used with caution, considering the possible negative effects of steroid therapy within 5 days of symptom onset or in patients with mild disease (APACHE II score <14).
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http://dx.doi.org/10.1371/journal.pntd.0009128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7928499PMC
February 2021

Serologic Evaluation of Healthcare Workers Caring for COVID-19 Patients in the Republic of Korea.

Front Microbiol 2020 20;11:587613. Epub 2020 Nov 20.

Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.

The safety of healthcare workers (HCWs) against severe acute respiratory syndrome virus 2 (SARS-CoV-2) transmission is an important aspect of managing the coronavirus disease 2019 (COVID-19) pandemic. In the South Korea, highly stringent infection prevention and control (IPC) guidelines are implemented, and reports of healthcare-associated SARS-CoV-2 transmission among HCWs are limited. However, subclinical infections may have been missed by the current symptom-based screening strategy. To evaluate the risk of undetected SARS-CoV-2 transmissions from COVID-19 patients to HCWs, we conducted a multicenter seroprevalence study after the first surge of the COVID-19 outbreak. A total of 432 HCWs were evaluated, comprising 309 HCWs designated to laboratory-confirmed COVID-19 patient care and 123 non-designated HCWs. Designated HCWs wore personal protective equipment including an N95 respirator, eye protection, hooded overalls, shoe covers, and inner and outer gloves. Use of a powered air-purifying respirator was recommended for aerosol-generating procedures or long-duration care activities. A high-sensitivity (99.1%) fluorescence immunoassay immunoglobulin G (IgG) kit was used as the initial screening test, and two enzyme-linked immunosorbent assay kits for total and IgG antibodies were used to confirm the test results. A microneutralization test was additionally performed to evaluate the neutralizing activity of positive specimens. Among the evaluated HCWs, none of the non-designated HCWs had a positive result, while one of the HCWs designated for COVID-19 patient care (1/309, 0.3%) was seropositive for SARS-CoV-2 with confirmed neutralizing activity (1:40). This finding suggests that subclinical seroconversion may occur among HCWs caring for COVID-19 patients, although the risk is low under strict IPC guidance.
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http://dx.doi.org/10.3389/fmicb.2020.587613DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7714715PMC
November 2020

RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops.

Hortic Res 2020 Nov 1;7(1):177. Epub 2020 Nov 1.

Washington State University, Pullman, WA, 99164, USA.

The Rosaceae crop family (including almond, apple, apricot, blackberry, peach, pear, plum, raspberry, rose, strawberry, sweet cherry, and sour cherry) provides vital contributions to human well-being and is economically significant across the U.S. In 2003, industry stakeholder initiatives prioritized the utilization of genomics, genetics, and breeding to develop new cultivars exhibiting both disease resistance and superior horticultural quality. However, rosaceous crop breeders lacked certain knowledge and tools to fully implement DNA-informed breeding-a "chasm" existed between existing genomics and genetic information and the application of this knowledge in breeding. The RosBREED project ("Ros" signifying a Rosaceae genomics, genetics, and breeding community initiative, and "BREED", indicating the core focus on breeding programs), addressed this challenge through a comprehensive and coordinated 10-year effort funded by the USDA-NIFA Specialty Crop Research Initiative. RosBREED was designed to enable the routine application of modern genomics and genetics technologies in U.S. rosaceous crop breeding programs, thereby enhancing their efficiency and effectiveness in delivering cultivars with producer-required disease resistances and market-essential horticultural quality. This review presents a synopsis of the approach, deliverables, and impacts of RosBREED, highlighting synergistic global collaborations and future needs. Enabling technologies and tools developed are described, including genome-wide scanning platforms and DNA diagnostic tests. Examples of DNA-informed breeding use by project participants are presented for all breeding stages, including pre-breeding for disease resistance, parental and seedling selection, and elite selection advancement. The chasm is now bridged, accelerating rosaceous crop genetic improvement.
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http://dx.doi.org/10.1038/s41438-020-00398-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7603521PMC
November 2020

Psychological distress among infectious disease physicians during the response to the COVID-19 outbreak in the Republic of Korea.

BMC Public Health 2020 Nov 27;20(1):1811. Epub 2020 Nov 27.

Division of Infectious Diseases, Department of Internal Medicine, School of Medicine, Kyungpook National University, 130 Dongdeok-ro, Daegu, Jung-gu, 41944, South Korea.

Background: This study aimed to investigate psychological distress among infectious disease (ID) physicians during the coronavirus disease 2019 (COVID-19) outbreak in the Republic of Korea.

Methods: Using an online-based survey link sent via text message and email, we conducted a survey from April 21 to 25, 2020, targeting all ID physicians currently working in ID (n = 265). The questionnaire was based on the Maslach Burnout Inventory-Human Services Survey and the Depression, Anxiety, and Stress Scales, and information was collected on factors protecting against psychological distress and difficulties in relation to COVID-19.

Results: Of 265 ID physicians, 115 (43.3%) responded, showing burnout (97, 90.4%), depression (20, 17.4%), anxiety (23, 20.0%), and stress (5, 4.3%). There were no differences in terms of distress between ID physicians who were directly involved in the care of patients with COVID-19 or not. Greater than 50% of physicians valued their work and felt recognized by others, whereas < 10% indicated that sufficient human and financial support and private time had been provided during the outbreak. The most challenging issues concerned a lack of attending physicians caring for COVID-19 patients or infection control practitioners, a shortage of personal protective equipment or airborne infection isolation rooms, pressure for research, and lack of guidelines for COVID-19 management.

Conclusions: During the COVID-19 outbreak in the Republic of Korea, most respondents reported psychological distress. Preparing strategies to secure human resources are crucial to prepare effectively for future epidemics and pandemics.
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http://dx.doi.org/10.1186/s12889-020-09886-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7691971PMC
November 2020

Prosthetic valve endocarditis by Trichosporon mucoides: A case report and review of literature.

Medicine (Baltimore) 2020 Oct;99(41):e22584

Department of Infectious Diseases, Chonnam National University Hospital.

Nationale: Trichosporon species are widely distributed in nature and are emerging opportunistic human pathogens. Trichosporon infections are associated with superficial cutaneous involvement in immunocompetent individuals to severe systemic disease in immunocompromised patients. Until now, there is no report in infective endocarditis by Trichosporon mucoides confirmed by molecular diagnostics PATIENT CONCERNS:: A 66-year-old man presented with a fever that had occurred for a period of 6 months. He had undergone aortic valve replacement 10 years prior. Transthoracic echocardiography showed vegetations on the prosthetic aortic valve and native mitral valve. T mucoides was detected in the cultures of blood and vegetations.

Diagnosis: DNA sequencing using D/D2 region of rRNA and internal transcribed spacer were performed.

Interventions: Infections were successfully controlled with valve replacement and voriconazole plus liposomal amphotericin B therapy.

Outcomes: There has been no sign of recurrence for 18-months after treatment completion.

Lessons: This is the first reported case of infective endocarditis due to T mucoides. Clinicians should consider Trichosporon species as causative agents of endocarditis in patients who have undergone cardiac surgery.
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http://dx.doi.org/10.1097/MD.0000000000022584DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7544388PMC
October 2020

What should we prepare for the next coronavirus disease 2019 outbreak? A survey on the opinions of infectious diseases specialists in South Korea.

Korean J Intern Med 2020 11 23;35(6):1270-1278. Epub 2020 Sep 23.

Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Korea.

Background/aims: This study aimed to collect information on the opinions of Korean infectious disease (ID) experts on coronavirus disease 2019 (COVID-19) and related issues in preparation for a future outbreak.

Methods: A survey was conducted over the course of 5 days (from April 21 to 25, 2020), targeting all adult ID specialists currently in the medical field in South Korea (n = 265). An online-based survey was forwarded via text message and e-mail. Only one response was accepted from each participant.

Results: Of these 265 ID specialists gotten to, 132 (49.8%) responded. The highest proportion of the respondents envisaged the current COVID-19 outbreak to end after December 2020 (47.7% for the domestic Korean outbreak and 70.5% for the global pandemic); moreover, 60.7% of them stated that a second nationwide wave is likely to occur between September and December 2020 in South Korea. N95 respirators were considered to be the most important item in hospitals in preparation for a second wave. The most important policy to be implemented at the national level was securing national hospitals designated for the treatment of ID (67.4%).

Conclusion: ID experts in South Korea believe that the COVID-19 pandemic may not be easily controlled and that a second nationwide wave is likely to occur in South Korea. Our results indicate that Korean ID specialists believe that a high level of preparation is needed in various aspects, including the procurement of personal protective equipment, to respond efficiently to a second outbreak.
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http://dx.doi.org/10.3904/kjim.2020.222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7652668PMC
November 2020

Viral Load Kinetics of SARS-CoV-2 Infection in Saliva in Korean Patients: a Prospective Multi-center Comparative Study.

J Korean Med Sci 2020 Aug 10;35(31):e287. Epub 2020 Aug 10.

Department of Infectious Diseases, Chonnam National University Hospital, Gwangju, Korea.

Background: This study was performed to compare the viral load and kinetics of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in saliva with those in standard nasopharyngeal/oropharyngeal (NP/OP) swabs.

Methods: Fifteen patients with SARS-CoV-2 infection from four hospitals were prospectively enrolled and matched samples of nasopharyngeal/oropharyngeal swabs and saliva were collected at Day 1 of admission and every other day till consequently negative for two times. Real-time reverse transcription polymerase chain reaction (rRT-PCR) was performed to detect the envelope (E) and RNA-dependent RNA polymerase (RdRP) genes.

Results: The cycle threshold values of saliva were comparable to those of NP/OP swabs overall ( = 0.720, Mann-Whitney U test). However, the overall sensitivity of rRT-PCR using saliva was 64% (34/53), which is lower than the 77% (41/53) using NP/OP swabs. The sensitivity of rRT-PCR using saliva was especially lower in early stage of symptom onset (1-5 days; 8/15; 53%) and in patients who did not have sputum (12/22; 55%).

Conclusion: Saliva sample itself is not appropriate for initial diagnosis of coronavirus disease 2019 (COVID-19) to replace NP/OP swabs, especially for the person who does not produce sputum. COVID-19 cannot be excluded when the test using saliva is negative, and it is necessary to retest using NP/OP swabs.
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http://dx.doi.org/10.3346/jkms.2020.35.e287DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7415999PMC
August 2020

A Rosaceae Family-Level Approach To Identify Loci Influencing Soluble Solids Content in Blackberry for DNA-Informed Breeding.

G3 (Bethesda) 2020 10 5;10(10):3729-3740. Epub 2020 Oct 5.

USDA-ARS National Clonal Germplasm Repository, Corvallis, OR

A Rosaceae family-level candidate gene approach was used to identify genes associated with sugar content in blackberry ( subgenus ). Three regions conserved among apple (), peach (), and alpine strawberry () were identified that contained previously detected sweetness-related quantitative trait loci (QTL) in at least two of the crops. Sugar related genes from these conserved regions and 789 sugar-associated apple genes were used to identify 279 candidate transcripts. A Hyb-Seq approach was used in conjunction with PacBio sequencing to generate haplotype level sequence information of sugar-related genes for 40 cultivars with high and low soluble solids content from the University of Arkansas and USDA blackberry breeding programs. Polymorphisms were identified relative to the 'Hillquist' blackberry () and ORUS 4115-3 black raspberry () genomes and tested for their association with soluble solids content (SSC). A total of 173 alleles were identified that were significantly (α = 0.05) associated with SSC. KASP genotyping was conducted for 92 of these alleles on a validation set of blackberries from each breeding program and 48 markers were identified that were significantly associated with SSC. One QTL, qSSC-Ruh-ch1.1, identified in both breeding programs accounted for an increase of 1.5 °Brix and the polymorphisms were detected in the intron space of a sucrose synthase gene. This discovery represents the first environmentally stable sweetness QTL identified in blackberry. The approach demonstrated in this study can be used to develop breeding tools for other crops that have not yet benefited directly from the genomics revolution.
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http://dx.doi.org/10.1534/g3.120.401449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7534445PMC
October 2020

Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases.

Database (Oxford) 2020 01;2020

Dept of Horticulture, Washington State University, 149 Johnson Hall 646414, Pullman, WA 99164-6414, USA.

Online biological databases housing genomics, genetic and breeding data can be constructed using the Tripal toolkit. Tripal is an open-source, internationally developed framework that implements FAIR data principles and is meant to ease the burden of constructing such websites for research communities. Use of a common, open framework improves the sustainability and manageability of such as site. Site developers can create extensions for their site and in turn share those extensions with others. One challenge that community databases often face is the need to provide tools for their users that analyze increasingly larger datasets using multiple software tools strung together in a scientific workflow on complicated computational resources. The Tripal Galaxy module, a 'plug-in' for Tripal, meets this need through integration of Tripal with the Galaxy Project workflow management system. Site developers can create workflows appropriate to the needs of their community using Galaxy and then share those for execution on their Tripal sites via automatically constructed, but configurable, web forms or using an application programming interface to power web-based analytical applications. The Tripal Galaxy module helps reduce duplication of effort by allowing site developers to spend time constructing workflows and building their applications rather than rebuilding infrastructure for job management of multi-step applications.
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http://dx.doi.org/10.1093/database/baaa032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334887PMC
January 2020

Age-Related Morbidity and Mortality among Patients with COVID-19.

Infect Chemother 2020 Jun 12;52(2):154-164. Epub 2020 Jun 12.

Department of Internal Medicine, Chonnam National University Medical School, Gwangju, Korea.

On March 11, 2020, the World Health Organization declared coronavirus disease (COVID-19), caused by the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a pandemic. During the COVID-19 pandemic, an age-associated vulnerability in the burden of disease has been uncovered. Understanding the spectrum of illness and the pathogenic mechanism of the disease in a vulnerable population is critical, especially during the pandemic. Herein, we reviewed published COVID-19 epidemiology data from several countries to identify any consistent trends in the relationship between age and COVID-19-associated morbidity or mortality. We also reviewed the literature for studies explaining the difference in the host response to SARS-CoV-2 infection according to age. The insights from these data will be useful in determining the treatment policies and preventive measures of COVID-19.
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http://dx.doi.org/10.3947/ic.2020.52.2.154DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7335648PMC
June 2020

Microbial Etiology of Pyogenic Vertebral Osteomyelitis According to Patient Characteristics.

Open Forum Infect Dis 2020 Jun 20;7(6):ofaa176. Epub 2020 May 20.

Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.

Background: It is difficult to select an appropriate empirical antibiotic treatment regimen for patients with culture-negative pyogenic vertebral osteomyelitis (PVO). Having knowledge of the distribution of microorganisms according to patient characteristics can help clinicians make informed choices regarding empirical antibiotics. The aim of this study was to determine the microbial distribution among individuals with PVO according to their demographic and clinical characteristics.

Methods: We reviewed the medical records of patients admitted to our hospital with culture-confirmed PVO between January 2005 and December 2017 and collected data on demographics, underlying diseases, and radiographic and microbiological results. Statistical analysis was performed to identify associations between specific bacteria and specific patient characteristics.

Results: A total of 586 patients were included in the study. The prevalence of infections was higher in young patients than in old patients, while gram-negative bacterial infections and were more prevalent in older patients. Gram-negative bacterial infections were more common in women than in men (32.1% vs 16.4%;  < .05), in patients with cirrhosis than in those without (32.7% vs 21.1%;  < .05), and in patients with a solid tumor than in those without (31.0% vs 20.7%;  < .05). Methicillin-resistant infections were more prevalent in patients with chronic renal disease than in those without (34.4% vs 14.7%;  < .05).

Conclusions: The microbial etiology of PVO varies according to patient characteristics. Patient characteristics should thus be considered when choosing empirical antibiotics in patients with culture-negative PVO.
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http://dx.doi.org/10.1093/ofid/ofaa176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7270706PMC
June 2020

Historical and Clinical Perspective of Infections in Korea.

Infect Chemother 2020 Jun 29;52(2):245-251. Epub 2020 May 29.

Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.

infection was first reported as a necrotizing skin disease of unknown cause in Korea in 1979. In the early days, this disease caused panic across the country due to dreadful wound and its high mortality. Since then, the nature of the disease has become better understood and the overwhelming public fear has dissipated. However, there are still a certain number of infected patients each year and the high mortality rate remains a major health and social problem. From this review on historical and clinical perspective, better understanding of infection would provide valuable information for public health planning.
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http://dx.doi.org/10.3947/ic.2020.52.2.245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7335640PMC
June 2020

Case report: nosocomial fungemia caused by Candida diddensiae.

BMC Infect Dis 2020 May 27;20(1):377. Epub 2020 May 27.

Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea.

Background: Candida diddensiae, a yeast found in olive oil, is considered non-pathogenic to humans. Here, we describe the first case of fungemia caused by C. diddensiae in a hospitalized patient with underlying diseases.

Case Presentation: A 62-year-old woman was admitted because of multiple contusions due to repeated falls and generalized weakness. She presented with chronic leukopenia due to systemic lupus erythematosus, and multiple cranial nerve neuropathies due to a recurring chordoma. She was given a lipid emulsion containing total parenteral nutrition (TPN) starting on the day of admission. Broad-spectrum antibiotics had been administered during her last hospital stay and from day 8 of this hospitalization. However, no central venous catheter was used during this hospital stay. Blood cultures obtained on hospital days 17, 23, and 24 yielded the same yeast, which was identified as C. diddensiae via sequence analyses of the internal transcribed spacer region and D1/D2 regions of the 26S ribosomal DNA of the rRNA gene. In vitro susceptibility testing showed that the minimum inhibitory concentration of fluconazole for all isolates was 8 μg/mL. On day 23, TPN was discontinued and fluconazole therapy was started. Blood cultures obtained on day 26 were negative. The fluconazole therapy was replaced with micafungin on day 26 and the patient exhibited improvements.

Conclusion: The use of lipid TPN may potentially contribute to the occurrence of nosocomial fungemia by C. diddensiae, an unusual Candida species.
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http://dx.doi.org/10.1186/s12879-020-05095-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7251903PMC
May 2020

Developmental Mechanisms of Fleshy Fruit Diversity in Rosaceae.

Annu Rev Plant Biol 2020 04;71:547-573

Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA; email:

Rosaceae (the rose family) is an economically important family that includes species prized for high-value fruits and ornamentals. The family also exhibits diverse fruit types, including drupe (peach), pome (apple), drupetum (raspberry), and achenetum (strawberry). Phylogenetic analysis and ancestral fruit-type reconstruction suggest independent evolutionary paths of multiple fleshy fruit types from dry fruits. A recent whole genome duplication in the Maleae/Pyreae tribe (with apple, pear, hawthorn, and close relatives; referred to as Maleae here) may have contributed to the evolution of pome fruit. MADS-box genes, known to regulate floral organ identity, are emerging as important regulators of fruit development. The differential competence of floral organs to respond to fertilization signals may explain the different abilities of floral organs to form fleshy fruit. Future comparative genomics and functional studies in closely related Rosaceae species with distinct fruit types will test hypotheses and provide insights into mechanisms of fleshy fruit diversity. These efforts will be facilitated by the wealth of genome data and resources in Rosaceae.
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http://dx.doi.org/10.1146/annurev-arplant-111119-021700DOI Listing
April 2020

Comparison of In Vivo Pharmacokinetics and Pharmacodynamics of Vancomycin Products Available in Korea.

Yonsei Med J 2020 Apr;61(4):301-309

Department of Infectious Diseases, Chonnam National University Medical School, Gwangju, Korea.

Purpose: Few studies have been investigated the in vivo efficacy of generic vancomycin products available outside of the United States. In this study, we aimed to compare the in vivo pharmacokinetics (PK) and pharmacodynamics (PD) of five generic vancomycin products available in Korea with those of the innovator.

Materials And Methods: The in vitro vancomycin purity of each product was examined using high-pressure liquid chromatography. Single-dose PK analyses were performed using neutropenic mice. The in vivo efficacy of vancomycin products was compared with that of the innovator in dose-effect experiments (25 to 400 mg/kg per day) using a thigh-infection model with neutropenic mice.

Results: Generic products had a lower proportion of vancomycin B (range: 90.3-93.8%) and a higher proportion of impurities (range: 6.2-9.7%) than the innovator (94.5% and 5.5%, respectively). In an in vivo single-dose PK study, the maximum concentration (C) values of each generic were lower than that of the innovator, and the geographic mean area under the curve ratios of four generics were significantly lower than that of the innovator (all <0.1). In the thigh-infection model, the maximum efficacies of generic products reflected in maximal effect (E) values were not significantly different from the innovator. However, the PD profile curves of some generic products differed significantly from that of the innovator in mice injected with a high level of Mu3 (all ≤0.05).

Conclusion: Some generic vancomycin products available in Korea showed inferior PK and PD profiles, especially in mice infected with hetero-vancomycin-resistant Staphylococcus aureus.
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http://dx.doi.org/10.3349/ymj.2020.61.4.301DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7105400PMC
April 2020

A roadmap for research in octoploid strawberry.

Hortic Res 2020 15;7:33. Epub 2020 Mar 15.

1University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma, Florida 33598 USA.

The cultivated strawberry ( × ) is an allo-octoploid species, originating nearly 300 years ago from wild progenitors from the Americas. Since that time the strawberry has become the most widely cultivated fruit crop in the world, universally appealing due to its sensory qualities and health benefits. The recent publication of the first high-quality chromosome-scale octoploid strawberry genome (cv. Camarosa) is enabling rapid advances in genetics, stimulating scientific debate and provoking new research questions. In this forward-looking review we propose avenues of research toward new biological insights and applications to agriculture. Among these are the origins of the genome, characterization of genetic variants, and big data approaches to breeding. Key areas of research in molecular biology will include the control of flowering, fruit development, fruit quality, and plant-pathogen interactions. In order to realize this potential as a global community, investments in genome resources must be continually augmented.
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http://dx.doi.org/10.1038/s41438-020-0252-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7072068PMC
March 2020

Clinical characteristics and risk factors for complications of candidaemia in adults: Focus on endophthalmitis, endocarditis, and osteoarticular infections.

Int J Infect Dis 2020 Apr 30;93:126-132. Epub 2020 Jan 30.

Department of Internal Medicine, Chonnam National University Medical School, Gwangju, South Korea. Electronic address:

Objectives: This study evaluated the incidence, risk factors, and clinical characteristics of complications of candidaemia in adults, with a focus on endophthalmitis, endocarditis, and osteoarticular infections.

Methods: All patients ≥18 years old with candidaemia in two Korean tertiary hospitals from 2007 to 2016 were investigated. Complications of candidaemia were defined as the presence of endophthalmitis, endocarditis, or osteoarticular infections documented in patients with candidaemia. The clinical characteristics and risk factors for candidaemia with complications were analysed in the patients who underwent ophthalmological examinations.

Results: Of 765 adult patients with candidaemia, 34 (4.4%) met the definition of complications, including endophthalmitis in 29 (3.8%), endocarditis in 4 (0.5%), and osteoarticular infections in 3 (0.4%). Of the 225 patients who underwent ophthalmological examinations, 29 (12.9%) had endophthalmitis. Candida albicans was an independent risk factor for complicated candidaemia (OR, 5.12; 95% CI, 2.17-12.09; P < 0.001). Although the mortality rate was no higher in complicated candidaemia, the duration of antifungal therapy was longer (23.1 ± 17.6 vs. 16.4 ± 10.8 days, P = 0.042), and 13 patients (39.3%) underwent additional procedures or surgery.

Conclusions: Complications of candidaemia occurred in 4.4% of adult patients. C. albicans was an independent risk factor for complicated candidaemia in adults. Complications of candidaemia might need prolonged treatment and additional procedures or surgery. Therefore, careful evaluation and active treatment of candidaemia with complications should be encouraged.
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http://dx.doi.org/10.1016/j.ijid.2020.01.049DOI Listing
April 2020

Tripal MapViewer: A tool for interactive visualization and comparison of genetic maps.

Database (Oxford) 2019 01;2019

Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA.

Tripal is an open-source, resource-efficient toolkit for construction of genomic, genetic and breeding databases. It facilitates development of biological websites by providing tools to integrate and display biological data using the generic database schema, Chado, together with Drupal, a popular website creation and content management system. Tripal MapViewer is a new interactive tool for visualizing genetic map data. Developed as a Tripal replacement for Comparative Map Viewer (CMap), it enables visualization of entire maps or linkage groups and features such as molecular markers, quantitative trait loci (QTLs) and heritable phenotypic markers. It also provides graphical comparison of maps sharing the same markers as well as dot plot and correspondence matrices. MapViewer integrates directly with the Tripal application programming interface framework, improving data searching capability and providing a more seamless experience for site visitors. The Tripal MapViewer interface can be integrated in any Tripal map page and linked from any Tripal page for markers, QTLs, heritable morphological markers or genes. Configuration of the display is available through a control panel and the administration interface. The administration interface also allows configuration of the custom database query for building materialized views, providing better performance and flexibility in the way data is stored in the Chado database schema. MapViewer is implemented with the D3.js technology and is currently being used at the Genome Database for Rosaceae (https://www.rosaceae.org), CottonGen (https://www.cottongen.org), Citrus Genome Database (https://citrusgenomedb.org), Vaccinium Genome Database (https://www.vaccinium.org) and Cool Season Food Legume Database (https://www.coolseasonfoodlegume.org). It is also currently in development on the Hardwood Genomics Web (https://hardwoodgenomics.org) and TreeGenes (https://treegenesdb.org). Database URL: https://gitlab.com/mainlabwsu/tripal_map.
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http://dx.doi.org/10.1093/database/baz100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6829499PMC
January 2019

Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases.

Database (Oxford) 2019 01;2019

Department of Horticulture, Washington State University, Pullman, WA, USA.

Community biological databases provide an important online resource for both public and private data, analysis tools and community engagement. These sites house genomic, transcriptomic, genetic, breeding and ancillary data for specific species, families or clades. Due to the complexity and increasing quantities of these data, construction of online resources is increasingly difficult especially with limited funding and access to technical expertise. Furthermore, online repositories are expected to promote FAIR data principles (findable, accessible, interoperable and reusable) that presents additional challenges. The open-source Tripal database toolkit seeks to mitigate these challenges by creating both the software and an interactive community of developers for construction of online community databases. Additionally, through coordinated, distributed co-development, Tripal sites encourage community-wide sustainability. Here, we report the release of Tripal version 3 that improves data accessibility and data sharing through systematic use of controlled vocabularies (CVs). Tripal uses the community-developed Chado database as a default data store, but now provides tools to support other data stores, while ensuring that CVs remain the central organizational structure for the data. A new site developer can use Tripal to develop a basic site with little to no programming, with the ability to integrate other data types using extension modules and the Tripal application programming interface. A thorough online User's Guide and Developer's Handbook are available at http://tripal.info, providing download, installation and step-by-step setup instructions.
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http://dx.doi.org/10.1093/database/baz077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6643302PMC
January 2019

Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment.

Front Plant Sci 2019 25;10:813. Epub 2019 Jun 25.

Department of Horticulture, Washington State University, Pullman, WA, United States.

Despite tremendous advancements in high throughput sequencing, the vast majority of tree genomes, and in particular, forest trees, remain elusive. Although primary databases store genetic resources for just over 2,000 forest tree species, these are largely focused on sequence storage, basic genome assemblies, and functional assignment through existing pipelines. The tree databases reviewed here serve as secondary repositories for community data. They vary in their focal species, the data they curate, and the analytics provided, but they are united in moving toward a goal of centralizing both data access and analysis. They provide frameworks to view and update annotations for complex genomes, interrogate systems level expression profiles, curate data for comparative genomics, and perform real-time analysis with genotype and phenotype data. The organism databases of today are no longer simply catalogs or containers of genetic information. These repositories represent integrated cyberinfrastructure that support cross-site queries and analysis in web-based environments. These resources are striving to integrate across diverse experimental designs, sequence types, and related measures through ontologies, community standards, and web services. Efficient, simple, and robust platforms that enhance the data generated by the research community, contribute to improving forest health and productivity.
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http://dx.doi.org/10.3389/fpls.2019.00813DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6603172PMC
June 2019

Four Taeniasis saginata Cases Diagnosed at a University Hospital in Korea.

Korean J Parasitol 2019 Jun 30;57(3):313-318. Epub 2019 Jun 30.

Department of Parasitology, College of Veterinary Medicine, Chonnam National University, Gwangju 61186, Korea.

In recent years, the taeniasis has been rarely reported in the Republic of Korea (Korea). But in this study, we intend to report 4 taeniasis cases caused by Taenia saginata during a 5-month period (February to June 2018) at a unversity hospital in Gwangju, Korea. Worm samples (proglottids) discharged from all cases were identified by phenotypic and molecular diagnostics. Mitochondrial cytochrome c oxidase subunit I sequences showed 99.4-99.9% identity with T. saginata but, differed by 4% from T. asiatica and by 7% from T. multiceps, respectively. We found that tapeworms in 2 cases (Cases 2 and 3) yielded exactly the same sequences between them, which differed from those in Cases 1 and 4, suggesting intra-species variation in tapeworms. These taeniasis cases by T. saginata infection in this study, which occurred within a limited time period and region, suggest the possibility of a mini-outbreak. This study highlights the need for further epidemiological investigation of potentially overlooked cases of T. saginata infection in Korea.
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http://dx.doi.org/10.3347/kjp.2019.57.3.313DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6616169PMC
June 2019

Safety and Effectiveness Analysis of Kivexa® (lamivudine/abacavir sulfate) in Human Immunodeficiency Virus Infected Korean Patients.

Infect Chemother 2019 Jun;51(2):150-160

Department of Internal Medicine, Kyungpook National University School of Medicine, Daegu, Korea.

Background: Lamivudine and abacavir sulfate are widely used nucleoside/tide reverse transcriptase inhibitors (NRTI) backbone agents, which are recommended in major international treatment guidelines. The fixed-dose combination of lamivudine and abacavir sulfate has been developed to contribute to low pill burden of antiretroviral therapy (ART) regimen and patient adherence. A mandatory post-marketing surveillance was conducted in Korea to monitor the safety of Kivexa (lamivudine 300 mg/abacavir 600 mg).

Materials And Methods: An open label, multi-center, non-interventional post-marketing surveillance was conducted to monitor the safety of Kivexa from July 2011 to July 2017 in 23 hospitals in Korea. Subjects over 12 years old taking Kivexa per prescribing information were enrolled. The primary outcome was defined as the occurrence of any adverse events during the study period. Secondary outcomes included the occurrence of adverse drug reaction, the occurrence of serious adverse events and the effectiveness of Kivexa.

Results: A total of 600 patients from 23 hospitals were enrolled within the 6 years of study. The total observation period was 1,004 person-years. Three hundred and ten patients reported 674 adverse events. The incidence of upper respiratory infection (65 cases, 10.9%) was the highest, followed by diarrhea (20 cases, 3.3%), and nausea (18 cases, 3.0%). 109 subjects reported 71 events of adverse drug reactions, and the most common reaction was nausea in 2.33% of the subjects. Thirty-one subjects reported serious adverse events, none of them were considered drug related. From the total of 600 subjects, excluding 48 subjects who were 'effectiveness unassessable' by investigators, 552 patients were eligible for the subjective effectiveness analysis. 459 (83.2%) were evaluated as 'improved'. Proportion of subjects whose human immunodeficiency virus-RNA is <50 copies/ml was 61.2% (309/505) at the beginning of observation and increased to 91.9% (464/505) at the end of study period.

Conclusions: The post-marketing surveillance showed the safety of Kivexa in HIV-1 patients in Korea. Ischemic cardiovascular events and hypersensitivity associated with Kivexa were few. There was no significant new safety information. This data may be helpful in implementing Kivexa and lamivudine/abacavir sulfate containing drugs in Korea.
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http://dx.doi.org/10.3947/ic.2019.51.2.150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6609745PMC
June 2019

Apple whole genome sequences: recent advances and new prospects.

Hortic Res 2019 5;6:59. Epub 2019 Apr 5.

1Department of Horticulture, Washington State University, Pullman, WA 99164 USA.

In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for "what's next" focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.
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http://dx.doi.org/10.1038/s41438-019-0141-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450873PMC
April 2019

genetics and applications after de novo genome sequencing: achievements and prospects.

Hortic Res 2019 5;6:58. Epub 2019 Apr 5.

1IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain.

Prior to the availability of whole-genome sequences, our understanding of the structural and functional aspects of tree genomes was limited mostly to molecular genetic mapping of important traits and development of EST resources. With public release of the peach genome and others that followed, significant advances in our knowledge of genomes and the genetic underpinnings of important traits ensued. In this review, we highlight key achievements in genetics and breeding driven by the availability of these whole-genome sequences. Within the structural and evolutionary contexts, we summarize: (1) the current status of whole-genome sequences; (2) preliminary and ongoing work on the sequence structure and diversity of the genomes; (3) the analyses of genome evolution driven by natural and man-made selection; and (4) provide insight into haploblocking genomes as a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based tree breeding programs worldwide. Functionally, we summarize recent and ongoing work that leverages whole-genome sequences to identify and characterize genes controlling 22 agronomically important traits. These include phenology, fruit quality, allergens, disease resistance, tree architecture, and self-incompatibility. Translationally, we explore the application of sequence-based marker-assisted breeding technologies and other sequence-guided biotechnological approaches for crop improvement. Finally, we present the current status of publically available genomics and genetics data housed mainly in the Genome Database for Rosaceae (GDR) and its updated functionalities for future bioinformatics-based genetics and genomics inquiry.
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http://dx.doi.org/10.1038/s41438-019-0140-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450939PMC
April 2019
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