Androgen receptor and its correlation with estrogen and progesterone receptors, aimed for identification of cases for future anti-androgen therapy in endometrial cancers.

INTRODUCTION: The expression of androgen receptor (AR) is not commonly tested or studied in uterine cancers, unlike estrogen receptor (ER) and progesterone receptor (PR) which are positive in most endometrial carcinomas. In this series, we evaluated the expression of AR and its comparison to ER and PR in different types of endometrial cancers and have reviewed the literature. MATERIALS AND METHODS: The status of AR, ER, and PR expression were evaluated in 71 cases which were categorized into endometrial endometrioid cancer (EEC), non-endometrioid endometrial cancers (NEEC), and metastatic carcinomas of endometrium. Expression of the receptors were compared to each other as well as to mismatch repair proteins (MMR), p53, and body mass index (BMI) using Fisher's Exact test in the StatPlus software. RESULTS: In EECs, the positivity was 97% for all the three receptors. In NEEC, positivity rates were 68%, 48%, and 35% for AR, ER, and PR respectively. In Metastatic carcinomas, AR and ER positivity was seen in 100% while PR was positive in 75% of the cases. In all cancers, the rates were 17% (11/66) for MMR loss, 57% (30/53) for p53 aberrant expression, and 76% (54/71) for the patients with BMI of ≥ 25 (kg/m2). CONCLUSION: AR is expressed in a high percentage of endometrial cancers. Its significance is more evident in high-grade NEEC where ER and PR may not be expressed. These findings warrant further evaluation of AR expression and candidacy of this pathway as a potential therapeutic target in endometrial cancers.

A Frameshift Mutation in the Mg-Chelatase I Subunit Gene OsCHLI Is Associated with a Lethal Chlorophyll-Deficient, Yellow Seedling Phenotype in Rice.

Chlorophyll biosynthesis is a crucial biological process in plants, and chlorophyll content is one of the most important traits in rice breeding programs. In this study, we identified a lethal, chlorophyll-deficient, yellow seedling (YS) phenotype segregating in progeny of CR5055-21, an F2 plant derived from a backcross between Korean japonica variety 'Hwaseong' (Oryza sativa) and CR5029, which is mostly Hwaseong with a small amount of Oryza grandiglumis chromosome segments. The segregation of the mutant phenotype was consistent with a single gene recessive mutation. Light microscopy of YS leaf cross-sections revealed loosely arranged mesophyll cells and sparse parenchyma in contrast to wildtype. In addition, transmission electron microscopy showed that chloroplasts did not develop in the mesophyll cells of the YS mutant. Quantitative trait loci (QTL)-seq analysis did not detect any significant QTL, however, examination of the individual delta-SNP index identified a 2-bp deletion (AG) in the OsCHLI gene, a magnesium (Mg)-chelatase subunit. A dCAPs marker was designed and genotyping of a segregating population (n = 275) showed that the mutant phenotype co-segregated with the marker. The 2-bp deletion was predicted to result in a frameshift mutation generating a premature termination. The truncated protein likely affects formation and function of Mg-chelatase, which consists of three different subunits that together catalyze the first committed step of chlorophyll biosynthesis. Transcriptome analysis showed that photosynthesis and carbohydrate metabolism pathways were significantly altered although expression of OsCHLI was not. Chlorophyll- and carotenoid-related genes were also differentially expressed in the YS mutant. Our findings demonstrated that OsCHLI plays an important role in leaf pigment biosynthesis and leaf structure development in rice.

Optimizing genomic selection of agricultural traits using K-wheat core collection.

The agricultural traits that constitute basic plant breeding information are usually quantitative or complex in nature. This quantitative and complex combination of traits complicates the process of selection in breeding. This study examined the potential of genome-wide association studies (GWAS) and genomewide selection (GS) for breeding ten agricultural traits by using genome-wide SNPs. As a first step, a trait-associated candidate marker was identified by GWAS using a genetically diverse 567 Korean (K)-wheat core collection. The accessions were genotyped using an Axiom® 35K wheat DNA chip, and ten agricultural traits were determined (awn color, awn length, culm color, culm length, ear color, ear length, days to heading, days to maturity, leaf length, and leaf width). It is essential to sustain global wheat production by utilizing accessions in wheat breeding. Among the traits associated with awn color and ear color that showed a high positive correlation, a SNP located on chr1B was significantly associated with both traits. Next, GS evaluated the prediction accuracy using six predictive models (G-BLUP, LASSO, BayseA, reproducing kernel Hilbert space, support vector machine (SVM), and random forest) and various training populations (TPs). With the exception of the SVM, all statistical models demonstrated a prediction accuracy of 0.4 or better. For the optimization of the TP, the number of TPs was randomly selected (10%, 30%, 50% and 70%) or divided into three subgroups (CC-sub 1, CC-sub 2 and CC-sub 3) based on the subpopulation structure. Based on subgroup-based TPs, better prediction accuracy was found for awn color, culm color, culm length, ear color, ear length, and leaf width. A variety of Korean wheat cultivars were used for validation to evaluate the prediction ability of populations. Seven out of ten cultivars showed phenotype-consistent results based on genomics-evaluated breeding values (GEBVs) calculated by the reproducing kernel Hilbert space (RKHS) predictive model. Our research provides a basis for improving complex traits in wheat breeding programs through genomics assisted breeding. The results of our research can be used as a basis for improving wheat breeding programs by using genomics-assisted breeding.

Digitalizing breeding in plants: A new trend of next-generation breeding based on genomic prediction.

As the world's population grows and food needs diversification, the demand for cereals and horticultural crops with beneficial traits increases. In order to meet a variety of demands, suitable cultivars and innovative breeding methods need to be developed. Breeding methods have changed over time following the advance of genetics. With the advent of new sequencing technology in the early 21st century, predictive breeding, such as genomic selection (GS), emerged when large-scale genomic information became available. GS shows good predictive ability for the selection of individuals with traits of interest even for quantitative traits by using various types of the whole genome-scanning markers, breaking away from the limitations of marker-assisted selection (MAS). In the current review, we briefly describe the history of breeding techniques, each breeding method, various statistical models applied to GS and methods to increase the GS efficiency. Consequently, we intend to propose and define the term digital breeding through this review article. Digital breeding is to develop a predictive breeding methods such as GS at a higher level, aiming to minimize human intervention by automatically proceeding breeding design, propagating breeding populations, and to make selections in consideration of various environments, climates, and topography during the breeding process. We also classified the phases of digital breeding based on the technologies and methods applied to each phase. This review paper will provide an understanding and a direction for the final evolution of plant breeding in the future.

Novel Yellow Azo Pyridone Derivatives with Different Halide Atoms for Image-Sensor Color Filters.

Novel yellow azo pyridone dye derivatives were synthesized for use in image-sensor color filters. The synthesized compounds have a basic chemical structure composed of azo, hydroxy, amide, and nitrile groups as well as different halide groups. New materials were evaluated on the basis of their optical, thermal, and surface properties under conditions mimicking those of a commercial device fabrication process. A comparison of their related performance revealed that, among the four prepared compounds, 5-((4,6-dichlorocyclohexa-2,4-dien-1-yl)diazenyl)-6-hydroxy-1,4-dimethyl-2-oxo-1,2-dihydropyridine-3-carbonitrile (Cl-PAMOPC) exhibited the best performance as an image-sensor color filter material, including a solubility greater than 0.1 wt% in propylene glycol monomethyl ether acetate solvent, a high decomposition temperature of 263 °C, and stable color difference values of 4.93 and 3.88 after a thermal treatment and a solvent-resistance test, respectively. The results suggest that Cl-PAMOPC can be used as a green dye additive in an image-sensor colorant.

Expression Profile of Sorghum Genes and Cis-Regulatory Elements under Salt-Stress Conditions.

Salinity stress is one of the most important abiotic stresses that causes great losses in crop production worldwide. Identifying the molecular mechanisms of salt resistance in sorghum will help develop salt-tolerant crops with high yields. Sorghum (Sorghum bicolor (L.) Moench) is one of the world's four major grains and is known as a plant with excellent adaptability to salt stress. Among the various genotypes of sorghum, a Korean cultivar Nampungchal is also highly tolerant to salt. However, little is known about how Nampungchal responds to salt stress. In this study, we measured various physiological parameters, including Na+ and K+ contents, in leaves grown under saline conditions and investigated the expression patterns of differentially expressed genes (DEGs) using QuantSeq analysis. These DEG analyses revealed that genes up-regulated in a 150 mM NaCl treatment have various functions related to abiotic stresses, such as ERF and DREB. In addition, transcription factors such as ABA, WRKY, MYB, and bZip bind to the CREs region of sorghum and are involved in the regulation of various abiotic stress-responsive transcriptions, including salt stress. These findings may deepen our understanding of the mechanisms of salt tolerance in sorghum and other crops.

Physio-chemical and co-expression network analysis associated with salt stress in sorghum.

BACKGROUND: Abiotic stress can damage crops and reduce productivity. Among them, salt stress is related to water stress such as osmosis and ions, and like other abiotic stresses, it can affect the growth of plants by changing gene expressions. Investigating the profiles of gene expression under salt stress may help us understand molecular mechanisms of plants to cope with unfavorable conditions. RESULTS: To study salt tolerance in sorghum, physiological and comparative transcriptomic studies were performed using a Korean sorghum cultivar 'Sodamchal' which is considered sensitive to soil salinity. In this study, the samples were treated with two concentrations of NaCl [0 (control) and 150 mM], and the leaves and roots were harvested at 0, 3, and 9 days after the treatment. For the physiological study, the levels of anthocyanin, proline, reducing sugar, and chlorophyll were evaluated in the control and the treatment group at each sampling point. The results show that the cultivar 'Sodamchal' has salt-susceptible profiles. We also analyzed the transcription profile in the presence of 0 and 150 mM NaCl to confirm the candidate genes under the saline stress condition. Between the control and salt treatment, we found a total of 1506 and 1510 differentially expressed genes (DEGs) in the leaves and roots, respectively. We also built a gene co-expression network to determine the association of the candidate genes in terms of biological pathways. CONCLUSIONS: Through the co-expression network, genes related to salt stress such as AP2/ERF and Dehydrin were identified. This study provides the physiological and genic markers that could be used during intense salt stress in sorghum. These markers could be used to lay the foundation for the distribution of high-quality seeds that are tolerant to salt in the future.

Management of Clitoral Melanoma Presenting as an Exophytic Clitoral Mass: A Case Report and Review of the Literature.

Primary mucosal melanomas of the female genital tract account for one percent or less of all cases of melanoma with even fewer originating in the clitoris. Given the rarity of diagnosis of clitoral melanoma, there is a paucity of data guiding management. There is no supporting evidence that radical vulvectomy (with or without inguinal lymphadenopathy) is associated with improved disease-free or overall survival compared to partial vulvectomy or wide local excision. Additionally, there is no data to evaluate the role of sentinel lymph node biopsy or extensive lymphadenectomy in clitoral melanoma, however previous evidence demonstrates the utility of regional lymph node sampling in predicting survival in women with female genital tract mucosal melanoma. Adjuvant therapy considerations are often extrapolated from their use in treating cutaneous melanomas, including immune checkpoint inhibitors and other immunotherapy agents. Adjuvant radiation therapy has limited utility except in cases of bulky, unresectable disease, or when inguinal lymph nodes are positive for metastasis. The 52 year-old patient presented in this review was diagnosed with locally invasive advanced stage clitoral melanoma presenting as an exophytic clitoral mass. She underwent diagnostic primary tumor resection, which demonstrated ulcerative melanoma with spindle cell features extending to a Breslow depth of at least 28 mm. She subsequently underwent secondary wide local excision with groin sentinel lymph node biopsy, and adjuvant treatment with pembrolizumab. This article also emphasizes the importance of a multidisciplinary team involving gynecologic oncology, medical oncology, radiology, and pathology for management of this rare type of primary mucosal melanoma of the female genital tract.

p16 is superior to Stathmin-1 and HSP27 in identifying cervical dysplasia.

BACKGROUND: The aim of this study was to determine how Stathmin-1 and Heat Shock Protein 27 (HSP27) can be used as adjunctive biomarkers to differentiate high-grade dysplasia from benign/reactive lesions in cervical tissues. In addition, we aimed to see if any of these markers can differentiate endometrial from endocervical adenocarcinomas. METHODS: Fifty cases including benign cervical tissue, low-grade squamous intraepithelial lesion (LSIL), high-grade squamous intraepithelial lesion (HSIL), adenocarcinoma in situ of the endocervix, invasive endocervical adenocarcinoma, and endometrial adenocarcinoma were selected. Stathmin-1 and HSP27 immunohistochemistry (IHC) were performed for each case and the results were compared to the previously available p16 IHC stains. RESULTS: p16 stained positively in 100% of HSIL, endocervical adenocarcinoma in situ, and invasive endocervical cases. Stathmin-1 stained positively in 43% of HSIL and 90% of endocervical adenocarcinoma in situ and all invasive endocervical cases. Stathmin-1 and p16 were negative in all benign cervical samples. Stathmin-1, HSP27, and p16 stained 100% of LSIL cases. HSP27 stained indiscriminately, including 100% of benign cervical tissue. 87% of the endometrial adenocarcinomas stained positively for p16, Stathmin-1, and HSP27. CONCLUSION: p16 remains superior to both Stathmin-1 and HSP27 in differentiating dysplasia from benign, reactive changes of the cervix.

Automated identification and assignment of colonoscopy surveillance recommendations for individuals with colorectal polyps.

BACKGROUND AND AIMS: Determining surveillance intervals for patients with colorectal polyps is critical but time-consuming and challenging to do reliably. We present the development and assessment of a pipeline that leverages natural language processing techniques to automatically extract and analyze relevant polyp findings from free-text colonoscopy and pathology reports. Using this information, we categorized individual patients into 6 postcolonoscopy surveillance intervals defined by the U.S. Multi-Society Task Force on Colorectal Cancer. METHODS: Using a set of 546 randomly selected colonoscopy and pathology reports from 324 patients in a single health system, we used a combination of statistical classifiers and rule-based methods to extract polyp properties from each report type, associate properties with unique polyps, and classify a patient into 1 of 6 risk categories by integrating information from both report types. We then assessed the pipeline's performance by determining the positive predictive value (PPV), sensitivity, and F-score of the algorithm, compared with the determination of surveillance intervals by a gastroenterologist. RESULTS: The pipeline was developed using 346 reports (224 colonoscopy and 122 pathology) from 224 patients and evaluated on an independent test set of 200 reports (100 colonoscopy and 100 pathology) from 100 patients. We achieved an average PPV, sensitivity, and F-score of .92, .95, and .93, respectively, across targeted entities for colonoscopy. Pathology extraction achieved a PPV, sensitivity, and F-score of .95, .97, and .96. The system achieved an overall accuracy of 92% in assigning the recommended interval for surveillance colonoscopy. CONCLUSIONS: This study demonstrates the feasibility of using machine learning to automatically extract findings and classify patients to appropriate risk categories and corresponding surveillance intervals. Incorporating this system can facilitate proactive and timely follow-up after screening colonoscopy and enable real-time quality assessment of prevention programs and providers.

Gastroenterology visitation and reminders predict surveillance uptake for patients with adenomas with high-risk features.

Individuals diagnosed with colorectal adenomas with high-risk features during screening colonoscopy have increased risk for the development of subsequent adenomas and colorectal cancer. While US guidelines recommend surveillance colonoscopy at 3 years in this high-risk population, surveillance uptake is suboptimal. To inform future interventions to improve surveillance uptake, we sought to assess surveillance rates and identify facilitators of uptake in a large integrated health system. We utilized a cohort of patients with a diagnosis of ≥ 1 tubular adenoma (TA) with high-risk features (TA ≥ 1 cm, TA with villous features, TA with high-grade dysplasia, or ≥ 3 TA of any size) on colonoscopy between 2013 and 2016. Surveillance colonoscopy completion within 3.5 years of diagnosis of an adenoma with high-risk features was our primary outcome. We evaluated surveillance uptake over time and utilized logistic regression to detect factors associated with completion of surveillance colonoscopy. The final cohort was comprised of 405 patients. 172 (42.5%) patients successfully completed surveillance colonoscopy by 3.5 years. Use of a patient reminder (telephone, electronic message, or letter) for due surveillance (adjusted odds = 1.9; 95%CI = 1.2-2.8) and having ≥ 1 gastroenterology (GI) visit after diagnosis of an adenoma with high-risk features (adjusted odds = 2.6; 95%CI = 1.6-4.2) significantly predicted surveillance colonoscopy completion at 3.5 years. For patients diagnosed with adenomas with high-risk features, surveillance colonoscopy uptake is suboptimal and frequently occurs after the 3-year surveillance recommendation. Patient reminders and visitation with GI after index colonoscopy are associated with timely surveillance completion. Our findings highlight potential health system interventions to increase timely surveillance uptake for patients diagnosed with adenomas with high-risk features.

Electrostatic interaction mechanism of visible light absorption broadening in ion-doped graphitic carbon nitride.

Broadening the light response of graphitic carbon nitride (CN) is helpful to improve its solar energy utilization efficiency in photocatalytic reaction. In this work, a facile synthesis method was developed via the treatment of potassium-doped CN (CN-K) with H2O2 in isopropanol solvent. Various characterizations indicate the basic structure of CN-K treated with H2O2 (CN-K-OOH) resembles that of CN-K, while it presents light absorption up to 650 nm. A series of control experiments and TGA-MS measurements suggest the weak electrostatic attraction between potassium ions and hydroperoxyl groups inside CN-K-OOH is responsible for its enhanced visible light absorption. As a consequence, compared to pristine CN, the photodegradation organic pollutant ability of CN-K-OOH is obviously improved under visible light irradiation (>470 nm). The current synthesis strategy might be universal and it could be applied to other cations.

The uterine pathological features associated with sentinel lymph node metastasis in endometrial carcinomas.

BACKGROUND: In recent years, sentinel lymph node excision and ultrastaging have been performed in endometrial carcinomas to obtain information about lymph node status, avoiding unnecessary complete pelvic and paraaortic lymphadenectomy. The purpose of this retrospective study was to provide a comprehensive evaluation of the pathological features of endometrial carcinomas and their significance in association with sentinel lymph node involvement. METHODS: Patients with endometrial carcinomas, preceded by sentinel lymph node mapping, were classified into Group-I and Group-II with negative and positive involvement, respectively. The pathological features, associated with sentinel lymph node involvement, were statistically analyzed, including determination of test performance parameters. RESULTS: Among 70 patients who had undergone hysterectomy and sentinel lymph node excision, 61 had carcinoma and 9 had atypical hyperplasia. There were 50 patients in Group-I and 10 in Group-II. In Group-II, the significant pathological features were: 1) lower uterine segment involvement (100%), 2) an average tumor size of ≥5 CM, 3) lymphovascular invasion (50%), 4) cervical stromal invasion (40%), and 5) depth of myometrial invasion of ≥50% (50%). The incidences of these pathological features were significantly less in Group-I. Statistical analyses singled out "lower uterine segment involvement" as the most important feature. CONCLUSIONS: We have identified five pathological features which are associated with sentinel lymph node involvement. Since lower uterine segment involvement has occurred in all cases of the Group-II cohort, we recommend FIGO and other organizations that determine staging rules should consider whether tumors that involve the lower uterine segment should be staged as higher than "1a", if the findings in this small series are confirmed by other studies. The results of this study may guide pathologists and oncologists in the diagnostic and therapeutic approaches to management of endometrial carcinomas.

Application of Genomic Big Data in Plant Breeding:Past, Present, and Future.

Plant breeding has a long history of developing new varieties that have ensured the food security of the human population. During this long journey together with humanity, plant breeders have successfully integrated the latest innovations in science and technologies to accelerate the increase in crop production and quality. For the past two decades, since the completion of human genome sequencing, genomic tools and sequencing technologies have advanced remarkably, and adopting these innovations has enabled us to cost down and/or speed up the plant breeding process. Currently, with the growing mass of genomic data and digitalized biological data, interdisciplinary approaches using new technologies could lead to a new paradigm of plant breeding. In this review, we summarize the overall history and advances of plant breeding, which have been aided by plant genomic research. We highlight the key advances in the field of plant genomics that have impacted plant breeding over the past decades and introduce the current status of innovative approaches such as genomic selection, which could overcome limitations of conventional breeding and enhance the rate of genetic gain.

Prediction of Dhurrin Metabolism by Transcriptome and Metabolome Analyses in Sorghum.

Sorghum (Sorghum bicolor (L.)) Moench is an important food for humans and feed for livestock. Sorghum contains dhurrin which can be degraded into toxic hydrogen cyanide. Here, we report the expression patterns of 14 candidate genes related to dhurrin ((S)-4-Hydroxymandelnitrile-ß-D-glucopyranoside) metabolism and the effects of the gene expression on specific metabolite content in selected sorghum accessions. Dhurrin-related metabolism is vigorous in the early stages of development of sorghum. The dhurrin contents of most accessions tested were in the range of approximately 6-22 µg mg-1 fresh leaf tissue throughout growth. The p-hydroxybenzaldehyde (pHB) contents were high at seedling stages, but almost nonexistent at adult stages. The contents of p-hydroxyphenylacetic acid (pHPAAc) were relatively low throughout growth compared to those of dhurrin or pHB. Generally, the expression of the candidate genes was higher at seedling stage than at other stages and decreased gradually as plants grew. In addition, we identified significant SNPs, and six of them were potentially associated with non-synonymous changes in CAS1. Our results may provide the basis for choosing breeding materials to regulate cyanide contents in sorghum varieties to prevent HCN toxicity of livestock or to promote drought tolerance or pathogen resistance.

Quantitative Trait Loci (QTLs) Associated with Microspore Culture in Raphanus sativus L. (Radish).

The radish is a highly self-incompatible plant, and consequently it is difficult to produce homozygous lines. Bud pollination in cross-fertilization plants should be done by opening immature pollen and attaching pollen to mature flowers. It accordingly takes a lot of time and effort to develop lines with fixed alleles. In the current study, a haploid breeding method has been applied to obtain homozygous plants in a short period of time by doubling chromosomes through the induction of a plant body in the haploid cells, in order to shorten the time to breed inbred lines. We constructed genetic maps with an F1 population derived by crossing parents that show a superior and inferior ability to regenerate microspores, respectively. Genetic maps were constructed from the maternal and parental maps, separately, using the two-way pseudo-testcross model. The phenotype of the regeneration rate was examined by microspore cultures and a quantitative trait loci (QTL) analysis was performed based on the regeneration rate. From the results of the culture of microspores in the F1 population, more than half of the group did not regenerate, and only a few showed a high regeneration rate. A total of five significant QTLs were detected in the F1 population, and five candidate genes were found based on the results. These candidate genes are divided into two classes, and appear to be related to either PRC2 subunits or auxin synthesis.

A neonatal pustule:Langerhans cell histiocytosis.

Langerhans cell histiocytosis (LCH) is a rare, clinically heterogeneous disease that most commonly occurs in pediatric populations. Congenital self-limited LCH is a benign variant of LCH. It most commonly presents as a diffuse eruption and reports of single lesion cases are infrequent in the literature. Even in the case of congenital self-limited LCH, there is potential for future multisystem relapse, making long-term follow-up important. We present a case of single lesion self-limited LCH in a full-term male infant with interesting morphology. Physical examination revealed a painless, 6 millimeter, well-demarcated, papule encircled by erythema with central hemorrhage. An infectious workup was negative and a punch biopsy was obtained, which showed a dermal infiltrate of histiocytes consistent with a diagnosis of LCH. The lesion healed without intervention within three weeks. Our case highlights the need for dermatologists to consider LCH in the differential diagnosis for lesions of varying morphology in children, as proper identification is necessary to monitor for multisystem recurrence.

Twenty-year-old woman presenting with typical Kawasaki disease.

We describe adult-onset Kawasaki disease (KD) and review clinical manifestations and treatment guidelines. Our patient is a 20-year-old female who initially presented to an outside hospital for fever, cervical lymphadenopathy, malaise, exudative tonsillitis, and skin eruption. She received antibiotics for suspected exudative pharyngitis, but experienced continued fevers and presented to the UCLA emergency room one week later. She had diffuse petechial macules coalescing into reticulated patches, fingertip peeling, conjunctival injection, oral erosions, and tongue swelling. Despite her age, given her constellation of symptoms, a diagnosis of typical KD was favored. She was started on high dose aspirin and IVIG, with improvement of rash and conjunctivitis. She was discharged on 325mg of aspirin daily with close follow-up. This case highlights the challenge of diagnosing KD in adults. Although this patient had classic symptoms, she was likely misdiagnosed because KD is rare in adults and without validated criteria. Our patient met the pediatric criteria, suggesting these should be considered when clinical suspicion for adult-onset KD is high. Adult-onset KD is most commonly misdiagnosed as toxic shock syndrome or drug-induced hypersensitivity syndrome and these are important to rule-out. Treatment with high-dose aspirin and IVIG is well established and should be initiated promptly.

Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology.

The whole genome sequencing (WGS) has become a crucial tool in understanding genome structure and genetic variation. The MinION sequencing of Oxford Nanopore Technologies (ONT) is an excellent approach for performing WGS and it has advantages in comparison with other Next-Generation Sequencing (NGS): It is relatively inexpensive, portable, has simple library preparation, can be monitored in real-time, and has no theoretical limits on reading length. Sorghum bicolor (L.) Moench is diploid (2n = 2x = 20) with a genome size of about 730 Mb, and its genome sequence information is released in the Phytozome database. Therefore, sorghum can be used as a good reference. However, plant species have complex and large genomes when compared to animals or microorganisms. As a result, complete genome sequencing is difficult for plant species. MinION sequencing that produces long-reads can be an excellent tool for overcoming the weak assembly of short-reads generated from NGS by minimizing the generation of gaps or covering the repetitive sequence that appears on the plant genome. Here, we conducted the genome sequencing for S. bicolor cv. BTx623 while using the MinION platform and obtained 895,678 reads and 17.9 gigabytes (Gb) (ca. 25× coverage of reference) from long-read sequence data. A total of 6124 contigs (covering 45.9%) were generated from Canu, and a total of 2661 contigs (covering 50%) were generated from Minimap and Miniasm with a Racon through a de novo assembly using two different tools and mapped assembled contigs against the sorghum reference genome. Our results provide an optimal series of long-read sequencing analysis for plant species while using the MinION platform and a clue to determine the total sequencing scale for optimal coverage that is based on various genome sizes.