Genome Analysis and Therapeutic Evaluation of a Novel Lytic Bacteriophage of Salmonella Typhimurium: Suggestive of a New Genus in the Subfamily Vequintavirinae

Salmonella Typhimurium, a foodborne pathogen, is a major concern for food safety. Its MDR serovars of animal origin pose a serious threat to the human population. Phage therapy can be an alternative for the treatment of such MDR Salmonella serovars. In this study, we report on detailed genome analyses of a novel Salmonella phage (Salmonella-Phage-SSBI34) and evaluate its therapeutic potential. The phage was evaluated for latent time, burst size, host range, and bacterial growth reduction in liquid cultures. The phage stability was examined at various pH levels and temperatures. The genome analysis (141.095 Kb) indicated that its nucleotide sequence is novel, as it exhibited only 1-7% DNA coverage. The phage genome features 44% GC content, and 234 putative open reading frames were predicted. The genome was predicted to encode for 28 structural proteins and 40 enzymes related to nucleotide metabolism, DNA modification, and protein synthesis. Further, the genome features 11 tRNA genes for 10 different amino acids, indicating alternate codon usage, and hosts a unique hydrolase for bacterial lysis. This study provides new insights into the subfamily Vequintavirinae, of which SSBI34 may represent a new genus.

Balancing Complex Signals for Robust Predictive Modeling

Robust predictive modeling is the process of creating, validating, and testing models to obtain better prediction outcomes. Datasets usually contain outliers whose trend deviates from the most data points. Conventionally, outliers are removed from the training dataset during preprocessing before building predictive models. Such models, however, may have poor predictive performance on the unseen testing data involving outliers. In modern machine learning, outliers are regarded as complex signals because of their significant role and are not suggested for removal from the training dataset. Models trained in modern regimes are interpolated (over trained) by increasing their complexity to treat outliers locally. However, such models become inefficient as they require more training due to the inclusion of outliers, and this also compromises the models’ accuracy. This work proposes a novel complex signal balancing technique that may be used during preprocessing to incorporate the maximum number of complex signals (outliers) in the training dataset. The proposed approach determines the optimal value for maximum possible inclusion of complex signals for training with the highest performance of the model in terms of accuracy, time, and complexity. The experimental results show that models trained after preprocessing with the proposed technique achieve higher predictive accuracy with improved execution time and low complexity as compared to traditional predictive modeling.

Age of First Oral Health Examination and Dental Treatment Needs of Medicaid-Enrolled Children

INTRODUCTION

Early childhood caries (ECC), despite being preventable, remains the most prevalent disease of childhood, particularly in children between the ages of 2 and 5 y. The association between the type of health care provider completing initial oral health examinations and subsequent dental caries in children under 6 y of age is unclear.

OBJECTIVE

The objective of the current study is to longitudinally assess the association between age at first oral health examination and provider type at first oral health examination on dental treatment for children under 6 y of age.

METHODS

Deidentified administrative claims data were used from the IBM Marketscan Multi-State Medicaid Database (n = 2.41 million Medicaid-enrolled children younger than 6 y in 13 states from 2012 to 2017). A Kaplan-Meier survival analysis was used to examine the association between age at first oral health examination and provider type with first treatment of dental caries at follow-up.

RESULTS

The adjusted hazard ratio (HR) of dental caries for children whose first oral health examination at 4 y of age is 5.425 times higher than for children whose first oral health examination was before 1 y of age (95% confidence interval [CI], 5.371-5.479). The adjusted HR of dental caries for children seen by pediatric dentists (HR = 1.215; 95% CI, 1.207-1.223) and physicians (HR = 2.618; 95% CI, 2.601-2.635) was higher than those seen by a general dentist.

CONCLUSIONS

Findings from this study highlight the importance of children having their first oral health examination no later than 12 mo of age in accordance with existing guidelines and referrals from physicians to prevent the need for invasive treatment.

KNOWLEDGE OF TRANSFER STATEMENT

Results of this study emphasize the need for a child's first oral health examination to be completed no later than 12 mo of age to prevent dental caries. Reinforcement and referrals by physicians based on this recommendation facilitate early establishment of a dental home in young children.

Comparative Chloroplast Genome Analyses of the Winter-Blooming Eastern Asian Endemic Genus Chimonanthus (Calycanthaceae) With Implications For Its Phylogeny and Diversification

Chimonanthus of Calycanthaceae is a small endemic genus in China, with unusual winter-blooming sweet flowers widely cultivated for ornamentals and medicinal uses. The evolution of Chimonanthus plastomes and its phylogenetic relationships remain unresolved due to limited availability of genetic resources. Here, we report fully assembled and annotated chloroplast genomes of five Chimonanthus species. The chloroplast genomes of the genus (size range 153,010 – 153,299 bp) reveal high similarities in gene content, gene order, GC content, codon usage, amino acid frequency, simple sequence repeats, oligonucleotide repeats, synonymous and non-synonymous substitutions, and transition and transversion substitutions. Signatures of positive selection are detected in atpF and rpoB genes in C. campanulatus. The correlations among substitutions, InDels, and oligonucleotide repeats reveal weak to strong correlations in distantly related species at the intergeneric levels, and very weak to weak correlations among closely related Chimonanthus species. Chloroplast genomes are used to reconstruct a well-resolved phylogenetic tree, which supports the monophyly of Chimonanthus. Within Chimonanthus, C. praecox and C. campanulatus form one clade, while C. grammatus, C. salicifolius, C. zhejiangensis, and C. nitens constitute another clade. Chimonanthus nitens appears paraphyletic and is closely related to C. salicifolius and C. zhejiangensis, suggesting the need to reevaluate the species delimitation of C. nitens. Chimonanthus and Calycanthus diverged in mid-Oligocene; the radiation of extant Chimonanthus species was dated to the mid-Miocene, while C. grammatus diverged from other Chimonanthus species in the late Miocene. C. salicifolius, C. nitens(a), and C. zhejiangensis are inferred to have diverged in the Pleistocene of the Quaternary period, suggesting recent speciation of a relict lineage in the subtropical forest regions in eastern China. This study provides important insights into the chloroplast genome features and evolutionary history of Chimonanthus and family Calycanthaceae.

Assessment of water, sanitation and hygiene practices for prevention and control of COVID-19 in Kenya

Background

Safely managed water, sanitation and hygiene (WASH) services are an essential part of preventing and protecting human health during infectious disease outbreaks, including the current coronavirus disease 2019 (COVID-19) pandemic. Additionally, adherence to COVID-19 measures, including washing hands using soap and proper waste disposal, no doubt can improve containment of the virus.

Methods

A cross-sectional survey was conducted in Kilifi and Mombasa Counties in Kenya. A total of 612 quantitative data were collected using a mobile data collection tool Open Data Kit. Parametric and non-parametric tests were used to examine factors associated with WASH practices and control of COVID-19 in Kenya.

Results

More than half of the respondents were from Kilifi, 431 (70.4%) were female and the mean age was 38.2±14.8 y. Households in Kilifi were most likely not to have enough water, while Mombasa households were more likely to pay for water. Sanitation coverage was 47.6%, with more than half sharing sanitation facilities. Sharing of latrines was significantly associated with county and income level. Accessing soap was worse compared with the month prior to the survey, only 3.9% had their garbage collected by formal service providers and only 17% reported wearing any protective gear while handling waste at home.

Conclusions

Water is disproportionately available in the two counties, with low sanitation coverage. There is low knowledge on hand washing and inadequate waste disposal services.

Safety and efficacy of nurse led intravitreal injection service with Precivia® injection assist device

INTRODUCTION

Intravitreal anti-VEGF injections are the most frequently performed outpatient procedure in the UK. Ophthalmic allied healthcare professionals are replacing medical professionals in delivering injections nationwide. The use of injection assist devices such as Precivia® has been well established and increasingly adopted to aid in their safe delivery. We present outcomes of nurse-led intravitreal injections using the Precivia® injection assist device over a five-year period in the UK.

METHODS

A retrospective review was completed of all anti-VEGF intravitreal injections delivered at the Great Western Hospital between May 2015 and May 2020.

RESULTS

Over the five-year study period, 2318 patients underwent a total of 26,923 intravitreal injections; 20,421 (75.8%) of which were delivered by appropriately trained ophthalmic nurses. The annual number of injections increased year-on-year from 2112 injections in 2015-2016 to 5410 injections in 2019-2020. The mean age of patients was 75.7±12.2 years with a female-to-male ratio was 1.17:1. Wet age-related macular degeneration represented the major indication for injections followed by retinal vein occlusion and diabetic maculopathy respectively. Three cases of post-injection endophthalmitis out of 20,421 (0.015%) injections in nurse injection group were identified during the study period. There were no cases of lens touch, retinal detachment or systemic thromboembolic events.

CONCLUSION

Use of the Precivia® intravitreal injection assist device by trained ophthalmic allied health professionals is a safe and cost-effective way to deliver intravitreal injections service.

Pseudogenization of the chloroplast threonine (trnT-GGU) gene in the sunflower family (Asteraceae)

The chloroplast genome evolves through the course of evolution. Various types of mutational events are found within the chloroplast genome, including insertions-deletions (InDels), substitutions, inversions, gene rearrangement, and pseudogenization of genes. The pseudogenization of the chloroplast threonine (trnT-GGU) gene was previously reported in Cryptomeria japonica (Cupressaceae), Pelargonium × hortorum (Geraniaceae), and Anaphalis sinica and Leontopodium leiolepis of the tribe Gnaphalieae (Asteroideae, Asteraceae). Here, we performed a broad analysis of the trnT-GGU gene among the species of 13 subfamilies of Asteraceae and found this gene as a pseudogene in core Asteraceae (Gymnarrhenoideae, Cichorioideae, Corymbioideae, and Asteroideae), which was linked to an insertion event within the 5' acceptor stem and is not associated with ecological factors such as habit, habitat, and geographical distribution of the species. The pseudogenization of trnT-GGU was not predicted in codon usage, indicating that the superwobbling phenomenon occurs in core Asteraceae in which a single transfer RNA (trnT-UGU) decodes all four codons of threonine. To the best of our knowledge, this is the first evidence of a complete clade of a plant species using the superwobbling phenomenon for translation.

1131 The Integration of Cardiothoracic Practical Skills Workshop in The Undergraduate Medical School Curriculum and Its Impact on Promoting Interest in Cardiothoracic Surgery

Aim

Assess if WETLAB workshop encourages the engagement of medical students in CTS surgery

Method

We hosted a cardiac WETLAB workshop, led by a consultant cardiothoracic surgeon. Attendees were taught how to carry out an end-to-side anastomosis on animal tissue. We used pre-and -post exposure questionnaires composed of 10 items to assess the ability of the workshop to improve undergraduate interest in cardiothoracic surgery. The questionnaire included questions around students’ interest in the speciality, previous exposure to the speciality and whether students want to pursue a career in the speciality.

Results

Out of the 12 attendees, 10 completed both questionnaires. The workshop was well received with the overall satisfaction of 9.64 out of 10. It significantly increased respondents’ interest in CTS(z=-0.06, p = 0.01) but did not show any significant difference in encouraging them to pursue surgery. 100% of respondents agreed that specialised practical workshops should be incorporated within the medical school curriculum and that if the opportunity arises, they will attend another in the future.

Conclusions

Specialised practical workshops have the potential to play a significant role in the medical school curriculum in order to enhance exposure to the field of cardiothoracic surgery. This may lead to a positive impact on the number of doctors wishing to pursue this speciality in the future.

783 Digital Weekend Handover an Effective Documentation

Aim

To assess quality of completion for weekend handover for surgical weekend and to plan and design a Digital handover, the implementation and effect of which is studied.

Method

Data collection from TRAKCARE for documentation completion criteriae including diagnosis, further investigations to chase (e.g., bloods, imaging), discharge plans, escalation and DNAR status identified.

First cycle collected in August 2020 for pre-implementation status and standard. Second cycle was collected after implementation and raising awareness about new system in October 2020.

Exclusion criteria: patients discharged prior to weekend

Results

32 (10f 22m) and 22 (9 f 13m) patients were studied in first and second cycle with a respective median length stay of 243 hours and 161.5 hours. Handover entries had improved from 40.6% completion rate to 77.3% these included a diagnosis and management plan. Required blood investigation plans were recorded in 54.5% patients (previously 9.4%). Escalation plans including DNACPR and ceiling of care were improved from 25% to 31%.

Conclusions

Digital Medical recording left a gap in documentation for weekend ward rounds when personnels are thinned and busy. To optimize clinical care, the use of a E weekend handover has improved documentation greatly. Future Ongoing project includes improving escalation plans further.

64 Seizing an Opportunity: Setting Up A Virtual Wetlab During the COVID19 Pandemic

Aim

The COVID19 pandemic has negatively impacted surgical training across the globe. In the UK, educational events and training days were cancelled for trainees at all levels. However, these unusual times provide opportunity to develop novel teaching methods. Our aim was to design a “virtual cardiac surgery wetlab” that allows real-time skills training.

Method

With support from industry partners Edwards Lifesciences, Wetlab and Connexon365 (Webinar Hosting Platform) all the necessary materials were distributed. A package was sent to trainer and trainees that included microinstruments, sutures, synthetic vessels and valve models, high-definition camera, along with printed instructions and video to outline set-up of the rig. Trainees only need to provide is a computer. A consultant surgeon demonstrated how to perform a coronary anastomosis and aortic valve replacement and was then able to supervise trainees and provide real-time feedback using the online platform.

Results

Feedback from trainer and trainees has shown that the system is an easy-to-set-up, effective training tool for teaching cardiac surgery skills including coronary anastomosis and valve surgery. The online platform enabled good vision and engagement between trainer and trainee and also enabled recording of the session. Distributing all of the materials nationwide means the virtual wetlab can take place anywhere, including in the comfort of home, for both trainee and trainer.

Conclusions

Surgical skills training can still take place effectively in the absence of “real life” wetlabs. Given the current COVID19 pandemic continues to interrupt traditional surgical teaching, this method has potential to be adopted nationwide to minimise the disruption.

Comparative analysis of the serum microbiome of HIV infected individuals

HIV infects the CD4 cells which marks the suppression of our immune system. DNA from serum of healthy, treated and untreated HIV infected individuals was extracted. The DNA was subjected to 16S metagenomic sequencing and analyzed using QIIME2 pipeline. 16S sequencing analysis showed serum microbiome was dominated by Firmicutes, Proteobacteria, Bacteroidota and Actinobacteria. Treated HIV infection showed highest abundance of Firmicutes (66.40%) significantly higher than untreated HIV infection (35.88%) and control (41.89%). Bacilli was most abundant class in treated (63.59%) and second most abundant in untreated (34.53%) while control group showed highest abundance of class Gamma-proteobacteria (45.86%). Untreated HIV infection group showed Enterococcus (10.72%) and Streptococcus (6.599%) as the most abundant species. Untreated HIV infection showed significantly higher (p = 0.0039) species richness than treated and control groups. An altered serum microbiome of treated HIV infection and higher microbial abundance in serum of untreated HIV infection was observed.

The GASA Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome Wide Identification and Expression Analysis

The gibberellic acid-stimulated Arabidopsis (GASA/GAST) gene family is widely distributed in plants and involved in various physiological and biological processes. These genes also provide resistance to abiotic and biotic stresses, including antimicrobial, antiviral, and antifungal. We are interested in characterizing the GASA gene family and determining its role in various physiological and biological process in Theobroma cacao. Here, we report 17 tcGASA genes distributed on six chromosomes in T. cacao. The gene structure, promoter region, protein structure and biochemical properties, expression, and phylogenetics of all tcGASAs were analyzed. Phylogenetic analyses divided tcGASA proteins into five groups. Among 17 tcGASA genes, nine segmentally duplicating genes were identified which formed four pairs and cluster together in phylogenetic tree. Differential expression analyses revealed that most of the tcGASA genes showed elevated expression in the seeds (cacao food), implying their role in seed development. The differential expression of tcGASAs was recorded between the tolerant and susceptible cultivars of cacao, which indicating their possible role as fungal resistant. Our findings provide new insight into the function, evolution, and regulatory system of the GASA family genes in T.cacao and may suggest new target genes for development of fungi-resistant cacao varieties in breeding programs.

Comparative plastome analysis of Blumea, with implications for genome evolution and phylogeny of Asteroideae

The genus Blumea (Asteroideae, Asteraceae) comprises about 100 species, including herbs, shrubs, and small trees. Previous studies have been unable to resolve taxonomic issues and the phylogeny of the genus Blumea due to the low polymorphism of molecular markers. Therefore, suitable polymorphic regions need to be identified. Here, we de novo assembled plastomes of the three Blumea species B. oxyodonta, B. tenella, and B. balsamifera and compared them with 26 other species of Asteroideae after correction of annotations. These species have quadripartite plastomes with similar gene content, genome organization, and inverted repeat contraction and expansion comprising 113 genes, including 80 protein-coding, 29 transfer RNA, and 4 ribosomal RNA genes. The comparative analysis of codon usage, amino acid frequency, microsatellite repeats, oligonucleotide repeats, and transition and transversion substitutions has revealed high resemblance among the newly assembled species of Blumea. We identified 10 highly polymorphic regions with nucleotide diversity above 0.02, including rps16-trnQ, ycf1, ndhF-rpl32, petN-psbM, and rpl32-trnL, and they may be suitable for the development of robust, authentic, and cost-effective markers for barcoding and inference of the phylogeny of the genus Blumea. Among these highly polymorphic regions, five regions also co-occurred with oligonucleotide repeats and support use of repeats as a proxy for the identification of polymorphic loci. The phylogenetic analysis revealed a close relationship between Blumea and Pluchea within the tribe Inuleae. At tribe level, our phylogeny supports a sister relationship between Astereae and Anthemideae rooted as Gnaphalieae, Calenduleae, and Senecioneae. These results are contradictory to recent studies which reported a sister relationship between "Senecioneae and Anthemideae" and "Astereae and Gnaphalieae" or a sister relationship between Astereae and Gnaphalieae rooted as Calenduleae, Anthemideae, and then Senecioneae using nuclear genome sequences. The conflicting phylogenetic signals observed at the tribal level between plastidt and nuclear genome data require further investigation.

Folic acid supplementation in postmenopausal women with hot flushes: phase III randomised double-blind placebo-controlled trial

OBJECTIVE

To assess whether folic acid supplementation ameliorates hot flushes.

DESIGN

Double-blind, placebo-controlled randomised trial.

SETTING

Nine hospitals in England.

POPULATION

Postmenopausal women experiencing ≥50 hot flushes weekly.

METHODS

Women (n = 164) were randomly assigned in a 1:1 ratio to receive folic acid 5 mg tablet or placebo daily for 12 weeks. Participants recorded frequency and severity of hot flushes in a Sloan Diary daily and completed Greene Climacteric and Utian Quality of Life (UQoL) Scales at 4-week intervals.

MAIN OUTCOME MEASURES

The change in daily Hot Flush Score at week 12 from randomisation based on Sloan Diary Composite Score B calculation.

RESULTS

Data of 143 (87%) women were available for the primary outcome. The mean change (SD) in Hot Flush Score at week 12 was -6.98 (10.30) and -4.57 (9.46) for folic acid and placebo group, respectively. The difference between groups in the mean change was -2.41 (95% CI -5.68 to 0.87) (P = 0.149) and in the adjusted mean change -2.61 (95% CI -5.72 to 0.49) (P = 0.098). Analysis of secondary outcomes indicated an increased benefit in the folic acid group regarding changes in total and emotional UQoL scores at week 8 when compared with placebo. The difference in the mean change from baseline was 5.22 (95% CI 1.16-9.28) and 1.88 (95% CI 0.23-3.52) for total and emotional score, respectively.

CONCLUSIONS

The study was not able to demonstrate that folic acid had a statistically significant greater benefit in reducing Hot Flush Score over 12 weeks in postmenopausal women when compared with placebo.

TWEETABLE ABSTRACT

Folic acid may ameliorate hot flushes in postmenopausal women but confirmation is required from a larger study.

40 Across the Pond: Why Are Junior Doctors Seeking Surgical Training Abroad?

Introduction

The loss of junior doctors from the NHS has been an ongoing issue. A subset are now seeking surgical training in other systems, such as the US. This is a costly and difficult process and many enter into undesignated positions with no guarantee of a job. With so much career uncertainty, why are trainees willing to take the risk?

Method

We performed a survey of trainees who graduated from British medical schools; all are currently enrolled in a US surgical training programme. They were asked about their experiences and perceptions of

Results

Nine trainees completed the survey. The most common time for trainees to move was during or after foundation training and the majority initially matched into preliminary positions. The most common reason cited to move was to receive better quality training. Many perceived the US training to be better and felt that they had a reasonable work-life balance.

Conclusions

The potential loss of the future NHS surgical workforce is worrying. Our survey highlights that surgical trainees place a high value on the quality of their training and were willing to enter an intense and uncertain process to achieve it. This needs to be addressed to retain potential trainees.

263 Airway, Voice and Swallow Outcomes Following Endotracheal Intubation and Mechanical Ventilation For COVID-19 Pneumonitis: Preliminary Results of a Prospective Cohort Study

Introduction

The COVID-19 pandemic has placed exceptional demands on Intensive Care Units (ICU) across the world – particularly requiring patients to be intubated and mechanically ventilated. Laryngeal injury following intubation is a common occurrence, therefore this study aims to analyse airway, voice, and swallow (AVS) outcomes of patients intubated for COVID-19 pneumonitis and compares it to intubated non-COVID-19 respiratory patients and other ICU admissions.

Method

We collected data from inpatient records, and follow-up clinics on intubated adult patients discharged from a tertiary care hospital ICU between 01/03/20 and 30/04/20. Patients were assessed with the AVS Scale, Voice Handicap Index-10 (VHI-10), and Eating Assessment Tool-10 (EAT-10).

Results

86 patients were admitted with COVID-19 pneumonitis, 17 patients were admitted with non-COVID-19 respiratory failure, and 26 patients were admitted with a non-respiratory diagnosis.

The COVID-19 cohort demonstrated higher rates of AVS difficulties (airway 59% vs 44% and 31%, voice 40% vs 19% and 19%, swallow 21% vs 6% and 12%). VHI-10 and EAT-10 scores showed no significant differences between groups.

Conclusions

Patients intubated for COVID-19 pneumonitis reported higher rates of AVS difficulties against non-COVID-19 reasons for intubation. Robust prospective screening protocols are essential to improving patient outcomes by highlighting and therefore managing laryngological sequelae that occur following intubation.

Asymptomatic urinary tract infections and associated risk factors in Pakistani Muslim type 2 diabetic patients

Background

One of the leading long-term complications of type 2 diabetes mellitus (T2DM) includes renal dysfunction and urinary tract infections (UTI) which are considered to be prevalent in uncontrolled diabetes. Moreover, physiological factors like age, gender, duration of diabetes, other diabetic complications like neuropathy, autonomic neuropathy and glycosuria are also considered as predisposing factors for increased prevalence of UTI in diabetes which can be symptomatic or asymptomatic.

Methods

This was a cross-sectional, multi-centre study including diabetic patients from 12 clinical sites spread across major cities of Pakistan. The inclusion criteria were adult Pakistani population of age between 18 to 75 years both genders and suffering from T2DM irrespective of duration. A detailed clinical history of the past 3 months was recorded and, biochemical investigations of blood samples were conducted. Urine culture analysis performed identified the type of pathogen present and was done only for asymptomatic patients.

Results

A total of 745 type 2 diabetic patients were initially screened, out of 545 patients considered for final analysis 501 (91.92%) were negative and the rest 44 (8.08%) had positive urine culture. Female gender had a significantly higher proportion of positive urine culture (77.27%, p-value< 0.001). Body mass index and mean age had insignificant distribution among the two groups of positive and negative urine culture, with age 40–59 years having higher proportion (70.45%) in the positive group. Escherichia coli was detected in most of the positive samples (52.3%). All bacterial samples were found resistant to Ciprofloxacin.

Conclusion

Diabetic Pakistani muslim female patients are identified to be at high risk of suffering from asymptomatic UTI and age more than 40 years is an important risk factor. Escherichia coli was the most common causative organism among people living in this geographical area.

The GASA Gene Family in Theobroma cacao: Genome wide Identification and Expression Analysis.. [DOI: 10.1101/2021.01.27.425041]

The gibberellic acid-stimulated Arabidopsis (GASA/GAST) gene family is widely distributed in plants. The role of the GASA gene family has been reported previously in various physiological and biological processes, such as cell division, root and seed development, stem growth, and fruit ripening. These genes also provide resistance to abiotic and biotic stresses including antimicrobial, antiviral, and antifungal. Here, we report 17 tcGASA genes in Theobroma cacao L. distributed on six chromosomes. The gene structure, promoter-region sequences, protein structure, and biochemical properties, expression, and phylogenetics of all tcGASAs were analyzed. Phylogenetic analyses divided tcGASA proteins into five groups. The nine segmentally duplicating genes form four pairs and cluster together in phylogenetic tree. Purifying selection pressure was recorded on tcGASA, including duplicated genes. Several stress/hormone-responsive cis-regulatory elements were also recognized in the promoter region of tcGASAs. Differential expression analyses revealed that most of the tcGASA genes showed elevated expression in the seeds (cacao food), implying their role in seed development. The black rod disease of genus Phytophthora caused up to 20–25% loss (700,000 metric tons) in world cacao production. The role of tcGASA genes in conferring fungal resistance was also explored based on RNAseq data against Phytophthora megakarya. The differential expression of tcGASA genes was recorded between the tolerant and susceptible cultivars of cacao plants, which were inoculated with the fungus for 24h and 72h. This differential expression indicating possible role of tcGASA genes to fungal resistant in cacao. Our findings provide new insight into the function, evolution, and regulatory system of the GASA family genes in T. cacao and provide new target genes for development of fungi-resistant cacao varieties in breeding programs.

Mutational Dynamics of Aroid Chloroplast Genomes II

The co-occurrence among single nucleotide polymorphisms (SNPs), insertions-deletions (InDels), and oligonucleotide repeats has been reported in prokaryote, eukaryote, and chloroplast genomes. Correlations among SNPs, InDels, and repeats have been investigated in the plant family Araceae previously using pair-wise sequence alignments of the chloroplast genomes of two morphotypes of one species, Colocasia esculenta belonging to subfamily Aroideae (crown group), and four species from the subfamily Lemnoideae, a basal group. The family Araceae is a large family comprising 3,645 species in 144 genera, grouped into eight subfamilies. In the current study, we performed 34 comparisons using 27 species from 7 subfamilies of Araceae to determine correlation coefficients among the mutational events at the family, subfamily, and genus levels. We express strength of the correlations as: negligible or very weak (0.10–0.19), weak (0.20–0.29), moderate (0.30–0.39), strong (0.40–0.69), very strong (0.70–0.99), and perfect (1.00). We observed strong/very strong correlations in most comparisons, whereas a few comparisons showed moderate correlations. The average correlation coefficient was recorded as 0.66 between “SNPs and InDels,” 0.50 between “InDels and repeats,” and 0.42 between “SNPs and repeats.” In qualitative analyses, 95–100% of the repeats at family and sub-family level, while 36–86% of the repeats at genus level comparisons co-occurred with SNPs in the same bins. Our findings show that such correlations among mutational events exist throughout Araceae and support the hypothesis of distribution of oligonucleotide repeats as a proxy for mutational hotspots.