Chromosome-Level Genome Assembly and Annotation of a Periodical Cicada Species: Magicicada septendecula.

We present a high-quality assembly and annotation of the periodical cicada species, Magicicada septendecula (Hemiptera: Auchenorrhyncha: Cicadidae). Periodical cicadas have a significant ecological impact, serving as a food source for many mammals, reptiles, and birds. Magicicada are well known for their massive emergences of 1 to 3 species that appear in different locations in the eastern United States nearly every year. These year classes ("broods") emerge dependably every 13 or 17 yr in a given location. Recently, it has become clear that 4-yr early or late emergences of a sizeable portion of a population are an important part of the history of brood formation; however, the biological mechanisms by which they track the passage of time remain a mystery. Using PacBio HiFi reads in conjunction with Hi-C proximity ligation data, we have assembled and annotated the first whole genome for a periodical cicada, an important resource for future phylogenetic and comparative genomic analysis. This also represents the first quality genome assembly and annotation for the Hemipteran superfamily Cicadoidea. With a scaffold N50 of 518.9 Mb and a complete BUSCO score of 96.7%, we are confident that this assembly will serve as a vital resource toward uncovering the genomic basis of periodical cicadas' long, synchronized life cycles and will provide a robust framework for further investigations into these insects.

Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity.

We report the first chromosome-length genome assemblies for three species in the mammalian order Pholidota: the white-bellied, Chinese, and Sunda pangolins. Surprisingly, we observe extraordinary karyotypic plasticity within this order and, in female white-bellied pangolins, the largest number of chromosomes reported in a Laurasiatherian mammal: 2n = 114. We perform the first karyotype analysis of an African pangolin and report a Y-autosome fusion in white-bellied pangolins, resulting in 2n = 113 for males. We employ a novel strategy to confirm the fusion and identify the autosome involved by finding the pseudoautosomal region (PAR) in the female genome assembly and analyzing the 3D contact frequency between PAR sequences and the rest of the genome in male and female white-bellied pangolins. Analyses of genetic variability show that white-bellied pangolins have intermediate levels of genome-wide heterozygosity relative to Chinese and Sunda pangolins, consistent with two moderate declines of historical effective population size. Our results reveal a remarkable feature of pangolin genome biology and highlight the need for further studies of these unique and endangered mammals.

A Chromosome-length Assembly of the Black Petaltail (Tanypteryx hageni) Dragonfly.

We present a chromosome-length genome assembly and annotation of the Black Petaltail dragonfly (Tanypteryx hageni). This habitat specialist diverged from its sister species over 70 million years ago, and separated from the most closely related Odonata with a reference genome 150 million years ago. Using PacBio HiFi reads and Hi-C data for scaffolding we produce one of the most high-quality Odonata genomes to date. A scaffold N50 of 206.6 Mb and a single copy BUSCO score of 96.2% indicate high contiguity and completeness.

Breast Cancer Management Consensus By The Society of Surgeons and Surgical Oncology Society of Pakistan.

The Society of Surgeons of Pakistan and The Society of Surgical Oncology of Pakistan with factions from various major centres comprising of surgical oncology, medical and radiation oncology collaborated to reach consensus on breast cancer management guidelines and a framework of "good practice" minimum standards of care. The aim of the task force was to enhance treatment standards, which have a direct correlation with improving patient mortality and morbidity and long-term survival whilst taking into consideration economic limitations of access to leading centers of excellence as well as minimum expertise required in health care. These multidisciplinary guidelines, whilst not exhaustive, aim to provide an algorithm of care for breast cancer patients at tertiary care centres and district level hospitals to provide most appropriate treatment.

A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population.

High-quality reference genomes are fundamental tools for understanding population history, and can provide estimates of genetic and demographic parameters relevant to the conservation of biodiversity. The federally endangered Pacific pocket mouse (PPM), which persists in three small, isolated populations in southern California, is a promising model for studying how demographic history shapes genetic diversity, and how diversity in turn may influence extinction risk. To facilitate these studies in PPM, we combined PacBio HiFi long reads with Omni-C and Hi-C data to generate a de novo genome assembly, and annotated the genome using RNAseq. The assembly comprised 28 chromosome-length scaffolds (N50 = 72.6 MB) and the complete mitochondrial genome, and included a long heterochromatic region on chromosome 18 not represented in the previously available short-read assembly. Heterozygosity was highly variable across the genome of the reference individual, with 18% of windows falling in runs of homozygosity (ROH) >1 MB, and nearly 9% in tracts spanning >5 MB. Yet outside of ROH, heterozygosity was relatively high (0.0027), and historical Ne estimates were large. These patterns of genetic variation suggest recent inbreeding in a formerly large population. Currently the most contiguous assembly for a heteromyid rodent, this reference genome provides insight into the past and recent demographic history of the population, and will be a critical tool for management and future studies of outbreeding depression, inbreeding depression, and genetic load.

Chromosome size affects sequence divergence between species through the interplay of recombination and selection.

The structure of the genome shapes the distribution of genetic diversity and sequence divergence. To investigate how the relationship between chromosome size and recombination rate affects sequence divergence between species, we combined empirical analyses and evolutionary simulations. We estimated pairwise sequence divergence among 15 species from three different mammalian clades-Peromyscus rodents, Mus mice, and great apes-from chromosome-level genome assemblies. We found a strong significant negative correlation between chromosome size and sequence divergence in all species comparisons within the Peromyscus and great apes clades but not the Mus clade, suggesting that the dramatic chromosomal rearrangements among Mus species may have masked the ancestral genomic landscape of divergence in many comparisons. Our evolutionary simulations showed that the main factor determining differences in divergence among chromosomes of different sizes is the interplay of recombination rate and selection, with greater variation in larger populations than in smaller ones. In ancestral populations, shorter chromosomes harbor greater nucleotide diversity. As ancestral populations diverge, diversity present at the onset of the split contributes to greater sequence divergence in shorter chromosomes among daughter species. The combination of empirical data and evolutionary simulations revealed that chromosomal rearrangements, demography, and divergence times may also affect the relationship between chromosome size and divergence, thus deepening our understanding of the role of genome structure in the evolution of species divergence.

Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater.

BACKGROUND: The helmeted honeyeater (Lichenostomus melanops cassidix) is a Critically Endangered bird endemic to Victoria, Australia. To aid its conservation, the population is the subject of genetic rescue. To understand, monitor, and modulate the effects of genetic rescue on the helmeted honeyeater genome, a chromosome-length genome and a high-density linkage map are required. RESULTS: We used a combination of Illumina, Oxford Nanopore, and Hi-C sequencing technologies to assemble a chromosome-length genome of the helmeted honeyeater, comprising 906 scaffolds, with length of 1.1 Gb and scaffold N50 of 63.8 Mb. Annotation comprised 57,181 gene models. Using a pedigree of 257 birds and 53,111 single-nucleotide polymorphisms, we obtained high-density linkage and recombination maps for 25 autosomes and Z chromosome. The total sex-averaged linkage map was 1,347 cM long, with the male map being 6.7% longer than the female map. Recombination maps revealed sexually dimorphic recombination rates (overall higher in males), with average recombination rate of 1.8 cM/Mb. Comparative analyses revealed high synteny of the helmeted honeyeater genome with that of 3 passerine species (e.g., 32 Hi-C scaffolds mapped to 30 zebra finch autosomes and Z chromosome). The genome assembly and linkage map suggest that the helmeted honeyeater exhibits a fission of chromosome 1A into 2 chromosomes relative to zebra finch. PSMC analysis showed a ∼15-fold decline in effective population size to ∼60,000 from mid- to late Pleistocene. CONCLUSIONS: The annotated chromosome-length genome and high-density linkage map provide rich resources for evolutionary studies and will be fundamental in guiding conservation efforts for the helmeted honeyeater.

3D genomics across the tree of life reveals condensin II as a determinant of architecture type.

We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes.

Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome.

BACKGROUND: Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. RESULTS: Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three dog breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative dog breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. CONCLUSIONS: The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific dog breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.

Limited Evidence for Parallel Evolution Among Desert-Adapted Peromyscus Deer Mice.

Warming climate and increasing desertification urge the identification of genes involved in heat and dehydration tolerance to better inform and target biodiversity conservation efforts. Comparisons among extant desert-adapted species can highlight parallel or convergent patterns of genome evolution through the identification of shared signatures of selection. We generate a chromosome-level genome assembly for the canyon mouse (Peromyscus crinitus) and test for a signature of parallel evolution by comparing signatures of selective sweeps across population-level genomic resequencing data from another congeneric desert specialist (Peromyscus eremicus) and a widely distributed habitat generalist (Peromyscus maniculatus), that may be locally adapted to arid conditions. We identify few shared candidate loci involved in desert adaptation and do not find support for a shared pattern of parallel evolution. Instead, we hypothesize divergent molecular mechanisms of desert adaptation among deer mice, potentially tied to species-specific historical demography, which may limit or enhance adaptation. We identify a number of candidate loci experiencing selective sweeps in the P. crinitus genome that are implicated in osmoregulation (Trypsin, Prostasin) and metabolic tuning (Kallikrein, eIF2-alpha kinase GCN2, APPL1/2), which may be important for accommodating hot and dry environmental conditions.

De novo chromosome-length assembly of the mule deer (Odocoileus hemionus) genome.

The mule deer (Odocoileus hemionus) is an ungulate species that is distributed in a range from western Canada to central Mexico. Mule deer are an essential source of food for many predators, are relatively abundant, and commonly make broad migration movements. A clearer understanding of the mule deer genome can improve our knowledge of its population genetics, movements, and demographic history, aiding in conservation efforts. Their large population size, continuous distribution, and diversity of habitat make mule deer excellent candidates for population genomics studies; however, few genomic resources are currently available for this species. Here, we sequence and assemble the mule deer genome into a highly contiguous chromosome-length assembly for use in future research using long-read sequencing and Hi-C technologies. We also provide a genome annotation and compare demographic histories of the mule deer and white-tailed deer using the pairwise sequentially Markovian coalescent model. We expect this assembly to be a valuable resource in the continued study and conservation of mule deer.

Modifying Surgical Practice in the Times of Current COVID-19 Pandemic.

In the times of current coronavirus disease 2019 (COVID-19) pandemic, the surgical practice is suffering. The present report summarises the impact of this pandemic on our surgical services and the changes that have been promulgated for the resumption of services with the purpose of providing valuable information for our surgical colleagues worldwide. Almost six months have passed since this pandemic started, and the total number of confirmed cases has exceeded 7 million; and over 400 thousand lives have been claimed till now. We need to find ways to continue providing essential medical services to patients, while fighting with this pandemic since it might take longer than expected to end. Key Words: COVID-19, Pandemic, Surgery, Personal protective equipment, N95 masks.

Lack of awareness among surgeons regarding safe use of electrosurgery. A cross sectional survey of surgeons in Pakistan.

OBJECTIVE: To assess our surgeons perceptive regarding the safe usage of electrosurgical devices. METHOD: ology: This cross sectional survey was carried out at two hospitals, A cancer hospital and a public sector general hospital. Consultants, fellows and senior residents (Resident year 3rd and year 4th) on the surgical floor were requested to fill up the questionnaire. Calculations were performed with Statistical Package for the Social Sciences (SPSS 20) for Windows version 20 statistical software. Data was described using median with minimum and maximum value for quantitative variables. For categorical variables, number of observations and percentages were reported. The study is complied with hospital guidelines on research involving human subjects. RESULTS: Out of 80 questionnaires 52 were filled and returned. 12 consultants, 16 fellows/Senior registrars and 24 senior residents filled their questionnaires. For the sake of anonymity no information was obtained regarding the level of training and experience. Total 12 questions were asked. An expert level was set for a score above 10/12. A moderate level was set at 8/12. A score of less than 8 was considered unsafe for using electrosurgical devices. Only 6 (11.5%) participants had an expert level of understanding. 16 (30.7%) had moderate understanding. 30 (57.7%) were considered unsafe regarding use of electrosurgical devices. 85% participants were not aware of the correct mode of current to use for coagulating vessels. 69% of surgeons would use electrocautery to control staple line bleeds. 67% participants weren't aware of the correct placement of dispersive electrode. 60% couldn't identify a safe device for use in patients with a pacemaker. 46% of surgeons would cut a dispersive electrode to fit it on a child. 69% believed that harmonic scalpel was a bipolar cautery. 61% couldn't differentiate between RFA and Microwave Ablation. 63% didn't know how to handle an operating room fire. CONCLUSION: In these two hospitals, high level of ignorance noticed regarding the procedure and indications of basic electrosurgical equipment which needs raising awareness and further training.

Invasive carcinoma in accessory axillary breast tissue: A case report.

INTRODUCTION: Accessory or ectopic breast tissue is an aberration of normal breast development. It is known to be a rare entity present anywhere along the embryologic mammary streak or milk line but more common in axilla. PRESENTATION OF CASE: We report a case of 36 year old female with accessory breast carcinoma who presented with a progressive lump in her left axilla for 1 year. On examination a 2 cm solitary mass was palpable in axilla. Ultrasound confirmed a 19 mm mass with no other lesion in breast and axilla. Core biopsy showed invasive ductal carcinoma. She was discussed in multidisciplinary board meeting and was offered upfront surgery with excision of accessory breast tissue and sentinel lymph node biopsy. Axillary lymph node dissection was omitted following ACOSG Z0011 criteria. She was offered adjuvant chemotherapy and radiation post operatively along with endocrine treatment as she was hormone receptor positive. DISCUSSION: Accessory breast development is hormone dependent just like normal breast. Breast cancer in accessory breast tissue is very rare. The incidence is around 6%. Most common pathology is invasive ductal carcinoma (50-75%). The most common location is axilla (60-70%) although it can present in other less common locations like infra-mammary region (5-10%) and rarely in thighs, perineum, groin, and vulva. CONCLUSION: Since accessory axillary breast tissue is out of the image of screening breast examination, it is necessary for the oncologists to be aware of this entity and associated pathologies. Their preventive excision in high risk women can also be considered.

Use of box simulators for improving intraoperative laparoscopic skills - an essential tool for the surgeon in training.

OBJECTIVE: To compare the improvement of intraoperative laparoscopic skills by measuring GOALS score between residents who have undergone simulator training with those who have not received any simulator training. STUDY DESIGN: A randomized controlled trial. PLACE AND DURATION OF STUDY: Department of Surgery, Services Hospital, Lahore, from August 2013 to February 2014. METHODOLOGY: Thirty residents belonging to year 1, 2 and 3 were included in the study. They were randomly divided into 2 groups. Both groups had a baseline evaluation with GOALS score while performing dissection of gallbladder from liver bed during laparoscopic cholecystectomy. Group-A underwent formal training on simulators whereas group-B did not receive any formal training on simulators. After 6 months, a repeat evaluation was done again by measuring GOALS score while performing gallbladder dissection. RESULTS: Baseline GOALS scores of both the groups were similar. Group-A baseline score was 7.66 ± 0.93 and group-B score was 7.46 ± 1.04 (p = 0.585). However repeat scores for group-A showed a significant improvement (an increase of 7.16 ± 1.48 to 14.76 ± 1.67, p < 0.001) from baseline scores. Residents in group-B improved their scores by 2.30 ± 0.99 to 9.76 ± 0.79 (p < 0.001). When inter group comparison was done the second score of group-A was significantly higher than that of group-B (14.76 ± 1.67 vs. 9.76 ± 0.79, p < 0.001). Inter-rater reliability was moderately significant (Kappa 0.540).