Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing.

Long-read sequencing is revolutionizing de-novo genome assemblies, with continued advancements making it more readily available for previously understudied, non-model organisms. Stony corals are one such example, with long-read de-novo genome assemblies now starting to be publicly available, opening the door for a wide array of 'omics-based research. Here we present a new de-novo genome assembly for the endangered Caribbean star coral, Orbicella faveolata, using PacBio circular consensus reads. Our genome assembly improved the contiguity (51 versus 1,933 contigs) and complete and single copy BUSCO orthologs (93.6% versus 85.3%, database metazoa_odb10), compared to the currently available reference genome generated using short-read methodologies. Our new de-novo assembled genome also showed comparable quality metrics to other coral long-read genomes. Telomeric repeat analysis identified putative chromosomes in our scaffolded assembly, with these repeats at either one, or both ends, of scaffolded contigs. We identified 32,172 protein coding genes in our assembly through use of long-read RNA sequencing (ISO-seq) of additional O. faveolata fragments exposed to a range of abiotic and biotic treatments, and publicly available short-read RNA-seq data. With anthropogenic influences heavily affecting O. faveolata, as well as its increasing incorporation into reef restoration activities, this updated genome resource can be used for population genomics and other 'omics analyses to aid in the conservation of this species.

A Rare Case of Postmenopausal Hirsutism Associated With a Serous Cystadenofibroma of the Ovary.

Hirsutism in females is most commonly associated with polycystic ovarian syndrome, but can also result from congenital adrenal hyperplasia and ovarian tumors like granulosa cell tumors, Sertoli-Leydig cell tumors, and hilus cell tumors. We present a case of a 54-year-old female with hirsutism, diagnosed with ovarian cystadenofibroma. She had a history of premature ovarian failure at the age of 35 and presented with new onset chin and upper lip hair, and scalp hair loss. Labs showed elevated total testosterone, normal dehydroepiandrosterone (DHEA) and sex hormone-binding globulin (SHBG), low estradiol, and postmenopausal range anti-Mullerian hormone (AMH), follicle-stimulating hormone (FSH), luteinizing hormone (LH), and prolactin. Cytogenetic testing showed a normal XX karyotype. Initial transvaginal ultrasound revealed a thickened endometrial stripe and unremarkable ovaries. Repeat ultrasound and MRI noted persistent endometrial thickening and a solid-cystic structure in the left ovary. The patient underwent total hysterectomy, bilateral salpingo-oophorectomy, and sentinel lymph node dissection. Endometrial biopsy showed FIGO grade 1 endometrioid carcinoma, and the left ovary biopsy revealed benign serous cystadenofibroma and endometriosis. Postoperatively, hirsutism resolved and testosterone levels normalized. Hirsutism in postmenopausal women should prompt evaluation for adrenal or ovarian sources, including tumors. Ovarian tumors cause about 1% of hirsutism cases. Our case highlights the need for thorough evaluation, as benign ovarian tumors can also cause androgen excess and associated conditions like endometrial cancer.

A Case of Adrenal Insufficiency Secondary to Bilateral Adrenal Hemorrhage in a Patient With Antiphospholipid Antibody Syndrome and Epstein-Barr Virus Infection.

Bilateral adrenal hemorrhage (AH) is linked to various causes, including bacterial and viral infections, coagulopathies, and postoperative states. Symptoms can range from mild adrenal insufficiency to shock from Waterhouse-Friedrichsen syndrome. We present a case of a 47-year-old male with antiphospholipid antibody syndrome (APS) on warfarin who presented to the emergency department (ED) with bilateral flank pain and was found to have bilateral AH. On exam, he was hypertensive, mildly tachycardic, and in severe pain. The abdomen was tender over the bilateral flank and costovertebral regions. Labs showed thrombocytopenia but normal international normalized ratio (INR) and fibrinogen. The CT and MRI confirmed bilateral AH. Further investigations revealed low ante meridiem (AM) cortisol and elevated adrenocorticotropic hormone (ACTH). The antinuclear antibody (ANA) test was negative, but the antiphospholipid antibody panel was positive. In addition, the patient had a positive Epstein-Barr virus (EBV) nuclear antigen with a significant IgM titer. He was treated with low-dose steroids and was placed on a prophylactic dose of enoxaparin with the resolution of symptoms. At discharge, he was advised to follow up with a hematologist in six weeks to restart full-dose anticoagulation, allowing time for the bleeding to resolve. This case highlights EBV infection as a possible trigger of adrenal insufficiency from adrenal bleeding in a patient with preexisting coagulopathy, necessitating prompt recognition and treatment.

Novel metagenomics analysis of stony coral tissue loss disease.

Stony coral tissue loss disease (SCTLD) has devastated coral reefs off the coast of Florida and continues to spread throughout the Caribbean. Although a number of bacterial taxa have consistently been associated with SCTLD, no pathogen has been definitively implicated in the etiology of SCTLD. Previous studies have predominantly focused on the prokaryotic community through 16S rRNA sequencing of healthy and affected tissues. Here, we provide a different analytical approach by applying a bioinformatics pipeline to publicly available metagenomic sequencing samples of SCTLD lesions and healthy tissues from 4 stony coral species. To compensate for the lack of coral reference genomes, we used data from apparently healthy coral samples to approximate a host genome and healthy microbiome reference. These reads were then used as a reference to which we matched and removed reads from diseased lesion tissue samples, and the remaining reads associated only with disease lesions were taxonomically classified at the DNA and protein levels. For DNA classifications, we used a pathogen identification protocol originally designed to identify pathogens in human tissue samples, and for protein classifications, we used a fast protein sequence aligner. To assess the utility of our pipeline, a species-level analysis of a candidate genus, Vibrio, was used to demonstrate the pipeline's effectiveness. Our approach revealed both complementary and unique coral microbiome members compared with a prior metagenome analysis of the same dataset.

Novel metagenomics analysis of stony coral tissue loss disease.

Stony coral tissue loss disease (SCTLD) has devastated coral reefs off the coast of Florida and continues to spread throughout the Caribbean. Although a number of bacterial taxa have consistently been associated with SCTLD, no pathogen has been definitively implicated in the etiology of SCTLD. Previous studies have predominantly focused on the prokaryotic community through 16S rRNA sequencing of healthy and affected tissues. Here, we provide a different analytical approach by applying a bioinformatics pipeline to publicly available metagenomic sequencing samples of SCTLD lesions and healthy tissues from four stony coral species. To compensate for the lack of coral reference genomes, we used data from apparently healthy coral samples to approximate a host genome and healthy microbiome reference. These reads were then used as a reference to which we matched and removed reads from diseased lesion tissue samples, and the remaining reads associated only with disease lesions were taxonomically classified at the DNA and protein levels. For DNA classifications, we used a pathogen identification protocol originally designed to identify pathogens in human tissue samples, and for protein classifications, we used a fast protein sequence aligner. To assess the utility of our pipeline, a species-level analysis of a candidate genus, Vibrio, was used to demonstrate the pipeline's effectiveness. Our approach revealed both complementary and unique coral microbiome members compared to a prior metagenome analysis of the same dataset.

Sediment source and dose influence the larval performance of the threatened coral Orbicella faveolata.

The effects of turbidity and sedimentation stress on early life stages of corals are poorly understood, particularly in Atlantic species. Dredging operations, beach nourishment, and other coastal construction activities can increase sedimentation and turbidity in nearby coral reef habitats and have the potential to negatively affect coral larval development and metamorphosis, reducing sexual reproduction success. In this study, we investigated the performance of larvae of the threatened Caribbean coral species Orbicella faveolata exposed to suspended sediments collected from a reef site in southeast Florida recently impacted by dredging (Port of Miami), and compared it to the performance of larvae exposed to sediments collected from the offshore, natal reef of the parent colonies. In a laboratory experiment, we tested whether low and high doses of each of these sediment types affected the survival, settlement, and respiration of coral larvae compared to a no-sediment control treatment. In addition, we analyzed the sediments used in the experiments with 16S rRNA gene amplicon sequencing to assess differences in the microbial communities present in the Port versus Reef sediments, and their potential impact on coral performance. Overall, only O. faveolata larvae exposed to the high-dose Port sediment treatment had significantly lower survival rates compared to the control treatment, suggesting an initial tolerance to elevated suspended sediments. However, significantly lower settlement rates were observed in both Port treatments (low- and high-dose) compared to the control treatment one week after exposure, suggesting strong latent effects. Sediments collected near the Port also contained different microbial communities than Reef sediments, and higher relative abundances of the bacteria Desulfobacterales, which has been associated with coral disease. We hypothesize that differences in microbial communities between the two sediments may be a contributing factor in explaining the observed differences in larval performance. Together, these results suggest that the settlement success and survival of O. faveolata larvae are more readily compromised by encountering port inlet sediments compared to reef sediments, with potentially important consequences for the recruitment success of this species in affected areas.