One-Year Recovery Among Survivors of Prolonged Severe COVID-19: A National Multicenter Cohort.

OBJECTIVES: Understanding the long-term effects of severe COVID-19 illness on survivors is essential for effective pandemic recovery planning. Therefore, we investigated impairments among hospitalized adults discharged to long-term acute care hospitals (LTACHs) for prolonged severe COVID-19 illness who survived 1 year. DESIGN: The Recovery After Transfer to an LTACH for COVID-19 (RAFT COVID) study was a national, multicenter, prospective longitudinal cohort study. SETTING AND PATIENTS: We included hospitalized English-speaking adults transferred to one of nine LTACHs in the United States between March 2020 and February 2021 and completed a survey. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Validated instruments for impairments and free response questions about recovering. Among 282 potentially eligible participants who provided permission to be contacted, 156 (55.3%) participated (median age, 65; 38.5% female; 61.3% in good prior health; median length of stay of 57 d; 77% mechanically ventilated for a median of 26 d; 42% had a tracheostomy). Approximately two-thirds (64%) had a persistent impairment, including physical (57%), respiratory (49%; 19% on supplemental oxygen), psychiatric (24%), and cognitive impairments (15%). Nearly half (47%) had two or more impairment types. Participants also experienced persistent debility from hospital-acquired complications, including mononeuropathies and pressure ulcers. Participants described protracted recovery, attributing improvements to exercise/rehabilitation, support, and time. While considered life-altering with 78.7% not returning to their usual health, participants expressed gratitude for recovering; 99% returned home and 60% of previously employed individuals returned to work. CONCLUSIONS: Nearly two-thirds of survivors of among the most prolonged severe COVID-19 illness had persistent impairments at 1 year that resembled post-intensive care syndrome after critical illness plus debility from hospital-acquired complications.

Disparities in Use of Novel Diabetes Medications by Insurance: A Nationally Representative Cohort Study.

BACKGROUND: Minority racial and ethnic populations have the highest prevalence of type 2 diabetes mellitus but lower use of sodium-glucose co-transporter-2 inhibitors (SGLT2i) and glucagon-like peptide-1 receptor agonists (GLP1ra), novel medications that reduce morbidity and mortality. Observed disparities may be due to differences in insurance coverage, which have variable cost-sharing, prior authorization, and formulary restrictions that influence medication access. OBJECTIVE: To assess whether racial/ethnic differences in SGLT2i and GLP1ra use differ by payer. DESIGN: Cross-sectional analysis of 2018 and 2019 Medical Expenditure Panel Survey data. PARTICIPANTS: Adults ≥ 18 years old with diabetes. MAIN MEASURES: We defined insurance as private, Medicare, or Medicaid using ≥ 7 months of coverage in the calendar year. We defined race/ethnicity as White (non-Hispanic) vs non-White (including Hispanic). The primary outcome was use of ≥ 1 SGLT2i or GLP1ra medication. We used multivariable logistic regression to assess the interaction between payer and race/ethnicity adjusted for cardiovascular, socioeconomic, and healthcare access factors. KEY RESULTS: We included 4997 adults, representing 24.8 million US adults annually with diabetes (mean age 63.6 years, 48.8% female, 38.8% non-White; 33.5% private insurance, 56.8% Medicare, 9.8% Medicaid). In our fully adjusted model, White individuals with private insurance had significantly more medication use versus non-White individuals (16.1% vs 8.3%, p < 0.001), which was similar for Medicare beneficiaries but more attenuated (14.7% vs 11.0%, p = 0.04). Medication rates were similar among Medicaid beneficiaries (10.0% vs 9.0%, p = 0.74). CONCLUSIONS: Racial/ethnic disparities in novel diabetes medications were the largest among those with private insurance. There was no disparity among Medicaid enrollees, but overall prescription rates were the lowest. Given that disparities vary considerably by payer, differences in insurance coverage may account for the observed disparities in SGLT2i and GLP1ra use. Future studies are needed to assess racial/ethnic differences in novel diabetes use by insurance formulary restrictions and out-of-pocket cost-sharing.

The impacts of cancer treatment on lifestyle habits and mental health in Vietnamese women: an exploratory qualitative study.

AIMS: This qualitative study explores the experiences of women after cancer treatment in terms of habit changes and mental health impact. METHOD: The study involved 10 women who had undergone cancer treatment, recruited from three major hospitals in Hanoi, Vietnam. Data were collected through semi-structured interviews, which were transcribed and analyzed using thematic analysis. RESULTS: The findings of the study shed light on the various factors influencing lifestyle behavior and mental health changes among women after cancer treatment. Ten participants, aged 39 to 64 years, shared experiences including dietary changes, sleep disruptions, and reliance on non-scientific sources for health decisions. Initially shocked by their diagnosis, many transitioned to acceptance, adopting a "giving-in" attitude. Cultural beliefs, word-of-mouth sharing, and social support networks played significant roles in shaping post-treatment lifestyle changes, coping mechanisms, information-seeking behaviors, and mental health. CONCLUSION: The study highlights the need for accessible and scientifically verified information for women after cancer treatment to make informed decisions about their health. It emphasizes the importance of addressing traditional beliefs and promoting evidence-based practices. Moreover, the study underscores the importance of social support and relationships in coping with the challenges of post-cancer experiences.

Acute cancer-related symptoms and concerns among patients receiving chemotherapy: current state of the science.

PURPOSE: This study provides an updated evaluation of the prevalence and severity of acute cancer-related symptoms and quality of life (QOL) concerns among patients treated with emetogenic chemotherapy. METHODS: Patients were recruited to a larger, multi-site observational study prior to starting chemotherapy. Participants completed sociodemographic questionnaires and clinical data were abstracted via medical record review. Symptoms and QOL were assessed 5 days after starting moderately or highly emetogenic chemotherapy. Functional Assessment of Cancer Therapy - General assessed QOL concerns. Patient Reported Outcomes version of the Common Terminology Criteria for Adverse Events evaluated symptoms. Symptoms were considered severe when participants responded "severe" or "very severe." RESULTS: Participants (N = 1174) were on average 58 ± 13 years, mostly female (73%), non-Hispanic (89%), and White (87%). Most participants were diagnosed with breast (38.1%), gynecological (20%), and gastrointestinal (17.1%) cancer. The most common QOL concerns of any severity were fatigue (94%), anhedonia (89%), dissatisfaction with QOL (86%), and sleep disturbance (86%). The most common severe QOL concerns were anhedonia (44%), fatigue (40%), and inability to work (38%). Decreased appetite (74%), pain (71%), and constipation (70%) were the most common symptoms of any severity, as well as most common severe symptoms (13%, 18%, and 18%, respectively). CONCLUSION: Herein, updates are provided in regard to QOL concerns and symptoms reported by patients in the days after chemotherapy and demonstrates that concerns and symptoms have shifted in the last decade.

A draft reference genome assembly of California Pipevine, Aristolochia californica Torr.

The California Pipevine, Aristolochia californica Torr., is the only endemic California species within the cosmopolitan birthwort family Aristolochiaceae. It occurs as an understory vine in riparian and chaparral areas and in forest edges and windrows. The geographic range of this plant species almost entirely overlaps with that of its major specialized herbivore, the California Pipevine Swallowtail Butterfly Battus philenor hirsuta. While this species pair is a useful, ecologically well-understood system to study co-evolution, until recently, genomic resources for both have been lacking. Here, we report a new, chromosome-level assembly of A. californica as part of the California Conservation Genomics Project (CCGP). Following the sequencing and assembly strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin proximity sequencing technology to produce a de novo assembled genome. Our genome assembly, the first for any species in the genus, contains 531 scaffolds spanning 661 megabase (Mb) pairs, with a contig N50 of 6.53 Mb, a scaffold N50 of 42.2 Mb, and BUSCO complete score of 98%. In combination with the recently published B. philenor hirsuta reference genome assembly, the A. californica reference genome assembly will be a powerful tool for studying co-evolution in a rapidly changing California landscape.

The genome assembly of Island Oak (Quercus tomentella), a relictual island tree species.

Island oak (Quercus tomentella) is a rare relictual island tree species that exists only on six islands off the coast of California and Mexico, but was once widespread throughout mainland California. Currently, this species is endangered by threats such as non-native plants, grazing animals, and human removal. Efforts for conservation and restoration of island oak currently underway could benefit from information about its range-wide genetic structure and evolutionary history. Here we present a high-quality genome assembly for Q. tomentella, assembled using PacBio HiFi and Omni-C sequencing, developed as part of the California Conservation Genomics Project (CCGP). The resulting assembly has a length of 781 Mb, with a contig N50 of 22.0 Mb and a scaffold N50 of 63.4 Mb. This genome assembly will provide a resource for genomics-informed conservation of this rare oak species. Additionally, this reference genome will be the first one available for a species in Quercus section Protobalanus, a unique oak clade present only in western North America.

A genome assembly of the Yuma myotis bat, Myotis yumanensis.

The Yuma myotis bat (Myotis yumanensis) is a small vespertilionid bat and one of 52 species of new world Myotis bats in the subgenus Pizonyx. While M. yumanensis populations currently appear relatively stable, it is one of 12 bat species known or suspected to be susceptible to white-nose syndrome, the fungal disease causing declines in bat populations across North America. Only two of these 12 species have genome resources available, which limits the ability of resource managers to use genomic techniques to track the responses of bat populations to white-nose syndrome generally. Here we present the first de novo genome assembly for Yuma myotis, generated as a part of the California Conservation Genomics Project. The M. yumanensis genome was generated using a combination of PacBio HiFi long reads and Omni-C chromatin-proximity sequencing technology. This high-quality genome is one of the most complete bat assemblies available, with a contig N50 of 28.03 Mb, scaffold N50 of 99.14 Mb, and BUSCO completeness score of 93.7%. The Yuma myotis genome provides a high-quality resource that will aid in comparative genomic and evolutionary studies, as well as inform conservation management related to white-nose syndrome.

A highly contiguous genome assembly for the pocket mouse Perognathus longimembris longimembris.

The little pocket mouse, Perognathus longimembris, and its nine congeners are small heteromyid rodents found in arid and seasonally arid regions of Western North America. The genus is characterized by behavioral and physiological adaptations to dry and often harsh environments, including nocturnality, seasonal torpor, food caching, enhanced osmoregulation, and a well-developed sense of hearing. Here we present a genome assembly of Perognathus longimembris longimembris generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing as part of the California Conservation Genomics Project. The assembly has a length of 2.35 Gb, contig N50 of 11.6 Mb, scaffold N50 of 73.2 Mb, and includes 93.8% of the BUSCO Glires genes. Interspersed repetitive elements constitute 41.2% of the genome. A comparison with the highly endangered Pacific pocket mouse, P. l. pacificus, reveals broad synteny. These new resources will enable studies of local adaptation, genetic diversity, and conservation of threatened taxa.

Reference genome of Townsend's big-eared bat, Corynorhinus townsendii.

Townsend's big-eared bat, Corynorhinus townsendii, is a cave- and mine-roosting species found largely in western North America. Considered a species of conservation concern throughout much of its range, protection efforts would greatly benefit from understanding patterns of population structure, genetic diversity, and local adaptation. To facilitate such research, we present the first de novo genome assembly of C. townsendii as part of the California Conservation Genomics Project (CCGP). Pacific Biosciences HiFi long reads and Omni-C chromatin-proximity sequencing technologies were used to produce a de novo genome assembly, consistent with the standard CCGP reference genome protocol. This assembly comprises 391 scaffolds spanning 2.1 Gb, represented by a scaffold N50 of 174.6 Mb, a contig N50 of 23.4 Mb, and a benchmarking universal single-copy ortholog (BUSCO) completeness score of 96.6%. This high-quality genome will be a key tool for informed conservation and management of this vulnerable species in California and across its range.

A genome assembly of the American black bear, Ursus americanus, from California.

The American black bear, Ursus americanus, is a widespread and ecologically important species in North America. In California, the black bear plays an important role in a variety of ecosystems and serves as an important species for recreational hunting. While research suggests that the populations in California are currently healthy, continued monitoring is critical, with genomic analyses providing an important surveillance tool. Here we report a high-quality, near chromosome-level genome assembly from a U. americanus sample from California. The primary assembly has a total length of 2.5 Gb contained in 316 scaffolds, a contig N50 of 58.9 Mb, a scaffold N50 of 67.6 Mb, and a BUSCO completeness score of 96%. This U. americanus genome assembly will provide an important resource for the targeted management of black bear populations in California, with the goal of achieving an appropriate balance between the recreational value of black bears and the maintenance of viable populations. The high quality of this genome assembly will also make it a valuable resource for comparative genomic analyses among black bear populations and among bear species.

De novo genome assembly of a Geomyid rodent, Botta's pocket gopher (Thomomys bottae bottae).

Botta's pocket gopher (Thomomys bottae) is a common and widespread subterranean rodent of the North American west. The species has been of long interest to evolutionary biologists due to the phenotypic diversity across its range and unusual levels of variation in chromosome number and composition. Here, we present a high-quality reference genome from a male T. b. bottae individual captured in the San Francisco Bay Area. The assembly is comprised of 2,792 scaffolds, with a scaffold N50 value of 23.6 Mb and a BUSCO score of 91.0%. This genome helps fill a significant taxonomic sampling gap in rodent genome resources. With this reference genome, we envision new opportunities to investigate questions regarding the genomics of adaptation to the belowground niche. Further, we can begin to explore the impact of associated life history traits, such as limited dispersal and low population connectivity, on intraspecific genetic and phenotypic variation, genome evolution, speciation, and phylogenetic relationships across the Geomyoidea.

A genome assembly for the Chryxus Arctic (Oeneis chryxus), the highest butterfly in North America.

We describe a highly contiguous and complete diploid genome assembly for the Chryxus Arctic, Oeneis chryxus (E. Doubleday, [1849]), a butterfly species complex spanning much of northern and western North America. One subspecies, the Ivallda Arctic (O. c. ivallda), is endemic to California's Sierra Nevada and of particular biogeographic interest and conservation concern. Extreme alpine habitats occupied by this subspecies include the summit of Mt. Whitney, California, representing the highest elevation butterfly population in North America. The assembly presented here consists of two haplotypes, 738.92 and 770.85 Mb in length, with contig N50 values of 10.49 and 10.13 Mb, scaffold N50 values of 25.35 and 25.69 Mb, scaffold L50 values of 13 and 14, and BUSCO completeness scores of 96.5 and 98.3%, respectively. More than 97% of the assembly is organized into 29 scaffolds, which likely represent whole chromosomes. This assembly is the first major genomic resource for Oeneis, providing a foundational reference for future genomic studies on the taxonomy, evolutionary history, and conservation of the genus. As part of the California Conservation Genomics Project, we will use this assembly in conjunction with short-read resequencing to resolve patterns of evolutionary differentiation, adaptive genomic variation, and gene flow among remaining O. c. ivallda populations. These data can and will be used to inform the subspecies' conservation as warming climatic conditions continue to lead to the loss and fragmentation of alpine habitats. We also provide genome assemblies for the O. chryxus mitochondrion and a Wolbachia endosymbiont.

A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia).

The Yellow Warbler (Setophaga petechia) is a small songbird in the wood-warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California's riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation in Yellow Warblers and can inform conservation management of this charismatic bird species.

The WW domain of IQGAP1 binds directly to the p110α catalytic subunit of PI 3-kinase.

IQGAP1 is a multi-domain cancer-associated protein that serves as a scaffold protein for multiple signaling pathways. Numerous binding partners have been found for the calponin homology, IQ and GAP-related domains in IQGAP1. Identification of a binding partner for its WW domain has proven elusive, however, even though a cell-penetrating peptide derived from this domain has marked anti-tumor activity. Here, using in vitro binding assays with human proteins and co-precipitation from human cells, we show that the WW domain of human IQGAP1 binds directly to the p110α catalytic subunit of phosphoinositide 3-kinase (PI3K). In contrast, the WW domain does not bind to ERK1/2, MEK1/2, or the p85α regulatory subunit of PI3K when p85α is expressed alone. However, the WW domain is able to bind to the p110α/p85α heterodimer when both subunits are co-expressed, as well as to the mutationally activated p110α/p65α heterodimer. We present a model of the structure of the IQGAP1 WW domain, and experimentally identify key residues in the hydrophobic core and beta strands of the WW domain that are required for binding to p110α. These findings contribute to a more precise understanding of IQGAP1-mediated scaffolding, and of how IQGAP1-derived therapeutic peptides might inhibit tumorigenesis.

Multilevel Determinants of Digital Health Equity: A Literature Synthesis to Advance the Field.

Current digital health approaches have not engaged diverse end users or reduced health or health care inequities, despite their promise to deliver more tailored and personalized support to individuals at the right time and the right place. To achieve digital health equity, we must refocus our attention on the current state of digital health uptake and use across the policy, system, community, individual, and intervention levels. We focus here on (a) outlining a multilevel framework underlying digital health equity; (b) summarizingfive types of interventions/programs (with example studies) that hold promise for advancing digital health equity; and (c) recommending future steps for improving policy, practice, and research in this space.

Assessing survival outcomes and complication profiles following surgical excision and radiotherapy as interventions for skull base chordoma: a systematic review of operative margins and surgical approaches.

INTRODUCTION: Despite their precarious behavioral classification (benign and low grade on histopathology yet behaviorally malignant), great strides have been taken to improve prognostication and treatment paradigms for patients with skull base chordoma. With respect to surgical techniques, lateral transcranial (TC) approaches have traditionally been used, however endoscopic endonasal approaches (EEA) have been advocated for midline lesions. Nonetheless, due to the rarity of this pathology (0.2% of all intracranial neoplasms), investigations within the literature remain limited to small retrospective series. Furthermore, radiotherapeutic treatments investigated to date have proven largely ineffective. METHODS: Accordingly, we performed a systematic review in order to profile surgical and survival outcomes for skull base chordoma. Fixed and random-effect meta-analyses were performed for categorical variables including GTR, STR, 5-year OS, 10-year OS, 5-year PFS, and 10-year PFS. Additionally, we pooled eligible studies for formal meta-analysis to compare outcomes by surgical approach (lateral versus midline). Statistical analyses were performed using R Studio 'metafor' package or Cochrane Review Manager. Furthermore, meta-analysis of pooled mortality rates and sub-analyses of operative margin and surgical complications were used to compare midline versus lateral approaches via the Mantel-Haenszel method. We considered all p-values < 0.05 to be statistically significant. RESULTS: Following the systematic search and screen, 55 studies published between 1993 and 2022 reporting data for 2453 patients remained eligible for analysis. Sex distribution was comparable between males and females, with a slight predominance of male-identifying patients (0.5625 [95% CI: 0.5418; 0.3909]). Average age at diagnosis was 42.4 ± 12.5 years, while average age of treatment initiation was 43.0 ± 10.6 years. Overall, I2 value indicated notable heterogeneity across the 55 studies [I2 = 56.3% (95%CI: 44.0%; 65.9%)]. With respect to operative margins, the rate of GTR was 0.3323 [95% CI: 0.2824; 0.3909], I2 = 91.9% [95% CI: 90.2%; 93.4%], while the rate of STR was significantly higher at 0.5167 [95% CI: 0.4596; 0.5808], I2 = 93.1% [95% CI: 91.6%; 94.4%]. The most common complication was CSF leak (5.4%). In terms of survival outcomes, 5-year OS rate was 0.7113 [95% CI: 0.6685; 0.7568], I2 = 91.9% [95% CI: 90.0%; 93.5%]. 10-year OS rate was 0.4957 [95% CI: 0.4230; 0.5809], I2 = 92.3% [95% CI: 89.2%; 94.4%], which was comparable to the 5-year PFS rate of 0.5054 [95% CI: 0.4394; 0.5813], I2 = 84.2% [95% CI: 77.6%; 88.8%] and 10-yr PFS rate of 0.4949 [95% CI: 0.4075; 0.6010], I2 = 14.9% [95% CI: 0.0%; 87.0%]. There were 55 reported deaths for a perioperative mortality rate of 2.5%. The relative risk for mortality in the midline group versus the lateral approach group did not indicate any substantial difference in survival according to laterality of approach (-0.93 [95% CI: -1.03, -0.97], I2 = 95%, (p < 0.001). CONCLUSION: Overall, these results indicate good 5-year survival outcomes for patients with skull base chordoma; however, 10-year prognosis for skull base chordoma remains poor due to its radiotherapeutic resistance and high recurrence rate. Furthermore, mortality rates among patients undergoing midline versus lateral skull base approaches appear to be equivocal.

A reference genome assembly for the continentally distributed ring-necked snake, Diadophis punctatus.

Snakes in the family Colubridae include more than 2,000 currently recognized species, and comprise roughly 75% of the global snake species diversity on Earth. For such a spectacular radiation, colubrid snakes remain poorly understood ecologically and genetically. Two subfamilies, Colubrinae (788 species) and Dipsadinae (833 species), comprise the bulk of colubrid species richness. Dipsadines are a speciose and diverse group of snakes that largely inhabit Central and South America, with a handful of small-body-size genera that have invaded North America. Among them, the ring-necked snake, Diadophis punctatus, has an incredibly broad distribution with 14 subspecies. Given its continental distribution and high degree of variation in coloration, diet, feeding ecology, and behavior, the ring-necked snake is an excellent species for the study of genetic diversity and trait evolution. Within California, six subspecies form a continuously distributed "ring species" around the Central Valley, while a seventh, the regal ring-necked snake, Diadophis punctatus regalis is a disjunct outlier and Species of Special Concern in the state. Here, we report a new reference genome assembly for the San Diego ring-necked snake, D. p. similis, as part of the California Conservation Genomics Project. This assembly comprises a total of 444 scaffolds spanning 1,783 Mb and has a contig N50 of 8.0 Mb, scaffold N50 of 83 Mb, and BUSCO completeness score of 94.5%. This reference genome will be a valuable resource for studies of the taxonomy, conservation, and evolution of the ring-necked snake across its broad, continental distribution.

The reference genome assembly of the bright cobblestone lichen, Acarospora socialis.

Acarospora socialis, the bright cobblestone lichen, is commonly found in southwestern North America. This charismatic yellow lichen is a species of key ecological significance as it is often a pioneer species in new environments. Despite their ecological importance virtually no research has been conducted on the genomics of A. socialis. To address this, we used long-read sequencing to generate the first high-quality draft genome of A. socialis. Lichen thallus tissue was collected from Pinkham Canyon in Joshua Tree National Park, California and deposited in the UC Riverside herbarium under accession #295874. The de novo assembly of the mycobiont partner of the lichen was generated from Pacific Biosciences HiFi long reads and Dovetail Omni-C chromatin capture data. After removing algal and bacterial contigs, the fungal genome was approximately 31.2 Mb consisting of 38 scaffolds with contig and scaffold N50 of 2.4 Mb. The BUSCO completeness score of the assembled genome was 97.5% using the Ascomycota gene set. Information on the genome of A. socialis is important for California conservation purposes given that this lichen is threatened in some places locally by wildfires due to climate change. This reference genome will be used for understanding the genetic diversity, population genomics, and comparative genomics of A. socialis species. Genomic resources for this species will support population and landscape genomics investigations, exploring the use of A. socialis as a bioindicator species for climate change, and in studies of adaptation by comparing populations that occur across aridity gradients in California.

A reference genome assembly of the declining tricolored blackbird, Agelaius tricolor.

The tricolored blackbird, Agelaius tricolor, is a gregarious species that forms enormous breeding and foraging colonies in wetland and agricultural habitats, primarily in California, USA. Once extremely abundant, species numbers have declined dramatically in the past century, largely due to losses of breeding and foraging habitats. Tricolored blackbirds are currently listed as Endangered by the IUCN, and Threatened under the California Endangered Species Act. Increased genetic information is needed to detail the evolutionary consequences of a species-wide bottleneck and inform conservation management. Here, we present a contiguous tricolored blackbird reference genome, assembled with PacBio HiFi long reads and Dovetail Omni-C data to generate a scaffold-level assembly containing multiple chromosome-length scaffolds. This genome adds a valuable resource for important evolutionary and conservation research on tricolored blackbirds and related species.

Reference genome of the Virginia rail, Rallus limicola.

The Virginia rail, Rallus limicola, is a member of the family Rallidae, which also includes many other species of secretive and poorly studied wetland birds. It is recognized as a single species throughout its broad distribution in North America where it is exploited as a game bird, often with generous harvest limits, despite a lack of systematic population surveys and evidence of declines in many areas due to wetland loss and degradation. To help advance understanding of the phylogeography, biology, and ecology of this elusive species, we report the first reference genome assembly for the Virginia rail, produced as part of the California Conservation Genomics Project (CCGP). We produced a de novo genome assembly using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology with an estimated sequencing error rate of 0.191%. The assembly consists of 1,102 scaffolds spanning 1.39 Gb, with a contig N50 of 11.0 Mb, scaffold N50 of 25.3 Mb, largest contig of 45 Mb, and largest scaffold of 128.4 Mb. It has a high BUSCO completeness score of 96.9% and represents the first genome assembly available for the genus Rallus. This genome assembly will help resolve questions about the complex evolutionary history of rails and evaluate the potential of rails for adaptive evolution in the face of growing threats from climate change and habitat loss and fragmentation. It will also provide a valuable resource for rail conservation efforts by quantifying Virginia rail vagility, population connectivity, and effective population sizes.