Dataset for genomic resources for the neotropical tree genus Cedrela (Meliaceae) and its relatives

This dataset is available as supplement for a research article submitted in 2018 and accepted in 2019. Genomic resources for the Neotropical tree genus Cedrela (Meliaceae) and its relatives. By Kristen N. Finch, B.A.; F. Andrew Jones, Ph.D.; Richard Cronn, Ph.D. Tree species in the genus Cedrela are threatened by timber overexploitation across the Neotropics. Genetic identification of processed timber can be used to supplement wood anatomy to assist in the taxonomic and source validation of protected species and populations of Cedrela. However, few genetic resources exist that enable both species and source identification of Cedrela timber products. We developed several genomic resources including a leaf transcriptome, chloroplast genome, and diagnostic single nucleotide polymorphisms (SNPs) that may assist the classification of Cedrela specimens to species and geographic origin. In this supplementary directory, we share the assembled transcriptome reference, hybridization capture probe sequences, and the chloroplast genome reference for a single specimen, CEOD_NYBG (C. odorata from the living collection at the New York Botanical Garden). We also include: chloroplast genome sequences for each of the 43 specimens screened in our diversity panel (as separate files and as a combined file, aligned and unaligned), the VCF file containing SNPs for species and origin prediction for Cedrela, and data sets to replicate our statistical analysis using R. By sharing these resources, we hope to enable future research on this widespread Neotropical tree genus

Genomic Resources for Phylogenetics, Species Delimitation, and Geographic Localization of Neotropical Tree Species Cedrela odorata L. (Meliaceae)

Biodiversity loss is of global concern, and is due in part to deforestation and high consumer demand for wood and wood products. The neotropical tree species Cedrela odorata (“Spanish cedar” or “cedro”) is economically valuable for its wood and faces threats of overexploitation. Due to strong similarities in wood features across species, overlapping geographic distributions, and taxonomic uncertainty, other Cedrela species may be intentionally or mistakenly substituted for C. odorata in trade. This pressure is expected to make these species more vulnerable if current logging practices proceed unchecked. This dissertation focuses on the development of genomic resources for C. odorata and five closely allied species in the genus Cedrela. Each chapter describes how the implementation of genomic data can be used to better understand and protect this historically overexploited plant group. Chapter 2 presents a C. odorata leaf transcriptome, chloroplast genome, and a set of probes that can be used to enrich target regions (genes) of the nuclear genome for DNA sequence analysis. I demonstrated that these “target capture” probes efficiently sampled thousands of genes from C. odorata specimens (~ 7,900 genes at 10X depth), the four Cedrela species included (3,000-9,500 genes), closely related and endangered Swietenia mahagoni (Caribbean mahogany; 4,000 genes), and distantly related Guarea guidonia (muskwood; 750 genes) and Trichilia tuberculata (550 genes). This list of genes adds significantly to the available genomic resources for these species (most are currently represented by fewer than 20 genes), and makes a large contribution to genomic resources for the mahogany family (Meliaceae). In Chapter 3, I used the target capture probes to sample the genomes of 168 Cedrela trees representing six co-occurring species, with the goal of determining whether named species can be verified as distinct genetic entities based on robust genomic sampling. Of particular interest was the possibility that C. odorata may contain multiple genetic lineages that are morphologically similar or identical (i.e., cryptic species). I inferred the phylogenetic relationships among C. odorata and closely allied species with nuclear SNPs and chloroplast genomes. I found that C. odorata was clearly represented as two lineages: one in Mesoamerica, and one in South America that included allied species C. fissilis, C. nebulosa, and C. saltensis. I compared seven species delimitation schemes to current taxonomy (i.e., models combining individuals identified as distinct species under the same taxonomic name and/or separating previously grouped individuals). In all cases, species definitions showing simplified taxonomy (fewer species) were better representations of the data than current taxonomy. The best model supported: (i) the separation of Mesoamerican C. odorata sensu stricto and South American C. odorata into distinct taxa, and (ii) combining two previously described species (C. nebulosa and C. saltensis) with South American C. odorata into a single species. If these findings were adopted for Cedrela taxonomy, they would result in reduced taxonomic uncertainty in this genus, and would help streamline documentation of Cedrela in trade. In Chapter 4, I developed and tested a single nucleotide polymorphism (“SNP”) genotyping assay for geographic source validation of C. odorata, a critical need for law enforcement. I demonstrated that array SNPs and resulting genotypes accurately estimate C. odorata geographic origin at the scale of Central vs. South America, and that SNPs provided a median prediction error of 188.7 km from the true origin. This approach has promise for assigning geographic origin of C. odorata wood, and provides useful information for enforcing restrictions on the harvest and trade of C. odorata across its range in the Neotropics. Chapter 5 provides a review the major findings presented in this dissertation, and presents unresolved areas of research that may benefit from these genomic resources. For example, the presented data and methods may provide a starting point for future phylogenetic studies of Cedrela that consider the entire genus. The genomic depth obtained with the probe set should also be adequate to investigate the role of hybridization in the genus Cedrela

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Dataset for predicting the geographic origin of Spanish Cedar (Cedrela odorata L.) based on DNA variation

The legality of wood products in trade often depends on their geographic origin, creating a need for forensic tools that can verify claims of provenance for wood and wood products. Cedrela odorata L. or Spanish cedar is a target of illegal logging. We developed a 140 SNP Agena™ MassARRAY® assay for geographic assignment of C. odorata specimens to their origin. Hybridization capture, target enrichment, and short-read sequencing of 192 Cedrela specimens allowed us to identify 140 spatially informative SNPs that differentiate C. odorata specimens by latitude, temperature, and precipitation. These SNPs were validated using 356 Cedrela specimens from eight species, and genetic clusters from discriminant analysis of principal components corresponded roughly to species groups. We used random forest classification and the R package SPASIBA to perform discrete and continuous spatial assignment of C. odorata sensu stricto specimens and to evaluate classification error. In this supplementary directory, a reduced representation nuclear genome reference for C. odorata, a VCF file containing 144,083 high quality SNPs for C. odorata which may be used to further refine out SNP genotyping assay for geographic assignment or other purposes, 140 SNP primers used for the Agena™ MassARRAY®, and data sets to replicate our statistical analysis using R. By sharing these resources, we hope to enable future research on this widespread Neotropical tree genus.Keywords: Logging; Cedrela; Forensic biology; Plants; Mahogany--South America; Meliaceae; Spanish ceda

Genomic resources for the Neotropical tree genus Cedrela (Meliaceae) and its relatives

Abstract Background Tree species in the genus Cedrela P. Browne are threatened by timber overexploitation across the Neotropics. Genetic identification of processed timber can be used to supplement wood anatomy to assist in the taxonomic and source validation of protected species and populations of Cedrela. However, few genetic resources exist that enable both species and source identification of Cedrela timber products. We developed several ‘omic resources including a leaf transcriptome, organelle genome (cpDNA), and diagnostic single nucleotide polymorphisms (SNPs) that may assist the classification of Cedrela specimens to species and geographic origin and enable future research on this widespread Neotropical tree genus. Results We designed hybridization capture probes to enrich for thousands of genes from both freshly preserved leaf tissue and from herbarium specimens across eight Meliaceae species. We first assembled a draft de novo transcriptome for C. odorata, and then identified putatively low-copy genes. Hybridization probes for 10,001 transcript models successfully enriched 9795 (98%) of these targets, and analysis of target capture efficiency showed that probes worked effectively for five Cedrela species, with each species showing similar mean on-target sequence yield and depth. The probes showed greater enrichment efficiency for Cedrela species relative to the other three distantly related Meliaceae species. We provide a set of candidate SNPs for species identification of four of the Cedrela species included in this analysis, and present draft chloroplast genomes for multiple individuals of eight species from four genera in the Meliaceae. Conclusions Deforestation and illegal logging threaten forest biodiversity globally, and wood screening tools offer enforcement agencies new approaches to identify illegally harvested timber. The genomic resources described here provide the foundation required to develop genetic screening methods for Cedrela species identification and source validation. Due to their transferability across the genus and family as well as demonstrated applicability for both fresh leaves and herbarium specimens, the genomic resources described here provide additional tools for studies examining the ecology and evolutionary history of Cedrela and related species in the Meliaceae

Predicting the geographic origin of Spanish cedar (Cedrela odorata L.) based on DNA variation

Funding for this study was provided by U. S. Agency for International Development (Award 19318814Y0010-140001) to the U.S. Forest Service International Programs, the U.S.D.A. Forest Service Pacific Northwest Research Station, and the Moldenke Endowment (Botany and Plant Pathology Department, Oregon State University).The legality of wood products often depends on their origin, creating a need for forensic tools that verify claims of provenance for wood products. The neotropical tree species Cedrela odorata (Spanish cedar) is economically valuable for its wood and faces threats of overexploitation. We developed a 140 SNP assay for geographic localization of C. odorata specimens. Target capture and short-read sequencing of 46 C. odorata specimens allowed us to identify 140 spatially informative SNPs that differentiate C. odorata specimens by latitude, temperature, and precipitation. We assessed the broad applicability of these SNPs on 356 specimens from eight Cedrela species, three tissue types, and a range of DNA mass inputs. Origin prediction error was evaluated with discrete and continuous spatial assignment methods focusing on C. odorata specimens. Discrete classification with random forests readily differentiated specimens originating in Central America versus South America (5.8% error), while uncertainty increased as specimens were divided into smaller regions. Continuous spatial prediction with SPASIBA showed a median prediction error of 188.7 km. Our results demonstrate that array SNPs and resulting genotypes accurately validate C. odorata geographic origin at the continental scale and show promise for country-level verification, but that finer-scale assignment likely requires denser spatial sampling. Our study underscores the important role of herbaria for developing genomic resources, and joins a growing list of studies that highlight the role of genomic tools for conservation of threatened species.Publisher PDFPeer reviewe

IL-1α/IL-1R1 expression in chronic obstructive pulmonary disease and mechanistic relevance to smoke-induced neutrophilia in mice.

BACKGROUND: Cigarette smoking is the main risk factor for the development of chronic obstructive pulmonary disease (COPD), a major cause of morbidity and mortality worldwide. Despite this, the cellular and molecular mechanisms that contribute to COPD pathogenesis are still poorly understood. METHODOLOGY AND PRINCIPAL FINDINGS: The objective of this study was to assess IL-1 α and β expression in COPD patients and to investigate their respective roles in perpetuating cigarette smoke-induced inflammation. Functional studies were pursued in smoke-exposed mice using gene-deficient animals, as well as blocking antibodies for IL-1α and β. Here, we demonstrate an underappreciated role for IL-1α expression in COPD. While a strong correlation existed between IL-1α and β levels in patients during stable disease and periods of exacerbation, neutrophilic inflammation was shown to be IL-1α-dependent, and IL-1β- and caspase-1-independent in a murine model of cigarette smoke exposure. As IL-1α was predominantly expressed by hematopoietic cells in COPD patients and in mice exposed to cigarette smoke, studies pursued in bone marrow chimeric mice demonstrated that the crosstalk between IL-1α+ hematopoietic cells and the IL-1R1+ epithelial cells regulates smoke-induced inflammation. IL-1α/IL-1R1-dependent activation of the airway epithelium also led to exacerbated inflammatory responses in H1N1 influenza virus infected smoke-exposed mice, a previously reported model of COPD exacerbation. CONCLUSIONS AND SIGNIFICANCE: This study provides compelling evidence that IL-1α is central to the initiation of smoke-induced neutrophilic inflammation and suggests that IL-1α/IL-1R1 targeted therapies may be relevant for limiting inflammation and exacerbations in COPD