From Pectinate to Divaricate: The Promise of NGS Genome Skimming for Phylogenetic Systematics of Oreocarya (Boraginaceae)

Includes bibliographical references (pages 35-41).Next-generation sequencing (NGS) is enabling plant systematists to capture orders of magnitude more sequence data for phylogenetic studies. As systematists grapple with how to best apply NGS to their taxa of interest, a deluge of review papers, methods, and analytic tools makes choosing the right method difficult. Oreocarya, a genus of 63 species in the Boraginaceae, is a good example of a group with few genomic resources and a lack of species-level resolution. Traditional methods, using PCR and Sanger sequencing of a few molecular markers, have failed to resolve species-level relationships. To test the utility of using NGS genome skimming for systematic studies within Oreocarya, 100-bp single-end Illumina reads were generated for 20 taxa (including two outgroups) in half of an Illumina HiSeq 2000 lane, resulting in 1.7-9 million reads per sample. A combination of de novo and reference-guided assemblies were used to recover the nuclear ribosomal cistron, the plastome, and nine mitochondrial genes; these data were used to infer phylogenies using Maximum Likelihood, Bayesian Inference and species-tree methods. Additionally, NGS data were used to inform future studies in Oreocarya, by identifying published conserved single-copy orthologous low-copy nuclear genes (LCNG), and calculating multiplexing levels. Although genome skimming provides a much-improved primary data collection method for phylogenetic resolution at the species level, and is suitable for systematic revision of Oreocarya at the sectional level; targeting of LCNG holds the most promise for a well-resolved phylogeny of Oreocarya in the future

School-Based Policies to Identify Adversity in Childhood and Mitigate the Effects of Toxic Stress in Texas

Drawing on evidence and example legislation, this policy research brief identifies school-based policy options for Texas to prevent and mitigate toxic stress caused by Adverse Childhood Experiences (ACEs). The term ACEs refers to the 10 common categories of adversity included in a landmark study from the Centers of Disease Control and Prevention and Kaiser Permanente (Felliti et al., 1998). These include physical, emotional, or sexual abuse, physical or emotional neglect, and a set of household challenges such as living with a person who is experiencing mental illness (Felliti et al., 1998). Of great concern is that even before the COVID-19 pandemic, ACEs were already widespread in the state, cutting across lines of race and income and potentially affecting constituents from every region and demographic group (Texas Behavioral Risk Factor Surveillance System, 2020). Over the past two years, COVID-19 related school and child-care center closures coupled with an economic recession has increased children’s risk of hunger, homelessness, and neglect (Welch & Haskins, 2020). The effects of ACEs are particularly concerning in Texas because the state is home to over 7.5 million children under 18 – more than any state other than California – and children under 18 make up more than 25% of the population of Texas – more than any state other than Utah (U.S. Census Bureau, 2020). Therefore, Texas’s school-based policies to mitigate the effects of toxic stress are particularly consequential now and in the future. The purpose of this policy research brief is to identify and describe nationwide legislative efforts to help Texas school district officials and Texas policymakers consider legislative remedies to reduce or mitigate the detrimental impact of ACEs.Educatio

cpDNA alignment

Contains the final cpDNA alignment used in analyses. Files are in both nexus and Geneious format

Final ML trees

Contains the final published phylogenetic trees for the nrDNA, cpDNA, and mtDNA in both nexus and Geneious format

mtDNA exon sequences

Contains the raw mtDNA exon sequences in both fasta and Geneious format. These were aligned and trimmed prior to analysis

mtDNA exon alignments

Contains the final exon alignments used in analyses. Files are in both nexus and Geneious format

Data from: Geneious! Simplified genome skimming methods for phylogenetic systematic studies: a case study in Oreocarya (Boraginaceae)

Premise of the study: As systematists grapple with how to best harness the power of next-generation sequencing (NGS), a deluge of review papers, methods, and analytical tools make choosing the right method difficult. Oreocarya (Boraginaceae), a genus of 63 species, is a good example of a group lacking both species-level resolution and genomic resources. The use of Geneious removes bioinformatic barriers and makes NGS genome skimming accessible to even the least tech-savvy systematists. Methods: A combination of de novo and reference-guided assemblies was used to process 100-bp single-end Illumina HiSeq 2000 reads. A subset of 25 taxa was used to test the suitability of genome skimming for future systematic studies in recalcitrant lineages like Oreocarya. Results: The nuclear ribosomal cistron, the plastome, and 12 mitochondrial genes were recovered from all 25 taxa. All data processing and phylogenomic analyses were performed in Geneious. We report possible future multiplexing levels and published low-copy nuclear genes represented within de novo contigs. Discussion: Genome skimming represents a much-improved primary data collection over PCR+Sanger sequencing when chloroplast DNA (cpDNA), nuclear ribosomal DNA (nrDNA), and mitochondrial DNA (mtDNA) are the target sequences. This study details methods that plant systematists can employ to study their own taxa of interest