Representation and participation across 20 years of plant genome sequencing

The field of plant genome sequencing has grown rapidly in the past 20 years, leading to increases in the quantity and quality of publicly available genomic resources. The growing wealth of genomic data from an increasingly diverse set of taxa provides unprecedented potential to better understand the genome biology and evolution of land plants. Here we provide a contemporary view of land plant genomics, including analyses on assembly quality, taxonomic distribution of sequenced species and national participation. We show that assembly quality has increased dramatically in recent years, that substantial taxonomic gaps exist and that the field has been dominated by affluent nations in the Global North and China, despite a wide geographic distribution of study species. We identify numerous disconnects between the native range of focal species and the national affiliation of the researchers studying them, which we argue are rooted in colonialism—both past and present. Luckily, falling sequencing costs, widening availability of analytical tools and an increasingly connected scientific community provide key opportunities to improve existing assemblies, fill sampling gaps and empower a more global plant genomics community.

Taphofacies and Petrofacies Theoretical Marine Models Applied to the Coquina of the Amaral Formation (Lusitanian Basin, Portugal)

The Amaral Formation has a wide geographic distribution within the Lusitanian Basin, at the western Iberian Margin (Portugal). The different depositional contexts for this unit enabled the distinction of three sectors: lagoon, lagoon-barrier, and marine-distal. The integration of the evolutionary taphonomic analysis of its fossil assemblages with the analysis of multiscale properties through the CAMURES methodology (Multiscale Reservoir Characterization) allowed the application of a methodology for the classification of coquina which was previously developed for the Morro do Chaves Formation (Sergipe–Alagoas Basin, Brazil). Here, it was adapted according to the complexity of the Amaral Formation deposits. The classification of ten taphofacies, in association with four lithofacies, allowed the definition of 84 petrofacies, based on the nature of the sedimentary and taphonomic processes. The relationship between the structural context, the systems tracts, the diversity of the fossil record, the classification of taphofacies and petrofacies, and the understanding of vertical and lateral variations of the sediments’ deposition within the unit support the construction of geological and theoretical models for coquina deposits. These models will allow for prediction of the spatial distribution of facies in other coquina analogous hydrocarbon reservoirs, as well as specifying the delimitation of reservoir zones for 3D geocellular modeling and flow simulation of hydrocarbon-producing reservoirs, thus improving predictive analyses.

Obstetric Capacity Strengthening in Ghana Results in Wide Geographic Distribution and Retention of Certified Obstetrician-Gynecologists: A Quantitative Analysis

Objectives: Our primary objective to determine the cumulative retention of Ob/Gyns since the inception of the program, to determine the demographic and practice characteristics of all Ob/Gyns who have been trained by the Ghana postgraduate Ob/Gyn programs, and to compare the geographic distribution of Ob/Gyns throughout Ghana between 2010 when a prior study was conducted and the current practice locations of all graduates in 2017. Design: Cross-sectional, Quantitative Investigation Setting: Fieldwork for this study was conducted in Ghana between June 21, 2017, and August 20, 2017. Methods: A roster of certified Ob/Gyns, year certified, and email contact information was obtained from the Ghana College of Physicians and Surgeons, a roster of practice locations was obtained from Ghana Medical Board. Main Outcome Measures: retention of Ob/Gyns, geographic distribution of providers, fand comparisons between 2010 and 2017 Results: Significant geographic spread and increase in in-country medical programs have occurred over the seven-year period. In recent years, the Ghana College of Physicians and Surgeons surpassed that of the West African College of Surgeons. Conclusion: Establishing an Ob/gyn training program with national certification provides a cadre of certified Ob/Gyns that can be trained and retained in low-income settings. Moreover, this allows for long term commitment in multiple relevant sectors that may serve to establish a comprehensive obstetric and gynecology capacity beyond urban centers.

Obstetric Capacity Strengthening in Ghana Results in Wide Geographic Distribution and Retention of Certified Obstetrician-Gynecologists: A Quantitative Analysis

Objectives: Our primary objective to determine the cumulative retention of Ob/Gyns since the inception of the program, to determine the demographic and practice characteristics of all Ob/Gyns who have been trained by the Ghana postgraduate Ob/Gyn programs, and to compare the geographic distribution of Ob/Gyns throughout Ghana between 2010 when a prior study was conducted and the current practice locations of all graduates in 2017. Design: Cross-sectional, Quantitative Investigation Setting: Fieldwork for this study was conducted in Ghana between June 21, 2017, and August 20, 2017. Methods: A roster of certified Ob/Gyns, year certified, and email contact information was obtained from the Ghana College of Physicians and Surgeons, a roster of practice locations was obtained from Ghana Medical Board. Main Outcome Measures: retention of Ob/Gyns, geographic distribution of providers, fand comparisons between 2010 and 2017 Results: Significant geographic spread and increase in in-country medical programs have occurred over the seven-year period. In recent years, the Ghana College of Physicians and Surgeons surpassed that of the West African College of Surgeons. Conclusion: Establishing an Ob/gyn training program with national certification provides a cadre of certified Ob/Gyns that can be trained and retained in low-income settings. Moreover, this allows for long term commitment in multiple relevant sectors that may serve to establish a comprehensive obstetric and gynecology capacity beyond urban centers.

Antibody Profile Comparison against MSP1 Antigens of Multiple Plasmodium Species in Human Serum Samples from Two Different Brazilian Populations Using a Multiplex Serological Assay

Plasmodium malariae has a wide geographic distribution, but mainly at very low parasitemias and in co-infections, leading to an underestimated prevalence of this species. Studies for the detection of antibodies against Plasmodium recombinant proteins are increasingly used to map geographical distributions, seroprevalence and transmission intensities of malaria infection. However, no seroepidemiological survey using recombinant P. malariae proteins has been conducted in Brazil. This work evaluated the antibody response in serum samples of individuals from endemic regions of Brazil (the Amazon region and Atlantic Forest) against five recombinant proteins of P. malariae merozoite surface protein 1 (MSP1), and the MSP1 C-terminal portions of P. vivax and P. falciparum, in a multiplex assay. The positivity was 69.5% of samples recognizing at least one MSP1 recombinant protein. The mean of the Reactivity Index for the C-terminal portion of the P. falciparum was significantly higher compared to the other recombinant proteins, followed by the C-terminal of P. vivax and the N-terminal of P. malariae. Among the recombinant P. malariae proteins, the N-terminal of P. malariae showed the highest Reactivity Index alone. This study validates the use of the multiplex assay to measure naturally acquired IgG antibodies against Plasmodium MSP1 proteins and demonstrate that these proteins are important tools for seroepidemiological surveys and could be used in malaria surveillance.

Rhipicephalus sanguineus Complex in the Americas: Systematic, Genetic Diversity, and Geographic Insights

The Rhipicephalus sanguineus group encompasses at least 12 validated species of Palearctic and Afrotropical hard ticks, which are relevant in veterinary medicine and public health. The taxonomy of R. sanguineus s.s., has been particularly intensely debated, due to its wide geographic distribution, morphological variants, parasite-host associations, and its capacity and vectorial competence for the transmission of several pathogens. By sequencing mitochondrial markers, it was possible to identify the existence of multiple lineages, among which the Tropical and the Temperate lineages stand out, particularly in America. However, the northern limit between these lineages is not clear due to the lack of extensive sampling across Mexico. For this reason, the aim of the present study was to determine the genetic diversity and structure of the R. sanguineus group in Mexico and to compare it with the populations reported in the Americas, in order to propose the northern limit of the R. sanguineus Tropical lineage and the potential regions of sympatry with R. sanguineus s.s. The findings of this study now confirm the presence of R. sanguineus s.s. in Mexico, showing a subtle genetic structure and high genetic diversity throughout its distribution in the Americas. In contrast, the Tropical lineage seems to be genetically less diverse in its overall distribution in the Americas. The genetic diversity of these two independent lineages could have important epidemiological implications in the transmission of tick pathogens.

Morphological variation in Bessera (Asparagaceae: Brodiaeoideae) allows for the recognition of two new species

Bessera (Asparagaceae: Brodiaeoideae) is a genus endemic to Mexico. It currently has two described species: B. elegans with a wide geographic distribution from Durango and Sinaloa in the Sierra Madre Occidental, across the Transmexican Volcanic Belt to Oaxaca in the Sierra Madre del Sur, and B. tuitensis which is endemic to the Sierra del Cuale in Jalisco. Most of the morphological variation in Bessera occurs in western Mexico. We measured ten morphological characters for 280 plants from 21 populations, including B. tuitensis, to answer the following questions: Can Moore’s Group B of B. elegans be recognized as a different species? Are the newly included B. elegans s. l. populations from Colima different from B. elegans s. str., and from B. elegans s. l. (Moore’s group B)? Is there a significant relationship between morphological variation and climate variables for these species? The statistical analyses (ANOVA, MANOVA, and discriminant analysis) allowed us to recognize two new Bessera species, described here as B. elegantissima and B. ramirezii. Additionally, we provide a morphological key for Bessera, illustrations, a distribution map, and photographs of all the species.

Argasid Ticks of Palearctic Bats: Distribution, Host Selection, and Zoonotic Importance

The soft ticks (Ixodida: Argasidae) are ectoparasites of terrestrial vertebrates with a wide geographic distribution, occurring on all continents. These ticks are obligate blood-feeders, most of them show high degrees of host-specialization and several species in arid and tropical regions are important parasites of livestock and men. Species commonly occurring on domestic animals and man are generally well-known, with many studies focusing on their ecology, distribution or vectorial role. However, wildlife-specialist soft ticks are less studied. Nearly half of all soft tick species are bat specialists, with five species (Carios vespertilionis, Chiropterargas boueti, Chiropterargas confusus, Reticulinasus salahi, and Secretargas transgariepinus) occurring in the Western Palearctic. There is no comprehensive study on the distribution, hosts or pathogens in these soft ticks, although most species were shown to carry several viral, bacterial, or protozoan pathogens and also to occasionally infest humans. Based on a literature survey and 1,120 distinct georeferenced records, we present here the geographical range, host selection and vectorial potential for bat-specialist soft ticks occurring in the Western Palearctic (chiefly Europe, North Africa, and the Middle East). Carios vespertilionis shows the largest distribution range and was found on most host species, being ubiquitous wherever crevice-roosting bats occur. All the other species were located only in areas with Mediterranean climate, with Ch. boueti, Chiropteraragas confusus, and R. salahi are missing entirely from Europe. These three species have a host spectrum of bats roosting primarily in caves, while S. transgariepinus and Ca. vespertilionis is feeding primarily on crevice-roosting bat species. All but one of these soft tick species are known to feed on humans and may be vectors of important disease agents (Rickettsia spp., Borrelia spp., Bartonella spp., Ehrlichia spp., Babesia spp., several nairo-, and flaviviruses). As several crevice-roosting bat species show a continuous adaptation to human-altered areas, with certain species becoming common city-dwellers in the Western Palearctic, the study of bat specialist soft ticks is also important from an epidemiologic point of view.

Lessons from 20 years of plant genome sequencing: an unprecedented resource in need of more diverse representation

The field of plant genomics has grown rapidly in the past 20 years, leading to dramatic increases in both the quantity and quality of publicly available genomic resources. With an ever-expanding wealth of genomic data from an increasingly diverse set of taxa, unprecedented potential exists to better understand the evolution and genome biology of plants. Here, we provide a contemporary view of plant genomics, including analyses on the quality of existing plant genome assemblies, the taxonomic distribution of sequenced species, and how national participation has influenced the fields development. We show that genome quality has increased dramatically in recent years, that substantial taxonomic gaps exist, and that the field has been dominated by affluent nations in the Global North, despite a wide geographic distribution of sequenced species. We identify multiple inconsistencies between the range of focal species and the national affiliation of the researchers studying the plants, which we argue are rooted in colonialism--both past and present. Falling sequencing costs paired with widening availability of analytical tools and an increasingly connected scientific community provide key opportunities to improve existing assemblies, fill sampling gaps, and, most importantly, empower a more global plant genomics community.