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Abstract Genome size has been measurable since the 1940s but we still do not understand genome size variation. Caenorhabditis nematodes show strong conservation of chromosome number but vary in genome size between closely related species. Androdioecy, where populations are composed of males and self-fertile hermaphrodites, evolved from outcrossing, female-male dioecy, three times in this group. In Caenorhabditis, androdioecious genomes are 10–30% smaller than dioecious species, but in the nematode Pristionchus, androdioecy evolved six times and does not correlate with genome size. Previous hypotheses include genome size evolution through: 1) Deletions and “genome shrinkage” in androdioecious species; 2) Transposable element (TE) expansion and DNA loss through large deletions (the “accordion model”); and 3) Differing TE dynamics in androdioecious and dioecious species. We analyzed nematode genomes and found no evidence for these hypotheses. Instead, nematode genome sizes had strong phylogenetic inertia with increases in a few dioecious species, contradicting the “genome shrinkage” hypothesis. TEs did not explain genome size variation with the exception of the DNA transposon Mutator which was twice as abundant in dioecious genomes. Across short and long evolutionary distances Caenorhabditis genomes evolved through small structural mutations including gene-associated duplications and insertions. Seventy-one protein families had significant, parallel decreases across androdioecious Caenorhabditis including genes involved in the sensory system, regulatory proteins and membrane-associated immune responses. Our results suggest that within a dynamic landscape of frequent small rearrangements in Caenorhabditis, reproductive mode mediates genome evolution by altering the precise fates of individual genes, proteins, and the phenotypes they underlie. 

The isolation ofBradyrhizobiumstrain I71 expands the distribution of acetylene-consuming microbes to include a group of economically important microorganisms. Members ofBradyrhizobiumare well studied for their abilities to improve plant health and increase crop yields by providing bioavailable nitrogen.

 

We report the genome ofRhodococcus opacusstrain MoAcy1 (DSM 44186), an aerobic soil isolate capable of using acetylene as its primary carbon and energy source (acetylenotrophy). The genome is composed of a single circular chromosome of ∼8 Mbp and two closed plasmids, with a G+C content of 67.3%.

 

The Adapt, Implement, and Research at Nebraska (AIR@NE) project, funded by the NSF CSforAll Researcher-Practitioner Partnership (RPP) program, examines the adaptation of a validated K-8 Computer Science (CS) curriculum in diverse school districts statewide. Our Research-Practitioner Partnership is primarily between the University of Nebraska-Lincoln, the Lincoln Public Schools, and other diverse school districts across Nebraska. Our primary goal is to study and document how different districts, including rural, predominantly minority, and Native American reservation, adopt the curriculum and broaden participation in CS. In addition, the project is developing instructional capacity for K-8 CS education with diverse learners. Our research also adapts and develops teacher and student CS assessments, and documents case studies using design-based research methodology to show how an adaptive curriculum broadens CS participation. Our Professional Development (PD) program for K-8 CS teachers is comprehensive. It consists of three summer courses for each cohort and a series of workshops during the academic year. Of the three summer courses, two are administered in the first year for a cohort: (1) an introduction to computer science course where teachers learn fundamental CS topics and programming in a high-level programming language (e.g., Python), and engage in problem solving and practice computational thinking, and (2) a course in pedagogy for teachers to learn how to teach K-8 CS, including lesson designs, use of instructional resources such as dot-and-dash robots, and assessments. Then, the following academic year after the summer, the PD program holds a series of workshops on five separate Saturdays to support teacher implementation of their lesson modules during the academic year, reflect and improve on their lessons, reinforce on CS concepts and pedagogy techniques, review and adopt alternative instructional resources, and share insights. These Saturday workshops also facilitate further community building and resource sharing. The third course occurs in the second year for a cohort, involving dissemination of research results from the team to the teachers, opportunities to discuss new resources and approaches on teaching CS concepts and computational thinking, and sharing of experiences and insights after teachers have completed one academic year of teaching CS. Unlike the first two courses that are required of teachers, this third course is an opt-in course that combines more in- depth pedagogy and elements of leadership. Thus far, we have had two cohorts and used the design methodology to revise our PD program, making our design more robust based on the lessons learned over the two years. The course materials, assessment, and survey instruments have also been improved. While the project is on-going we have data to that indicates the impact of the work so far. There were significant pre-post gains for both cohorts in teachers’ knowledge of computer science concepts and computational thinking. Scores on the computational thinking assessment were higher than those for CS concepts, which was to be expected given their CS teaching experience. Moreover, in both cohorts, the teachers’ confidence in teaching CS improved significantly. 

Bumble bees are ecologically and economically important insect pollinators. Three abundant and widespread species in western North America, Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii, have been the focus of substantial research relating to diverse aspects of bumble bee ecology and evolutionary biology. We present de novo genome assemblies for each of the three species using hybrid assembly of Illumina and Oxford Nanopore Technologies sequences. All three assemblies are of high quality with large N50s (> 2.2 Mb), BUSCO scores indicating > 98% complete genes, and annotations producing 13,325 - 13,687 genes, comparing favorably with other bee genomes. Analysis of synteny against the most complete bumble bee genome, Bombus terrestris, reveals a high degree of collinearity. These genomes should provide a valuable resource for addressing questions relating to functional genomics and evolutionary biology in these species. 

A Gram-stain-negative, strictly anaerobic, non-motile, rod-shaped bacterium, designated SFB93^T, was isolated from the intertidal sediments of South San Francisco Bay, located near Palo Alto, CA, USA. SFB93^Twas capable of acetylenotrophic and diazotrophic growth, grew at 22–37 °C, pH 6.3–8.5 and in the presence of 10–45 g l⁻¹NaCl. Phylogenetic analyses based on 16S rRNA gene sequencing showed that SFB93^Trepresented a member of the genusSyntrophotaleawith highest 16S rRNA gene sequence similarities toSyntrophotalea acetylenicaDSM 3246^T(96.6 %),Syntrophotalea carbinolicaDSM 2380^T(96.5 %), andSyntrophotalea venetianaDSM 2394^T(96.7 %). Genome sequencing revealed a genome size of 3.22 Mbp and a DNA G+C content of 53.4 %. SFB93^Thad low genome-wide average nucleotide identity (81–87.5 %) and <70 % digital DNA–DNA hybridization value with other members of the genusSyntrophotalea. The phylogenetic position of SFB93^Twithin the familySyntrophotaleaceaeand as a novel member of the genusSyntrophotaleawas confirmed via phylogenetic reconstruction based on concatenated alignments of 92 bacterial core genes. On the basis of the results of phenotypic, genotypic and phylogenetic analyses, a novel species,Syntrophotalea acetylenivoranssp. nov., is proposed, with SFB93^T(=DSM 106009^T=JCM 33327^T=ATCC TSD-118^T) as the type strain.

 

Many species use dormant stages for habitat selection by tying recovery to informative external cues. Other species have an undiscerning strategy in which they recover randomly despite having advanced sensory systems. We investigated whether elements of a species' habitat structure and life history can bar it from developing a discerning recovery strategy. The nematodeCaenorhabditis eleganshas a dormant stage called the dauer larva that disperses between habitat patches. On one hand,C. eleganscolonization success is profoundly influenced by the bacteria found in its habitat patches, so we might expect this to select for a discerning strategy. On the other hand,C. elegans' habitat structure and life history suggest that there is no fitness benefit to varying recovery, which might select for an undiscerning strategy. We exposed dauers of three genotypes to a range of bacteria acquired from the worms' natural habitat. We found thatC. elegansdauers recover in all conditions but increase recovery on certain bacteria depending on the worm's genotype, suggesting a combination of undiscerning and discerning strategies. Additionally, the worms' responses did not match the bacteria's objective quality, suggesting that their decision is based on other characteristics.