Biology subjects

Phillips, A. R.

Publications and source records attributed to Phillips, A. R..

4 recordsLinked to original sources

bioRxiv2025

The origins and adaptive consequences of polyploidy in a dominant prairie grass

Polyploidy is ubiquitous across North American prairies, which provide essential ecosystem services and rich soil for agriculture. Yet the mechanism driving polyploid abundance is unclear. Multiple hypotheses have been proposed including polyploid abundance is proportional to the opportunity for whole genome duplication (WGD), and WGD alters phenotypes that may increase fitness. We tested these two hypotheses together in the mixed-ploidy species Andropogon gerardi, a dominant grass species in endangered North American tallgrass prairies. Leveraging a novel, phased allopolyploid reference genome, we found the A. gerardi hexaploid arose after the C4 grassland expansion in the early Pleistocene, when glacial cycles likely increased secondary contact between the diploid progenitors. We sequenced A. gerardi from 25 popula-tions and examined cytotype performance and morphology in a controlled environment to investigate the consequences of the contemporary mixed-ploidy populations. We found the 9x A. gerardi cytotype is a neopolyploid and a result of recurrent WGD events. Further, we demonstrate the 9x neopolyploids have greater growth and a decreased stomatal pore index, which is adaptive in xeric climates where the 9x cy-totype is most common. Together, our results support both hypotheses for polyploid abundance in North America: WGD is a product of opportunity and can have immediate fitness consequences. Although the changes to fitness may provide an advantage to 9x A. gerardi, the establishment of 9x may lower overall population fitness due to the lower reproductive viability of 9x individuals. Significance statementPolyploid species are abundant in North American prairies and make up many of the dominant species in the ecosystem. This prominence could be a result of whole genome duplication conferring an advantage that increases the frequency of polyploids or could simply indicate that the opportunity for whole genome duplication is higher in this ecosystem, or both. Through examining three polyploidization events in A. gerardi, the dominant species in endangered tallgrass North American prairies, we found whole genome duplication is both surprisingly common and confers traits that are beneficial in some environments.

plant biology↗

bioRxiv2024

Current genomic deep learning architectures generalize across grass species but not alleles

Non-coding regions of the genome are just as important as coding regions for understanding the mapping from genotype to phenotype. Interpreting deep learning models trained on RNA-seq is an emerging method to highlight functional sites within non-coding regions. Most of the work on RNA abundance models has been done within humans and mice, with little attention paid to plants. Here, we benchmark four genomic deep learning model architectures with genomes and RNA-seq data from 18 species closely related to maize and sorghum within the Andropogoneae. The Andropogoneae are a tribe of C4 grasses that have adapted to a wide range of environments worldwide since diverging 18 million years ago. Hundreds of millions of years of evolution across these species has produced a large, diverse pool of training alleles across species sharing a common physiology. As model input, we extracted 1,026 base pairs upstream of each genes translation start site. We held out maize as our test set and two closely related species as our validation set, training each architecture on the remaining Andropogoneae genomes. Within a panel of 26 maize lines, all architectures predict expression across genes moderately well but poorly across alleles. DanQ consistently ranked highest or second highest among all architectures yet performance was generally very similar across architectures despite orders of magnitude differences in size. This suggests that state-of-the-art supervised genomic deep learning models are able to generalize moderately well across related species but not sensitively separate alleles within species, the latter of which agrees with recent work within humans. We are releasing the preprocessed data and code for this work as a community benchmark to evaluate new architectures on our across-species and across-allele tasks.

genomics↗

bioRxiv2022

A happy accident: a novel turfgrass reference genome

Poa pratensis, commonly known as Kentucky bluegrass, is a popular cool-season grass species used as turf in lawns and recreation areas globally. Despite its substantial economic value, a reference genome had not previously been assembled due to the genomes relatively large size and biological complexity that includes apomixis, polyploidy, and interspecific hybridization. We report here a fortuitous de novo assembly and annotation of a P. pratensis genome. Instead of sequencing the genome of a C4 grass, we accidentally sampled and sequenced tissue from a weedy P. pratensis whose stolon was intertwined with that of the C4 grass. The draft assembly consists of 6.09 Gbp with an N50 scaffold length of 65.1 Mbp, and a total of 118 scaffolds, generated using PacBio long reads and Bionano optical map technology. We annotated 256K gene models and found 58% of the genome to be composed of transposable elements. To demonstrate the applicability of the reference genome, we evaluated population structure and estimated genetic diversity in P. pratensis collected from three North American prairies, two in Manitoba, Canada and one in Colorado, USA. Our results support previous studies that found high genetic diversity and population structure within the species. The reference genome and annotation will be an important resource for turfgrass breeding and study of bluegrasses.

plant biology↗

bioRxiv2019

High-resolution 3D imaging and topological mapping of the lymph node conduit system

The conduit network is a hallmark of lymph node microanatomy, but lack of suitable imaging technology has prevented comprehensive investigation of its topology. We employed an extended-volume imaging system to capture the conduit network of an entire murine lymph node ({approx}280,000 segments). The extensive 3D images provide a comprehensive overview of the regions supplied by conduits including perivascular sleeves, and distinctive \"follicular reservoirs\" within B cell follicles, surrounding follicular dendritic cells. A 3D topology map of conduits within the T cell zone showed homogeneous branching, but conduit density was significantly higher in the superficial T cell zone compared to the deep zone, where distances between segments are sufficient for T cells to lose contact with fibroblastic reticular cells. This topological mapping of the conduit anatomy can now aid modeling of its roles in lymph node function, as we demonstrate by simulating T cell motility in the different T cell zones.

immunology↗