Biology subjects

Hartwick, N.

Publications and source records attributed to Hartwick, N..

3 recordsLinked to original sources

bioRxiv2021

The genetic and epigenetic landscape of the Arabidopsis centromeres

Centromeres attach chromosomes to spindle microtubules during cell division and, despite this conserved role, show paradoxically rapid evolution and are typified by complex repeats. We used ultra-long-read sequencing to generate the Col-CEN Arabidopsis thaliana genome assembly that resolves all five centromeres. The centromeres consist of megabase-scale tandemly repeated satellite arrays, which support high CENH3 occupancy and are densely DNA methylated, with satellite variants private to each chromosome. CENH3 preferentially occupies satellites with least divergence and greatest higher-order repetition. The centromeres are invaded by ATHILA retrotransposons, which disrupt genetic and epigenetic organization of the centromeres. Crossover recombination is suppressed within the centromeres, yet low levels of meiotic DSBs occur that are regulated by DNA methylation. We propose that Arabidopsis centromeres are evolving via cycles of satellite homogenization and retrotransposon-driven diversification. One-sentence summaryLong read sequencing and assembly of the Arabidopsis centromeres reveals their genetic and epigenetic topography.

genomics↗

bioRxiv2021

LoopViz: A uLoop Assembly Clone Verification Tool for Nanopore Sequencing Reads

Cloning has been an integral part of most laboratory research questions and continues to be an essential tool in defining the genetic elements determining life. Cloning can be difficult and time consuming as each plasmid is unique to a particular project and each sequence must be carefully selected, cloned and sequenced to determine correctness. Loop assembly (uLOOP) is a recursive, Golden Gate-like assembly method that allows rapid cloning of domesticated DNA fragments to robustly refactor novel pathways. With uLOOP methodologies, one can clone several sequences directionally to generate a library of transcriptional units (TUs) in plasmids within a single reaction but analysis of the plasmid population has been impeded by current sequencing and analysis methods. Here we develop LoopViz, a quality control tool that quantifies and visualizes results from assembly reactions using long-read Oxford Nanopore Technologies (ONT) sequencing. LoopViz identifies full length reads originating from a single plasmid in the population, and visualizes them in terms of a user input DNA fragments file, and provides QC statistics. This methodology enables validation and analysis of cloning and sequencing reactions in less than a day, determination of the entire plasmids sequence, and sequencing through repetitive meta-regions that cannot be meaningfully assembled. Finally, LoopViz represents a new paradigm in determining plasmid sequences that is rapid, cost-effective and performed in-lab. LoopViz is made publicly available at https://gitlab.com/marielelensink325/loopseq

bioinformatics↗

bioRxiv2020

Genome and time-of-day transcriptome of Wolffia australiana link morphological extreme minimization with un-gated plant growth

Wolffia is the fastest growing plant genus on Earth with a recorded doubling time of less than a day. Wolffia has a dramatically reduced body plan, primarily growing through a continuous, budding-type asexual reproduction with no obvious phase transition. Most plants are bound by the 24-hour light-dark cycle with the majority of processes such as gene expression partitioned or phased to a specific time-of-day (TOD). However, the role that TOD information and the circadian clock plays in facilitating the growth of a fast-growing plant is unknown. Here we generated draft reference genomes for Wolffia australiana (Benth.) Hartog & Plas to monitor gene expression over a two-day time course under light-dark cycles. Wolffia australiana has the smallest genome size in the genus at 357 Mb and has a dramatically reduced gene set at 15,312 with a specific loss of root (WOX5), vascular (CASP), circadian (TOC1), and light-signaling (NPH3) genes. Remarkably, it has also lost all but one of the NLR genes that are known to be involved in innate immunity. In addition, only 13% of its genes cycle, which is far less than in other plants, with an overrepresentation of genes associated with carbon processing and chloroplast-related functions. Despite having a focused set of cycling genes, TOD cis-elements are conserved in W. australiana, consistent with the overall conservation of transcriptional networks. In contrast to the model plants Arabidopsis thaliana and Oryza sativa, the reduction in cycling genes correlates with fewer pathways under TOD control in Wolffia, which could reflect a release of functional gating. Since TOD networks and the circadian clock work to gate activities to specific times of day, this minimization of regulation may enable Wolffia to grow continuously with optimal economy. Wolffia is an ideal model to study the transcriptional control of growth and the findings presented here could serve as a template for plant improvement.

plant biology↗