A5063553871- Chromosomal and Genetic Variations
- Epigenetics and DNA Methylation
- Genomics and Phylogenetic Studies
- Single-cell and spatial transcriptomics
- Plant tissue culture and regeneration
- Plant nutrient uptake and metabolism
- Photosynthetic Processes and Mechanisms
- Plant Molecular Biology Research
- Genomics and Chromatin Dynamics
- Cancer Genomics and Diagnostics
- Plant Reproductive Biology
- Cytomegalovirus and herpesvirus research
- CRISPR and Genetic Engineering
- Congenital heart defects research
- Genetic Syndromes and Imprinting
- RNA and protein synthesis mechanisms
Salk Institute for Biological Studies
2017-2021
Methylation and the single neuronal cell The presence or absence of methylation on chromosomal DNA can drive repress gene expression. Now, a comprehensive map variation in populations, including between-species comparison, illustrates how epigenetic diversity plays important roles development. Luo et al. examined is both similar different within neurons at single-nucleus level humans mice. They identified 16 mouse 21 human clusters, with greater complexity excitatory deep brain layers than...
Abstract The handheld Oxford Nanopore MinION sequencer generates ultra-long reads with minimal cost and time requirements, which makes sequencing genomes at the bench feasible. Here, we sequence gold standard Arabidopsis thaliana genome (KBS-Mac-74 accession) on sequencer, assemble using typical consumer computing hardware (4 Cores, 16 Gb RAM) into chromosome arms (62 contigs an N50 length of 12.3 Mb). We validate contiguity quality assembly two independent single-molecule technologies,...
Abstract Single-cell DNA methylome profiling has enabled the study of epigenomic heterogeneity in complex tissues and during cellular reprogramming. However, broader applications method have been impeded by modest quality sequencing libraries. Here we report snmC-seq2, which provides improved read mapping, reduced artifactual reads, enhanced throughput, as well increased library complexity coverage uniformity compared to snmC-seq. snmC-seq2 is an efficient strategy suited for large-scale...
The bacterium Agrobacterium tumefaciens has been the workhorse in plant genome engineering. Customized replacement of native tumor-inducing (Ti) plasmid elements enabled insertion a sequence interest called Transfer-DNA (T-DNA) into any genome. Although these transfer mechanisms are well understood, detailed understanding structure and epigenomic status events was limited by current technologies. Here we applied two single-molecule technologies analyzed Arabidopsis thaliana lines from three...
Rootless plants in the genus Wolffia are some of fastest growing known on Earth. have a reduced body plan, primarily multiplying through budding type asexual reproduction. Here, we generated draft reference genomes for australiana (Benth.) Hartog & Plas, which has smallest genome size at 357 Mb and set predicted protein-coding genes about 15,000. Comparison between multiple high-quality sequences from W. clones confirmed loss several hundred that highly conserved among flowering plants,...
Abstract Recent experimental advances have enabled high-throughput single-cell measurement of gene expression, chromatin accessibility and DNA methylation. We previously used integrative non-negative matrix factorization (iNMF) to jointly learn interpretable low-dimensional representations from multiple datasets using dataset-specific shared metagene factors. These factors provide a principled, quantitative definition cellular identity how it varies across biological contexts. However,...
Abstract While many evolutionary questions can be answered by short read re-sequencing, presence/absence polymorphisms of genes and/or transposons have been largely ignored in large-scale intraspecific studies. To enable the rigorous analysis such variants, multiple high quality and contiguous genome assemblies are essential. Similarly, while based on reads made genomics accessible for non-reference species, these limitations due to low contiguity. Long-read sequencers long-read technologies...
Abstract Over the last 35 years soil bacterium Agrobacterium tumefaciens has been workhorse tool for plant genome engineering. Replacement of native tumor-inducing (Ti) plasmid elements with customizable cassettes enabled insertion a sequence interest called Transfer DNA (T-DNA) into any genome. Although these T-DNA transfer mechanisms are well understood, detailed understanding structure and epigenomic status events was limited by current technologies. To fill this gap, we analyzed...
Single-cell DNA methylome profiling has enabled the study of epigenomic heterogeneity in complex tissues and during cellular reprogramming. However, broader applications method have been impeded by modest quality sequencing libraries. Here we report snmC-seq2, which provides improved read mapping, reduced artifactual reads, enhanced throughput, as well increased library complexity coverage uniformity compared to snmC-seq. snmC-seq2 is an efficient strategy suited for large scale single-cell studies.
Abstract Wolffia is the fastest growing plant genus on Earth with a recorded doubling time of less than day. has dramatically reduced body plan, primarily through continuous, budding-type asexual reproduction no obvious phase transition. Most plants are bound by 24-hour light-dark cycle majority processes such as gene expression partitioned or phased to specific time-of-day (TOD). However, role that TOD information and circadian clock plays in facilitating growth fast-growing unknown. Here...