Robert Laport
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Robert Laport
@robertlaport.bsky.social
840 followers 660 following 13 posts
College of Idaho; Assistant Professor & Director of the Herbarium; Plant Evolutionary Ecologist; Botanist; Polyploidy; Views my own
www.robertlaport.com
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Reposted by Robert Laport
stairwaytokevin.bsky.social
In the most extreme case, an accession from Armenia (Ames 32873) has nearly unprecedented levels of genomic rearrangement: only 25% syntenic to the reference genotype. However, those rearrangements are entirely located in the pericentromeres and don't contribute to higher levels of gene PAV. 4/
Figure 3 | Macrosynteny and genome structure across the Brassicaceae. Horizontal blue/black/orange bands represent the chromosomes of Arabidopsis thaliana, A. lyrata, MN106, and Brassica rapa (top to bottom). Chromosomes are ordered by their number from left to right. Colors represent genomic content binned hierarchically in sliding windows (400kb-overlapping 500kb) as follow: (1) within a gene annotation (including intron and UTR, orange), (2) within EDTA-annotated repeats categorized as Ty3, (3) Ty1 (copia), (4) within another repeat category, or (5) un-annotated. Grey bands are sequence-based syntenic blocks between each pair of genomes. Pennycress and B. rapa are phylogenetically proximate (both in Brassicodae supertribe), but have reduced synteny in part because of genome reshuffling in B. rapa following a whole-genome triplication event. The seven pennycress genome assemblies (horizontal bars) are binned into TRASH-defined centromeres (orange), pericentromeres (dark blue), chromosome arms (light blue) and telomeres (dark red). The colors along the chromosome segments scale physically with the size of the bin, except that centromeres and telomeres have a 1pt buffer to make it easier to see these typically small regions. Each genome is connected to its neighbor by grey polygons that represent sequence-based syntenic blocks. Plots, genomic bins, and syntenic blocks were built with DEEPSPACE (github.com/jtlovell/DEEPSPACE). Genome-wide classification of sequence alignments between each genome and the MN106 reference genome from SyRI. Alignments are broken down into syntenic, not alignable to MN106, duplicated, inverted, inverted and translocated, and “highly-diverged region”
September 28, 2025 at 5:25 PM
Reposted by Robert Laport
stairwaytokevin.bsky.social
Genome size variation (455Mb-466Mb) and gene level presence/absence variation between genotypes was small (~80% core), but the pangenomic variation in genome graph was larger (~53% core), suggesting more going on beneath the surface. 2/
Figure 2 | Pan-genome variation in pennycress. A The amount of sequence in the genome graph that is shared by different numbers of haplotypes (assemblies). This figure only represents sequence in the final graph and does not contain sequences ‘clipped out.’ B Breakdown of core, dispensable, and unique orthogroups among our seven genomes. C Growth curves describing patterns of 31-mer sharing across assemblies; a steeper curve indicates a smaller degree of k-mer sharing among assemblies for that sequence class.
September 28, 2025 at 5:25 PM
Reposted by Robert Laport
stairwaytokevin.bsky.social
Whole-genome alignments revealed pennycress has nearly dichotomous genome compartmentalization: huge gene-poor pericentromeric regions (~300Mb; <1% genic) with frequent rearrangements and highly syntenic gene-rich chromosome arms (~150Mb; ~20% genic). What we call a "two-speed" genome structure. 3/
Figure 3 | Macrosynteny and genome structure across the Brassicaceae. Horizontal blue/black/orange bands represent the chromosomes of Arabidopsis thaliana, A. lyrata, MN106, and Brassica rapa (top to bottom). Chromosomes are ordered by their number from left to right. Colors represent genomic content binned hierarchically in sliding windows (400kb-overlapping 500kb) as follow: (1) within a gene annotation (including intron and UTR, orange), (2) within EDTA-annotated repeats categorized as Ty3, (3) Ty1 (copia), (4) within another repeat category, or (5) un-annotated. Grey bands are sequence-based syntenic blocks between each pair of genomes. Pennycress and B. rapa are phylogenetically proximate (both in Brassicodae supertribe), but have reduced synteny in part because of genome reshuffling in B. rapa following a whole-genome triplication event. The seven pennycress genome assemblies (horizontal bars) are binned into TRASH-defined centromeres (orange), pericentromeres (dark blue), chromosome arms (light blue) and telomeres (dark red). The colors along the chromosome segments scale physically with the size of the bin, except that centromeres and telomeres have a 1pt buffer to make it easier to see these typically small regions. Each genome is connected to its neighbor by grey polygons that represent sequence-based syntenic blocks. Plots, genomic bins, and syntenic blocks were built with DEEPSPACE (github.com/jtlovell/DEEPSPACE).
September 28, 2025 at 5:25 PM