Selection on positive length variants contributed to genome shrinkage in Arabidopsis Robin Burns, Magnus Nordborg Gregor Mendel Institute of Plant Molecular Biology, Vienna BioCenter Introduction The genome of the outcrossing perennial A. lyrata (207Mb) is larger than that of the selfing annual A. thaliana (125Mb), despite the two species diverging only about 6 Mya. This difference was previously attributed to numerous small deletions occuring in A. thaliana after the species split [1], and this was based on the use of a single reference genome for both species. Could, instead of just deletions, selection acting against positive length variants from standing variation have contibuted to the smaller genome size of A. thaliana? By comparing whole genome alignments for multiple long read assemblies of both species. We find that these indels are segregating in A. lyrata in agreement with selection against positive length variants contributing to genome shrinkage. Examination of short reads for a population of A. lyrata is ongoing. or a b A. thaliana reference (125 Mb) A. lyrata reference (207 Mb) ancestor (~200 Mb - family average) ancestral population A. thaliana population A. lyrata population / = Presence/Absence of Indels 1. More than half the A. lyrata reference is missing from A. thaliana 2. Long read assemblies show that these same indels are segregating in A. lyrata 3. Kmer approach to calling presence or absence of indels in short reads A. ly A. th insertion Whole Genome Alignment k-mers 1. 2. 3. presence/absence Chromosome level assembly of 2 Nanopore A. lyrata genomes 7 published A. thaliana long read assemblies available [2] 5. References 4. Conclusions and follow up Search for matching k-mers in short Illumina reads in a population of A. lyrata lines k-mers specific to sequences present in A. lyrata reference but missing from A. thaliana Aly.Unaligned Ath.Unaligned Aly.Aligned Ath.Aligned Alyrata Athaliana 0.0e+00 5.0e+07 1.0e+08 1.5e+08 2.0e+08 Base−pairs N unassigned DNAtes RNAtes intergenic introns CDS a ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ● ● ●●●●● ● 0e+00 3e+07 6e+07 9e+07 0e+00 1e+06 2e+06 Size of indel Cumulative length species ● Alyrata b ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ● ●●●● ● 0e+00 1e+07 2e+07 3e+07 4e+07 0 20000 40000 60000 Size of indel Cumulative length species ● Athaliana c 0 30 60 lat Location of Arabidopsis lyrata sub-species A. lyrata lyrata A. lyrata arenicola A. lyrata petraea A. lyrata petraeaumbrosa Self compatible Self incompatible 4. 0 20000 40000 60000 2 4 6 Athaliana Individual Frequency count a 0.0e+00 2.5e+07 5.0e+07 7.5e+07 1.0e+08 Deletions Base pairs Species Al At b ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ● ● ● ● 0e+00 1e+07 2e+07 3e+07 0 500000 1000000 1500000 2000000 Size of indel Cumulative length (34Mb), N=21748 c Population level whole genome alignments reveal that regions related to genome size differences between the A. thaliana and A. lyrata references are segregating in A.lyrata. Caution for such future comparions. SNPs around the locations will be examined along with kmer analysis for a population of A. lyrata. How does selection act on these regions in A. lyrata. Different mating types? Use of outgroups hindere