The Capsella rubella genome and the genomic consequences of rapid mating system evolution

Abstract

3 1 l e t t e r sThe shift from outcrossing to selfing is common in flowering plants 1,2 , but the genomic consequences and the speed at which they emerge remain poorly understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self compatible <200,000 years ago. We report a C. rubella reference genome sequence and compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor Capsella grandiflora. We found a clear shift in the expression of genes associated with flowering phenotypes, similar to that seen in Arabidopsis, in which self fertilization evolved about 1 million years ago. Comparisons of the two Capsella species showed evidence of rapid genome-wide relaxation of purifying selection in C. rubella without a concomitant change in transposable element abundance. Overall we document that the transition to selfing may be typified by parallel shifts in gene expression, along with a measurable reduction of purifying selection.

The BOY NAMED SUE Quantitative Trait Locus Confers Increased Meiotic Stability to an Adapted Natural Allopolyploid of Arabidopsis

“…Two were consistent with rearrangement between the A. lyrata and A. arenosa genomes. One of these was also confirmed by the karyotypes of several of our dosage variants ( Figure 7B, inset) and was also detected in a population of Capsella rubella (Slotte et al, 2013). Taken together, these results suggest that it might originate from erroneous assembly of that particular segment of the A. lyrata genome (Slotte et al, 2013).…”

“…One of these was also confirmed by the karyotypes of several of our dosage variants ( Figure 7B, inset) and was also detected in a population of Capsella rubella (Slotte et al, 2013). Taken together, these results suggest that it might originate from erroneous assembly of that particular segment of the A. lyrata genome (Slotte et al, 2013). Only the third rearrangement was consistent with an inversion between the two parental genomes (A. arenosa Care-1 and A. suecica Sue-1).…”

Two linked pairs of Arabidopsis TNL resistance genes independently confer recognition of bacterial effector AvrRps4

“…We used nucleotidenucleotide BLAST 2.2.29 þ 58 , specifically the megablast algorithm 38 , to search ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms7338 the predicted coding sequence databases from A. lyrata 39 , C. rubella 40 and B. rapa 41 with the A. thaliana Col-0-coding sequences of RRS1, RPS4, RRS1B and RPS4B. Following the identification of putatively orthologous genes, MUSCLE 59 and CLUSTAL W 60 nucleotide and protein sequence alignments were used to generate phylogenetic trees using the Neighbour-Joining and Maximum Likelihood (Tamura-Nei model) methods, each with 1,000 bootstraps.…”

“…NATURE COMMUNICATIONS | DOI: 10.1038/ncomms7338 ARTICLE A. thaliana. Using the nucleotide sequences of each gene from each pair in megablast searches 38 , we found that in the genomes of the sister species Arabidopsis lyrata 39 , and the closely related species Capsella rubella 40 , there are distinct putatively orthologous pairs matching both the 'A' pair (RRS1/RPS4) and 'B' pair (RRS1B/RPS4B). In A. lyrata, we also found an apparent duplication of the 'B' pair, resulting in a paralogous 'C' pair with a high level of identity to the 'B' pair (Fig.…”

Genomic analysis reveals major determinants ofcis-regulatory variation inCapsella grandiflora

“…An example script with all program versions and flags used for bioinformatic analyses, filtered vcf files, and a collated dataset and scripts used to identify genomic predictors of ASE are available on Figshare: https://doi.org/10.17045/sthlmuni.c.3654650. structure (20) and a large, stable effective population size (21,22). Indeed, selection on both protein-coding (23) and regulatory regions (18) is highly efficient in C. grandiflora, and high levels of polymorphism enhance the power to detect cis-regulatory variation and quantify selection.…”