Legends for Supporting Information
Figure S1. Schemes for recombination between chloroplast IR-1 (a) or DR-1 (b)
repeats.
IR-1 and DR-1 loci and their flanking regions are represented schematically:
boxes represent exons, and lines between boxes represent introns or noncoding flanking
sequences. IR-1 and DR-1 repeats are represented by triangles surrounded by boxes.
Primers used in the qPCR assay are represented by arrows. Copy 1 and 2 denote copies of
parental sequences, and type 1 and 2 denote reciprocal recombination products.
Recombination between IR-1 repeats causes truncation of trnG and rpl16 (A).
Recombination between DR-1 repeats causes chimerization of psaA and psaB, because the
reading frame of the recombination product is not shifted relative to that of psaA or psaB
(b).
Figure S2. Analysis of DNA and RNA in RECA2 KO chloroplasts.
(a) Relative copy
number of IR-1 or DR-1 parental sequences. Relative copy number of copy 1 and 2 of IR-1
or DR-1 determined by qPCR was normalized by that of nuclear gene actin. Data from
biological replicates are expressed as means ± SD (n = 3).
(b) RT-PCR analysis of
psaA-psaB chimeric transcript. psaA-psaB chimeric transcripts derived from DNA
recombined between DR-1 was amplified using total RNA with (+) or without (-) reverese
transcription (RT). Actin was used as an internal control.
Table S1. Shorter repeats involved in P. patens chloroplast genomic instability.
Table S2. primers used in this study