Biased gene introgression and adaptation in face of chloroplast capture in Aquilegia amurensis

Chloroplast capture, a phenomenon that can occur through interspecific hybridization and introgression, has been frequently suggested as an explanation for cytonuclear discordance in plants. In theory, the captured donor chloroplasts may not cooperate with the recipient nuclear genome, especially chloroplast-targeted nuclear genes. However, relatively few studies have documented the mechanisms of cytonuclear coevolution and its potential species differentiation and possible functional differences in the face of chloroplast capture. To explore this crucial question, we chose the Aquilegia genus, which is known for having minimal sterility among the species, and we inferred that A. amurensis captured the plastome of A. parviflora based on cytonuclear discordance and gene flow between these two species. We focused on the introgression region and its differentiation with closely related species, especially its composition in a chloroplast capture scenario. We found that nuclear genes encodi..., The raw reads were quality-checked using FASTQC (Andrews, 2010). The available chloroplast genome (MH142265) of Semiaquilegia adoxoides and the nuclear reference genome of Aquilegia coerulae (v3.1) were downloaded from GenBank and Phytozome, respectively. Then, we used Burrows-Wheeler Aligner (BWA) (Li & Durbin, 2009) to map the genomic reads of each individual against the chloroplast and nuclear reference at the default setting. Then, the single nucleotide polymorphisms (SNPs) were detected using SAMtools’ mpileup command (Li et al., 2009; Li, 2011) at the default setting appropriate for diploid organisms. Raw SNPs were filtered using VCFtools, requiring a minimum depth (DP) of 3, minimum mapping quality (MQ) of 30, minor allele frequency (MAF) of 0.04, and maximum missing rate of 0.5, and all non-biallelic SNPs were filtered, which may be caused by sequencing. Additionally, each sample of Paraquilegia microphylla and Semiaquilegia adoxoides (SRX127267) was used as an outgroup for ..., , ass_filter_CHR_genus_filter.recode.vcf

* SNPs across nuclear genome of 17 Aquilegia species

cp_aquilegia_samtools.filter.recode.vcf

* SNPs across chloroplast genome of 17 Aquilegia species

aquilegia_hua.recode.vcf

* SNPs across nuclear genome of four species

supplementary_figures.docx

* fig. S1 - fig. S7

supplementary_Tables.xlsx

* Tab. S1-Tab. S10

ass_filter_CHR_genus_filter.recode.min4.fasta.treefile

* The Newick format file of the phylogenetic tree based on the dataset of nuclear genome of 17 Aquilegia species

gene_seq.fasta.treefile

* The Newick format file of the phylogenetic tree based on the dataset of nuclear gene regions of 17 Aquilegia species

inter_seq.fasta.treefile

* The Newick format file of the phylogenetic tree based on the dataset of nuclear intergenic regions of 17 Aquilegia species

cp_aquilegia_samtools.filter.recode.min4.fasta.treefile

* The Newick format file of the phylogenetic tree based on the dataset of chlorolplast genome of ...