DOI: 10.5061/dryad.kprr4xh80
title: Biased gene introgression and adaptation in face of chloroplast capture in Aquilegia amurensis

description: 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 encoding
 cytonuclear enzyme complexes or organelle localized (CECs) were
 significantly enriched in the introgression regions, indicating that the
 CEC genes of chloroplast donor species were selectively retained and
 displaced the original CEC genes in chloroplast receptor species due to
 cytonuclear interactions during introgression. Notably, the intrinsic
 factor of cytonuclear compatibility may have a higher degree of
 evolutionary distance for the introgressed CEC genes between A. amurensis
 and A. parviflora. Introgression from A. parviflora promotes the
 differentiation of A. amurensis and A. japonica. Furthermore, we found
 that one of the overrepresented gene ontology terms in these introgressed
 genes was terpene synthase activity (GO: 0010333) in which more than
 one-third of the genes were CEC genes, showing that A. amurensis had
 similar release patterns for terpenes in flowers of A. parviflora when
 compared with A. japonica. Altogether, this study helps to clarify the
 mechanisms of cytonuclear coevolution, species differentiation and
 functional differences in face of chloroplast capture and highlights a
 critical role of chloroplast capture in adaptation.
description: The raw reads were
 quality-checked using FASTQC (Andrews, 2010). The available chloroplast genome
 (MH142265) of <em>Semiaquilegia</em>
 <em>adoxoides</em> and the nuclear reference genome of
 <em>Aquilegia</em> <em>coerulae</em> (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 <em>Paraquilegia</em>
 <em>microphylla</em> and <em>Semiaquilegia</em>
 <em>adoxoides</em> (SRX127267) was used as an outgroup for
 downstream analyses, and the approach of variant calling was the same as
 that above.
description: 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 17 Aquilegia species