Comparative chloroplast genomics of 75 Asparagus species reveals conserved genome architecture, gene-specific positive selection, and chloroplast–nuclear phylogenetic discordance

Abstract

The chloroplast genome offers a compact, maternally inherited resource for resolving evolutionary relationships in plants, yet in Asparagus it has received limited genus-wide attention relative to recent nuclear genomic efforts. Here, we de novo assembled 35 chloroplast genomes: one from newly generated sequencing data and 34 from publicly available sequencing reads downloaded from the National Center for Biotechnology Information, and integrated them with 40 published genomes, yielding 75 species in total. All genomes retained the canonical quadripartite architecture, with conserved genome size (155,654 − 157,211 bp), gene content (131 genes; 113 unique), and inverted-repeat boundaries, indicating strong structural stasis despite the genus’s ecological and morphological diversity. Selection analyses identified episodic diversifying selection in ycf1 , ccsA , rps8 , and rbcL , with ycf1 and rbcL showing the strongest signals, which were corroborated by PAML site-model analysis; ccsA showed a signal restricted to two codon sites and rps8 a gene-wide signal not recovered at individual sites. The ccsA signal was recovered by PAML branch-site analysis; the rps8 signal was not. Nucleotide diversity was substantially higher in non-coding than coding regions, highlighting rps15 and ycf1 among coding loci and psbC - trnS-UGA , ccsA - ndhD , and rps3 - rpl22 among intergenic spacers as candidate species-identification markers. Maximum-likelihood analysis recovered twelve previously recognized infrageneric clades with strong within-clade support and a well-supported backbone in the complete chloroplast genome tree but weaker support in the CDS-based tree. Quantitative comparison with the published nuclear species tree (59 shared species) revealed substantial topological discordance at backbone nodes (Robinson–Foulds distance = 72, normalized RF = 0.64), indicating only partial congruence between the chloroplast and nuclear phylogenies. These results establish the first genus-wide chloroplast genome resource for Asparagus , clarify the balance of structural conservation and gene-specific selection shaping its evolution, and provide a foundation for integrating organellar and nuclear data in future phylogenomic and conservation-genetic studies of this medicinally and economically important genus.