The evolutionary fate of the chloroplast and nuclear rps16 genes as revealed through the sequencing and comparative analyses of four novel legume chloroplast genomes from Lupinus

Abstract

The Fabaceae family is considered as a model system for understanding chloroplast genome evolution due to the presence of extensive structural rearrangements, gene losses and localized hypermutable regions. Here, we provide sequences of four chloroplast genomes from the Lupinus genus, belonging to the underinvestigated Genistoid clade. Notably, we found in Lupinus species the functional loss of the essential rps16 gene, which was most likely replaced by the nuclear rps16 gene that encodes chloroplast and mitochondrion targeted RPS16 proteins. To study the evolutionary fate of the rps16 gene, we explored all available plant chloroplast, mitochondrial and nuclear genomes. Whereas no plant mitochondrial genomes carry an rps16 gene, many plants still have a functional nuclear and chloroplast rps16 gene. Ka/Ks ratios revealed that both chloroplast and nuclear rps16 copies were under purifying selection. However, due to the dual targeting of the nuclear rps16 gene product and the absence of a mitochondrial copy, the chloroplast gene may be lost. We also performed comparative analyses of lupine plastomes (SNPs, indels and repeat elements), identified the most variable regions and examined their phylogenetic utility. The markers identified here will help to reveal the evolutionary history of lupines, Genistoids and closely related clades.

Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole‐genome duplications in Brassica

“…Plastid genome assemblies were performed using the pipeline previously published by Keller et al . (). Briefly, de novo assemblies were built using the organelle assembler (Coissac et al ., ).…”

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“…Aconitum due to the loss of one CDS region (Table 2). As has been revealed in other studies, the functional loss of the rps16 gene might be compensated by the dual targeting of the nuclear rps16 gene product (Keller et al, 2017).…”

The Intertwined Chloroplast and Nuclear Genome Coevolution in Plants

“…Similarly, faster evolution has been observed in the clpP gene in Mimosoid [29]. In Lupinus (Fabaceae), two hypervariable regions have been identified (ycf1 gene and psaA-ycf4 region) and are characterized by high numbers of indels (with length usually superior to 20 bp) and mutations [22].…”

“…This relaxation of selective constraint allows for non-sense mutations that may render the chloroplast copy non-functional [19,20]. In addition, genes can become non-functional following the loss of their splicing capacity, as observed for rps16 [21,22]. The plastome gene content reduction is even more pronounced in non-chlorophyll organisms, such as parasites and obligate symbionts.…”