ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2017
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.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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60 citing papers in PubMed, 108 citations in OpenAlex.
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- Comparative chloroplast genomes of Sophora species: identification of variable DNA markers and phylogenetic relationships within the genus.BMC plant biology · 2025Article
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- Comparative analysis of chloroplast genomes reveals molecular evolution and phylogenetic relationships within the Papilionoideae of Fabaceae.BMC plant biology · 2025Article
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- The complete chloroplast genomes and comparative study of the two tung trees of Vernicia (Euphorbiaceae).BMC genomics · 2024Article
- Comparative Plastome Analysis Between Endangered Mangrove SpeciesEcology and evolution · 2024Article
- Comparative analysis of chloroplast genomes in ten holly (Ilex) species: insights into phylogenetics and genome evolution.BMC ecology and evolution · 2024Article
- Plastome evolution of Engelhardia facilitates phylogeny of Juglandaceae.BMC plant biology · 2024Article
- Comparative chloroplast genomes of Dactylicapnos species: insights into phylogenetic relationships.BMC plant biology · 2024Article
- Dynamic changes in the plastid and mitochondrial genomes of the angiosperm Corydalis pauciovulata (Papaveraceae).BMC plant biology · 2024Article
- Genomic exploration of Sesuvium sesuvioides: comparative study and phylogenetic analysis within the order Caryophyllales from Cholistan desert, Pakistan.BMC plant biology · 2023Article
- Complete Chloroplast Genomes ofCurrent genomics · 2023Article
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Authors and funding
11 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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