The complete plastome of macaw palm [Acrocomia aculeata (Jacq.) Lodd. ex Mart.] and extensive molecular analyses of the evolution of plastid genes in Arecaceae

Abstract

The plastome of macaw palm was sequenced allowing analyses of evolution and molecular markers. Additionally, we demonstrated that more than half of plastid protein-coding genes in Arecaceae underwent positive selection. Macaw palm is a native species from tropical and subtropical Americas. It shows high production of oil per hectare reaching up to 70% of oil content in fruits and an interesting plasticity to grow in different ecosystems. Its domestication and breeding are still in the beginning, which makes the development of molecular markers essential to assess natural populations and germplasm collections. Therefore, we sequenced and characterized in detail the plastome of macaw palm. A total of 221 SSR loci were identified in the plastome of macaw palm. Additionally, eight polymorphism hotspots were characterized at level of subfamily and tribe. Moreover, several events of gain and loss of RNA editing sites were found within the subfamily Arecoideae. Aiming to uncover evolutionary events in Arecaceae, we also analyzed extensively the evolution of plastid genes. The analyses show that highly divergent genes seem to evolve in a species-specific manner, suggesting that gene degeneration events may be occurring within Arecaceae at the level of genus or species. Unexpectedly, we found that more than half of plastid protein-coding genes are under positive selection, including genes for photosynthesis, gene expression machinery and other essential plastid functions. Furthermore, we performed a phylogenomic analysis using whole plastomes of 40 taxa, representing all subfamilies of Arecaceae, which placed the macaw palm within the tribe Cocoseae. Finally, the data showed here are important for genetic studies in macaw palm and provide new insights into the evolution of plastid genes and environmental adaptation in Arecaceae.

The Complete Plastome Sequences of Eleven Capsicum Genotypes: Insights into DNA Variation and Molecular Evolution

“…In the present study, SSRs were mainly localized in intergenic regions and in the LSC. This finding is in agreement with previous results for species belonging to Solanaceae, Poaceae, and Arecaceae [ 5 , 30 , 54 , 55 ]; indeed, the low number of SSRs within IRs is due to its duplicative nature that implies copy-correction activity [ 54 ]. Mono-(p1), di-(p2), and trinucleotide (p3) SSR types were detected in all genotypes under investigation.…”

“…In particular, SNPs present in psbA and atpI were specific for the C B complex, whereas SNPs in atpB allowed discrimination among species belonging to the C A complex. The use of SSRs in intergenic regions as molecular markers was widely suggested, since these regions evolve faster than coding sequences [ 31 , 55 ]. Among them, we identified the variation in the atpB–rbcL region, already reported by Walsh and Hoot [ 20 ], that elucidated relationships between Capsicum spp., thereby contributing to their taxonomic grouping.…”

Complete chloroplast genome sequence of Fagopyrum dibotrys: genome features, comparative analysis and phylogenetic relationships

“…Because the NDH monomer is sensitive to high light intensity, we deduced that the genes encoded NAD(P)H dehydrogenase might have changed drastically to develop new functions for stress resistance 45 , 46 . Previous research reported that genes belong to subunits of cytochrome were under positive selection in some species 47 , 48 , we therefore inferred that petL for cytochrome b6/f complex subunit proteins may have a high evolution rate in the cp genome of F. luojishanense . The gene rpoC2 was associated with PPR7 protein, we thus speculated it may have coevolved with nuclear genes 49 .…”

The complete plastid genomes of Ophrys iricolor and O. sphegodes (Orchidaceae) and comparative analyses with other orchids

“…sphegodes with few differences: ccs A (5 sites), atp A (3 sites), psa B (2 sites), rps 14 (2 sites), atp F (2 sites) ( S2 Table ) which suggest a general conservation of the RNA editing mechanism within Ophrys but also that RNA editing evolution accumulated enough differences to differentiate two Ophrys species. A previous study has also found that the number of RNA editing sites predicted for protein-coding genes in orchids species is high in comparison with other monocots [ 51 ].Likelihood ratio test between a null model and an alternative model carried out following [ 52 ] shows that 24 genes are under positive selection ( S3 Table ); overall, the most divergent genes have the stronger signatures of positive selection ( S2 Fig ). In details, the positively selected genes were involved in different essential functions such as photosynthesis, PSII ( psb A, psb B, psb E, psb H, psb M, psbN genes), large subunits of rubisco ( rbc L), ATP synthase ( atp I gene), cytochrome b6f ( pet B gene), subunits of RNA polymerase ( rpo A, rpo B, rpo C1, rpo C2 genes), RNA maturation ( mat K gene), ribosomal proteins ( rpl 20, rpl 22, rpl 32, rpl 33, rps 12, rps 19 genes), fatty acid biosynthesis ( acc D gene), cytochrome biosynthesis ( ccs A gene), import of protein in the plastid ( ycf 1 gene), and unknown function ( ycf 2 gene).…”

“…In particular, and as already suggested for other monocots as Arecaceae, many tropical orchid species grow as epiphytes in tropical forests and are shade adapted. The transition to the terrestrial habitus of all temperate orchid lineages (as Ophrys ) may have promoted a new selective pressure for improving the photosynthesis efficiency under the new terrestrial ecological conditions [ 52 ].…”