Highly accelerated rates of genomic rearrangements and nucleotide substitutions in plastid genomes of Passiflora subgenus Decaloba

Plastome Evolution in Dolomiaea (Asteraceae, Cardueae) Using Phylogenomic and Comparative Analyses

“…Due to the lack of recombination, usually uniparental inheritance and high copy numbers per cells (Wicke et al, 2011;Ruhlman and Jansen, 2014), whole plastome sequences have been extensively used in reconstructing the plant Tree of Life (e.g., Jansen et al, 2007;Moore et al, 2007;Ruhfel et al, 2014;Gitzendanner et al, 2018;Li et al, 2019). Comparative plastome studies provide the opportunity to explore sequence variation and the molecular evolutionary patterns associated with genome rearrangements (e.g., Knox, 2014;Weng et al, 2014;Rabah et al, 2019;Shrestha et al, 2019) as well as gene loss, duplication, and transfer events (e.g., Downie and Jansen, 2015;Wu and Chaw, 2016;Sun et al, 2017), while also detecting signatures of positive selection in plastid genes facilitating our understanding of plants adapting to extreme environments (e.g., alpine areas) (Bock et al, 2014;Jiang et al, 2018;Liu et al, 2018). Highly divergent regions and simple sequence repeats (SSRs) obtained from whole plastome sequence hold promise as efficient molecular markers implemented in species delimitation and population genetics Cui et al, 2019).…”

Characterization of the complete chloroplast genome of a purple passion flower variety ‘Pingtang No.1’ (Passiflora edulia Sims) in China and phylogenetic relationships

“…There are more than 700 plant species in the family, most of which belongs to the genus Passiflora. Many chloroplast genomes of plant species from Passiflora have been reported (Rabah et al 2019;Shrestha et al 2019), which is very helpful for the Pssaiflora species evolutionary and genetic studies. Passion flower can be divided into yellow passion flower and purple passion flower according to the color of the fruit skin.…”

Genome-wide signatures of plastid-nuclear coevolution point to repeated perturbations of plastid proteostasis systems across angiosperms

“…Not surprisingly, angiosperms that lose photosynthetic function and transition to parasitic/heterotrophic lifestyles exhibit massive plastome decay and rapid protein sequence evolution (Wicke et al, 2016), in extreme cases resulting in outright loss of the entire plastome (Molina et al, 2014). However, even among angiosperms that remain fully photosynthetic, there have been repeated accelerations in rates of plastid gene evolution (Jansen et al, 2007;Guisinger et al, 2008;Knox, 2014;Sloan, Triant, Forrester, et al, 2014;Dugas et al, 2015;Nevill et al, 2019;Shrestha et al, 2019). These accelerations in angiosperms that retain a photosynthetic lifestyle can be highly gene-specific (Magee et al, 2010) and are often most pronounced in non-photosynthetic genes, such as those that encode ribosomal proteins, RNA polymerase subunits, the plastid caseinolytic protease (Clp) subunit ClpP1, the acetyl-CoA carboxylase (ACCase) subunit AccD, and the essential chloroplast factors Ycf1 and Ycf2 (Guisinger et al, 2008;Sloan, Triant, Forrester, et al, 2014;Seongjun Park et al, 2017;Shrestha et al, 2019).…”

“…However, even among angiosperms that remain fully photosynthetic, there have been repeated accelerations in rates of plastid gene evolution (Jansen et al, 2007;Guisinger et al, 2008;Knox, 2014;Sloan, Triant, Forrester, et al, 2014;Dugas et al, 2015;Nevill et al, 2019;Shrestha et al, 2019). These accelerations in angiosperms that retain a photosynthetic lifestyle can be highly gene-specific (Magee et al, 2010) and are often most pronounced in non-photosynthetic genes, such as those that encode ribosomal proteins, RNA polymerase subunits, the plastid caseinolytic protease (Clp) subunit ClpP1, the acetyl-CoA carboxylase (ACCase) subunit AccD, and the essential chloroplast factors Ycf1 and Ycf2 (Guisinger et al, 2008;Sloan, Triant, Forrester, et al, 2014;Seongjun Park et al, 2017;Shrestha et al, 2019). Accelerated protein sequence evolution has frequently been accompanied by other forms of plastome instability, including structural rearrangements and gene duplication (Guisinger et al, 2011;Knox, 2014;Sloan, Triant, Forrester, et al, 2014;Shrestha et al, 2019) as well as accelerated mitochondrial genome evolution in some cases (Cho et al, 2004;Parkinson et al, 2005;Jansen et al, 2007;Mower et al, 2007;Sloan et al, 2009;Seongjun Park et al, 2017).…”

“…These accelerations in angiosperms that retain a photosynthetic lifestyle can be highly gene-specific (Magee et al, 2010) and are often most pronounced in non-photosynthetic genes, such as those that encode ribosomal proteins, RNA polymerase subunits, the plastid caseinolytic protease (Clp) subunit ClpP1, the acetyl-CoA carboxylase (ACCase) subunit AccD, and the essential chloroplast factors Ycf1 and Ycf2 (Guisinger et al, 2008;Sloan, Triant, Forrester, et al, 2014;Seongjun Park et al, 2017;Shrestha et al, 2019). Accelerated protein sequence evolution has frequently been accompanied by other forms of plastome instability, including structural rearrangements and gene duplication (Guisinger et al, 2011;Knox, 2014;Sloan, Triant, Forrester, et al, 2014;Shrestha et al, 2019) as well as accelerated mitochondrial genome evolution in some cases (Cho et al, 2004;Parkinson et al, 2005;Jansen et al, 2007;Mower et al, 2007;Sloan et al, 2009;Seongjun Park et al, 2017). Several explanations have been proposed for the cause of these cases of rapid plastome evolution, but they remain largely a mystery (Guisinger et al, 2008;Seongjun Park et al, 2017;Williams et al, 2019).…”