The plastome sequence of the endemic Amazonian conifer, Retrophyllum piresii (Silba) C.N.Page, reveals different recombination events and plastome isoforms

Abstract

Retrophyllum piresii (Podocarpaceae) is an endemic conifer species from the Brazilian Amazonian Region, and very few data related to ecological and genetic characteristics of this species are available. Plastome sequencing is an efficient tool to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as to probe the structural and functional evolution of plants. Usually, the plastome of photosynthetic land plants is quadripartite, with two copies of the inverted repeats (IRs) separating the small and large single-copy regions. However, in gymnosperms, IR can vary from large in size to completely absent, being constituted principally by transfer RNA (tRNA) genes, or a part of sequence of other genes. Here, we sequenced and characterized the complete plastome of R. piresii. This plastome was determined to be 133,291 bp (~480-fold coverage), presenting a total of 120 identified genes, of which 118 were single copy and two genes, trnN-GUU and trnD-GUC, were found to be duplicated and occurring as inverted and directed repeat (DR) sequences, respectively. These repeated regions presented recombinationally active sites, resulting in an IR-mediated inversion and a DR-mediated deletion. However, the isoform resulted from DR-mediated deletion may result in unviable plastome, with deletion of photosynthetic and expression machinery-related genes.

Unprecedented Intraindividual Structural Heteroplasmy in Eleocharis (Cyperaceae, Poales) Plastomes

“…2011 ), whereas other studies of conifers suggested a repeat-mediated homologous recombination mechanism based on a circular unit genome ( Guo et al. 2014 ; do Nascimento Vieira et al. 2016 ; Hsu et al.…”

Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide

“…In addition, Sciadopitys contains specific IRs (called rpoC2 -IRs) that are proven to be re-combinable 7 . The trnN -IRs that were proposed to be responsible for formation of isomeric plastomes 8 are common in Podocarpaceae 51 . All three Araucariaceae genera possess rrn5 -IRs, though their recombinant activity has not been assessed 51 .…”

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

“…Plastome sequences are also of great importance to understand evolutionary events in plants based on the knowledge of gene content, recombination events, loss of genes, gene transfer to the nucleus and genome rearrangements (Vieira et al 2016b;Bock 2017;Lopes et al 2017;Park et al 2017;Ruhlman et al 2017), as well as for plastid transformation aiming basic research (Rogalski et al 2006(Rogalski et al , 2008Alkatib et al 2012) and biotechnological applications (Daniell et al 2016;Zhang et al 2017) since the complete sequence of plastome is a prerequisite to choose target intergenic regions for insertion of transgenes and development of transplastomic plants (Daniell et al 2016;Fuentes et al 2017). The plastid transformation has been used efficiently for metabolic engineering (Daniell et al 2016;Fuentes et al 2017) and it is a viable alternative to manipulate plastid fatty acid biosynthesis (Rogalski and Carrer 2011) given that several efficient protocols of plant regeneration based on somatic embryogenesis are available for macaw palm (Moura et al 2009;Luis and Scherwinski-Pereira 2014;Padilha et al 2015).…”