Complete plastid genome sequence ofPrimula sinensis(Primulaceae): structure comparison, sequence variation and evidence foraccDtransfer to nucleus

Abstract

Species-rich genus Primula L. is a typical plant group with which to understand genetic variance between species in different levels of relationships. Chloroplast genome sequences are used to be the information resource for quantifying this difference and reconstructing evolutionary history. In this study, we reported the complete chloroplast genome sequence of Primula sinensis and compared it with other related species. This genome of chloroplast showed a typical circular quadripartite structure with 150,859 bp in sequence length consisting of 37.2% GC base. Two inverted repeated regions (25,535 bp) were separated by a large single-copy region (82,064 bp) and a small single-copy region (17,725 bp). The genome consists of 112 genes, including 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Among them, seven coding genes, seven tRNA genes and four rRNA genes have two copies due to their locations in the IR regions. The accD and infA genes lacking intact open reading frames (ORF) were identified as pseudogenes. SSR and sequence variation analyses were also performed on the plastome of Primula sinensis, comparing with another available plastome of P. poissonii. The four most variable regions, rpl36–rps8, rps16–trnQ, trnH–psbA and ndhC–trnV, were identified. Phylogenetic relationship estimates using three sub-datasets extracted from a matrix of 57 protein-coding gene sequences showed the identical result that was consistent with previous studies. A transcript found from P. sinensis transcriptome showed a high similarity to plastid accD functional region and was identified as a putative plastid transit peptide at the N-terminal region. The result strongly suggested that plastid accD has been functionally transferred to the nucleus in P. sinensis.

Novel genetic code and record-setting AT-richness in the highly reduced plastid genome of the holoparasitic plant Balanophora

“…Close to extinction are the extremely genereduced plastomes of the holoparasite Pilostyles and the mycoheterotrophs Thismia and S. thaidanica, which appear to contain only a single raison d'être gene, accD (19,21,22). Loss of these genomes sparked by accD transfer to the nucleus would hardly be surprising given the gene's functional transfer to the nucleus in multiple lineages of seed plants (84)(85)(86).…”

Highly variable chloroplast genome from two endangered Papaveraceae lithophytes Corydalis saxicola and C. tomentella

“…Furthermore, several studies have shown that the accD gene has been transferred into the nucleus, and the proteins it encodes are transported from the nucleus to the chloroplast to function in the form of a transfer peptide [37][38][39][40][41][42][43][44][45][46][47][48][50][51]. Whether the C. tomentella and C. saxicola accD genes have been lost or transferred to the nucleus, the effects on development are currently unknown.…”

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

“…Even though these genes have been identified with essential functions beyond photosynthesis and retained in the plastome of most embryophytes (Drescher et al, 2000;Kuroda and Maliga, 2003;Kode et al, 2005;Kikuchi et al, 2013;Parker et al, 2014;Dong et al, 2015), there are several other plants where these genes are missing from the chloroplast genome (Kim, 2004;Magee et al, 2010;Lei et al, 2016;Graham et al, 2017). The pseudogenization or loss of the accD, rpl22 and several genes of the ndh suite from the plastids has been reported to be a consequence of them being transferred to the nuclear genome (Jansen et al, 2011;Jansen and Ruhlman 2012;Sanderson et al 2015;Cauz-Santos et al, 2017;Liu et al 2016). Plastid gene transfer to the nucleus remains to be examined in O. quimilo and related…”