Rearrangement and duplication as main forces in chloroplast genome evolution in Pines

Abstract

The entire nucleotide sequence of the chloroplast genome (117,190bp) of Korean pine (Pinus koraiensis) was determined and compared with the already published genome of Japanese black pine. As in the case ofJapanese black pine, it retains 475 bp inverted repeats containing 3' portion of psbA gene but lacking rRNA genes. The translated amino acid sequences of respective potential coding genes showed 77% to 100% sequence similarity to those of corresponding genes of P. thunbergii. When compared with Japanese black pine, the order of the genes is fairly conserved except for the psaM gene and ndh pseudo genes. Thirteen indels that are larger than 100 bp wereidentified from the alignment of the two pine genomes. Except for the region containing ndh pseudo genes and that between psaI and accD,all the large indels occur near the potential rearrangement breakpoints involving several tRNA genes and their neighboring sequencesas repeat units. Multiple rearrangement events appeared to be responsible for the loss of a copy of psaM gene and rps4 and ycf12 pseudo genes found in Japanese black pine. In addition,the further proceeded truncation of ndhK pseudo gene in Korean pine and ndhB pseudo gene in Japanese black pine indicate that thesegenes are functionally redundant in pines. Surprisingly, the loss of the gene and pseudo genes are conserved among haploxylon pinesand not in diploxylon pines, suggesting that they occurred simultaneously at the time of divergence or within a short period of timeafter divergence of the two pine subgenera and that since then little change has occurred. There also appeared many indels that are lessthan 50 bps. Many of these indels appeared to be the tandem duplication products of the adjacent sequences. These tandem repeats are also very well conserved among haploxylon and among diploxylon pines.