The Complete Chloroplast Genome Sequence of Cephalotaxus oliveri (Cephalotaxaceae): Evolutionary Comparison of Cephalotaxus Chloroplast DNAs and Insights into the Loss of Inverted Repeat Copies in Gymnosperms

Abstract

We have determined the complete chloroplast (cp) genome sequence of Cephalotaxus oliveri. The genome is 134,337 bp in length, encodes 113 genes, and lacks inverted repeat (IR) regions. Genome-wide mutational dynamics have been investigated through comparative analysis of the cp genomes of C. oliveri and C. wilsoniana. Gene order transformation analyses indicate that when distinct isomers are considered as alternative structures for the ancestral cp genome of cupressophyte and Pinaceae lineages, it is not possible to distinguish between hypotheses favoring retention of the same IR region in cupressophyte and Pinaceae cp genomes from a hypothesis proposing independent loss of IRA and IRB. Furthermore, in cupressophyte cp genomes, the highly reduced IRs are replaced by short repeats that have the potential to mediate homologous recombination, analogous to the situation in Pinaceae. The importance of repeats in the mutational dynamics of cupressophyte cp genomes is also illustrated by the accD reading frame, which has undergone extreme length expansion in cupressophytes. This has been caused by a large insertion comprising multiple repeat sequences. Overall, we find that the distribution of repeats, indels, and substitutions is significantly correlated in Cephalotaxus cp genomes, consistent with a hypothesis that repeats play a role in inducing substitutions and indels in conifer cp genomes.

The Complete Chloroplast Genome Sequence of a Relict Conifer Glyptostrobus pensilis: Comparative Analysis and Insights into Dynamics of Chloroplast Genome Rearrangement in Cupressophytes and Pinaceae

“…After IRB were lost from the cp genomes of Pinaceae, evolution endowed this conifer clade specific repeats to complement the residual IRs [61]. Although similar repeats were also found in the cupressophyte cp genomes [47], our results indicated that this conifer clade contained less potential functional repeats after losing IRA, leading to relatively extensive cp genome rearrangements compared to Pinaceae. We anticipate that the results presented here will be helpful both for deeper research on this endangered species and greater understanding of the complex evolutionary history of conifer cp genomes.…”

“…The GC content at the first, second and third codon positions of protein-coding genes is 45.94, 36.82 and 27.50%, respectively (Table 1). This trend of decreasing GC content at the three codon positions and the bias toward a lower GC content at the third codon position has been observed in many other sequenced plant cp genomes, and this pattern contributes to the relatively high AT content throughout the cp genome [47–51]. With regard to amino acid and codon usage, the most- and least-frequently coded amino acids are leucine (2660, 10.83%) and cysteine (279, 1.14%), respectively, whearea AAA (1176, 4.79%) and CGG (77, 0.31%) are the most and least used, respectively (S2 Fig and S7 Table).…”

The complete chloroplast genome sequence of the relict woody plant Metasequoia glyptostroboides Hu et Cheng

“…Analysis of the Cephalotaxus oliveri cp genome further supports that repeats are crucial in inducing substitutions and indels (Yi et al, 2013). For repeat analysis, 11 forward repeats, nine palindromic repeats, and 15 tandem repeats were detected in the M. glyptostroboides cp genome (Supplementary Table S3).…”

Complete Chloroplast Genome of the Wollemi Pine (Wollemia nobilis): Structure and Evolution

“…Nonetheless, they are known to be associated with gene duplication [60], gene expansion [23,49] and chloroplast DNA rearrangement [61]. We identified 28 tandem repeats of more than 20 bp in length in the W .…”