Abstract
Comparative chloroplast genome analyses are mostly carried out at lower taxonomic levels, such as the family and genus levels. At higher taxonomic levels, chloroplast genomes are generally used to reconstruct phylogenies. However, little attention has been paid to chloroplast genome evolution within orders. Here, we present the chloroplast genome of Sedum sarmentosum and take advantage of several available (or elucidated) chloroplast genomes to examine the evolution of chloroplast genomes in Saxifragales. The chloroplast genome of S. sarmentosum is 150,448 bp long and includes 82,212 bp of a large single-copy (LSC) region, 16.670 bp of a small single-copy (SSC) region, and a pair of 25,783 bp sequences of inverted repeats (IRs).The genome contains 131 unique genes, 18 of which are duplicated within the IRs. Based on a comparative analysis of chloroplast genomes from four representative Saxifragales families, we observed two gene losses and two pseudogenes in Paeonia obovata, and the loss of an intron was detected in the rps16 gene of Penthorum chinense. Comparisons among the 72 common protein-coding genes confirmed that the chloroplast genomes of S. sarmentosum and Paeonia obovata exhibit accelerated sequence evolution. Furthermore, a strong correlation was observed between the rates of genome evolution and genome size. The detected genome size variations are predominantly caused by the length of intergenic spacers, rather than losses of genes and introns, gene pseudogenization or IR expansion or contraction. The genome sizes of these species are negatively correlated with nucleotide substitution rates. Species with shorter duration of the life cycle tend to exhibit shorter chloroplast genomes than those with longer life cycles.
Highlights
Chloroplasts are one of the main distinctive characteristics of plant cells
The complete chloroplast genome of S. sarmentosum (JX427551) is 150,448 bp in size and exhibits a typical circular structure including a pair of inverted repeats (IRs) (25,783 bp each) that separate the genome into two single-copy regions (LSC 82,212 bp; small single copy (SSC) 16,670 bp; Figure 1)
There are a total of 113 genes in the genome, including 79 protein-coding genes, 30 transfer RNAs (tRNAs) genes, and 4 ribosomal RNA genes (Figure 1 and Table S2)
Summary
Chloroplasts are one of the main distinctive characteristics of plant cells. The major function of chloroplasts is to perform photosynthesis [1]. Most chloroplast genomes contain 110–130 distinct genes; the majority of these genes (approximately 79) encode proteins, which are mostly involved in photosynthesis, while the remainder of the genes encode transfer RNAs (approximately 30) or ribosomal RNAs (4) [2]. The chloroplast genomes of vascular plants are highly conserved in their basic structures, comparative genomic studies have revealed occasional structural changes, such as inversions, gene or intron losses, and rearrangements among plant lineages. Loss of chloroplast genes is rare in photosynthetic species but can occur if a gene has been transferred to the nuclear genome or functionally replaced by a nuclear gene [8]. The introns of the rpoC1, rpl, and atpF genes have been independently lost from the chloroplast genomes of some angiosperm lineages [10,12,13,14,15]. Extensions or contractions of IR regions that cause variations in genome size, together with gene losses and nucleotide insertions/ deletions (indels), are frequently observed within intergenic spacers [16]
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