Abstract
The variation of GC content is a key genome feature because it is associated with fundamental elements of genome organization. However, the reason for this variation is still an open question. Different kinds of hypotheses have been proposed to explain the variation of GC content during genome evolution. However, these hypotheses have not been explicitly investigated in whole plastome sequences. Dendrobium is one of the largest genera in the orchid species. Evolutionary studies of the plastomic organization and base composition are limited in this genus. In this study, we obtained the high-quality plastome sequences of D. loddigesii and D. devonianum. The comparison results showed a nearly identical organization in Dendrobium plastomes, indicating that the plastomic organization is highly conserved in Dendrobium genus. Furthermore, the impact of three evolutionary forces—selection, mutational biases, and GC-biased gene conversion (gBGC)—on the variation of GC content in Dendrobium plastomes was evaluated. Our results revealed: (1) consistent GC content evolution trends and mutational biases in single-copy (SC) and inverted repeats (IRs) regions; and (2) that gBGC has influenced the plastome-wide GC content evolution. These results suggest that both mutational biases and gBGC affect GC content in the plastomes of Dendrobium genus.
Highlights
Chloroplasts, responsible for photosynthesis and other biosynthesis processes in plants, have essential effects on plant growth and development
A total of approximately 3.84 Gb of 150 bp pair-end reads each for D. loddigesii and D. devonianum was obtained from the Illumina paired-end sequencing
This study is the first to observe the impact of evolutionary forces, selection, mutational biases, and GC-biased gene conversion on the variation of GC content in the whole plastome sequences
Summary
Chloroplasts, responsible for photosynthesis and other biosynthesis processes in plants, have essential effects on plant growth and development. Their own genomes (plastomes) are usually uniparentally inherited and highly conserved in their quadripartite structure, which consists of a pair of inverted repeats (IRs) regions and two single-copy (SC) regions [1]. The variation of GC content is a key genome feature because it is associated with fundamental elements of genome organization [4,5]. GC-rich regions exhibit higher gene density, more conserved mutation rates, and higher recombination rates, relative to GC-poor regions. Resolving the origin and causes of the variation in base composition has practical significance for a better understanding of the plastome organization
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